[med-svn] r7661 - trunk/packages/autodocksuite/trunk/debian/patches
Steffen Möller
moeller at alioth.debian.org
Sun Sep 4 18:47:24 UTC 2011
Author: moeller
Date: 2011-09-04 18:47:24 +0000 (Sun, 04 Sep 2011)
New Revision: 7661
Removed:
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_10.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_25.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_2nd.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_30.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_55.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_60.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_85.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_90.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_FILEpointer.patch
trunk/packages/autodocksuite/trunk/debian/patches/const_suggetsions_gcc4.6_1st_iteration.patch
trunk/packages/autodocksuite/trunk/debian/patches/manual_const_1.patch
trunk/packages/autodocksuite/trunk/debian/patches/series
Log:
Interim set of patches that was not intended for Debian but for upstream.
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_10.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_10.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_10.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,1076 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.cc 2010-07-31 00:07:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.cc 2010-07-31 23:20:08.000000000 +0200
-@@ -52,11 +52,11 @@
- // B_include_1_4_interactions, scale_1_4, qsp_abs_charge, B_use_non_bond_cutoff );
-
- EnergyBreakdown calculateEnergies(
-- const int natom, // input number of atoms
-- const int ntor, // input number of torsions
-- const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-- const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-- const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-+ const int natom, // input number of atoms
-+ const int ntor, // input number of torsions
-+ const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-+ const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-+ const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-
- // trilinterp
- const Real tcoord[MAX_ATOMS][SPACE], // input coordinates of atoms to be trilinearly-interpolated
-@@ -64,13 +64,13 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- const int B_outside, // input boolean whether some atoms are outside grid box
-- const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-+ const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int B_outside, // input boolean whether some atoms are outside grid box
-+ const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-- Real *p_elec_total, // output if not NULL - total electrostatic energy
-- Real *p_emap_total, // output if not NULL - total intermolecular energy
-+ Real *const p_elec_total, // output if not NULL - total electrostatic energy
-+ Real *const p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
- const NonbondParam *const nonbondlist, // input list of nonbonds
-@@ -80,7 +80,7 @@
- const Boole B_include_1_4_interactions,// input boolean whether to include 1,4 interactions as non-bonds
- const Real scale_1_4, // input scaling factor for 1,4 interactions, if included
- const Real qsp_abs_charge[MAX_ATOMS], // input q-solvation parameters
-- const Boole B_use_non_bond_cutoff // input boolean whether to use a nonbond distance cutoff
-+ const Boole B_use_non_bond_cutoff // input boolean whether to use a nonbond distance cutoff
-
- )
-
-@@ -178,13 +178,13 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
- const int B_outside, // input boolean whether some atoms are outside grid box
-- int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-+ const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-- Real *p_elec_total, // output if not NULL - total electrostatic energy
-- Real *p_emap_total, // output if not NULL - total intermolecular energy
-+ Real *const p_elec_total, // output if not NULL - total electrostatic energy
-+ Real *const p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
- const NonbondParam *const nonbondlist, // input list of nonbonds
-@@ -237,7 +237,7 @@
- return eb;
- } // calculateBindingEnergies()
-
--void update_binding_energy_breakdown( EnergyBreakdown * eb, Unbound_Model ad4_unbound_model )
-+void update_binding_energy_breakdown( /* not const */ EnergyBreakdown *const eb, const Unbound_Model ad4_unbound_model )
- {
- // total intermolecular energy = (1) + (4)
- eb->e_inter = eb->e_inter_moving_fixed + eb->e_inter_moving_moving;
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.h 2010-07-31 00:07:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.h 2010-07-31 23:18:32.000000000 +0200
-@@ -44,7 +44,7 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
- const int B_outside, // input boolean whether some atoms are outside grid box
- const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- /* not const */ Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
-@@ -84,13 +84,13 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
- const int B_outside, // input boolean whether some atoms are outside grid box
- const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-- Real *p_elec_total, // output if not NULL - total electrostatic energy
-- Real *p_emap_total, // output if not NULL - total intermolecular energy
-+ Real *const p_elec_total, // output if not NULL - total electrostatic energy
-+ Real *const p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
- const NonbondParam *const nonbondlist, // input list of nonbonds
-@@ -105,7 +105,7 @@
-
- );
-
--void update_binding_energy_breakdown( EnergyBreakdown * eb, const Unbound_Model ad4_unbound_model
-+void update_binding_energy_breakdown( /* not const */ EnergyBreakdown * eb, const Unbound_Model ad4_unbound_model
- );
-
- void initialise_binding_energy_breakdown ( EnergyBreakdown * eb,
-Index: autodocksuite-4.2.3/autodock/changeState.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/changeState.cc 2010-07-30 22:45:41.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/changeState.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -35,12 +35,12 @@
- #include "changeState.h"
-
-
--State changeState( State last, /* ...must be a normalized quaternion! */
-- Real trnStep,
-- Real torStep,
-- int ntor,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS])
-+State changeState( const State last, /* ...must be a normalized quaternion! */
-+ const Real trnStep,
-+ const Real torStep,
-+ const int ntor,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS])
-
- {
- register int i;
-Index: autodocksuite-4.2.3/autodock/changeState.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/changeState.h 2010-07-30 22:47:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/changeState.h 2010-07-30 22:48:16.000000000 +0200
-@@ -27,10 +27,10 @@
- #ifndef CHANGESTATE
- #define CHANGESTATE
-
--State changeState( State last, /* ...must be a normalized quaternion! */
-- Real trnStep,
-- Real torStep,
-- int ntor,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS]);
-+State changeState( const State last, /* ...must be a normalized quaternion! */
-+ const Real trnStep,
-+ const Real torStep,
-+ const int ntor,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/cnv_state_to_coords.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cnv_state_to_coords.cc 2010-07-30 23:41:01.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cnv_state_to_coords.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -49,7 +49,7 @@
- const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor,
- const Real crdpdb[MAX_ATOMS][SPACE],
-- Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const int natom)
-
- {
-Index: autodocksuite-4.2.3/autodock/cnv_state_to_coords.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cnv_state_to_coords.h 2010-07-30 23:41:01.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cnv_state_to_coords.h 2010-07-30 23:42:13.000000000 +0200
-@@ -37,6 +37,6 @@
- const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor,
- const Real crdpdb[MAX_ATOMS][SPACE],
-- Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const int natom);
- #endif
-Index: autodocksuite-4.2.3/autodock/getInitialState.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getInitialState.cc 2010-07-30 23:55:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getInitialState.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -46,12 +46,12 @@
-
- void getInitialState(
-
-- Real *Addr_e0total,
-- Real e0max,
-+ /* not const */ Real *const Addr_e0total,
-+ const Real e0max,
-
-- State *sInit, /* was qtn0[QUAT] and tor0[MAX_TORS] */
-- State *sMinm, /* was qtnMin[QUAT] and torMin[MAX_TORS] */
-- State *sLast, /* was qtnLast[QUAT] and torLast[MAX_TORS] */
-+ /* not const */ State *const sInit, /* was qtn0[QUAT] and tor0[MAX_TORS] */
-+ /* not const */ State *const sMinm, /* was qtnMin[QUAT] and torMin[MAX_TORS] */
-+ /* not const */ State *const sLast, /* was qtnLast[QUAT] and torLast[MAX_TORS] */
-
- const Boole B_RandomTran0,
- const Boole B_RandomQuat0,
-Index: autodocksuite-4.2.3/autodock/getInitialState.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getInitialState.h 2010-07-30 23:55:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getInitialState.h 2010-07-31 00:00:50.000000000 +0200
-@@ -38,12 +38,12 @@
- #include "timesys.h"
-
- void getInitialState(
-- Real *Addr_e0,
-- Real e0max,
-+ /* not const */ Real *const Addr_e0,
-+ const Real e0max,
-
-- State *sInit,
-- State *sMin,
-- State *sLast,
-+ /* not const */ State *const sInit,
-+ /* not const */ State *const sMin,
-+ /* not const */ State *const sLast,
-
- const Boole B_RandomTran0,
- const Boole B_RandomQuat0,
-@@ -52,13 +52,13 @@
- const Real charge[MAX_ATOMS],
- const Real abs_charge[MAX_ATOMS],
- const Real qsp_abs_charge[MAX_ATOMS],
-- const Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const Real crdpdb[MAX_ATOMS][SPACE],
- const char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real elec[MAX_ATOMS],
-- Real emap[MAX_ATOMS],
-+ /* not const */ Real elec[MAX_ATOMS],
-+ /* not const */ Real emap[MAX_ATOMS],
-
-- EnergyTables *const ptr_ad_energy_tables,
-+ const EnergyTables *const ptr_ad_energy_tables,
-
- const Boole B_calcIntElec,
- #include "map_declare.h"
-@@ -71,9 +71,9 @@
- const Real vt[MAX_TORS][SPACE],
- const int irun1,
- const int outlev,
-- const int MaxRetries,
-+ const int MaxRetries,
-
-- const Real torsFreeEnergy,
-+ const Real torsFreeEnergy,
-
- const int ligand_is_inhibitor,
-
-Index: autodocksuite-4.2.3/autodock/hybrids.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/hybrids.h 2010-07-31 00:13:27.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/hybrids.h 2010-07-31 00:14:39.000000000 +0200
-@@ -115,6 +115,6 @@
- #ifndef MMM
- #define MMM
-
--void minmeanmax( FILE *const fp, Population &pop, const int num_its, const GridMapSetInfo *const info );
-+void minmeanmax( FILE *const fp, const Population &pop, const int num_its, const GridMapSetInfo *const info );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/mkNewState.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/mkNewState.cc 2010-07-30 23:36:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/mkNewState.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -33,21 +33,21 @@
- #include "mkNewState.h"
-
-
--void mkNewState( State *now,
-- State *last, /* ...must be a normalized quaternion! */
-- State *change,
-+void mkNewState( /* not const */ State *const now,
-+ const State *const last, /* ...must be a normalized quaternion! */
-+ /* not const */ State *const change,
-
-- Real vt[MAX_TORS][NTRN],
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int ntor,
-- Real crd[MAX_ATOMS][NTRN],
-- Real crdpdb[MAX_ATOMS][NTRN],
-- int natom,
-- Real trnStep,
-- Real qtwStep,
-- Real torStep,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS])
-+ const Real vt[MAX_TORS][NTRN],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int ntor,
-+ /* not const */ Real crd[MAX_ATOMS][NTRN],
-+ const Real crdpdb[MAX_ATOMS][NTRN],
-+ const int natom,
-+ const Real trnStep,
-+ const Real qtwStep,
-+ const Real torStep,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS])
- // Create a new state, based on the current state
- {
- register int i;
-Index: autodocksuite-4.2.3/autodock/mkNewState.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/mkNewState.h 2010-07-30 23:36:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/mkNewState.h 2010-07-30 23:43:41.000000000 +0200
-@@ -31,9 +31,9 @@
- #include "qmultiply.h"
- #include "cnv_state_to_coords.h"
-
--void mkNewState( State *now,
-- State *last,
-- State *change,
-+void mkNewState( State *const now,
-+ const State *const last,
-+ State *const change,
- /*
- ** Real qtn[NQTN],
- ** Real tor[MAX_TORS],
-@@ -42,15 +42,15 @@
- ** Real qtnChange[NQTN],
- ** Real torChange[MAX_TORS],
- */
-- Real vt[MAX_TORS][NTRN],
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int ntor,
-- Real crd[MAX_ATOMS][NTRN],
-- Real crdpdb[MAX_ATOMS][NTRN],
-- int natom,
-- Real trnStep,
-- Real qtwStep,
-- Real torStep,
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS]);
-+ const Real vt[MAX_TORS][NTRN],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int ntor,
-+ /* not const */ Real crd[MAX_ATOMS][NTRN],
-+ const Real crdpdb[MAX_ATOMS][NTRN],
-+ const int natom,
-+ const Real trnStep,
-+ const Real qtwStep,
-+ const Real torStep,
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/output_state.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/output_state.cc 2010-07-30 23:46:21.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/output_state.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -52,7 +52,7 @@
- const char lastmove,
- const Boole B_watch,
- const char *const FN_watch,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
- const int natom,
- const Real crd[MAX_ATOMS][SPACE])
- /*----------------------------------------------------------------------------*/
-Index: autodocksuite-4.2.3/autodock/output_state.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/output_state.h 2010-07-30 23:46:21.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/output_state.h 2010-07-30 23:47:59.000000000 +0200
-@@ -28,16 +28,16 @@
- #ifndef OUTPUT_STATE
- #define OUTPUT_STATE
- #include "constants.h"
--void output_state( FILE *fp,
-- State S,
-- int ntor,
-- int istep,
-- Real energy,
-- Real eint,
-- char lastmove,
-- Boole B_watch,
-- char *FN_watch,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int natom,
-- Real crd[MAX_ATOMS][SPACE]);
-+void output_state( FILE *const fp,
-+ const State S,
-+ const int ntor,
-+ const int istep,
-+ const Real energy,
-+ const Real eint,
-+ const char lastmove,
-+ const Boole B_watch,
-+ const char *const FN_watch,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const int natom,
-+ const Real crd[MAX_ATOMS][SPACE]);
- #endif
-Index: autodocksuite-4.2.3/autodock/qtransform.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qtransform.cc 2010-07-31 00:32:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qtransform.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -36,7 +36,7 @@
-
- void qtransform( const Coord T,
- const Quat q,
-- Real tcoord[MAX_ATOMS][SPACE],
-+ /* not const */ Real tcoord[MAX_ATOMS][SPACE],
- const int natom)
-
- /******************************************************************************/
-@@ -129,16 +129,16 @@
- void reorient( FILE *const logFile,
- const int true_ligand_atoms,
- const char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crdpdb[MAX_ATOMS][SPACE], // original PDB coordinates from input
-- Real charge[MAX_ATOMS],
-+ /* not const */ Real crdpdb[MAX_ATOMS][SPACE], // original PDB coordinates from input
-+ const Real charge[MAX_ATOMS],
- const int type[MAX_ATOMS],
-- ParameterEntry parameterArray[MAX_ATOM_TYPES],
-- Quat q_reorient,
-- Coord origin,
-+ const ParameterEntry parameterArray[MAX_ATOM_TYPES],
-+ const Quat q_reorient,
-+ const Coord origin,
- const int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Molecule *ptr_ligand,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE],
-+ /* not const */ Molecule *ptr_ligand,
- const int debug )
- {
- // Print out the un-reoriented coordinates
-Index: autodocksuite-4.2.3/autodock/qtransform.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qtransform.h 2010-07-31 00:32:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qtransform.h 2010-07-31 01:04:16.000000000 +0200
-@@ -37,21 +37,21 @@
-
- void qtransform( const Coord T,
- const Quat q,
-- Real tcoord[MAX_ATOMS][SPACE],
-+ /* not const */ Real tcoord[MAX_ATOMS][SPACE],
- const int natom);
-
--void reorient( FILE *logFile,
-+void reorient( FILE *const logFile,
- const int true_ligand_atoms,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crdpdb[MAX_ATOMS][SPACE], // original PDB coordinates from input
-- Real charge[MAX_ATOMS],
-- int type[MAX_ATOMS],
-- ParameterEntry parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
-- Quat q_reorient,
-- Coord origin,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real crdpdb[MAX_ATOMS][SPACE], // original PDB coordinates from input
-+ const Real charge[MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const ParameterEntry parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
-+ const Quat q_reorient,
-+ const Coord origin,
- const int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Molecule *ptr_ligand,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE],
-+ /* not const */ Molecule *ptr_ligand,
- const int debug );
- #endif
-Index: autodocksuite-4.2.3/autodock/readPDBQT.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readPDBQT.cc 2010-07-31 00:48:29.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readPDBQT.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -93,12 +93,12 @@
- int *const P_ntorsdof,
- const int outlev,
- int ignore_inter[MAX_ATOMS],
-- int B_include_1_4_interactions,
-+ const int B_include_1_4_interactions,
-
- Atom atoms[MAX_ATOMS],
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ /* not const */ char PDBQT_record[MAX_RECORDS][LINE_LEN],
-
-- int end_of_branch[MAX_TORS]
-+ /* not const */ /* not const */ int end_of_branch[MAX_TORS]
- )
-
- {
-Index: autodocksuite-4.2.3/autodock/readPDBQT.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readPDBQT.h 2010-07-31 00:48:29.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readPDBQT.h 2010-07-31 00:56:55.000000000 +0200
-@@ -42,60 +42,60 @@
- #include "stack.h"
-
- void readPDBQTLine( char line[LINE_LEN],
-- int *ptr_serial,
-+ int *const ptr_serial,
- Real crd[SPACE],
-- Real *P_q,
-+ Real *const P_q,
- ParameterEntry *thisparm);
-
- Molecule readPDBQT( char line[LINE_LEN],
-
- int num_atm_maps,
-
-- int *P_natom,
-+ int *const P_natom,
- Real crdpdb[MAX_ATOMS][NTRN],
- Real crdreo[MAX_ATOMS][NTRN],
- Real charge[MAX_ATOMS],
-- Boole *P_B_haveCharges,
-+ Boole *const P_B_haveCharges,
- int type[MAX_ATOMS],
- int bondtype[MAX_ATOMS],
- char pdbaname[MAX_ATOMS][5],
-
-- char *pdbqFileName,
-- char *FN_flexres,
-+ char *const pdbqFileName,
-+ char *const FN_flexres,
- Boole B_have_flexible_residues,
-
- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int *P_n_heavy_atoms_in_ligand,
-+ int *const P_n_heavy_atoms_in_ligand,
-
-- Boole *P_B_constrain,
-- int *P_atomC1,
-- int *P_atomC2,
-- Real *P_sqlower,
-- Real *P_squpper,
--
-- int *P_ntor1,
-- int *P_ntor,
-- int *P_ntor_ligand,
-+ Boole *const P_B_constrain,
-+ int *const P_atomC1,
-+ int *const P_atomC2,
-+ Real *const P_sqlower,
-+ Real *const P_squpper,
-+
-+ int *const P_ntor1,
-+ int *const P_ntor,
-+ int *const P_ntor_ligand,
- int tortree[MAX_TORS][MAX_ATOMS],
- Real vt[MAX_TORS][NTRN],
-
-- int *P_Nnb,
-- NonbondParam *nonbondlist,
-+ int *const P_Nnb,
-+ NonbondParam *const nonbondlist,
-
-- Clock jobStart,
-- struct tms tms_jobStart,
-- char hostnm[MAX_CHARS],
-+ const Clock jobStart,
-+ const struct tms tms_jobStart,
-+ const char hostnm[MAX_CHARS],
-
-- int *P_ntorsdof,
-- int outlev,
-+ int *const P_ntorsdof,
-+ const int outlev,
-
- int ignore_inter[MAX_ATOMS],
-
-- int B_include_1_4_interactions,
-+ const int B_include_1_4_interactions,
-
- Atom atoms[MAX_ATOMS],
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ /* not const */ char PDBQT_record[MAX_RECORDS][LINE_LEN],
-
-- int end_of_branch[MAX_TORS]
-+ /* not const */ int end_of_branch[MAX_TORS]
- );
- #endif
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.h 2010-07-31 00:06:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.h 2010-07-31 00:07:05.000000000 +0200
-@@ -43,7 +43,7 @@
- char * report_parameter_library();
-
- void setup_distdepdiel( const int outlev,
-- const EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
-+ EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
- );
-
-
-Index: autodocksuite-4.2.3/autodock/simanneal.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/simanneal.cc 2010-07-30 22:49:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/simanneal.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -44,92 +44,92 @@
- extern char *programname;
-
-
--void simanneal ( int *Addr_nconf,
-- int Nnb,
-- Real WallEnergy,
-+void simanneal ( int *const Addr_nconf,
-+ const int Nnb,
-+ const Real WallEnergy,
- char atomstuff[MAX_ATOMS][MAX_CHARS],
- Real charge[MAX_ATOMS],
- Real abs_charge[MAX_ATOMS],
- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-+ const Boole B_calcIntElec,
- Real crd[MAX_ATOMS][SPACE],
- Real crdpdb[MAX_ATOMS][SPACE],
-- char *FN_dpf,
-+ const char *const FN_dpf,
-
-- EnergyTables *ptr_ad_energy_tables,
-+ EnergyTables *const ptr_ad_energy_tables,
-
-- Real econf[MAX_RUNS],
-- Boole B_either,
-+ /* not const */ Real econf[MAX_RUNS],
-+ const Boole B_either,
- Real elec[MAX_ATOMS],
- Real emap[MAX_ATOMS],
-- int NcycMax,
-- int irunmax,
-- Clock jobStart,
-+ const int NcycMax,
-+ const int irunmax,
-+ const Clock jobStart,
- #include "map_declare.h"
-- int naccmax,
-- int natom,
-- NonbondParam *nonbondlist,
-- int nrejmax,
-- int ntor1,
-- int ntor,
-- int outlev,
-+ const int naccmax,
-+ const int natom,
-+ NonbondParam *const nonbondlist,
-+ const int nrejmax,
-+ const int ntor1,
-+ const int ntor,
-+ const int outlev,
-
- State sInit, /* tor0, qtn0 */
-- State sHist[MAX_RUNS], /* was qtnHist, torHist */
-+ /* not const */ State sHist[MAX_RUNS], /* was qtnHist, torHist */
-
-- Real qtwFac,
-- Boole B_qtwReduc,
-- Real qtwStep0,
-- Boole B_selectmin,
-- char *FN_ligand,
-- Real lig_center[SPACE],
-- Real RT0,
-- Boole B_RTChange,
-- Real RTFac,
-+ const Real qtwFac,
-+ const Boole B_qtwReduc,
-+ const Real qtwStep0,
-+ const Boole B_selectmin,
-+ const char *const FN_ligand,
-+ const Real lig_center[SPACE],
-+ const Real RT0,
-+ const Boole B_RTChange,
-+ const Real RTFac,
- struct tms tms_jobStart,
- int tlist[MAX_TORS][MAX_ATOMS],
-- Real torFac,
-- Boole B_torReduc,
-- Real torStep0,
-- char *FN_trj,
-- int trj_cyc_max,
-- int trj_cyc_min,
-- int trj_freq,
-- Real trnFac,
-- Boole B_trnReduc,
-- Real trnStep0,
-- int type[MAX_ATOMS],
-+ const Real torFac,
-+ const Boole B_torReduc,
-+ const Real torStep0,
-+ const char *const FN_trj,
-+ const int trj_cyc_max,
-+ const int trj_cyc_min,
-+ const int trj_freq,
-+ const Real trnFac,
-+ const Boole B_trnReduc,
-+ const Real trnStep0,
-+ const int type[MAX_ATOMS],
- Real vt[MAX_TORS][SPACE],
-- Boole B_writeTrj,
-- Boole B_constrain,
-- int atomC1,
-- int atomC2,
-- Real sqlower,
-- Real squpper,
-- Boole B_linear_schedule,
-- Real RTreduc,
-+ const Boole B_writeTrj,
-+ const Boole B_constrain,
-+ const int atomC1,
-+ const int atomC2,
-+ const Real sqlower,
-+ const Real squpper,
-+ const Boole B_linear_schedule,
-+ const Real RTreduc,
- /*Real maxrad,*/
-- Boole B_watch,
-- char *FN_watch,
-- Boole B_isGaussTorCon,
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Boole B_isTorConstrained[MAX_TORS],
-- Boole B_ShowTorE,
-- unsigned short US_TorE[MAX_TORS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- Boole B_RandomTran0,
-- Boole B_RandomQuat0,
-- Boole B_RandomDihe0,
-- Real e0max,
-+ const Boole B_watch,
-+ const char *const FN_watch,
-+ const Boole B_isGaussTorCon,
-+ /* not const */ unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const Boole B_ShowTorE,
-+ /* not const */ unsigned short US_TorE[MAX_TORS],
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS],
-+ const Boole B_RandomTran0,
-+ const Boole B_RandomQuat0,
-+ const Boole B_RandomDihe0,
-+ const Real e0max,
-
-- Real torsFreeEnergy,
-+ const Real torsFreeEnergy,
-
-- int MaxRetries,
-+ const int MaxRetries,
-
-- int ligand_is_inhibitor,
-+ const int ligand_is_inhibitor,
-
-- int ignore_inter[MAX_ATOMS],
-+ const int ignore_inter[MAX_ATOMS],
-
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-@@ -138,11 +138,11 @@
-
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-- Unbound_Model ad4_unbound_model
-+ GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ const Unbound_Model ad4_unbound_model
- )
-
- {
-Index: autodocksuite-4.2.3/autodock/simanneal.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/simanneal.h 2010-07-30 23:11:10.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/simanneal.h 2010-07-30 23:51:09.000000000 +0200
-@@ -38,98 +38,98 @@
- #include "eintcal.h"
- #include "writePDBQT.h"
-
--void simanneal( int *P_nconf,
-- int Nnb,
-- Real WallEnergy,
-+void simanneal( int *const P_nconf,
-+ const int Nnb,
-+ const Real WallEnergy,
- char atomstuff[MAX_ATOMS][MAX_CHARS],
- Real charge[MAX_ATOMS],
- Real abs_charge[MAX_ATOMS],
- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-+ const Boole B_calcIntElec,
- Real crd[MAX_ATOMS][SPACE],
- Real crdpdb[MAX_ATOMS][SPACE],
-- char *dpfFN,
-+ const char *const dpfFN,
-
-- EnergyTables *ptr_ad_energy_tables,
-+ EnergyTables *const ptr_ad_energy_tables,
-
-- Real econf[MAX_RUNS],
-- Boole B_either,
-+ /* not const */ Real econf[MAX_RUNS],
-+ const Boole B_either,
- Real elec[MAX_ATOMS],
- Real emap[MAX_ATOMS],
-- int icyclemax,
-- int irunmax,
-- Clock jobStart,
-+ const int icyclemax,
-+ const int irunmax,
-+ const Clock jobStart,
- #include "map_declare.h"
-- int naccmax,
-- int natom,
-- NonbondParam *nonbondlist,
-- int nrejmax,
-- int ntor1,
-- int ntor,
-- int outlev,
-+ const int naccmax,
-+ const int natom,
-+ NonbondParam *const nonbondlist,
-+ const int nrejmax,
-+ const int ntor1,
-+ const int ntor,
-+ const int outlev,
-
- State sInit, /* Real qtn0[QUAT],
- Real tor0[MAX_TORS], */
-- State sHist[MAX_RUNS], /* Real qtnHist[MAX_RUNS][QUAT],
-+ /* not const */ State sHist[MAX_RUNS], /* Real qtnHist[MAX_RUNS][QUAT],
- Real torHist[MAX_RUNS][MAX_TORS], */
-- Real qtwFac,
-- Boole B_qtwReduc,
-- Real qtwStep0,
-- Boole B_selectmin,
-- char *smFileName,
-- Real sml_center[SPACE],
-- Real RT0,
-- Boole B_RTChange,
-- Real RTFac,
-+ const Real qtwFac,
-+ const Boole B_qtwReduc,
-+ const Real qtwStep0,
-+ const Boole B_selectmin,
-+ const char *const smFileName,
-+ const Real sml_center[SPACE], // named lig_center in .cc file
-+ const Real RT0,
-+ const Boole B_RTChange,
-+ const Real RTFac,
- struct tms tms_jobStart,
- int tlist[MAX_TORS][MAX_ATOMS],
-- Real torFac,
-- Boole B_torReduc,
-- Real torStep0,
-- char *trjFileName,
-- int trj_cyc_max,
-- int trj_cyc_min,
-- int trj_freq,
-- Real trnFac,
-- Boole B_trnReduc,
-- Real trnStep0,
-- int type[MAX_ATOMS],
-+ const Real torFac,
-+ const Boole B_torReduc,
-+ const Real torStep0,
-+ const char *const trjFileName,
-+ const int trj_cyc_max,
-+ const int trj_cyc_min,
-+ const int trj_freq,
-+ const Real trnFac,
-+ const Boole B_trnReduc,
-+ const Real trnStep0,
-+ const int type[MAX_ATOMS],
- Real vt[MAX_TORS][SPACE],
-- Boole B_write_trj,
-- Boole B_constrain,
-- int atomC1,
-- int atomC2,
-- Real sqlower,
-- Real squpper,
-- Boole B_linear_schedule,
-- Real RTreduc,
-+ const Boole B_write_trj,
-+ const Boole B_constrain,
-+ const int atomC1,
-+ const int atomC2,
-+ const Real sqlower,
-+ const Real squpper,
-+ const Boole B_linear_schedule,
-+ const Real RTreduc,
- /*Real maxrad,*/
-- Boole B_watch,
-- char *FN_watch,
-- Boole B_isGaussTorCon,
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Boole B_isTorConstrained[MAX_TORS],
-- Boole B_ShowTorE,
-- unsigned short US_TorE[MAX_TORS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- Boole B_RandomTran0,
-- Boole B_RandomQuat0,
-- Boole B_RandomDihe0,
-- Real e0max,
-- Real torsFreeEnergy,
-- int MaxRetries,
-- int ligand_is_inhibitor,
-- int ignore_inter[MAX_ATOMS],
-+ const Boole B_watch,
-+ const char *const FN_watch,
-+ const Boole B_isGaussTorCon,
-+ /* not const */ unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const Boole B_ShowTorE,
-+ /* not const */ unsigned short US_TorE[MAX_TORS],
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS],
-+ const Boole B_RandomTran0,
-+ const Boole B_RandomQuat0,
-+ const Boole B_RandomDihe0,
-+ const Real e0max,
-+ const Real torsFreeEnergy,
-+ const int MaxRetries,
-+ const int ligand_is_inhibitor,
-+ const int ignore_inter[MAX_ATOMS],
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
- const ParameterEntry parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-- Unbound_Model ad4_unbound_model);
-+ GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ const Unbound_Model ad4_unbound_model);
-
- #endif
-Index: autodocksuite-4.2.3/autodock/torNorVec.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/torNorVec.cc 2010-07-31 00:36:59.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/torNorVec.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -39,10 +39,10 @@
- extern FILE *logFile;
-
-
--void torNorVec( Real crdpdb[MAX_ATOMS][SPACE],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE] )
-+void torNorVec( const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE] )
- {
-
- register int xyz = 0;
-@@ -95,12 +95,12 @@
- return;
- }
-
--void update_torsion_vectors( Real crdpdb[MAX_ATOMS][SPACE],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Molecule *ligand,
-- int debug )
-+void update_torsion_vectors( const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE],
-+ /* not const */ Molecule *ligand,
-+ const int debug )
- { // Update the unit vectors for the torsion rotations
- register int i=0, j=0;
- if (debug > 0) {
-Index: autodocksuite-4.2.3/autodock/torNorVec.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/torNorVec.h 2010-07-31 00:42:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/torNorVec.h 2010-07-31 00:43:30.000000000 +0200
-@@ -31,16 +31,16 @@
- #include "stop.h"
- #include "structs.h"
-
--void torNorVec( Real crdpdb[MAX_ATOMS][SPACE],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE] );
-+void torNorVec( const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE] );
-
--void update_torsion_vectors( Real crdpdb[MAX_ATOMS][SPACE],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Molecule *ligand,
-- int debug );
-+void update_torsion_vectors( const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real vt[MAX_TORS][SPACE],
-+ /* not const */ Molecule *ligand,
-+ const int debug );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/usage.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/usage.h 2010-07-31 00:26:13.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/usage.h 2010-07-31 00:26:42.000000000 +0200
-@@ -26,5 +26,5 @@
-
- #ifndef USAGE
- #define USAGE
--void usage(FILE * file, char * programname );
-+void usage(FILE *const file, const char *const programname );
- #endif
-Index: autodocksuite-4.2.3/autodock/writePDBQT.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/writePDBQT.cc 2010-07-30 23:52:15.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/writePDBQT.cc 2010-07-31 01:09:19.000000000 +0200
-@@ -67,8 +67,8 @@
- const Real vt[MAX_TORS][SPACE],
- const int tlist[MAX_TORS][MAX_ATOMS],
- const Real crdpdb[MAX_ATOMS][SPACE],
-- const NonbondParam *nonbondlist,
-- const EnergyTables *ptr_ad_energy_tables,
-+ const NonbondParam *const nonbondlist,
-+ const EnergyTables *const ptr_ad_energy_tables,
- const int type[MAX_ATOMS], // aka 'map_index' in 'ParameterEntry' structures
- const int Nnb,
- const Boole B_calcIntElec,
-@@ -80,7 +80,7 @@
- const ParameterEntry parameterArray[MAX_ATOM_TYPES],
- const Real unbound_internal_FE,
-
-- const GridMapSetInfo *info,
-+ const GridMapSetInfo *const info,
- const int state_type, // 0 means the state is unbound, 1 means the state is docked
- const char PDBQT_record[MAX_RECORDS][LINE_LEN],
- const Boole B_use_non_bond_cutoff,
-Index: autodocksuite-4.2.3/autodock/writePDBQT.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/writePDBQT.h 2010-07-30 23:52:15.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/writePDBQT.h 2010-07-30 23:53:30.000000000 +0200
-@@ -34,14 +34,14 @@
- #include "cnv_state_to_coords.h"
- #include "stateLibrary.h"
-
--void writePDBQT(const int irun,FourByteLong seed[2],
-+void writePDBQT(const int irun, const FourByteLong seed[2],
- const char *const smFileName,
- const char *dpfFN,
- const Real sml_center[SPACE],
- /* not const */ State state,
- const int ntor,
-- Real (*const Ptr_eintra),
-- Real (*const Ptr_einter),
-+ /* not const */ Real (*const Ptr_eintra),
-+ /* not const */ Real (*const Ptr_einter),
- const int natom,
- const char atomstuff[MAX_ATOMS][MAX_CHARS],
- /* not const */ Real crd[MAX_ATOMS][SPACE],
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_25.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_25.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_25.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,85 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/coliny.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/coliny.cc 2010-07-31 23:29:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/coliny.cc 2010-07-31 23:45:36.000000000 +0200
-@@ -51,7 +51,7 @@
- //
- // The AutoDock 'objective function' used within Coliny
- //
--double ADEvalFn(double* x, int n);
-+double ADEvalFn(/* not const */ double *const x, const int n);
-
- #ifdef COLIN_3_0
-
-@@ -69,7 +69,7 @@
- //// Initialize the "algname" optimizer over the given domain. An initial
- //// point is generate as the midpoint over the domain.
- ////
--void coliny_init(char* algname, char* domain, int num_vars)
-+void coliny_init(const char *const algname, const char *const domain, const int num_vars)
- {
- //
- // If 'algname' equals "help", then print the list of supported
-@@ -143,9 +143,9 @@
- ////
- //// To turn on "full debugging", set the false flag to true.
- ////
--void coliny_minimize(int seed, std::vector<double>& initpt,
-- std::vector<double>& finalpt,
-- int& neval, int& niters)
-+void coliny_minimize(const int seed, const std::vector<double>& initpt,
-+ /* not const */ std::vector<double>& finalpt,
-+ /* unused */ const int& neval, /* unused */ const int& niters)
- {
- coliny_problem->reset();
-
-@@ -259,9 +259,9 @@
- ////
- //// To turn on "full debugging", set the false flag to true.
- ////
--void coliny_minimize(int seed, std::vector<double>& initpt,
-- std::vector<double>& finalpt,
-- int& neval, int& niters)
-+void coliny_minimize(const int seed, const std::vector<double>& initpt,
-+ /* not const */ std::vector<double>& finalpt,
-+ /* unused */ const int& neval, /* unused */ const int& niters)
- {
- coliny_problem.reset_neval();
-
-Index: autodocksuite-4.2.3/autodock/coliny.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/coliny.h 2010-07-31 23:29:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/coliny.h 2010-07-31 23:41:42.000000000 +0200
-@@ -40,15 +40,15 @@
- //
- // Initialize the 'algname' coliny optimizer over 'domain'
- //
--void coliny_init(char* algname, char* domain, int num_vars);
-+void coliny_init(const char *const algname, const char *const domain, const int num_vars);
-
- //
- // Perform minimization with a given seed and initial point. Return
- // summary statistics
- //
--void coliny_minimize(int seed, std::vector<double>& initpt,
-- std::vector<double>& finalpt,
-- int& neval, int& niters);
-+void coliny_minimize(const int seed, const std::vector<double>& initpt,
-+ /* not const */ std::vector<double>& finalpt,
-+ /* unused */ const int& neval, /* unused */ const int& niters);
-
- #endif
-
-Index: autodocksuite-4.2.3/autodock/eval.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.cc 2010-07-31 23:31:36.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.cc 2010-07-31 23:33:19.000000000 +0200
-@@ -320,7 +320,7 @@
-
- extern Eval evaluate;
-
--double ADEvalFn(double* x, int n)
-+double ADEvalFn(/* not const */ double *const x, const int n)
- {
- //
- // Normalize the data
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_2nd.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_2nd.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_2nd.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,57 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/stateLibrary.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.cc 2010-07-21 19:53:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.cc 2010-07-22 21:18:56.000000000 +0200
-@@ -103,9 +103,9 @@
- D->e = S.e;
- }
-
--void printState( FILE *fp,
-+void printState( FILE *const fp,
- State S,
-- int detail )
-+ const int detail )
- {
- register int i;
- Real torDegTmp;
-@@ -153,7 +153,7 @@
- }
- }
-
--void writeState( FILE *fp, State S )
-+void writeState( FILE *const fp, State S )
- {
- register int i;
- Real torDegTmp;
-@@ -259,7 +259,7 @@
- return(retval);
- }
-
--Molecule copyStateToMolecule(State *S, Molecule *mol) /* S is the source */
-+Molecule copyStateToMolecule(const State *const S, Molecule *const mol) /* S is the source */
- {
- register int i;
- mol->S.T.x = S->T.x;
-Index: autodocksuite-4.2.3/autodock/stateLibrary.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.h 2010-07-22 21:17:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.h 2010-07-22 21:19:20.000000000 +0200
-@@ -37,14 +37,14 @@
- void copyState( State *destination,
- State source);
-
--void printState( FILE *fp,
-+void printState( FILE *const fp,
- State state,
-- int detail );
-+ const int detail );
-
--void writeState( FILE *fp,
-+void writeState( FILE *const fp,
- State state );
-
- int checkState( const State *D );
-
--Molecule copyStateToMolecule(State *source, Molecule *mol);
-+Molecule copyStateToMolecule(const State *const source, Molecule *const mol);
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_30.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_30.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_30.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,527 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/print_2x.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_2x.h 2010-07-31 23:48:12.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_2x.h 2010-07-31 23:48:31.000000000 +0200
-@@ -29,7 +29,7 @@
-
- #include "constants.h"
-
--void print_2x( FILE *stream1,
-- FILE *stream2,
-+void print_2x( FILE *const stream1,
-+ FILE *const stream2,
- const char *string );
- #endif
-Index: autodocksuite-4.2.3/autodock/rep.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/rep.cc 2010-07-31 23:49:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/rep.cc 2010-08-01 00:47:31.000000000 +0200
-@@ -70,7 +70,7 @@
- //
- // This constructor is used to generate the initial (random) instances
- // of an integer vector.
--IntVector::IntVector(int number_of_els)
-+IntVector::IntVector(const int number_of_els)
- : Representation(number_of_els)
- {
- register int i;
-@@ -88,7 +88,7 @@
-
- //______________________________________________________________________________
- //
--IntVector::IntVector(int num_els, FourByteLong init_low, FourByteLong init_high)
-+IntVector::IntVector(const int num_els, const FourByteLong init_low, const FourByteLong init_high)
- : Representation(num_els)
- {
- register int i;
-@@ -132,7 +132,7 @@
-
- //______________________________________________________________________________
- //
--void IntVector::write(unsigned char value, int gene)
-+void IntVector::write(const unsigned char value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -145,7 +145,7 @@
-
- //______________________________________________________________________________
- //
--void IntVector::write(FourByteLong value, int gene)
-+void IntVector::write(const FourByteLong value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -163,7 +163,7 @@
-
- //______________________________________________________________________________
- //
--void IntVector::write(double value, int gene)
-+void IntVector::write(const double value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -176,7 +176,7 @@
-
- //______________________________________________________________________________
- //
--void IntVector::write(const Element value, int gene)
-+void IntVector::write(const Element value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -197,7 +197,7 @@
-
- //______________________________________________________________________________
- //
--const Element IntVector::gene(unsigned int gene_number) const
-+const Element IntVector::gene(const unsigned int gene_number) const
- {
- Element retval;
-
-@@ -233,14 +233,13 @@
- Representation &IntVector::operator=(const Representation &original)
- {
- register unsigned int i;
-- FourByteLong *array;
-
- #ifdef DEBUG
- (void)fprintf(logFile, "\nrep.cc/Representation &IntVector::operator=(const Representation &original) \n");
- #endif /* DEBUG */
-
-
-- array = (FourByteLong *)original.internals();
-+ const FourByteLong *const array = (FourByteLong *)original.internals();
- if (original.type()==T_IntV) {
- number_of_pts = original.number_of_points();
- if (vector!=NULL) {
-@@ -268,7 +267,7 @@
- // This constructor is used to initialize the starting population,
- // with random values between REALV_LOW and REALV_HIGH.
- //
--RealVector::RealVector(int num_els)
-+RealVector::RealVector(/* not const */ int num_els)
- : Representation(num_els)
- {
- #ifdef DEBUG
-@@ -292,7 +291,7 @@
- // with elements of the vector set to random values between
- // the user-specified values, init_low and init_high.
- //
--RealVector::RealVector(int num_els, double init_low, double init_high)
-+RealVector::RealVector(/* not const */ int num_els, const double init_low, const double init_high)
- : Representation(num_els)
- {
- #ifdef DEBUG
-@@ -319,7 +318,7 @@
- // but the first value in this vector is set to the value supplied as the last argument.
- // This is useful for specifying an initial axis-angle rotation angle.
- //
--RealVector::RealVector(int num_els, double init_low, double init_high, double init_first_value)
-+RealVector::RealVector(const int num_els, const double init_low, const double init_high, const double init_first_value)
- : Representation(num_els)
- {
- #ifdef DEBUG
-@@ -351,7 +350,7 @@
- // nx, ny, and nz.
- // This is useful for specifying an initial orientation's axis components
- //
--RealVector::RealVector( int num_els, double init_low, double init_high, double nx, double ny, double nz )
-+RealVector::RealVector( const int num_els, const double init_low, const double init_high, const double nx, const double ny, const double nz )
- : Representation(num_els)
- {
- #ifdef DEBUG
-@@ -380,7 +379,7 @@
- // w, x, y, z
- // This is useful for specifying an initial quaternion rotation' unit vector.
- //
--RealVector::RealVector( int num_els, double init_low, double init_high, double x, double y, double z, double w)
-+RealVector::RealVector( const int num_els, const double init_low, const double init_high, const double x, const double y, const double z, const double w)
- : Representation(num_els)
- {
- #ifdef DEBUG
-@@ -434,7 +433,7 @@
-
- //______________________________________________________________________________
- //
--void RealVector::write(unsigned char value, int gene)
-+void RealVector::write(const unsigned char value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -447,7 +446,7 @@
-
- //______________________________________________________________________________
- //
--void RealVector::write(FourByteLong value, int gene)
-+void RealVector::write(const FourByteLong value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -460,7 +459,7 @@
-
- //______________________________________________________________________________
- //
--void RealVector::write(double value, int gene)
-+void RealVector::write(const double value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -485,7 +484,7 @@
-
- //______________________________________________________________________________
- //
--void RealVector::write(const Element value, int gene)
-+void RealVector::write(const Element value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -503,7 +502,7 @@
-
- //______________________________________________________________________________
- //
--const Element RealVector::gene(unsigned int gene_number) const
-+const Element RealVector::gene(const unsigned int gene_number) const
- {
-
- #ifdef DEBUG
-@@ -579,7 +578,7 @@
-
- //______________________________________________________________________________
- //
--ConstrainedRealVector::ConstrainedRealVector(int num_els)
-+ConstrainedRealVector::ConstrainedRealVector(/* not const */ int num_els)
- : Representation(num_els)
- {
-
-@@ -599,7 +598,7 @@
-
- //______________________________________________________________________________
- //
--ConstrainedRealVector::ConstrainedRealVector(int num_els, double init_low, double init_high)
-+ConstrainedRealVector::ConstrainedRealVector(/* not const */ int num_els, const double init_low, const double init_high)
- : Representation(num_els)
- {
-
-@@ -644,7 +643,7 @@
-
- //______________________________________________________________________________
- //
--void ConstrainedRealVector::write(unsigned char value, int gene)
-+void ConstrainedRealVector::write(const unsigned char value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -657,7 +656,7 @@
-
- //______________________________________________________________________________
- //
--void ConstrainedRealVector::write(FourByteLong value, int gene)
-+void ConstrainedRealVector::write(const FourByteLong value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -670,7 +669,7 @@
-
- //______________________________________________________________________________
- //
--void ConstrainedRealVector::write(double value, int gene)
-+void ConstrainedRealVector::write(const double value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -722,7 +721,7 @@
- }
- //______________________________________________________________________________
- //
--void ConstrainedRealVector::write(const Element value, int gene)
-+void ConstrainedRealVector::write(const Element value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -742,7 +741,7 @@
-
- //______________________________________________________________________________
- //
--void ConstrainedRealVector::normalize(void)
-+void ConstrainedRealVector::normalize(void) /* not const */
- {
- #ifdef DEBUG
- (void)fprintf(logFile, "rep.cc/void ConstrainedRealVector::normalize(void) const \n");
-@@ -772,7 +771,7 @@
-
- //______________________________________________________________________________
- //
--const Element ConstrainedRealVector::gene(unsigned int gene_number) const
-+const Element ConstrainedRealVector::gene(const unsigned int gene_number) const
- {
- Element retval;
-
-@@ -845,7 +844,7 @@
- // This constructor is used to initialize the first
- // generation of any particular bitvector. Right
- // now bits are assumed to be unsigned chars.
--BitVector::BitVector(int num_els)
-+BitVector::BitVector(/* not const */ int num_els)
- : Representation(num_els)
- {
-
-@@ -862,7 +861,7 @@
-
- //______________________________________________________________________________
- //
--BitVector::BitVector(int num_els, Real prob)
-+BitVector::BitVector(/* not const */ int num_els, const Real prob)
- : Representation(num_els)
- {
-
-@@ -903,7 +902,7 @@
-
- //______________________________________________________________________________
- //
--void BitVector::write(unsigned char value, int gene)
-+void BitVector::write(const unsigned char value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -915,7 +914,7 @@
-
- //______________________________________________________________________________
- //
--void BitVector::write(FourByteLong value, int gene)
-+void BitVector::write(const FourByteLong value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -928,7 +927,7 @@
-
- //______________________________________________________________________________
- //
--void BitVector::write(double value, int gene)
-+void BitVector::write(const double value, const int gene)
- {
-
- #ifdef DEBUG
-@@ -942,7 +941,7 @@
-
- //______________________________________________________________________________
- //
--void BitVector::write(const Element value, int gene)
-+void BitVector::write(const Element value, const int gene) /* not const */
- {
-
- #ifdef DEBUG
-@@ -955,7 +954,7 @@
-
- //______________________________________________________________________________
- //
--const Element BitVector::gene(unsigned int gene_number) const
-+const Element BitVector::gene(const unsigned int gene_number) const
- {
- Element retval;
-
-Index: autodocksuite-4.2.3/autodock/rep.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/rep.h 2010-07-31 23:49:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/rep.h 2010-08-01 00:50:41.000000000 +0200
-@@ -72,7 +72,7 @@
-
- public:
- Representation(void);
-- Representation(unsigned int);
-+ Representation(const unsigned int);
- virtual ~Representation(void);
- virtual Representation &operator=(const Representation &) = 0;
- unsigned int number_of_points(void) const;
-@@ -80,11 +80,11 @@
- void set_normalized_true(void);
- void set_normalized_false(void);
- virtual RepType type(void) const;
-- virtual void write(unsigned char, int) = 0;
-- virtual void write(FourByteLong, int) = 0;
-- virtual void write(double, int) = 0;
-+ virtual void write(const unsigned char, const int) = 0; /* not const, e.g. in bitvector */
-+ virtual void write(const FourByteLong, const int) = 0;
-+ virtual void write(const double, const int) = 0; /* not const, e.g. in RealVector */
- virtual void write(const Element, int) = 0;
-- virtual const Element gene(unsigned int) const = 0;
-+ virtual const Element gene(const unsigned int) const = 0;
- virtual Representation *clone(void) const = 0;
- virtual const void *internals(void) const = 0;
- };
-@@ -101,17 +101,17 @@
-
- public:
- IntVector(void);
-- IntVector(int);
-- IntVector(int, FourByteLong *);
-- IntVector(int, FourByteLong, FourByteLong);
-+ IntVector(const int);
-+ IntVector(const int, FourByteLong *const);
-+ IntVector(const int, const FourByteLong, const FourByteLong);
- IntVector(const IntVector &);
- ~IntVector(void);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-- void write(double, int);
-- void write(const Element, int);
-+ void write(const unsigned char, const int); /* not const - inherited */
-+ void write(const FourByteLong, const int); /* not const */
-+ void write(const double, const int);
-+ void write(const Element, const int); /* not const */
- Representation &operator=(const Representation &);
-- const Element gene(unsigned int) const;
-+ const Element gene(const unsigned int) const;
- };
-
- class RealVector : public Representation
-@@ -133,20 +133,20 @@
- mytype = T_RealV;
- }
-
-- RealVector(int);
-- RealVector(int, double *);
-- RealVector(int, double, double);
-+ RealVector(/* not const */ int);
-+ RealVector(const int, double *const);
-+ RealVector(/* not const */ int, const double, const double);
- // Use this to set the first value in the vector--useful for random quaternions
-- RealVector(int, double, double, double);
-- RealVector(int, double, double, double, double, double, double); // sets a quaternion's x,y,z,w values
-+ RealVector(const int, const double, const double, const double);
-+ RealVector(const int, const double, const double, const double, const double, const double, const double); // sets a quaternion's x,y,z,w values
- // Use this to create a vector of length 3 with these values--useful for random quaternions
-- RealVector(int, double, double, double, double, double );
-+ RealVector(const int, const double, const double, const double, const double, const double );
- RealVector(const RealVector &);
- ~RealVector(void);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-+ void write(const unsigned char, const int) /* not const - inherited */;
-+ void write(const FourByteLong, const int); /* not const, e.g. in IntVector */
- // void write(const void *, int);
-- void write(const Element, int);
-+ void write(const Element, const int) /* not const */;
- Representation &operator=(const Representation &);
- // const void *gene(unsigned int) const;
- #ifdef DEBUG
-@@ -166,11 +166,11 @@
- }
- */
- // non-inlined versions, possibly with range checking
-- void write(double, int);
-- const Element gene(unsigned int) const;
-+ void write(const double, const int) /* not const */;
-+ const Element gene(const unsigned int) const;
- #else
- // non-inlined versions, possibly with range checking
-- void write(double, int);
-+ void write(const double, const int) /* not const */;
- const Element gene(unsigned int) const;
- #endif
- };
-@@ -186,22 +186,22 @@
-
- const void *internals(void) const;
- Representation *clone(void) const;
-- void normalize(void);
-+ void normalize(void); /* not const */
-
- public:
- ConstrainedRealVector(void);
-- ConstrainedRealVector(int);
-- ConstrainedRealVector(int, double *);
-- ConstrainedRealVector(int, double, double);
-+ ConstrainedRealVector(/* not const */ int);
-+ ConstrainedRealVector(int, double *const);
-+ ConstrainedRealVector(/* not const */ int, const double, const double);
- ConstrainedRealVector(const ConstrainedRealVector &);
- ~ConstrainedRealVector(void);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-- void write(double, int);
-- void write(const Element, int);
-+ void write(const unsigned char, const int) /* not const - inherited */;
-+ void write(const FourByteLong, const int) /* not const - e.g. in IntVector */;
-+ void write(const double, const int); /* not const */
-+ void write(const Element, const int); /* not const */
- void write(double, double, double, double);
- Representation &operator=(const Representation &);
-- const Element gene(unsigned int) const;
-+ const Element gene(const unsigned int) const;
- };
-
- class BitVector : public Representation
-@@ -216,19 +216,19 @@
-
- public:
- BitVector(void);
-- BitVector(int);
-- BitVector(int, unsigned char *);
-- BitVector(int, Real);
-+ BitVector(/* not const */ int);
-+ BitVector(int, unsigned char *const);
-+ BitVector(/* not const */ int, const Real);
- BitVector(const BitVector &);
- ~BitVector(void);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-- void write(double, int);
-+ void write(const unsigned char, const int); /* not const */
-+ void write(const FourByteLong, const int); /* not const - inherited */
-+ void write(const double, const int); /* not const - inherited */
- // void write(const void *, int);
-- void write(const Element, int);
-+ void write(const Element, const int); /* not const */
- Representation &operator=(const Representation &);
- // const void *gene(unsigned int) const;
-- const Element gene(unsigned int) const;
-+ const Element gene(const unsigned int) const;
- };
-
- /**************************************************************************
-@@ -241,7 +241,7 @@
- mytype = T_BASE;
- }
-
--inline Representation::Representation(unsigned int pts)
-+inline Representation::Representation(const unsigned int pts)
- : number_of_pts(pts)
- {
- }
-@@ -288,7 +288,7 @@
- }
-
- // This constructor does a shallow copy of the array
--inline IntVector::IntVector(int num_els, FourByteLong *array)
-+inline IntVector::IntVector(const int num_els, FourByteLong *const array)
- : Representation(num_els), vector(array)
- {
- mytype = T_IntV;
-@@ -308,7 +308,7 @@
- }
-
- // This performs a shallow copy of the array
--inline RealVector::RealVector(int num_els, double *array)
-+inline RealVector::RealVector(const int num_els, double *const array)
- : Representation(num_els), high(REALV_HIGH), low(REALV_LOW),
- vector(array)
- {
-@@ -336,7 +336,7 @@
- mytype = T_CRealV;
- }
-
--inline ConstrainedRealVector::ConstrainedRealVector(int num_els, double *array)
-+inline ConstrainedRealVector::ConstrainedRealVector(const int num_els, double *const array)
- : Representation(num_els)
- {
- normalized = 0;
-@@ -365,7 +365,7 @@
- }
-
- // Do a shallow copy
--inline BitVector::BitVector(int num_els, unsigned char *array)
-+inline BitVector::BitVector(int num_els, unsigned char *const array)
- : Representation(num_els)
- {
- vector = array;
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,692 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/com.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/com.cc 2010-08-01 00:52:47.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/com.cc 2010-08-01 01:08:29.000000000 +0200
-@@ -36,10 +36,10 @@
-
- extern FILE *logFile;
-
--void advnst(FourByteLong k)
-+void advnst(const FourByteLong k)
- /*
- **********************************************************************
-- void advnst(FourByteLong k)
-+ void advnst(const FourByteLong k)
- ADV-a-N-ce ST-ate
- Advances the state of the current generator by 2^K values and
- resets the initial seed to that value.
-@@ -54,7 +54,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern void gscgn(FourByteLong getset,FourByteLong *g);
- extern FourByteLong Xm1,Xm2,Xa1,Xa2,Xcg1[],Xcg2[];
- static FourByteLong g,i,ib1,ib2;
-@@ -80,7 +80,7 @@
- */
- #undef numg
- }
--void getsd(FourByteLong *iseed1,FourByteLong *iseed2)
-+void getsd(FourByteLong *const iseed1,FourByteLong *const iseed2)
- /*
- **********************************************************************
- void getsd(FourByteLong *iseed1,FourByteLong *iseed2)
-@@ -98,7 +98,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern void gscgn(FourByteLong getset,FourByteLong *g);
- extern FourByteLong Xcg1[],Xcg2[];
- static FourByteLong g;
-@@ -133,9 +133,9 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
--extern void gssst(FourByteLong getset,FourByteLong *qset);
--extern void gscgn(FourByteLong getset,FourByteLong *g);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
-+extern void gssst(const FourByteLong getset,FourByteLong *const qset);
-+extern void gscgn(const FourByteLong getset,FourByteLong *const g);
- extern void inrgcm(void);
- extern FourByteLong Xm1,Xm2,Xa1,Xa2,Xcg1[],Xcg2[];
- extern FourByteLong Xqanti[];
-@@ -171,7 +171,7 @@
- return ignlgi;
- #undef numg
- }
--void initgn(FourByteLong isdtyp)
-+void initgn(const FourByteLong isdtyp)
- /*
- **********************************************************************
- void initgn(FourByteLong isdtyp)
-@@ -193,7 +193,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern void gscgn(FourByteLong getset,FourByteLong *g);
- extern FourByteLong Xm1,Xm2,Xa1w,Xa2w,Xig1[],Xig2[],Xlg1[],Xlg2[],Xcg1[],Xcg2[];
- static FourByteLong g;
-@@ -244,7 +244,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern FourByteLong Xm1,Xm2,Xa1,Xa2,Xa1w,Xa2w,Xa1vw,Xa2vw;
- extern FourByteLong Xqanti[];
- static FourByteLong T1;
-@@ -273,7 +273,7 @@
- gsrgs(1L,&T1);
- #undef numg
- }
--void setall(FourByteLong iseed1,FourByteLong iseed2)
-+void setall(const FourByteLong iseed1,const FourByteLong iseed2)
- /*
- **********************************************************************
- void setall(FourByteLong iseed1,FourByteLong iseed2)
-@@ -293,9 +293,9 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
--extern void gssst(FourByteLong getset,FourByteLong *qset);
--extern void gscgn(FourByteLong getset,FourByteLong *g);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
-+extern void gssst(const FourByteLong getset,FourByteLong *const qset);
-+extern void gscgn(const FourByteLong getset,FourByteLong *const g);
- extern FourByteLong Xm1,Xm2,Xa1vw,Xa2vw,Xig1[],Xig2[];
- static FourByteLong T1;
- static FourByteLong g,ocgn;
-@@ -324,7 +324,7 @@
- gscgn(1L,&ocgn);
- #undef numg
- }
--void setant(FourByteLong qvalue)
-+void setant(const FourByteLong qvalue)
- /*
- **********************************************************************
- void setant(FourByteLong qvalue)
-@@ -347,7 +347,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern void gscgn(FourByteLong getset,FourByteLong *g);
- extern FourByteLong Xqanti[];
- static FourByteLong g;
-@@ -365,7 +365,7 @@
- Xqanti[g-1] = qvalue;
- #undef numg
- }
--void setsd(FourByteLong iseed1,FourByteLong iseed2)
-+void setsd(const FourByteLong iseed1,const FourByteLong iseed2)
- /*
- **********************************************************************
- void setsd(FourByteLong iseed1,FourByteLong iseed2)
-@@ -384,7 +384,7 @@
- */
- {
- #define numg 32L
--extern void gsrgs(FourByteLong getset,FourByteLong *qvalue);
-+extern void gsrgs(const FourByteLong getset,FourByteLong *const qvalue);
- extern void gscgn(FourByteLong getset,FourByteLong *g);
- extern FourByteLong Xig1[],Xig2[];
- static FourByteLong g;
-Index: autodocksuite-4.2.3/autodock/ranlib.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ranlib.cc 2010-08-01 01:01:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ranlib.cc 2010-08-01 15:55:22.000000000 +0200
-@@ -38,12 +38,12 @@
- #define MIN(a,b) ((a) <= (b) ? (a) : (b))
- #define MAX(a,b) ((a) >= (b) ? (a) : (b))
-
--void ftnstop(const char*);
-+void ftnstop(const char *const);
-
- extern FILE *logFile;
-
-
--Real genbet(Real aa,Real bb)
-+Real genbet(const Real aa,const Real bb)
- /*
- **********************************************************************
- Real genbet(Real aa,Real bb)
-@@ -206,7 +206,7 @@
- #undef expmax
- #undef infnty
- }
--Real genchi(Real df)
-+Real genchi(const Real df)
- /*
- **********************************************************************
- Real genchi(Real df)
-@@ -233,7 +233,7 @@
- genchi = 2.0*gengam(1.0,df/2.0);
- return genchi;
- }
--Real genexp(Real av)
-+Real genexp(const Real av)
- /*
- **********************************************************************
- Real genexp(Real av)
-@@ -260,7 +260,7 @@
- genexp = sexpo()*av;
- return genexp;
- }
--Real genf(Real dfn,Real dfd)
-+Real genf(const Real dfn,const Real dfd)
- /*
- **********************************************************************
- Real genf(Real dfn,Real dfd)
-@@ -302,7 +302,7 @@
- S30:
- return genf;
- }
--Real gengam(Real a,Real r)
-+Real gengam(const Real a,const Real r)
- /*
- **********************************************************************
- Real gengam(Real a,Real r)
-@@ -339,7 +339,7 @@
- gengam /= a;
- return gengam;
- }
--void genmn(Real *parm,Real *x,Real *work)
-+void genmn(const Real *const parm,/* not const */ Real *const x,/* not const */ Real *const work)
- /*
- **********************************************************************
- void genmn(Real *parm,Real *x,Real *work)
-@@ -390,7 +390,7 @@
- *(x+i-1) = ae+*(parm+i);
- }
- }
--void genmul(FourByteLong n,Real *p,FourByteLong ncat,FourByteLong *ix)
-+void genmul(const FourByteLong n,const Real *const p,const FourByteLong ncat,/* not const */ FourByteLong *const ix)
- /*
- **********************************************************************
-
-@@ -451,7 +451,7 @@
- */
- return;
- }
--Real gennch(Real df,Real xnonc)
-+Real gennch(const Real df,const Real xnonc)
- /*
- **********************************************************************
- Real gennch(Real df,Real xnonc)
-@@ -482,7 +482,7 @@
- gennch = genchi(df-1.0)+pow(gennor(sqrt(xnonc),1.0),2.0);
- return gennch;
- }
--Real gennf(Real dfn,Real dfd,Real xnonc)
-+Real gennf(const Real dfn,const Real dfd,const Real xnonc)
- /*
- **********************************************************************
- Real gennf(Real dfn,Real dfd,Real xnonc)
-@@ -534,7 +534,7 @@
- S30:
- return gennf;
- }
--Real gennor(Real av,Real sd)
-+Real gennor(const Real av,const Real sd)
- /*
- **********************************************************************
- Real gennor(Real av,Real sd)
-@@ -561,7 +561,7 @@
- gennor = sd*snorm()+av;
- return gennor;
- }
--void genprm(FourByteLong *iarray,int larray)
-+void genprm(/* not const */ FourByteLong *const iarray,const int larray)
- /*
- **********************************************************************
- void genprm(FourByteLong *iarray,int larray)
-@@ -582,7 +582,7 @@
- *(iarray+i-1) = itmp;
- }
- }
--Real genunf(Real low,Real high)
-+Real genunf(const Real low,const Real high)
- /*
- **********************************************************************
- Real genunf(Real low,Real high)
-@@ -605,7 +605,7 @@
- genunf = low+(high-low)*ranf();
- return genunf;
- }
--void gscgn(FourByteLong getset,FourByteLong *g)
-+void gscgn(const FourByteLong getset,FourByteLong *const g)
- /*
- **********************************************************************
- void gscgn(FourByteLong getset,FourByteLong *g)
-@@ -630,7 +630,7 @@
- }
- #undef numg
- }
--void gsrgs(FourByteLong getset,FourByteLong *qvalue)
-+void gsrgs(const FourByteLong getset,FourByteLong *const qvalue)
- /*
- **********************************************************************
- void gsrgs(FourByteLong getset,FourByteLong *qvalue)
-@@ -647,7 +647,7 @@
- if(getset == 0) *qvalue = qinit;
- else qinit = *qvalue;
- }
--void gssst(FourByteLong getset,FourByteLong *qset)
-+void gssst(const FourByteLong getset,FourByteLong *const qset)
- /*
- **********************************************************************
- void gssst(FourByteLong getset,FourByteLong *qset)
-@@ -663,7 +663,7 @@
- if(getset != 0) qstate = 1;
- else *qset = qstate;
- }
--FourByteLong ignbin(FourByteLong n,Real pp)
-+FourByteLong ignbin(const FourByteLong n,const Real pp)
- /*
- **********************************************************************
- FourByteLong ignbin(FourByteLong n,Real pp)
-@@ -920,7 +920,7 @@
- ignbin = ix;
- return ignbin;
- }
--FourByteLong ignnbn(FourByteLong n,Real p)
-+FourByteLong ignnbn(const FourByteLong n,const Real p)
- /*
- **********************************************************************
-
-@@ -967,7 +967,7 @@
- ignnbn = ignpoi(y);
- return ignnbn;
- }
--FourByteLong ignpoi(Real mu)
-+FourByteLong ignpoi(const Real mu)
- /*
- **********************************************************************
- FourByteLong ignpoi(Real mu)
-@@ -1206,7 +1206,7 @@
- ignpoi = k;
- return ignpoi;
- }
--FourByteLong ignuin(FourByteLong low,FourByteLong high)
-+FourByteLong ignuin(const FourByteLong low,const FourByteLong high)
- /*
- **********************************************************************
- FourByteLong ignuin(FourByteLong low,FourByteLong high)
-@@ -1261,7 +1261,7 @@
- #undef err1
- #undef err2
- }
--FourByteLong lennob( char *str )
-+FourByteLong lennob( const char *const str )
- /*
- Returns the length of str ignoring trailing blanks but not
- other white space.
-@@ -1273,7 +1273,7 @@
- if ( *(str+i) != ' ' ) i_nb = i;
- return (i_nb+1);
- }
--FourByteLong mltmod(FourByteLong a,FourByteLong s,FourByteLong m)
-+FourByteLong mltmod(const FourByteLong a,const FourByteLong s,const FourByteLong m)
- /*
- **********************************************************************
- FourByteLong mltmod(FourByteLong a,FourByteLong s,FourByteLong m)
-@@ -1367,7 +1367,7 @@
- return mltmod;
- #undef h
- }
--void phrtsd(char* phrase,FourByteLong *seed1,FourByteLong *seed2)
-+void phrtsd(const char *const phrase,FourByteLong *const seed1,FourByteLong *const seed2)
- /*
- **********************************************************************
- void phrtsd(char* phrase,FourByteLong *seed1,FourByteLong *seed2)
-@@ -1406,7 +1406,7 @@
- 1L,64L,4096L,262144L,16777216L
- };
- static FourByteLong i,ichr,j,lphr,values[5];
--extern FourByteLong lennob(char *str);
-+extern FourByteLong lennob(const char *const str);
-
- *seed1 = 1234567890L;
- *seed2 = 123456789L;
-@@ -1453,7 +1453,7 @@
- ranf = ignlgi()*4.656613057E-10;
- return ranf;
- }
--void setgmn(Real *meanv,Real *covm,FourByteLong p,Real *parm)
-+void setgmn(const Real *const meanv,Real *const covm,const FourByteLong p,Real *const parm)
- /*
- **********************************************************************
- void setgmn(Real *meanv,Real *covm,FourByteLong p,Real *parm)
-@@ -1477,7 +1477,7 @@
- **********************************************************************
- */
- {
--extern void spofa(Real *a,FourByteLong lda,FourByteLong n,FourByteLong *info);
-+extern void spofa(/* not const */ Real *const a,const FourByteLong lda,const FourByteLong n,/* not const */ FourByteLong *const info);
- /* not used: static FourByteLong T1; */
- static FourByteLong i,icount,info,j,D2,D3,D4,D5;
- /* not used: T1 = p*(p+3)/2+1; */
-@@ -1929,7 +1929,7 @@
- FTNSTOP:
- Prints msg to standard error and then exits
- ************************************************************************/
--void ftnstop(const char* msg)
-+void ftnstop(const char *const msg)
- /* msg - error message */
- {
- if (msg != NULL) fprintf(stderr,"%s\n",msg);
-Index: autodocksuite-4.2.3/autodock/ranlib.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ranlib.h 2010-08-01 00:57:46.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ranlib.h 2010-08-01 15:48:17.000000000 +0200
-@@ -31,38 +31,38 @@
-
- #include "typedefs.h"
-
--extern void advnst(FourByteLong k);
--extern Real genbet(Real aa,Real bb);
--extern Real genchi(Real df);
--extern Real genexp(Real av);
--extern Real genf(Real dfn, Real dfd);
--extern Real gengam(Real a,Real r);
--extern void genmn(Real *parm,Real *x,Real *work);
--extern void genmul(FourByteLong n,Real *p,FourByteLong ncat,FourByteLong *ix);
--extern Real gennch(Real df,Real xnonc);
--extern Real gennf(Real dfn, Real dfd, Real xnonc);
--extern Real gennor(Real av,Real sd);
--extern void genprm(FourByteLong *iarray,int larray);
--extern Real genunf(Real low,Real high);
--extern void getsd(FourByteLong *iseed1,FourByteLong *iseed2);
--extern void gscgn(FourByteLong getset,FourByteLong *g);
--extern FourByteLong ignbin(FourByteLong n,Real pp);
--extern FourByteLong ignnbn(FourByteLong n,Real p);
-+extern void advnst(const FourByteLong k);
-+extern Real genbet(const Real aa,const Real bb);
-+extern Real genchi(const Real df);
-+extern Real genexp(const Real av);
-+extern Real genf(const Real dfn, const Real dfd);
-+extern Real gengam(const Real a,const Real r);
-+extern void genmn(const Real *const parm, /* not const */ Real *const x, /* not const */ Real *const work);
-+extern void genmul(const FourByteLong n,const Real *const p,const FourByteLong ncat,/* not const */ FourByteLong *const ix);
-+extern Real gennch(const Real df,const Real xnonc);
-+extern Real gennf(const Real dfn, const Real dfd, const Real xnonc);
-+extern Real gennor(const Real av,const Real sd);
-+extern void genprm(/* not const */FourByteLong *const iarray,const int larray);
-+extern Real genunf(const Real low,const Real high);
-+extern void getsd(FourByteLong *const iseed1,FourByteLong *const iseed2);
-+extern void gscgn(const FourByteLong getset,const FourByteLong *g);
-+extern FourByteLong ignbin(const FourByteLong n,const Real pp);
-+extern FourByteLong ignnbn(const FourByteLong n,const Real p);
- extern FourByteLong ignlgi(void);
--extern FourByteLong ignpoi(Real mu);
--extern FourByteLong ignuin(FourByteLong low,FourByteLong high);
--extern void initgn(FourByteLong isdtyp);
--extern FourByteLong mltmod(FourByteLong a,FourByteLong s,FourByteLong m);
--extern void phrtsd(char* phrase,FourByteLong* seed1,FourByteLong* seed2);
-+extern FourByteLong ignpoi(const Real mu);
-+extern FourByteLong ignuin(const FourByteLong low,const FourByteLong high);
-+extern void initgn(const FourByteLong isdtyp);
-+extern FourByteLong mltmod(const FourByteLong a,const FourByteLong s,const FourByteLong m);
-+extern void phrtsd(const char *const phrase,FourByteLong *const seed1,FourByteLong *const seed2);
- extern Real ranf(void);
--extern void setall(FourByteLong iseed1,FourByteLong iseed2);
--extern void setant(FourByteLong qvalue);
--extern void setgmn(Real *meanv,Real *covm,FourByteLong p,Real *parm);
--extern void setsd(FourByteLong iseed1,FourByteLong iseed2);
-+extern void setall(const FourByteLong iseed1,const FourByteLong iseed2);
-+extern void setant(const FourByteLong qvalue);
-+extern void setgmn(const Real *const meanv,Real *const covm,const FourByteLong p,Real *const parm);
-+extern void setsd(const FourByteLong iseed1,const FourByteLong iseed2);
- extern Real sexpo(void);
- extern Real sgamma(Real a);
- extern Real snorm(void);
--extern Real rcauchy(Real, Real);
-+extern Real rcauchy(const Real, const Real);
- extern Real scauchy1(void);
- extern Real scauchy2(void);
-
-Index: autodocksuite-4.2.3/autodock/gencau.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/gencau.cc 2010-08-01 15:47:27.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/gencau.cc 2010-08-01 15:47:54.000000000 +0200
-@@ -33,7 +33,7 @@
- #include "ranlib.h"
-
-
--Real rcauchy(Real alpha, Real beta)
-+Real rcauchy(const Real alpha, const Real beta)
- /*
- **********************************************************************
- Real rcauchy(Real alpha, Real beta)
-Index: autodocksuite-4.2.3/autodock/linpack.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/linpack.cc 2010-08-01 15:42:47.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/linpack.cc 2010-08-01 15:45:04.000000000 +0200
-@@ -43,7 +43,7 @@
- sdot = stemp;
- return sdot;
- }
--void spofa(Real *a,FourByteLong lda,FourByteLong n,FourByteLong *info)
-+void spofa(/* not const */ Real *const a,const FourByteLong lda,const FourByteLong n,/* not const */ FourByteLong *const info)
- /*
- SPOFA FACTORS A REAL SYMMETRIC POSITIVE DEFINITE MATRIX.
- SPOFA IS USUALLY CALLED BY SPOCO, BUT IT CAN BE CALLED
-Index: autodocksuite-4.2.3/autodock/cluster_analysis.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cluster_analysis.cc 2010-08-01 20:04:01.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cluster_analysis.cc 2010-08-01 20:10:59.000000000 +0200
-@@ -32,21 +32,21 @@
- #include "cluster_analysis.h"
-
-
--int cluster_analysis( Real clus_rms_tol,
-- int cluster[MAX_RUNS][MAX_RUNS],
-- int num_in_clus[MAX_RUNS],
-- int isort[MAX_RUNS],
-- int nconf,
-- int natom,
-- int type[MAX_ATOMS],
-- Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- Real sml_center[SPACE],
-- Real clu_rms[MAX_RUNS][MAX_RUNS],
-- Boole B_symmetry_flag,
-- Real ref_crds[MAX_ATOMS][SPACE],
-- int ref_natoms,
-- Real ref_rms[MAX_RUNS])
-+int cluster_analysis( const Real clus_rms_tol,
-+ /* not const */ int cluster[MAX_RUNS][MAX_RUNS],
-+ /* not const */ int num_in_clus[MAX_RUNS],
-+ const int isort[MAX_RUNS],
-+ const int nconf,
-+ const int natom,
-+ const int type[MAX_ATOMS],
-+ const Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real sml_center[SPACE],
-+ /* not const */ Real clu_rms[MAX_RUNS][MAX_RUNS],
-+ const Boole B_symmetry_flag,
-+ /* not const */ Real ref_crds[MAX_ATOMS][SPACE],
-+ const int ref_natoms,
-+ /* not const */ Real ref_rms[MAX_RUNS])
- {
- /* __________________________________________________________________________
- | Cluster Analysis |
-Index: autodocksuite-4.2.3/autodock/cluster_analysis.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cluster_analysis.h 2010-08-01 20:04:01.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cluster_analysis.h 2010-08-01 20:11:26.000000000 +0200
-@@ -30,19 +30,19 @@
- #include "getrms.h"
-
-
--int cluster_analysis( Real clus_rms_tol,
-- int cluster[MAX_RUNS][MAX_RUNS],
-- int num_in_clus[MAX_RUNS],
-- int isort[MAX_RUNS],
-- int nconf,
-- int natom,
-- int type[MAX_ATOMS],
-- Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- Real sml_center[SPACE],
-- Real clu_rms[MAX_RUNS][MAX_RUNS],
-- Boole B_symmetry_flag,
-- Real ref_crds[MAX_ATOMS][SPACE],
-- int ref_natoms,
-- Real ref_rms[MAX_RUNS]);
-+int cluster_analysis( const Real clus_rms_tol,
-+ /* not const */ int cluster[MAX_RUNS][MAX_RUNS],
-+ /* not const */ int num_in_clus[MAX_RUNS],
-+ const int isort[MAX_RUNS],
-+ const int nconf,
-+ const int natom,
-+ const int type[MAX_ATOMS],
-+ const Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real sml_center[SPACE],
-+ /* not const */ Real clu_rms[MAX_RUNS][MAX_RUNS],
-+ const Boole B_symmetry_flag,
-+ /* not const */ Real ref_crds[MAX_ATOMS][SPACE],
-+ const int ref_natoms,
-+ /* not const */ Real ref_rms[MAX_RUNS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/getrms.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getrms.cc 2010-08-01 20:12:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getrms.cc 2010-08-01 20:13:46.000000000 +0200
-@@ -32,11 +32,11 @@
- #include "getrms.h"
-
-
--Real getrms ( Real Crd[MAX_ATOMS][SPACE],
-- Real CrdRef[MAX_ATOMS][SPACE],
-- Boole B_symmetry_flag,
-- int natom,
-- int type[MAX_ATOMS] )
-+Real getrms ( const Real Crd[MAX_ATOMS][SPACE],
-+ const Real CrdRef[MAX_ATOMS][SPACE],
-+ const Boole B_symmetry_flag,
-+ const int natom,
-+ const int type[MAX_ATOMS] )
-
- {
- double sqrSum, sqrMin, dc[SPACE];
-Index: autodocksuite-4.2.3/autodock/getrms.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getrms.h 2010-08-01 20:12:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getrms.h 2010-08-01 20:13:30.000000000 +0200
-@@ -29,9 +29,9 @@
-
- #include "constants.h"
-
--Real getrms( Real Crd[MAX_ATOMS][SPACE],
-- Real CrdRef[MAX_ATOMS][SPACE],
-- Boole B_symmetry_flag,
-- int natom,
-- int type[MAX_ATOMS] );
-+Real getrms( const Real Crd[MAX_ATOMS][SPACE],
-+ const Real CrdRef[MAX_ATOMS][SPACE],
-+ const Boole B_symmetry_flag,
-+ const int natom,
-+ const int type[MAX_ATOMS] );
- #endif
-Index: autodocksuite-4.2.3/autodock/clmode.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/clmode.cc 2010-08-01 20:15:47.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/clmode.cc 2010-08-01 20:17:11.000000000 +0200
-@@ -41,17 +41,17 @@
- extern FILE *logFile;
- extern char *programname;
-
--void clmode( int num_atm_maps,
-- Real clus_rms_tol,
-- char *hostnm,
-- Clock jobStart,
-+void clmode( const int num_atm_maps,
-+ const Real clus_rms_tol,
-+ const char *const hostnm,
-+ const Clock jobStart,
- struct tms tms_jobStart,
-- Boole write_all_clusmem,
-- char *clusFN,
-- Real crdpdb[MAX_ATOMS][SPACE],
-- Real sml_center[SPACE],
-- Boole symmetry_flag,
-- char *rms_ref_crds )
-+ const Boole write_all_clusmem,
-+ const char *const clusFN,
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real sml_center[SPACE],
-+ const Boole symmetry_flag,
-+ const char *const rms_ref_crds )
-
- {
- FILE *clusFile;
-Index: autodocksuite-4.2.3/autodock/clmode.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/clmode.h 2010-08-01 20:15:47.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/clmode.h 2010-08-01 20:17:43.000000000 +0200
-@@ -39,15 +39,15 @@
- #include "success.h"
- #include "qmultiply.h"
- #include "openfile.h"
--void clmode( int num_atm_maps,
-- Real clus_rms_tol,
-- char hostnm[MAX_CHARS],
-- Clock jobStart,
-+void clmode( const int num_atm_maps,
-+ const Real clus_rms_tol,
-+ const char hostnm[MAX_CHARS],
-+ const Clock jobStart,
- struct tms tms_jobStart,
-- Boole B_write_all_clusmem,
-- char *clusFN,
-- Real crdpdb[MAX_ATOMS][SPACE],
-- Real sml_center[SPACE],
-- Boole B_symmetry_flag,
-- char *rms_ref_crds );
-+ const Boole B_write_all_clusmem,
-+ const char *const clusFN,
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real sml_center[SPACE],
-+ const Boole B_symmetry_flag,
-+ const char *const rms_ref_crds );
- #endif
-Index: autodocksuite-4.2.3/autodock/getpdbcrds.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getpdbcrds.cc 2010-08-01 20:18:17.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getpdbcrds.cc 2010-08-01 20:19:02.000000000 +0200
-@@ -40,8 +40,8 @@
- extern char *programname;
-
-
--int getpdbcrds( char *rms_ref_crds_FN,
-- Real ref_crds[MAX_ATOMS][SPACE] )
-+int getpdbcrds( const char *const rms_ref_crds_FN,
-+ /* not const */ Real ref_crds[MAX_ATOMS][SPACE] )
- {
- int ii=0;
- int natoms=0;
-Index: autodocksuite-4.2.3/autodock/getpdbcrds.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getpdbcrds.h 2010-08-01 20:18:17.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getpdbcrds.h 2010-08-01 20:19:17.000000000 +0200
-@@ -30,6 +30,6 @@
- #include "constants.h"
- #include "openfile.h"
-
--int getpdbcrds( char *rms_ref_crds_FN,
-- Real ref_crds[MAX_ATOMS][SPACE] );
-+int getpdbcrds( const char *const rms_ref_crds_FN,
-+ /* not const */ Real ref_crds[MAX_ATOMS][SPACE] );
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,721 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/ls.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.cc 2010-08-01 20:21:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.cc 2010-08-01 20:33:53.000000000 +0200
-@@ -85,7 +85,7 @@
- // This has only one value of rho, for all genes.
- // SW mapped individual
- // SW returns TRUE if it modifies the individual
--Boole Solis_Wets::SW(Phenotype &vector)
-+Boole Solis_Wets::SW(/* not const */ Phenotype &vector)
- {
- register unsigned int i, j, num_successes = 0, num_failures = 0;
- register Real temp_rho = rho;
-@@ -106,10 +106,10 @@
- #ifdef DEBUG
- //convenience function for debugging
- #define traceState(msg,vector) printDState(logFile,msg,vector,i,prevxyz,startxyz,prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates)
--void printDState(FILE *const logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-- Real startxyz[3], Quat prevQuat, Quat startQuat,
-- unsigned int num_successes, unsigned int num_failures,
-- Real temp_rho, Real * bias, Real * deviates);
-+void printDState(FILE *const logFile, const char *const msg,Phenotype &newPh, const int i, const Real prevxyz[3],
-+ const Real startxyz[3], const Quat prevQuat, const Quat startQuat,
-+ const unsigned int num_successes, const unsigned int num_failures,
-+ const Real temp_rho, Real *const bias, Real *const deviates);
- Real xyz[3];
- Real prevxyz[3];
- Real startxyz[3];
-@@ -245,7 +245,7 @@
- // This has a different value of rho for each gene.
- // PSW mapped individual
- // PSW returns TRUE if it modifies the individual
--Boole Pseudo_Solis_Wets::SW(Phenotype &vector)
-+Boole Pseudo_Solis_Wets::SW(/* not const */ Phenotype &vector)
- {
- register unsigned int i, j, num_successes = 0, num_failures = 0, all_rho_stepsizes_too_small = 1;
-
-@@ -523,10 +523,10 @@
- return newPoint;
- }
- //void printDState(logFile,msg,vector,i,prevxyz,startxyz, prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates);
--void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-- Real startxyz[3], const Quat prevQuat, const Quat startQuat,
-- unsigned int num_successes, unsigned int num_failures,
-- Real temp_rho, Real * bias, Real * deviates)
-+void printDState(FILE *logFile, const char *const msg,Phenotype &newPh, const int i, const Real prevxyz[3],
-+ const Real startxyz[3], const Quat prevQuat, const Quat startQuat,
-+ const unsigned int num_successes, const unsigned int num_failures,
-+ const Real temp_rho, const Real *const bias, const Real *const deviates)
- {
- #ifdef DEBUG
- Real dt; // translation step scalar
-Index: autodocksuite-4.2.3/autodock/ls.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.h 2010-08-01 20:21:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.h 2010-08-01 20:34:27.000000000 +0200
-@@ -92,8 +92,8 @@
- Solis_Wets_Base(void);
- Solis_Wets_Base(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
- virtual ~Solis_Wets_Base(void);
-- virtual double gen_deviates(Real) = 0;
-- virtual Boole SW(Phenotype &) = 0;
-+ virtual double gen_deviates(const Real) const = 0;
-+ virtual Boole SW(/* not const */ Phenotype &) = 0;
- virtual void reset(void);
- virtual int terminate(void) const;
- int search(Individual &);
-@@ -108,8 +108,8 @@
- Solis_Wets(void);
- Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
- virtual ~Solis_Wets(void);
-- virtual double gen_deviates(Real) = 0;
-- Boole SW(Phenotype &);
-+ virtual double gen_deviates(const Real) const = 0;
-+ Boole SW(/* not const */ Phenotype &);
- };
-
- class Pseudo_Solis_Wets : public Solis_Wets_Base
-@@ -123,7 +123,7 @@
- Pseudo_Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
- Pseudo_Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
- virtual ~Pseudo_Solis_Wets(void);
-- virtual double gen_deviates(Real) = 0;
-+ virtual double gen_deviates(const Real) const = 0;
- Boole SW(Phenotype &);
- };
-
-@@ -133,7 +133,7 @@
- Solis_Wets1(void);
- Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
- ~Solis_Wets1(void);
-- double gen_deviates(Real);
-+ double gen_deviates(const Real) const;
- };
-
- class Solis_Wets2 : public Solis_Wets
-@@ -142,7 +142,7 @@
- Solis_Wets2(void);
- Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
- ~Solis_Wets2(void);
-- double gen_deviates(Real);
-+ double gen_deviates(const Real) const;
- };
-
- class Pseudo_Solis_Wets1 : public Pseudo_Solis_Wets
-@@ -152,7 +152,7 @@
- Pseudo_Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
- Pseudo_Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
- ~Pseudo_Solis_Wets1(void);
-- double gen_deviates(Real);
-+ double gen_deviates(const Real) const;
- };
-
- class Pseudo_Solis_Wets2 : public Pseudo_Solis_Wets
-@@ -162,7 +162,7 @@
- Pseudo_Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
- Pseudo_Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
- ~Pseudo_Solis_Wets2(void);
-- double gen_deviates(Real);
-+ double gen_deviates(const Real) const;
- };
-
- // Inline Functions
-@@ -288,7 +288,7 @@
- {
- }
-
--inline double Solis_Wets1::gen_deviates(Real rho)
-+inline double Solis_Wets1::gen_deviates(const Real rho) const
- {
- return(gennor(0.0, rho));
- }
-@@ -310,7 +310,7 @@
- {
- }
-
--inline double Solis_Wets2::gen_deviates(Real rho)
-+inline double Solis_Wets2::gen_deviates(const Real rho) const
- {
- return(genunf(-rho/2.0, rho/2.0));
- }
-@@ -343,7 +343,7 @@
- {
- }
-
--inline double Pseudo_Solis_Wets1::gen_deviates(Real rho)
-+inline double Pseudo_Solis_Wets1::gen_deviates(const Real rho) const
- {
- return(gennor(0.0, rho));
- }
-@@ -376,7 +376,7 @@
- {
- }
-
--inline double Pseudo_Solis_Wets2::gen_deviates(Real rho)
-+inline double Pseudo_Solis_Wets2::gen_deviates(const Real rho) const
- {
- return(genunf(-rho/2.0, rho/2.0));
- }
-Index: autodocksuite-4.2.3/autodock/call_cpso.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/call_cpso.cc 2010-08-01 21:12:55.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/call_cpso.cc 2010-08-01 21:20:16.000000000 +0200
-@@ -48,7 +48,7 @@
-
-
-
--Individual cnv_state_to_ind2(const State &original, int ntor)
-+Individual cnv_state_to_ind2(const State &original, const int ntor)
- {
- // BEGIN ADDITION
- // Added by gmm, 27-MAR-97, to solve these compiler warnings:
-@@ -71,13 +71,13 @@
-
-
- State call_cpso(Local_Search * local_method,
-- State sInit,
-- int n_exec, int S, //swarm size
-- int D, //number of dimensions:7 + ntor
-- double *xmin, double *xmax,
-- unsigned int num_evals,
-- int K, double c1, double c2,
-- int outlev)
-+ const State sInit,
-+ const int n_exec, int S, //swarm size
-+ const int D, //number of dimensions:7 + ntor
-+ double *const xmin, double *const xmax,
-+ const unsigned int num_evals,
-+ const int K, const double c1, const double c2,
-+ const int outlev)
- {
- int nb_eval = 0;
- Position Xi[S_max]; //Max swarm size set to 1024 in constants.h
-Index: autodocksuite-4.2.3/autodock/support.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.cc 2010-08-01 20:43:23.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.cc 2010-08-01 21:39:19.000000000 +0200
-@@ -74,7 +74,7 @@
- lhb to size-1 *in reverse order*.
- */
-
--void Population::swap(Individual &individual1, Individual &individual2)
-+void Population::swap(Individual &individual1, Individual &individual2) const
- {
- Individual temp;
-
-@@ -92,7 +92,7 @@
- between lhb and size-1 and that the new individual is in
- position lhb-1.
- */
--void Population::SiftUp(void)
-+void Population::SiftUp(void) /* not const */
- {
- int i, parent;
-
-@@ -112,7 +112,7 @@
- /* This routine assumes that the heap condition is satisfied
- between lhb & size-2 initially, and that the individual at size-1
- needs to be accomodated.*/
--void Population::SiftDown(void)
-+void Population::SiftDown(void) /* not const */
- {
- int i, child;
-
-@@ -138,7 +138,7 @@
- }
- }
-
--void Population::msort(int m)
-+void Population::msort(const int m)
- {
- register int i;
-
-@@ -445,7 +445,7 @@
- }
-
- Genotype::Genotype(unsigned int init_number_of_vectors, Representation **
--init_rep_vector)
-+const init_rep_vector)
- : number_of_vectors(init_number_of_vectors), rep_vector(init_rep_vector),
- modified(0)
- {
-@@ -475,6 +475,9 @@
- }
- }
-
-+#if 0
-+ # steffen thinks this is redundant with the const variant
-+ # http://en.wikipedia.org/wiki/Copy_constructor
- Genotype::Genotype(Genotype &original)
- {
- register unsigned int i;
-@@ -501,8 +504,9 @@
- lookup[i] = original.lookup[i];
- }
- }
-+#endif
-
--Genotype::Genotype(Genotype const &original)
-+Genotype::Genotype(const Genotype &original)
- {
- register unsigned int i;
-
-@@ -592,7 +596,7 @@
- }
-
-
--void Genotype::write(Element value, int gene_number)
-+void Genotype::write(const Element value, const int gene_number) /* not const */
- {
-
- #ifdef DEBUG
-@@ -603,7 +607,7 @@
- rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Genotype::write(unsigned char value, int gene_number)
-+void Genotype::write(const unsigned char value, const int gene_number) /* not const */
- {
-
- #ifdef DEBUG
-@@ -614,7 +618,7 @@
- rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Genotype::write(FourByteLong value, int gene_number)
-+void Genotype::write(const FourByteLong value, const int gene_number) /* not const */
- {
-
- #ifdef DEBUG
-@@ -625,7 +629,7 @@
- rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Genotype::write(double value, int gene_number)
-+void Genotype::write(const double value, const int gene_number) /* not const */
- {
-
- #ifdef DEBUG
-@@ -636,7 +640,7 @@
- rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Genotype::write(const Representation &value, int gene_number)
-+void Genotype::write(const Representation &value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -648,7 +652,7 @@
- *(rep_vector[gene_number]) = value;
- }
-
--Quat Genotype::readQuat()
-+Quat Genotype::readQuat() const
- {
- Quat q;
- q.x = gread(3).real;
-@@ -659,7 +663,7 @@
- return q;
- }
-
--void Genotype::writeQuat( Quat q )
-+void Genotype::writeQuat( const Quat q )
- {
- write( q.x, 3 );
- write( q.y, 4 );
-@@ -667,7 +671,7 @@
- write( q.w, 6 );
- }
-
--Quat Phenotype::readQuat()
-+Quat Phenotype::readQuat() const
- {
- Quat q;
- q.x = gread(3).real;
-@@ -678,7 +682,7 @@
- return q;
- }
-
--void Phenotype::writeQuat( Quat q )
-+void Phenotype::writeQuat( const Quat q )
- {
- write( q.x, 3 );
- write( q.y, 4 );
-@@ -687,7 +691,7 @@
- }
-
- // Maybe we should evaluate the Phenotype?
--Phenotype::Phenotype(unsigned int init_number_of_dimensions, Representation **init_value_vector)
-+Phenotype::Phenotype(const unsigned int init_number_of_dimensions, Representation **const init_value_vector)
- : number_of_dimensions(init_number_of_dimensions), value_vector(init_value_vector),
- value(0.0), evalflag(0)
- {
-@@ -809,7 +813,7 @@
- }
- }
-
--void Phenotype::write(Element value, int gene_number)
-+void Phenotype::write(const Element value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -820,7 +824,7 @@
- value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Phenotype::write(unsigned char value, int gene_number)
-+void Phenotype::write(const unsigned char value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -831,7 +835,7 @@
- value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Phenotype::write(FourByteLong value, int gene_number)
-+void Phenotype::write(const FourByteLong value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -842,7 +846,7 @@
- value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Phenotype::write(double value, int gene_number)
-+void Phenotype::write(const double value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -853,7 +857,7 @@
- value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
- }
-
--void Phenotype::write(const Representation &value, int gene_number)
-+void Phenotype::write(const Representation &value, const int gene_number)
- {
-
- #ifdef DEBUG
-@@ -865,7 +869,7 @@
- *(value_vector[gene_number]) = value;
- }
-
--double Phenotype::evaluate(EvalMode mode)
-+double Phenotype::evaluate(const EvalMode mode) /* not const */
- {
-
- #ifdef DEBUG
-@@ -932,7 +936,7 @@
- }
- }
-
--State Individual::state(int ntor) const
-+State Individual::state(const int ntor) const
- {
-
- #ifdef DEBUG
-@@ -942,7 +946,7 @@
- return(phenotyp.make_state(ntor));
- }
-
--void Individual::getMol(Molecule *returnedMol)
-+void Individual::getMol(Molecule * /* not const */ returnedMol) const // Steffen : bug candidate here
- {
- // Converts phenotype to mol's state and returns this individual's mol data.
-
-@@ -951,7 +955,7 @@
-
- molState = phenotyp.make_state(mol->S.ntor);
- molcopy = copyStateToMolecule(&molState, mol);
-- returnedMol = &molcopy;
-+ returnedMol = &molcopy; // Steffen : or here, molcopy is not returned
- }
-
- void Individual::printIndividualsState(FILE *const filePtr, const int ntor, const int detail) const
-@@ -964,7 +968,7 @@
- fprintf( filePtr, "\n" );
- }
-
--void Individual::incrementAge(void)
-+void Individual::incrementAge(void) /* not const */
- {
- ++age;
- }
-Index: autodocksuite-4.2.3/autodock/support.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.h 2010-08-01 20:43:23.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.h 2010-08-01 21:40:15.000000000 +0200
-@@ -171,25 +171,30 @@
-
- public:
- Genotype(void);
-+#if 0
-+ # Steffen thinks this is redundant with the const variant
-+ # http://en.wikipedia.org/wiki/Copy_constructor
- Genotype(Genotype &); /* copy constructor */
-- Genotype(Genotype const &);
-- Genotype(unsigned int, Representation **); /* creates a genotype from the
-+#endif
-+ Genotype(const Genotype &);
-+ Genotype(unsigned int, Representation **const); /* creates a genotype from the
- representation & total # vectors */
-+ /* Steffen's comment - representation is apparently unused */
- ~Genotype(void); /* destructor */
- Genotype &operator=(const Genotype &);
- unsigned int num_vectors(void); /* e.g. "real,bit,bit,int" would = 4 */
- unsigned int num_genes(void); /* returns number_of_genes (see above) */
- RepType gtype(int); /* returns the type (real,bit,int) for
- a particular gene */
-- const Element gread(int);
-- const Representation *vread(int);
-- void write(Element, int);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-- void write(double, int);
-- void write(const Representation &, int);
-- Quat readQuat();
-- void writeQuat( Quat q );
-+ const Element gread(const int) const;
-+ const Representation *vread(int) const;
-+ void write(const Element, const int); /* not const */
-+ void write(const unsigned char, const int); /* not const */
-+ void write(const FourByteLong, const int); /* not const */
-+ void write(const double, const int); /* not const */
-+ void write(const Representation &, const int); /* not const */
-+ Quat readQuat() const;
-+ void writeQuat( const Quat q );
- };
-
- // Should Phenotype automatically evaluate itself upon construction?
-@@ -208,23 +213,23 @@
- Phenotype(void);
- Phenotype(const Phenotype &);
- //Phenotype(const Genotype &);//to do
-- Phenotype(unsigned int, Representation **);
-+ Phenotype(const unsigned int, Representation **const);
- ~Phenotype(void);
- Phenotype &operator=(const Phenotype &);
- RepType gtype(int);
-- const Element gread(int);
-- const Representation *vread(int);
-- void write(Element, int);
-- void write(unsigned char, int);
-- void write(FourByteLong, int);
-- void write(double, int);
-- void write(const Representation &, int);
-- double evaluate(EvalMode); // This should return evaluation if that's the right answer, and it should evaluate otherwise.
-+ const Element gread(const int) const;
-+ const Representation *vread(int) const;
-+ void write(const Element, const int);
-+ void write(const unsigned char, const int);
-+ void write(const FourByteLong, const int);
-+ void write(const double, const int);
-+ void write(const Representation &, const int);
-+ double evaluate(const EvalMode) /* not const */ ; // This should return evaluation if that's the right answer, and it should evaluate otherwise.
- State make_state(int) const;
-- unsigned int num_dimensions(void);
-- unsigned int num_pts(void);
-- Quat readQuat();
-- void writeQuat( Quat q );
-+ unsigned int num_dimensions(void) const; // Steffen : implementation not found
-+ unsigned int num_pts(void) const;
-+ Quat readQuat() const;
-+ void writeQuat( const Quat q );
- };
-
- // This should be an encapsulated class within Population
-@@ -248,11 +253,11 @@
- Individual &inverse_mapping(void); //updates genotype from current phenotype values
- //Phenotype mapping(void); /* takes the genotype and converts it into a phenotype. */
- //Genotype inverse_mapping(void); // Scott should do: Also copy Phenotype's value
-- double value(EvalMode); /* evaluation of the individual gives its value */
-- State state(int) const; /* state variables in AutoDock */
-- void getMol(Molecule *); /* converts phenotype to mol's state and returns this individual's mol data */
-+ double value(EvalMode); /* not const */ /* evaluation of the individual gives its value */ /* not const */
-+ State state(const int) const; /* state variables in AutoDock */
-+ void getMol(Molecule * /* not const */) const; /* converts phenotype to mol's state and returns this individual's mol data */
- void printIndividualsState(FILE *const, const int, const int) const; /* print out the state of this individual */
-- void incrementAge(); /* make individual grow 1 generation older */
-+ void incrementAge(); /* not const */ /* make individual grow 1 generation older */
- int serial; // serial number of this individual
- };
-
-@@ -263,9 +268,9 @@
- int lhb; // These keep track of the lower & upper heap bounds
- int size; /* the number of individuals in the population */
- Individual *heap; /* a heap of individuals -- special binary tree */
-- void swap(Individual &, Individual &); /* for maintaining the heap order*/
-- void SiftUp(void); /* for maintaining the heap order*/
-- void SiftDown(void); /* for maintaining the heap order*/
-+ void swap(Individual &, Individual &) const; /* for maintaining the heap order*/
-+ void SiftUp(void); /* not const */ /* for maintaining the heap order*/
-+ void SiftDown(void); /* not const */ /* for maintaining the heap order*/
- int end_of_branch[MAX_TORS]; // For Branch Crossover Mode
-
- public:
-@@ -277,7 +282,7 @@
- Individual &operator[](const int) const; /* for accessing a particular indiv.in pop*/
- Population &operator=(const Population &);
- unsigned int num_individuals(void) const; /* returns the size of the pop. */
-- void msort(int); /* sorts the first m individuals using heap properties */
-+ void msort(const int); /* sorts the first m individuals using heap properties */
- // void print(ostream &, int); /* prints top int energies */
- void print(FILE *const, const int) const; /* like above */
- int printPopulationStatistics(FILE *const, const int, const Boole) const; /* prints best, worse, mean, etc energies */
-@@ -317,12 +322,12 @@
- return(rep_vector[lookup[gene_number].vector]->type());
- }
-
--inline const Element Genotype::gread(int gene_number)
-+inline const Element Genotype::gread(const int gene_number) const
- {
- return(rep_vector[lookup[gene_number].vector]->gene(lookup[gene_number].index));
- }
-
--inline const Representation *Genotype::vread(int vector_number)
-+inline const Representation *Genotype::vread(int vector_number) const
- {
- return(rep_vector[vector_number]);
- }
-@@ -343,17 +348,17 @@
- return(value_vector[lookup[gene_number].vector]->type());
- }
-
--inline const Element Phenotype::gread(int gene_number)
-+inline const Element Phenotype::gread(const int gene_number) const
- {
- return(value_vector[lookup[gene_number].vector]->gene(lookup[gene_number].index));
- }
-
--inline const Representation *Phenotype::vread(int vector_number)
-+inline const Representation *Phenotype::vread(int vector_number) const
- {
- return(value_vector[vector_number]);
- }
-
--inline unsigned int Phenotype::num_pts(void)
-+inline unsigned int Phenotype::num_pts(void) const
- {
- return(number_of_points);
- }
-@@ -392,7 +397,7 @@
- return(*this);
- }
-
--inline double Individual::value(EvalMode mode)
-+inline double Individual::value(EvalMode mode) /* not const */
- { // TO DO: check if mapping from genotyp to phenotyp is up-to-date
- // note that phenotyp.evaluate only does evaluation if evalflag is false
- return(phenotyp.evaluate(mode));
-Index: autodocksuite-4.2.3/autodock/swap.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/swap.cc 2010-08-01 20:40:54.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/swap.cc 2010-08-01 20:43:03.000000000 +0200
-@@ -39,8 +39,8 @@
- #endif /* DEBUG */
-
- void swap ( int v[],
-- int i,
-- int j )
-+ const int i,
-+ const int j )
-
- {
- int temp;
-Index: autodocksuite-4.2.3/autodock/swap.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/swap.h 2010-08-01 20:40:54.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/swap.h 2010-08-01 20:43:12.000000000 +0200
-@@ -26,5 +26,5 @@
-
- #ifndef SWAP
- #define SWAP
--void swap( int v[], int i, int j );
-+void swap( int v[], const int i, const int j );
- #endif
-Index: autodocksuite-4.2.3/autodock/timesys.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/timesys.cc 2010-08-01 20:38:40.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/timesys.cc 2010-08-01 20:39:58.000000000 +0200
-@@ -43,9 +43,9 @@
-
- /*----------------------------------------------------------------------------*/
-
--void timesys( Clock duration,
-- struct tms *start,
-- struct tms *end)
-+void timesys( const Clock duration,
-+ const struct tms *const start,
-+ const struct tms *const end)
-
- /*----------------------------------------------------------------------------*/
-
-Index: autodocksuite-4.2.3/autodock/timesys.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/timesys.h 2010-08-01 20:38:40.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/timesys.h 2010-08-01 20:40:13.000000000 +0200
-@@ -33,7 +33,7 @@
- #include <time.h>
- #include "autocomm.h"
-
--void timesys( Clock duration,
-- struct tms *start,
-- struct tms *end );
-+void timesys( const Clock duration,
-+ const struct tms *const start,
-+ const struct tms *const end );
- #endif
-Index: autodocksuite-4.2.3/autodock/torsion.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/torsion.cc 2010-08-01 20:37:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/torsion.cc 2010-08-01 20:38:11.000000000 +0200
-@@ -35,7 +35,7 @@
-
-
- void torsion( const State now,
-- Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const Real v[MAX_TORS][SPACE],
- const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor )
-Index: autodocksuite-4.2.3/autodock/torsion.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/torsion.h 2010-08-01 20:37:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/torsion.h 2010-08-01 20:38:28.000000000 +0200
-@@ -28,7 +28,7 @@
- #define TORSION
-
- void torsion( const State now,
-- Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const Real vt[MAX_TORS][SPACE],
- const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor );
-Index: autodocksuite-4.2.3/autodock/warn_bad_file.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/warn_bad_file.cc 2010-08-01 20:35:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/warn_bad_file.cc 2010-08-01 20:35:23.000000000 +0200
-@@ -37,8 +37,8 @@
-
- /*----------------------------------------------------------------------------*/
-
--void warn_bad_file( char *filename,
-- char message[LINE_LEN] )
-+void warn_bad_file( const char *const filename,
-+ const char message[LINE_LEN] )
-
- /*----------------------------------------------------------------------------*/
- {
-Index: autodocksuite-4.2.3/autodock/warn_bad_file.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/warn_bad_file.h 2010-08-01 20:35:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/warn_bad_file.h 2010-08-01 20:35:33.000000000 +0200
-@@ -29,6 +29,6 @@
- #include "constants.h"
- #include "print_2x.h"
-
--void warn_bad_file( char *filename,
-- char *message );
-+void warn_bad_file( const char *const filename,
-+ const char *const message );
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_55.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_55.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_55.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,344 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/sort_enrg.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/sort_enrg.cc 2010-08-01 22:08:16.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/sort_enrg.cc 2010-08-01 22:09:56.000000000 +0200
-@@ -32,9 +32,9 @@
-
- extern FILE *logFile;
-
--void sort_enrg( Real econf[MAX_RUNS],
-- int isort[MAX_RUNS],
-- int nconf )
-+void sort_enrg( const Real econf[MAX_RUNS],
-+ /* not const */ int isort[MAX_RUNS],
-+ const int nconf )
-
- {
- /*__________________________________________________________________________
-Index: autodocksuite-4.2.3/autodock/sort_enrg.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/sort_enrg.h 2010-08-01 22:08:16.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/sort_enrg.h 2010-08-01 22:10:00.000000000 +0200
-@@ -32,7 +32,7 @@
- #include "constants.h"
- #include "quicksort.h"
-
--void sort_enrg( Real econf[MAX_RUNS],
-- int isort[MAX_RUNS],
-- int nconf );
-+void sort_enrg( const Real econf[MAX_RUNS],
-+ /* not const */ int isort[MAX_RUNS],
-+ const int nconf );
- #endif
-Index: autodocksuite-4.2.3/autodock/quicksort.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/quicksort.cc 2010-08-01 22:21:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/quicksort.cc 2010-08-01 22:22:01.000000000 +0200
-@@ -45,10 +45,10 @@
- extern FILE *logFile;
- #endif /* DEBUG */
-
--void quicksort( Real e[],
-- int isort[],
-- int left,
-- int right )
-+void quicksort( const Real e[],
-+ /* not const */ int isort[],
-+ const int left,
-+ const int right )
-
- {
- int i, last;
-Index: autodocksuite-4.2.3/autodock/quicksort.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/quicksort.h 2010-08-01 22:21:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/quicksort.h 2010-08-01 22:22:34.000000000 +0200
-@@ -29,8 +29,8 @@
- #include "swap.h"
- #include "typedefs.h"
-
--void quicksort( Real e[],
-- int isort[],
-- int left,
-- int right );
-+void quicksort( const Real e[],
-+ /* not const */ int isort[],
-+ const int left,
-+ const int right );
- #endif
-Index: autodocksuite-4.2.3/autodock/readfield.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readfield.cc 2010-08-01 22:18:24.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readfield.cc 2010-08-01 22:19:07.000000000 +0200
-@@ -39,8 +39,8 @@
- extern FILE *logFile;
-
- //FIXME: tms_jobStart could be passed by reference
--void readfield( GridMapSetInfo *info,
-- char line[LINE_LEN],
-+void readfield( /* not const */ GridMapSetInfo *const info,
-+ /* not const */ char line[LINE_LEN],
- const Clock jobStart,
- const struct tms tms_jobStart )
-
-Index: autodocksuite-4.2.3/autodock/readfield.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readfield.h 2010-08-01 22:18:24.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readfield.h 2010-08-01 22:20:16.000000000 +0200
-@@ -52,10 +52,10 @@
- struct tms tms_jobStart );
- */
-
--void readfield( GridMapSetInfo *info, // *ptr_map_set_info
-- char line[LINE_LEN],
-- Clock jobStart,
-- struct tms tms_jobStart );
-+void readfield( GridMapSetInfo *const info, // *ptr_map_set_info
-+ /* not const */ char line[LINE_LEN],
-+ const Clock jobStart,
-+ const struct tms tms_jobStart );
-
-
- #endif
-Index: autodocksuite-4.2.3/autodock/stack.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stack.cc 2010-08-01 22:10:25.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stack.cc 2010-08-01 22:11:18.000000000 +0200
-@@ -19,7 +19,7 @@
- return s;
- }
-
--int stack_pop(stack s)
-+int stack_pop(/* not const */ stack s)
- {
- (s->top)--;
- if (s->top < 0) {
-@@ -34,7 +34,7 @@
- return s->base[s->top];
- }
-
--void stack_push(stack s, const int i)
-+void stack_push(/* not const */ stack s, const int i)
- {
- if (s->trace != NULL) fprintf(s->trace, "Stack(%d/%d) push %d\n",
- s->top, s->size,i);
-Index: autodocksuite-4.2.3/autodock/stateLibrary.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.cc 2010-08-01 22:11:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.cc 2010-08-01 22:14:15.000000000 +0200
-@@ -35,7 +35,7 @@
-
- extern FILE *logFile;
-
--void initialiseState( State *S )
-+void initialiseState( /* not const */ State *const S )
- {
- register int i;
- S->T.x = 0.0;
-@@ -48,7 +48,7 @@
- }
- }
-
--void initialiseQuat( Quat *Q )
-+void initialiseQuat( /* not const */ Quat *const Q )
- {
- Q->nx = 1.0;
- Q->ny = 0.0;
-@@ -61,7 +61,7 @@
- Q->qmag = 1.0;
- }
-
--void copyState( State *D, /* Destination -- copy to here */
-+void copyState( /* not const */ State *const D, /* Destination -- copy to here */
- const State S ) /* Source -- copy this. */
- {
- register int i;
-@@ -189,7 +189,7 @@
- // (void)fprintf( fp, "\n");
- }
-
--int checkState( const State *D )
-+int checkState( const State *const D )
- {
- register int i;
- int retval = 1;
-@@ -259,7 +259,7 @@
- return(retval);
- }
-
--Molecule copyStateToMolecule(const State *const S, Molecule *const mol) /* S is the source */
-+Molecule copyStateToMolecule(const State *const S, /* not const */ Molecule *const mol) /* S is the source */
- {
- register int i;
- mol->S.T.x = S->T.x;
-Index: autodocksuite-4.2.3/autodock/stateLibrary.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.h 2010-08-01 22:11:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.h 2010-08-01 22:16:05.000000000 +0200
-@@ -30,21 +30,21 @@
- #include "structs.h"
- #include "constants.h"
-
--void initialiseState( State *S );
-+void initialiseState( /* not const */ State *const S );
-
--void initialiseQuat( Quat *Q );
-+void initialiseQuat( /* not const */ Quat *const Q );
-
--void copyState( State *destination,
-+void copyState( State *const destination,
- const State source);
-
- void printState( FILE *const fp,
- /* not const */ State state,
- const int detail );
-
--void writeState( FILE *const fp,
-+void writeState( /* not const */ FILE *const fp,
- /* not const */ State state );
-
--int checkState( const State *D );
-+int checkState( const State *const D );
-
--Molecule copyStateToMolecule(const State *const source, Molecule *const mol);
-+Molecule copyStateToMolecule(const State *const source, /* not const */ Molecule *const mol);
- #endif
-Index: autodocksuite-4.2.3/autodock/stop.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stop.cc 2010-08-01 22:17:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stop.cc 2010-08-01 22:17:19.000000000 +0200
-@@ -40,7 +40,7 @@
-
-
- /*----------------------------------------------------------------------------*/
--void stop(const char *reason)
-+void stop(const char *const reason)
- /*----------------------------------------------------------------------------*/
- {
-
-Index: autodocksuite-4.2.3/autodock/stop.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stop.h 2010-08-01 22:17:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stop.h 2010-08-01 22:17:28.000000000 +0200
-@@ -30,5 +30,5 @@
- #include "constants.h"
- #include "print_2x.h"
-
--void stop(const char* reason);
-+void stop(const char *const reason);
- #endif
-Index: autodocksuite-4.2.3/autodock/weedbonds.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/weedbonds.cc 2010-08-01 22:23:19.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/weedbonds.cc 2010-08-01 22:29:48.000000000 +0200
-@@ -40,16 +40,16 @@
- extern int Nnb_array[3];
-
-
--void weedbonds( int natom,
-- char pdbaname[MAX_ATOMS][5],
-- int rigid_piece[MAX_ATOMS],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-- int *Addr_Nnb,
-- NonbondParam *nonbondlist,
-- int outlev,
-- int type[MAX_ATOMS] )
-+void weedbonds( const int natom,
-+ const char pdbaname[MAX_ATOMS][5],
-+ const int rigid_piece[MAX_ATOMS],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-+ /* not const */ int *const Addr_Nnb,
-+ /* not const */ NonbondParam *nonbondlist,
-+ const int outlev,
-+ const int type[MAX_ATOMS] )
-
- {
- int a11=0;
-@@ -233,16 +233,16 @@
-
-
- void print_nonbonds(
-- int natom,
-- char pdbaname[MAX_ATOMS][5],
-- int rigid_piece[MAX_ATOMS],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-- int Nnb,
-- NonbondParam *nonbondlist,
-- int outlev,
-- int type[MAX_ATOMS])
-+ const int natom,
-+ const char pdbaname[MAX_ATOMS][5],
-+ const int rigid_piece[MAX_ATOMS],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-+ const int Nnb,
-+ const NonbondParam *const nonbondlist,
-+ const int outlev,
-+ const int type[MAX_ATOMS])
-
- {
- register int i = 0;
-Index: autodocksuite-4.2.3/autodock/weedbonds.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/weedbonds.h 2010-08-01 22:23:19.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/weedbonds.h 2010-08-01 22:29:32.000000000 +0200
-@@ -31,16 +31,16 @@
- #include "stop.h"
- #include "structs.h"
-
--void weedbonds( int natom,
-- char pdbaname[MAX_ATOMS][5],
-- int piece[MAX_ATOMS],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int nbmatrix_binary[MAX_ATOMS][MAX_ATOMS],
-- int *P_Nnb,
-- NonbondParam *nonbondlist,
-- int outlev,
-- int type[MAX_ATOMS]);
-+void weedbonds( const int natom,
-+ const char pdbaname[MAX_ATOMS][5],
-+ const int piece[MAX_ATOMS],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ int nbmatrix_binary[MAX_ATOMS][MAX_ATOMS],
-+ /* not const */ int *P_Nnb,
-+ /* not const */ NonbondParam *const nonbondlist,
-+ const int outlev,
-+ const int type[MAX_ATOMS]);
- #endif
-
-
-@@ -52,15 +52,15 @@
- #include "structs.h"
-
- void print_nonbonds(
-- int natom,
-- char pdbaname[MAX_ATOMS][5],
-- int piece[MAX_ATOMS],
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-- int Nnb,
-- NonbondParam *nonbondlist,
-- int outlev,
-- int type[MAX_ATOMS]);
-+ const int natom,
-+ const char pdbaname[MAX_ATOMS][5],
-+ const int piece[MAX_ATOMS],
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-+ const int Nnb,
-+ const NonbondParam *nonbondlist,
-+ const int outlev,
-+ const int type[MAX_ATOMS]);
- #endif
-
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_60.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_60.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_60.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,381 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/parse_dpf_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_dpf_line.cc 2010-08-02 22:42:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_dpf_line.cc 2010-08-02 22:42:32.000000000 +0200
-@@ -35,7 +35,7 @@
-
-
-
--int parse_dpf_line( char line[LINE_LEN] )
-+int parse_dpf_line( const char line[LINE_LEN] )
-
- /******************************************************************************/
- /* Name: parse_dpf_line */
-Index: autodocksuite-4.2.3/autodock/parse_dpf_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_dpf_line.h 2010-08-02 22:42:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_dpf_line.h 2010-08-02 22:42:36.000000000 +0200
-@@ -28,6 +28,6 @@
- #define PARSE_DPF_LINE
-
- #include "constants.h"
--int parse_dpf_line( char line[LINE_LEN] );
-+int parse_dpf_line( const char line[LINE_LEN] );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/parse_param_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_param_line.cc 2010-08-02 22:42:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_param_line.cc 2010-08-02 22:42:11.000000000 +0200
-@@ -36,7 +36,7 @@
- extern int debug;
- extern FILE *logFile;
-
--int parse_param_line( char line[LINE_LEN] )
-+int parse_param_line( const char line[LINE_LEN] )
-
- /******************************************************************************/
- /* Name: parse_param_line */
-Index: autodocksuite-4.2.3/autodock/parse_param_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_param_line.h 2010-08-02 22:42:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_param_line.h 2010-08-02 22:42:17.000000000 +0200
-@@ -28,6 +28,6 @@
- #define PARSE_PAR_LINE
-
- #include "constants.h"
--int parse_param_line( char line[LINE_LEN] );
-+int parse_param_line( const char line[LINE_LEN] );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/parse_trj_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_trj_line.cc 2010-08-02 22:41:25.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_trj_line.cc 2010-08-02 22:41:35.000000000 +0200
-@@ -35,7 +35,7 @@
- #include "trjtokens.h"
-
-
--int parse_trj_line( char line[LINE_LEN] )
-+int parse_trj_line( const char line[LINE_LEN] )
-
- /******************************************************************************/
- /* Name: parse_trj_line */
-Index: autodocksuite-4.2.3/autodock/parse_trj_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_trj_line.h 2010-08-02 22:41:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_trj_line.h 2010-08-02 22:41:40.000000000 +0200
-@@ -29,5 +29,5 @@
- #include "constants.h"
- #include "strindex.h"
-
--int parse_trj_line( char line[LINE_LEN] );
-+int parse_trj_line( const char line[LINE_LEN] );
- #endif
-Index: autodocksuite-4.2.3/autodock/parsetypes.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parsetypes.cc 2010-08-02 22:40:15.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parsetypes.cc 2010-08-02 22:41:03.000000000 +0200
-@@ -29,7 +29,7 @@
- #include <ctype.h>
- #include "parsetypes.h"
-
--int parsetypes(char * line, char *words[], int maxwords)
-+int parsetypes(const char *const line, char *words[], const int maxwords)
- /*utility func for parsing types*/
- {
- /******************************************************************************/
-Index: autodocksuite-4.2.3/autodock/parsetypes.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parsetypes.h 2010-08-02 22:40:15.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parsetypes.h 2010-08-02 22:41:15.000000000 +0200
-@@ -27,7 +27,7 @@
- #ifndef _PARSETYPES
- #define _PARSETYPES
-
--int parsetypes(char * line, char *words[], int maxwords);
-+int parsetypes(const char *const line, char *words[], const int maxwords);
-
- #endif
-
-Index: autodocksuite-4.2.3/autodock/prClusterHist.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/prClusterHist.cc 2010-08-02 22:38:50.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/prClusterHist.cc 2010-08-02 22:39:16.000000000 +0200
-@@ -36,14 +36,14 @@
-
- extern FILE *logFile;
-
--void prClusterHist( int ncluster,
-- int irunmax,
-- Real clus_rms_tol,
-- int num_in_clu[MAX_RUNS],
-- int cluster[MAX_RUNS][MAX_RUNS],
-- Real econf[MAX_RUNS],
-- Real clu_rms[MAX_RUNS][MAX_RUNS],
-- Real ref_rms[MAX_RUNS])
-+void prClusterHist( const int ncluster,
-+ const int irunmax,
-+ const Real clus_rms_tol,
-+ const int num_in_clu[MAX_RUNS],
-+ const int cluster[MAX_RUNS][MAX_RUNS],
-+ const Real econf[MAX_RUNS],
-+ const Real clu_rms[MAX_RUNS][MAX_RUNS],
-+ const Real ref_rms[MAX_RUNS])
- {
- Real etot = 0.,
- eavg = 0.;
-Index: autodocksuite-4.2.3/autodock/prClusterHist.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/prClusterHist.h 2010-08-02 22:38:50.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/prClusterHist.h 2010-08-02 22:39:24.000000000 +0200
-@@ -29,12 +29,12 @@
-
- #include "constants.h"
-
--void prClusterHist(int ncluster,
-- int irunmax,
-- Real clus_rms_tol,
-- int num_in_clu[MAX_RUNS],
-- int cluster[MAX_RUNS][MAX_RUNS],
-- Real econf[MAX_RUNS],
-- Real clu_rms[MAX_RUNS][MAX_RUNS],
-- Real ref_rms[MAX_RUNS]);
-+void prClusterHist(const int ncluster,
-+ const int irunmax,
-+ const Real clus_rms_tol,
-+ const int num_in_clu[MAX_RUNS],
-+ const int cluster[MAX_RUNS][MAX_RUNS],
-+ const Real econf[MAX_RUNS],
-+ const Real clu_rms[MAX_RUNS][MAX_RUNS],
-+ const Real ref_rms[MAX_RUNS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/prTorConList.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/prTorConList.cc 2010-08-02 22:32:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/prTorConList.cc 2010-08-02 22:34:07.000000000 +0200
-@@ -39,11 +39,11 @@
-
- extern FILE *logFile;
-
--void prTorConList( int ntor,
-- Boole B_isTorConstrained[MAX_TORS],
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS])
-+void prTorConList( const int ntor,
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS])
-
- {
- char graph[NROWS][LINE_LEN];
-Index: autodocksuite-4.2.3/autodock/prTorConList.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/prTorConList.h 2010-08-02 22:32:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/prTorConList.h 2010-08-02 22:33:39.000000000 +0200
-@@ -28,9 +28,9 @@
- #define PRTORCONLIST
- #include "constants.h"
-
--void prTorConList( int ntor,
-- Boole B_isTorConstrained[MAX_TORS],
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS]);
-+void prTorConList( const int ntor,
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ const int N_con[MAX_TORS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/print_rem.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_rem.h 2010-08-02 22:34:14.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_rem.h 2010-08-02 22:35:25.000000000 +0200
-@@ -29,9 +29,9 @@
-
- #include "typedefs.h"
-
--void print_rem( FILE *outFile,
-- int Rank,
-- int NumMem,
-- int Run,
-- Real ref_rms);
-+void print_rem( FILE *const outFile,
-+ const int Rank,
-+ const int NumMem,
-+ const int Run,
-+ const Real ref_rms);
- #endif
-Index: autodocksuite-4.2.3/autodock/printdate.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printdate.h 2010-08-02 22:36:23.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printdate.h 2010-08-02 22:36:36.000000000 +0200
-@@ -29,5 +29,5 @@
-
- #include "autocomm.h"
-
--void printdate( FILE *fp, int flag );
-+void printdate( FILE *const fp, const int flag );
- #endif
-Index: autodocksuite-4.2.3/autodock/printhms.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printhms.cc 2010-08-02 22:35:33.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printhms.cc 2010-08-02 22:35:47.000000000 +0200
-@@ -33,7 +33,7 @@
-
- extern FILE *logFile;
-
--void printhms( Real t )
-+void printhms( const Real t )
-
- {
- int h,
-Index: autodocksuite-4.2.3/autodock/printhms.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printhms.h 2010-08-02 22:35:33.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printhms.h 2010-08-02 22:35:52.000000000 +0200
-@@ -27,5 +27,5 @@
- #ifndef PRINTHMS
- #define PRINTHMS
- #include "typedefs.h"
--void printhms( Real t );
-+void printhms( const Real t );
- #endif
-Index: autodocksuite-4.2.3/autodock/qmultiply.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.cc 2010-08-02 22:43:43.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.cc 2010-08-02 22:51:54.000000000 +0200
-@@ -37,9 +37,9 @@
- extern FILE *logFile;
-
-
--void qmultiply( Quat *q, //result
-- register const Quat *ql, //left
-- register const Quat *qr ) //right
-+void qmultiply( Quat *const q, //result
-+ register const Quat *const ql, //left
-+ register const Quat *const qr ) //right
-
- /******************************************************************************/
- /* Name: qmultiply */
-@@ -76,9 +76,9 @@
- q->w = w;
- }
-
--void qconjmultiply( Quat *q,
-- register const Quat *ql,
-- register const Quat *qr )
-+void qconjmultiply( Quat *const q,
-+ register const Quat *const ql,
-+ register const Quat *const qr )
- // __
- // q = ql . qr
- {
-@@ -86,7 +86,7 @@
- qmultiply( q, &conj_ql, qr );
- }
-
--void mkUnitQuat( Quat *q )
-+void mkUnitQuat( Quat *const q )
- // essentially, convertRotToQuat( Quat q )
- {
- const double inv_nmag = 1. / hypotenuse( q->nx, q->ny, q->nz );
-@@ -137,7 +137,7 @@
- printQuat( fp, q );
- }
-
--Quat normQuat( Quat q )
-+Quat normQuat( /* not const */ Quat q )
- // Normalise the 4D quaternion, x,y,z,w
- {
- register double mag4 = hypotenuse4( q.x, q.y, q.z, q.w );
-@@ -165,7 +165,7 @@
- #define assertQuatOK( q ) {register double aQOK_mag4 = hypotenuse4( (q).x, (q).y, (q).z, (q).w ); assert((aQOK_mag4 > ONE_MINUS_EPSILON) && (aQOK_mag4 < ONE_PLUS_EPSILON)); }
- */
-
--Quat normRot( Quat q )
-+Quat normRot( /* not const */ Quat q )
- // Normalise the 3D rotation axis or vector nx,ny,nz
- {
- const double mag3 = hypotenuse( q.nx, q.ny, q.nz );
-@@ -193,7 +193,7 @@
-
-
- //FIXME: this routine does not need to change argument q, but it does
--Quat convertQuatToRot( Quat q )
-+Quat convertQuatToRot( /* not const */ Quat q )
- // Convert the quaternion components (x,y,z,w) of the quaternion q,
- // to the corresponding rotation-about-axis components (nx,ny,nz,ang)
- {
-@@ -307,7 +307,7 @@
- return q;
- }
-
--void unitQuat2rotation( Quat *const q )
-+void unitQuat2rotation( /* not const */ Quat *const q )
- // Convert from a unit quaternion to a rotation about an unit 3D-vector
- {
- double inv_sin_half_ang;
-@@ -337,7 +337,7 @@
- return;
- } // Print message about q_reorient
-
--void create_random_orientation( Quat *const ptr_quat )
-+void create_random_orientation( /* not const */ Quat *const ptr_quat )
- {
- // Generate a random initial orientation for the ligand
- // Generate a uniformly-distributed quaternion:
-@@ -591,7 +591,7 @@
- return a;
- }
-
--Real alerp( Real a, Real b, const Real fract )
-+Real alerp( /* not const */ Real a, /* not const */ Real b, const Real fract )
- {
- // if fract==0, return a
- // if fract==1, return b
-Index: autodocksuite-4.2.3/autodock/qmultiply.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.h 2010-08-02 22:43:43.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.h 2010-08-02 22:54:00.000000000 +0200
-@@ -35,8 +35,8 @@
- Quat convertQuatToRot( /* not const */ Quat q );
- Quat convertRotToQuat( const Quat q );
- Quat raaToQuat( const Real raa[3], Real angle );
--Quat normQuat( Quat q );
--Quat normRot( Quat q );
-+Quat normQuat( /* not const */ Quat q );
-+Quat normRot( /* not const */ Quat q );
- Real quatDifferenceToAngle( const Quat ql, const Quat qr );
- Real quatDifferenceToAngleDeg( const Quat ql, const Quat qr );
- Quat conjugate( const Quat q );
-@@ -48,19 +48,19 @@
- Quat axisDegreeToQuat( const Real ax, const Real ay, const Real az, const Real angle );
- Quat quatComponentsToQuat( const Real qx, const Real qy, const Real qz, const Real qw );
-
--void qmultiply( Quat *q, register const Quat *ql, register const Quat *qr );
--void qconjmultiply( Quat *q, register const Quat *ql, register const Quat *qr );
--void mkUnitQuat( Quat *q );
-+void qmultiply( Quat *const q, register const Quat *const ql, register const Quat *const qr );
-+void qconjmultiply( Quat *const q, register const Quat *const ql, register const Quat *const qr );
-+void mkUnitQuat( Quat *const q );
- void printQuat_q( FILE *const fp, const Quat q );
- void printQuat_r( FILE *const fp, const Quat q );
- void printQuat( FILE *const fp, const Quat q );
- void debugQuat( FILE *const fp, const Quat q, const unsigned int linenumber, const char *message );
- Quat uniformQuatByAmount( const Real amount );
--void unitQuat2rotation( Quat *const q );
-+void unitQuat2rotation( /* not const */ Quat *const q );
- void print_q_reorient_message( FILE *const logFile, const Quat q_reorient );
--void create_random_orientation( Quat *const ptr_quat );
-+void create_random_orientation( /* not const */ Quat *const ptr_quat );
- //void assertQuatOK( const Quat q );
- const Quat identityQuat();
--Real a_range_reduction( const Real a );
--Real alerp( const Real a, const Real b, const Real fract );
-+Real a_range_reduction( /* not const */ Real a );
-+Real alerp( /* not const */ Real a, /* not const */ Real b, const Real fract );
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,183 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/nbe.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/nbe.cc 2010-08-02 23:49:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/nbe.cc 2010-08-02 23:50:19.000000000 +0200
-@@ -56,9 +56,9 @@
-
- extern FILE *logFile;
-
--void nbe( GridMapSetInfo *info,
-- EnergyTables *ptr_ad_energy_tables,
-- int num_atm_maps )
-+void nbe( const GridMapSetInfo *const info,
-+ const EnergyTables *const ptr_ad_energy_tables,
-+ const int num_atm_maps )
-
- {
-
-Index: autodocksuite-4.2.3/autodock/nbe.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/nbe.h 2010-08-02 23:49:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/nbe.h 2010-08-02 23:50:29.000000000 +0200
-@@ -30,7 +30,7 @@
- #include "constants.h"
- #include "structs.h"
-
--void nbe( GridMapSetInfo *info,
-- EnergyTables *ptr_ad_energy_tables,
-- int num_atm_maps );
-+void nbe( const GridMapSetInfo *const info,
-+ const EnergyTables *const ptr_ad_energy_tables,
-+ const int num_atm_maps );
- #endif
-Index: autodocksuite-4.2.3/autodock/nonbonds.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/nonbonds.cc 2010-08-02 23:50:36.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/nonbonds.cc 2010-08-02 23:58:03.000000000 +0200
-@@ -41,12 +41,12 @@
-
- using namespace std;
-
--void nonbonds(const Real crdpdb[MAX_ATOMS][SPACE],
-- int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-- const int natom,
-- const int bond_index[MAX_ATOMS],
-- int B_include_1_4_interactions,
-- int bonded[MAX_ATOMS][6])
-+void nonbonds(const Real crdpdb[MAX_ATOMS][SPACE],
-+ /* not const */ int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-+ const int natom,
-+ const int bond_index[MAX_ATOMS],
-+ const int B_include_1_4_interactions,
-+ const int bonded[MAX_ATOMS][6])
- {
- int i,j,k,l;
- int nonbond_type;
-@@ -123,10 +123,10 @@
- /*----------------------------------------------------------------------------*/
-
- void getbonds(const Real crdpdb[MAX_ATOMS][SPACE],
-- const int from_atom,
-- const int to_atom,
-- const int bond_index[MAX_ATOMS],
-- int bonded[MAX_ATOMS][6])
-+ const int from_atom,
-+ const int to_atom,
-+ const int bond_index[MAX_ATOMS],
-+ /* not const */ int bonded[MAX_ATOMS][6])
- {
- int i,j;
- double dist,dx,dy,dz;
-@@ -221,7 +221,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void printbonds(const int natom, const int bonded[MAX_ATOMS][6], const char *message, const int B_print_all_bonds)
-+void printbonds(const int natom, const int bonded[MAX_ATOMS][6], const char *const message, const int B_print_all_bonds)
- {
- register int i, j;
- pr(logFile, message);
-@@ -242,7 +242,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void print_1_4_message(FILE *const file, const Boole B_include_1_4_interactions, const Real scale_1_4)
-+void print_1_4_message(FILE *const file, const Boole B_include_1_4_interactions, const Real scale_1_4)
- {
- if (B_include_1_4_interactions == FALSE) {
- pr(file, "1,4-interactions will be _ignored_ in the non-bonded internal energy calculation.\n\n");
-Index: autodocksuite-4.2.3/autodock/nonbonds.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/nonbonds.h 2010-08-02 23:50:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/nonbonds.h 2010-08-02 23:58:15.000000000 +0200
-@@ -28,32 +28,32 @@
- #define NONBONDS
- #include "constants.h"
- void nonbonds( const Real crdpdb[MAX_ATOMS][SPACE],
-- int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-- const int natom,
-- const int bond_index[MAX_ATOMS],
-- int B_include_1_4_interactions,
-- int bonded[MAX_ATOMS][6]);
-+ /* not const */ int nbmatrix[MAX_ATOMS][MAX_ATOMS],
-+ const int natom,
-+ const int bond_index[MAX_ATOMS],
-+ const int B_include_1_4_interactions,
-+ const int bonded[MAX_ATOMS][6]);
- #endif
-
- #ifndef GETBONDS
- #define GETBONDS
- #include "constants.h"
- void getbonds(const Real crdpdb[MAX_ATOMS][SPACE],
-- const int from_atom,
-- const int to_atom,
-- const int bond_index[MAX_ATOMS],
-- int bonded[MAX_ATOMS][6]);
-+ const int from_atom,
-+ const int to_atom,
-+ const int bond_index[MAX_ATOMS],
-+ /* not const */ int bonded[MAX_ATOMS][6]);
- #endif
-
- #ifndef PRINTBONDS
- #define PRINTBONDS
- #include "constants.h"
--void printbonds(const int natom, const int bonded[MAX_ATOMS][6], const char *message, const int B_print_all_bonds);
-+void printbonds(const int natom, const int bonded[MAX_ATOMS][6], const char *const message, const int B_print_all_bonds);
- #endif
-
- #ifndef PRINT14
- #define PRINT14
- #include "constants.h"
- #include <stdio.h>
--void print_1_4_message(FILE *file, Boole B_include_1_4_interactions, Real scale_1_4);
-+void print_1_4_message(FILE *const file, const Boole B_include_1_4_interactions, const Real scale_1_4);
- #endif
-Index: autodocksuite-4.2.3/autodock/openfile.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/openfile.cc 2010-08-02 23:46:29.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/openfile.cc 2010-08-02 23:48:44.000000000 +0200
-@@ -72,7 +72,7 @@
- /*----------------------------------------------------------------------------*/
- int openfile( const char *const filename,
- const char mode[],
-- FILE **fp )
-+ FILE **const fp )
-
- {
- if ( (*fp = ad_fopen(filename, mode)) == NULL ) {
-@@ -86,9 +86,9 @@
- /*----------------------------------------------------------------------------*/
- int openFile( const char *const filename,
- const char mode[],
-- FILE **fp,
-+ FILE **const fp,
- const Clock start,
-- struct tms tms_start,
-+ const struct tms tms_start,
- const Boole mayExit)
-
- {
-Index: autodocksuite-4.2.3/autodock/openfile.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/openfile.h 2010-08-02 23:46:29.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/openfile.h 2010-08-02 23:49:09.000000000 +0200
-@@ -36,14 +36,14 @@
-
- int openfile( const char *const filename,
- const char mode[],
-- FILE **fp );
-+ FILE **const fp );
-
-
- int openFile( const char *const filename,
- const char mode[],
-- FILE **fp,
-+ FILE **const fp,
- const Clock start,
-- struct tms tms_start,
-+ const struct tms tms_start,
- const Boole mayExit);
-
- FILE *ad_fopen(const char *const path, const char *const mode);
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,328 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/mkTorTree.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/mkTorTree.cc 2010-08-03 00:02:11.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/mkTorTree.cc 2010-08-03 00:07:06.000000000 +0200
-@@ -42,24 +42,24 @@
- extern char *programname;
-
-
--void mkTorTree( int atomnumber[ MAX_RECORDS ],
-- char Rec_line[ MAX_RECORDS ][ LINE_LEN ],
-- int nrecord,
--
-- int tlist[ MAX_TORS ][ MAX_ATOMS ],
-- int *P_ntor,
-- int *P_ntor_ligand,
--
-- char *smFileName,
--
-- char pdbaname[ MAX_ATOMS ][ 5 ],
-- Boole *P_B_constrain,
-- int *P_atomC1,
-- int *P_atomC2,
-- Real *P_sqlower,
-- Real *P_squpper,
-- int *P_ntorsdof,
-- int ignore_inter[MAX_ATOMS])
-+void mkTorTree( const int atomnumber[ MAX_RECORDS ],
-+ const char Rec_line[ MAX_RECORDS ][ LINE_LEN ],
-+ const int nrecord,
-+
-+/* not const */ int tlist[ MAX_TORS ][ MAX_ATOMS ],
-+/* not const */ int *const P_ntor,
-+/* not const */ int *const P_ntor_ligand,
-+
-+ const char *const smFileName,
-+
-+ const char pdbaname[ MAX_ATOMS ][ 5 ],
-+/* not const */ Boole *const P_B_constrain,
-+/* not const */ int *const P_atomC1,
-+/* not const */ int *const P_atomC2,
-+/* not const */ Real *const P_sqlower,
-+/* not const */ Real *const P_squpper,
-+/* not const */ int *const P_ntorsdof,
-+/* not const */ int ignore_inter[MAX_ATOMS])
-
- {
-
-Index: autodocksuite-4.2.3/autodock/mkTorTree.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/mkTorTree.h 2010-08-03 00:02:11.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/mkTorTree.h 2010-08-03 00:07:50.000000000 +0200
-@@ -31,19 +31,19 @@
- #include "parse_PDBQT_line.h"
- #include "stop.h"
-
--void mkTorTree(int atomnumber[MAX_RECORDS],
-- char record[MAX_RECORDS][LINE_LEN],
-- int nrecord,
-+void mkTorTree(const int atomnumber[MAX_RECORDS],
-+ const char record[MAX_RECORDS][LINE_LEN],
-+ const int nrecord,
- int tlist[MAX_TORS][MAX_ATOMS],
-- int *P_ntor,
-- int *P_ntor_ligand,
-- char *smFileName,
-- char pdbaname[MAX_ATOMS][5],
-- Boole *P_B_constrain,
-- int *P_atomC1,
-- int *P_atomC2,
-- Real *P_sqlower,
-- Real *P_squpper,
-- int *P_ntorsdof,
-+ int *const P_ntor,
-+ int *const P_ntor_ligand,
-+ const char *const smFileName,
-+ const char pdbaname[MAX_ATOMS][5],
-+ Boole *const P_B_constrain,
-+ int *const P_atomC1,
-+ int *const P_atomC2,
-+ Real *const P_sqlower,
-+ Real *const P_squpper,
-+ int *const P_ntorsdof,
- int ignore_inter[MAX_ATOMS]);
- #endif
-Index: autodocksuite-4.2.3/autodock/input_state.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/input_state.cc 2010-08-03 00:52:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/input_state.cc 2010-08-03 00:52:41.000000000 +0200
-@@ -37,7 +37,7 @@
-
- int input_state( State *const S,
- FILE *const fp,
-- char line[LINE_LEN],
-+ const char line[LINE_LEN],
- const int ntor,
- int *const p_istep,
- Real *const p_energy,
-Index: autodocksuite-4.2.3/autodock/input_state.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/input_state.h 2010-08-03 00:52:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/input_state.h 2010-08-03 00:52:50.000000000 +0200
-@@ -31,7 +31,7 @@
-
- int input_state( State *S,
- FILE *const fp,
-- char line[LINE_LEN],
-+ const char line[LINE_LEN],
- const int ntor,
- int *const P_istep,
- Real *const P_energy,
-Index: autodocksuite-4.2.3/autodock/intnbtable.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/intnbtable.cc 2010-08-03 00:53:31.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/intnbtable.cc 2010-08-03 00:53:47.000000000 +0200
-@@ -53,7 +53,7 @@
- extern FILE *logFile;
- extern int debug;
-
--void intnbtable( Boole *P_B_havenbp,
-+void intnbtable( Boole *const P_B_havenbp,
- const int a1,
- const int a2,
- const GridMapSetInfo *const info,
-Index: autodocksuite-4.2.3/autodock/intnbtable.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/intnbtable.h 2010-08-03 00:53:28.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/intnbtable.h 2010-08-03 00:53:56.000000000 +0200
-@@ -30,7 +30,7 @@
- #include "timesys.h"
- #include "structs.h"
-
--void intnbtable(/* not const */ Boole *P_B_havenbp,
-+void intnbtable(/* not const */ Boole *const P_B_havenbp,
- const int a1,
- const int a2,
- const GridMapSetInfo *const info,
-Index: autodocksuite-4.2.3/autodock/investigate.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/investigate.cc 2010-08-03 00:54:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/investigate.cc 2010-08-03 01:03:32.000000000 +0200
-@@ -47,49 +47,49 @@
- extern char *programname;
-
-
--void investigate( int Nnb,
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-+void investigate( const int Nnb,
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const Boole B_calcIntElec,
-+ /* not const */ Real crd[MAX_ATOMS][SPACE], // mod in cnv_state_to_coords
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-
-- EnergyTables *ptr_ad_energy_tables,
-+ const EnergyTables *const ptr_ad_energy_tables,
-
-- int maxTests,
-+ const int maxTests,
- #include "map_declare.h"
-- int natom,
-- NonbondParam *nonbondlist,
-- int ntor,
-- int outlev,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Boole B_isGaussTorCon,
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Boole B_isTorConstrained[MAX_TORS],
-- Boole B_ShowTorE,
-- unsigned short US_TorE[MAX_TORS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- Boole B_symmetry_flag,
-- char *FN_rms_ref_crds,
-- int OutputEveryNTests,
-- int NumLocalTests,
-- Real trnStep,
-- Real torStep,
-+ const int natom,
-+ const NonbondParam *const nonbondlist,
-+ const int ntor,
-+ const int outlev,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const Boole B_isGaussTorCon,
-+ const unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const Boole B_ShowTorE,
-+ /* not const */ unsigned short US_TorE[MAX_TORS],
-+ /* not const */ Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2], // mod in mkRandomState
-+ /* not const */ int N_con[MAX_TORS], // mod in mkRandomState
-+ const Boole B_symmetry_flag,
-+ const char *const FN_rms_ref_crds,
-+ const int OutputEveryNTests,
-+ const int NumLocalTests,
-+ const Real trnStep,
-+ const Real torStep,
-
-- int ignore_inter[MAX_ATOMS],
-+ const int ignore_inter[MAX_ATOMS],
-
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-
-
- const Real unbound_internal_FE,
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues)
-+ /* not const */ GridMapSetInfo *const info, // mod in mkRandomState
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues)
-
- {
- Boole B_outside = FALSE;
-Index: autodocksuite-4.2.3/autodock/investigate.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/investigate.h 2010-08-03 00:54:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/investigate.h 2010-08-03 01:01:25.000000000 +0200
-@@ -45,46 +45,46 @@
-
- void investigate(
- int Nnb,
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const Boole B_calcIntElec,
-+ const Real crd[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-
-- EnergyTables *ptr_ad_energy_tables,
-+ const EnergyTables *const ptr_ad_energy_tables,
-
-- int maxTests,
-+ const int maxTests,
- #include "map_declare.h"
-- int natom,
-- NonbondParam *nonbondlist,
-- int ntor,
-- int outlev,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- Boole B_isGaussTorCon,
-- unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-- Boole B_isTorConstrained[MAX_TORS],
-- Boole B_ShowTorE,
-- unsigned short US_TorE[MAX_TORS],
-- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- int N_con[MAX_TORS],
-- Boole B_symmetry_flag,
-- char *FN_rms_ref_crds,
-- int OutputEveryNTests,
-- int NumLocalTests,
-- Real trnStep,
-- Real torStep,
-+ const int natom,
-+ const NonbondParam *const nonbondlist,
-+ const int ntor,
-+ const int outlev,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const Boole B_isGaussTorCon,
-+ const unsigned short US_torProfile[MAX_TORS][NTORDIVS],
-+ const Boole B_isTorConstrained[MAX_TORS],
-+ const Boole B_ShowTorE,
-+ const unsigned short US_TorE[MAX_TORS],
-+ /* not const */ Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ /* not const */ int N_con[MAX_TORS],
-+ const Boole B_symmetry_flag,
-+ const char *FN_rms_ref_crds,
-+ const int OutputEveryNTests,
-+ const int NumLocalTests,
-+ const Real trnStep,
-+ const Real torStep,
-
-- int ignore_inter[MAX_ATOMS],
-+ const int ignore_inter[MAX_ATOMS],
-
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-
-
- const Real unbound_internal_FE,
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues);
-+ /* not const */ GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues);
- #endif
-Index: autodocksuite-4.2.3/autodock/linpack.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/linpack.cc 2010-08-03 00:11:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/linpack.cc 2010-08-03 00:12:45.000000000 +0200
-@@ -13,7 +13,7 @@
- #include <math.h>
- #include "structs.h"
-
--Real sdot(FourByteLong n,Real *sx,FourByteLong incx,Real *sy,FourByteLong incy)
-+Real sdot(const FourByteLong n,const Real *const sx,const FourByteLong incx,const Real *const sy,const FourByteLong incy)
- {
- static FourByteLong i,ix,iy,m,mp1;
- static Real sdot,stemp;
-@@ -74,7 +74,7 @@
- INTERNAL VARIABLES
- */
- {
--extern Real sdot(FourByteLong n,Real *sx,FourByteLong incx,Real *sy,FourByteLong incy);
-+extern Real sdot(const FourByteLong n,const Real *const sx,const FourByteLong incx,const Real *const sy,const FourByteLong incy);
- static FourByteLong j,jm1,k;
- static Real t,s;
- /*
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,71 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/call_glss.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/call_glss.cc 2010-08-03 01:07:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/call_glss.cc 2010-08-03 01:10:15.000000000 +0200
-@@ -55,7 +55,7 @@
-
- Eval evaluate;
-
--Representation **generate_R(const int num_torsions, GridMapSetInfo *info)
-+Representation **generate_R(const int num_torsions, GridMapSetInfo *const info)
- {
- Representation **retval;
- Quat q;
-@@ -249,8 +249,8 @@
- }
- #endif
-
--State call_glss(Global_Search *global_method, Local_Search *local_method,
-- State sInit,
-+State call_glss(/* not const */ Global_Search *const global_method, /* not const */ Local_Search *const local_method,
-+ const State sInit,
- const unsigned int num_evals, const unsigned int pop_size,
- const int outlev,
- const unsigned int extOutputEveryNgens, Molecule *const mol,
-Index: autodocksuite-4.2.3/autodock/hybrids.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/hybrids.h 2010-08-03 01:06:53.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/hybrids.h 2010-08-03 01:11:08.000000000 +0200
-@@ -44,8 +44,8 @@
- #ifndef CALL_GLSS
- #define CALL_GLSS
-
--State call_glss(Global_Search *global_method, Local_Search *local_method,
-- State now, const unsigned int num_evals, const unsigned int pop_size,
-+State call_glss(Global_Search *const global_method, Local_Search *const local_method,
-+ const State now, const unsigned int num_evals, const unsigned int pop_size,
- const int outlev, const unsigned int extOutputEveryNgens, Molecule *const mol,
- const Boole B_RandomTran0, const Boole B_RandomQuat0, const Boole B_RandomDihe0,
- const GridMapSetInfo *const info, const char *const FN_pop_file,
-Index: autodocksuite-4.2.3/autodock/investigate.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/investigate.h 2010-08-03 23:22:01.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/investigate.h 2010-08-03 23:27:01.000000000 +0200
-@@ -44,12 +44,12 @@
-
-
- void investigate(
-- int Nnb,
-+ const int Nnb,
- const Real charge[MAX_ATOMS],
- const Real abs_charge[MAX_ATOMS],
- const Real qsp_abs_charge[MAX_ATOMS],
- const Boole B_calcIntElec,
-- const Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
- const Real crdpdb[MAX_ATOMS][SPACE],
-
- const EnergyTables *const ptr_ad_energy_tables,
-@@ -67,9 +67,9 @@
- const unsigned short US_torProfile[MAX_TORS][NTORDIVS],
- const Boole B_isTorConstrained[MAX_TORS],
- const Boole B_ShowTorE,
-- const unsigned short US_TorE[MAX_TORS],
-- /* not const */ Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-- /* not const */ int N_con[MAX_TORS],
-+ /* not const */ unsigned short US_TorE[MAX_TORS],
-+ /* not const */ Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
-+ /* not const */ int N_con[MAX_TORS],
- const Boole B_symmetry_flag,
- const char *FN_rms_ref_crds,
- const int OutputEveryNTests,
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,294 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/eintcal.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eintcal.cc 2010-08-03 23:36:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eintcal.cc 2010-08-03 23:37:28.000000000 +0200
-@@ -61,7 +61,7 @@
- extern FILE *logFile;
-
- // Calculate internal energy and print out a detailed report
--Real eintcalPrint( NonbondParam * const nonbondlist,
-+Real eintcalPrint( const NonbondParam * const nonbondlist,
- const EnergyTables *ptr_ad_energy_tables,
- const Real tcoord[MAX_ATOMS][SPACE],
- const int Nnb,
-Index: autodocksuite-4.2.3/autodock/eintcalPrint.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eintcalPrint.h 2010-08-03 23:37:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eintcalPrint.h 2010-08-03 23:37:59.000000000 +0200
-@@ -27,7 +27,7 @@
- #ifndef _EINTCALPRINT
- #define _EINTCALPRINT
-
--Real eintcalPrint( NonbondParam * const nonbondlist,
-+Real eintcalPrint( const NonbondParam * const nonbondlist,
- const EnergyTables *ad_energy_tables,
- const Real tcoord[MAX_ATOMS][SPACE],
- const int Nnb,
-Index: autodocksuite-4.2.3/autodock/eval.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.cc 2010-08-03 23:38:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.cc 2010-08-03 23:41:42.000000000 +0200
-@@ -65,7 +65,7 @@
- tor 1, ..., tor N are the ntor torsion angles
- */
-
--void make_state_from_rep(const Representation *const *const rep, State *stateNow) /* not a member function */
-+void make_state_from_rep(const Representation *const *const rep, /* not const */ State *const stateNow) /* not a member function */
- /*
- This routine modifies the various components of stateNow to correspond
- to the chromosome.
-@@ -120,7 +120,7 @@
- return eval();
- }
-
--double Eval::operator()(const Representation *const *const rep, int term)
-+double Eval::operator()(const Representation *const *const rep, const int term)
- {
- make_state_from_rep(rep, &stateNow);
- return eval(term);
-@@ -283,14 +283,14 @@
- }
-
- #if defined(USING_COLINY) // {
--double Eval::operator()(double* vec, const int len)
-+double Eval::operator()(const double* const vec, const int len)
- {
- make_state_from_rep(vec, len, &stateNow);
- return eval();
- }
-
-
--void make_state_from_rep(double *rep, const int n, State *now)
-+void make_state_from_rep(const double *const rep, const int n, /* not const */ State *const now)
- {
- # ifdef DEBUG
- (void)fprintf(logFile, "eval.cc/make_state_from_rep(double *rep, int n, State *now)\n");
-@@ -351,7 +351,7 @@
- //
- #endif // USING_COLINY // }
-
--double Eval::evalpso(State *state)
-+double Eval::evalpso(/* not const */ State *const state)
- {
- register int i;
- int B_outside = 0;
-Index: autodocksuite-4.2.3/autodock/eval.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.h 2010-08-03 23:41:51.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.h 2010-08-04 00:17:10.000000000 +0200
-@@ -46,10 +46,10 @@
- #endif
-
- #if defined(USING_COLINY)
--void make_state_from_rep(double *x, const int n, State *now);
-+void make_state_from_rep(const double *const x, const int n, State *const now);
- #endif
-
--void make_state_from_rep(const Representation *const *const rep, State *stateNow);
-+void make_state_from_rep(const Representation *const *const rep, State *const stateNow);
-
- class Eval
- {
-@@ -81,38 +81,43 @@
-
- public:
- Eval(void);
-- void setup( Real init_crd[MAX_ATOMS][SPACE],
-- Real init_charge[MAX_ATOMS],
-- Real init_abs_charge[MAX_ATOMS],
-- Real init_qsp_abs_charge[MAX_ATOMS],
-- int init_type[MAX_ATOMS], int init_natom,
-- Real init_map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
--
-- Real init_elec[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-- Real init_emap[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
--
-- NonbondParam *init_nonbondlist,
-- EnergyTables *init_ptr_ad_energy_tables,
-- int init_Nnb,
-- Boole init_B_calcIntElec,
-- Boole init_B_isGaussTorCon, Boole init_B_isTorConstrained[MAX_TORS],
-- Boole init_B_ShowTorE, unsigned short init_US_TorE[MAX_TORS],
-- unsigned short init_US_torProfile[MAX_TORS][NTORDIVS],
-- Real init_vt[MAX_TORS][SPACE], int init_tlist[MAX_TORS][MAX_ATOMS],
-- Real init_crdpdb[MAX_ATOMS][SPACE],
-- Real init_crdreo[MAX_ATOMS][SPACE],
-- State stateInit, Molecule molInit,
-- int init_ignore_inter[MAX_ATOMS],
-- Boole init_B_include_1_4_interactions, // gmm 2005-01-8, for scaling 1-4 nonbonds
-- Real init_scale_1_4, // gmm 2005-01-8, for scaling 1-4 nonbonds
-+ void setup( /* not const */ Real init_crd[MAX_ATOMS][SPACE], // not const since pointers are copied, not contents
-+ /* not const */ Real init_charge[MAX_ATOMS],
-+ /* not const */ Real init_abs_charge[MAX_ATOMS],
-+ /* not const */ Real init_qsp_abs_charge[MAX_ATOMS],
-+ /* not const */ int init_type[MAX_ATOMS],
-+ const int init_natom,
-+ /* not const */ Real init_map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
-+
-+ /* not const */ Real init_elec[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-+ /* not const */ Real init_emap[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-+
-+ /* not const */ NonbondParam *const init_nonbondlist,
-+ /* not const */ EnergyTables *const init_ptr_ad_energy_tables,
-+ const int init_Nnb,
-+ const Boole init_B_calcIntElec,
-+ const Boole init_B_isGaussTorCon,
-+ /* not const */ Boole init_B_isTorConstrained[MAX_TORS], // pointers are copied, not values
-+ const Boole init_B_ShowTorE,
-+ /* not const */ unsigned short init_US_TorE[MAX_TORS],
-+ /* not const */ unsigned short init_US_torProfile[MAX_TORS][NTORDIVS],
-+ /* not const */ Real init_vt[MAX_TORS][SPACE],
-+ /* not const */ int init_tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real init_crdpdb[MAX_ATOMS][SPACE],
-+ /* not const */ Real init_crdreo[MAX_ATOMS][SPACE],
-+ const State stateInit,
-+ const Molecule molInit,
-+ const int init_ignore_inter[MAX_ATOMS], // values are copied
-+ const Boole init_B_include_1_4_interactions, // gmm 2005-01-8, for scaling 1-4 nonbonds
-+ const Real init_scale_1_4, // gmm 2005-01-8, for scaling 1-4 nonbonds
- //ParameterEntry init_parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
-- Real init_unbound_internal_FE,
-- GridMapSetInfo *init_info,
-- Boole init_B_use_non_bond_cutoff, // set this to FALSE if we are computing unbound extended conformations
-- Boole init_B_have_flexible_residues
-+ const Real init_unbound_internal_FE,
-+ /* not const */ GridMapSetInfo *const init_info,
-+ const Boole init_B_use_non_bond_cutoff, // set this to FALSE if we are computing unbound extended conformations
-+ const Boole init_B_have_flexible_residues
- );
- void update_crds( Real init_crdreo[MAX_ATOMS][SPACE],
-- Real init_vt[MAX_TORS][SPACE] );
-+ Real init_vt[MAX_TORS][SPACE]);
-
- double operator()(const Representation *const *const );
- double operator()(const Representation *const *const , int); // GMM - allows calculation of a particular term of the total energy
-@@ -124,8 +129,8 @@
- UnsignedFourByteLong evals(void);
- void reset(void);
- int write(FILE *const out_file, const Representation *const *const rep);
-- double evalpso(State *state);
-- void compute_intermol_energy(Boole init_B_compute_intermol_energy); // for computing unbound state
-+ double evalpso(/* not const */ State *const state);
-+ void compute_intermol_energy(const Boole init_B_compute_intermol_energy); // for computing unbound state
- };
-
- inline Eval::Eval(void)
-@@ -133,43 +138,43 @@
- {
- }
-
--inline void Eval::setup(Real init_crd[MAX_ATOMS][SPACE],
-- Real init_charge[MAX_ATOMS],
-- Real init_abs_charge[MAX_ATOMS],
-- Real init_qsp_abs_charge[MAX_ATOMS],
-- int init_type[MAX_ATOMS],
-- int init_natom,
-- Real init_map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
--
-- Real init_elec[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-- Real init_emap[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-- NonbondParam *init_nonbondlist,
-- EnergyTables *init_ptr_ad_energy_tables,
-- int init_Nnb,
-- Boole init_B_calcIntElec,
-- Boole init_B_isGaussTorCon,
-- Boole init_B_isTorConstrained[MAX_TORS],
-- Boole init_B_ShowTorE,
-- unsigned short init_US_TorE[MAX_TORS],
-- unsigned short init_US_torProfile[MAX_TORS][NTORDIVS],
-- Real init_vt[MAX_TORS][SPACE],
-- int init_tlist[MAX_TORS][MAX_ATOMS],
-- Real init_crdpdb[MAX_ATOMS][SPACE],
-- Real init_crdreo[MAX_ATOMS][SPACE],
-- State stateInit,
-- Molecule molInit,
-+inline void Eval::setup(/* not const */ Real init_crd[MAX_ATOMS][SPACE], // not const since pointers are copied, not values
-+ /* not const */ Real init_charge[MAX_ATOMS],
-+ /* not const */ Real init_abs_charge[MAX_ATOMS],
-+ /* not const */ Real init_qsp_abs_charge[MAX_ATOMS],
-+ /* not const */ int init_type[MAX_ATOMS],
-+ const int init_natom,
-+ /* not const */ Real init_map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
-+
-+ /* not const */ Real init_elec[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-+ /* not const */ Real init_emap[MAX_ATOMS], // gmm added 21-Jan-1998, for writePDBQState
-+ /* not const */ NonbondParam *const init_nonbondlist,
-+ /* not const */ EnergyTables *const init_ptr_ad_energy_tables,
-+ const int init_Nnb,
-+ const Boole init_B_calcIntElec,
-+ const Boole init_B_isGaussTorCon,
-+ /* not const */ Boole init_B_isTorConstrained[MAX_TORS], // again, values are not copied but pointers
-+ const Boole init_B_ShowTorE,
-+ /* not const */ unsigned short init_US_TorE[MAX_TORS],
-+ /* not const */ unsigned short init_US_torProfile[MAX_TORS][NTORDIVS],
-+ /* not const */ Real init_vt[MAX_TORS][SPACE],
-+ /* not const */ int init_tlist[MAX_TORS][MAX_ATOMS],
-+ /* not const */ Real init_crdpdb[MAX_ATOMS][SPACE],
-+ /* not const */ Real init_crdreo[MAX_ATOMS][SPACE],
-+ const State stateInit,
-+ const Molecule molInit,
-
-- int init_ignore_inter[MAX_ATOMS],
-+ const int init_ignore_inter[MAX_ATOMS], // values are copied
-
-- Boole init_B_include_1_4_interactions,
-- Real init_scale_1_4,
-+ const Boole init_B_include_1_4_interactions,
-+ const Real init_scale_1_4,
-
- //ParameterEntry init_parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
-
-- Real init_unbound_internal_FE,
-- GridMapSetInfo *init_info,
-- Boole init_B_use_non_bond_cutoff, // set this to FALSE if we are computing unbound extended conformations
-- Boole init_B_have_flexible_residues
-+ const Real init_unbound_internal_FE,
-+ /* not const */ GridMapSetInfo *const init_info,
-+ const Boole init_B_use_non_bond_cutoff, // set this to FALSE if we are computing unbound extended conformations
-+ const Boole init_B_have_flexible_residues
- )
-
- {
-@@ -224,13 +229,13 @@
- }
-
- inline void Eval::update_crds( Real init_crdreo[MAX_ATOMS][SPACE],
-- Real init_vt[MAX_TORS][SPACE] )
-+ Real init_vt[MAX_TORS][SPACE])
- {
- crdreo = init_crdreo;
- vt = init_vt;
- }
-
--inline void Eval::compute_intermol_energy(Boole init_B_compute_intermol_energy)
-+inline void Eval::compute_intermol_energy(const Boole init_B_compute_intermol_energy)
- // For computing the conformation and the internal energy of the unbound state.
- {
- B_compute_intermol_energy = init_B_compute_intermol_energy;
-Index: autodocksuite-4.2.3/autodock/get_atom_type.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/get_atom_type.cc 2010-08-03 23:29:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/get_atom_type.cc 2010-08-03 23:30:41.000000000 +0200
-@@ -43,9 +43,9 @@
- extern int debug;
-
-
--int get_atom_type( char aname[4] )
-+int get_atom_type( const char aname[4] )
- {
-- ParameterEntry * found_parm;
-+ const ParameterEntry * /* not const */ found_parm;
- ParameterEntry thisparm;
- int map_index = -1;
- int bond_index = -1;
-Index: autodocksuite-4.2.3/autodock/get_atom_type.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/get_atom_type.h 2010-08-03 23:29:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/get_atom_type.h 2010-08-03 23:30:48.000000000 +0200
-@@ -29,5 +29,5 @@
-
- #include "autocomm.h"
-
--int get_atom_type( char aname[4] );
-+int get_atom_type( const char aname[4] );
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_85.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_85.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_85.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,189 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/dimLibrary.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/dimLibrary.cc 2010-08-04 22:56:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/dimLibrary.cc 2010-08-04 23:07:09.000000000 +0200
-@@ -10,7 +10,7 @@
- extern FILE *logFile;
-
-
--void copyDimension( State *S, Position R)
-+void copyDimension( /* not const */ State *const S, const Position R)
- {
- register int i, j;
- S->T.x = R.x[0];
-@@ -27,7 +27,7 @@
- }
-
-
--void copyState2Dimension(Position *R , State S)
-+void copyState2Dimension(Position *const R , const State S)
- {
- register int i, j;
- R->x[0] = S.T.x;
-@@ -44,7 +44,7 @@
- }
-
-
--void initialiseDimension(GridMapSetInfo * info, double *xmin, double *xmax, int D)
-+void initialiseDimension(const GridMapSetInfo *const info, /* not const */ double *const xmin, /* not const */ double *const xmax, const int D)
- {
- int d;
-
-@@ -88,7 +88,7 @@
- }
-
-
--void initialiseParticle(int s, int D, Position *Xi, Velocity *Vi, double *xmin, double *xmax, double *Vmin, double *Vmax)
-+void initialiseParticle(const int s, const int D, /* not const */ Position *const Xi, /* not const */ Velocity *const Vi, const double *const xmin, const double *const xmax, double *const Vmin, double *const Vmax)
- {
- int d;
- double temp;
-@@ -125,7 +125,7 @@
- //printf("end initialiseParticle: s=%d, D=%d, Xi=%f \n",s,D,*Xi);
- }
-
--void swarmActivity(int S, int D, Position *Xi, int nb_eval, int outlev)
-+void swarmActivity(const int S, const int D, const Position *const Xi, const int nb_eval, const int outlev)
- {
- int s, d;
- double swarm_activity;
-Index: autodocksuite-4.2.3/autodock/dimLibrary.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/dimLibrary.h 2010-08-04 22:56:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/dimLibrary.h 2010-08-04 23:07:21.000000000 +0200
-@@ -9,13 +9,13 @@
- //void initialiseState( State *S );
- //void copyState( State *destination, State source);
-
--void copyDimension( State *S, Position R);
--void copyState2Dimension( Position *R, State S);
-+void copyDimension( /* not const */ State *const S, const Position R);
-+void copyState2Dimension( /* not const */ Position *const R, const State S);
- //void copyState2Dimension( Position R, State *S);
--void initialiseDimension(GridMapSetInfo * info, double *xmin, double *xmax, int D);
-+void initialiseDimension(const GridMapSetInfo *const info, /* not const */ double *const xmin, /* not const */ double *const xmax, const int D);
- //void initialiseDimension(float xlo, float xhi, float ylo, float yhi, float zlo, float zhi, double *xmin, double *xmax, int D);
--void initialiseParticle(int s, int D, Position *Xi, Velocity *Vi, double *xmin, double *xmax, double *Vmin, double *Vmax);
--void swarmActivity(int S, int D, Position *Xi, int nb_eval, int outlev);
-+void initialiseParticle(const int s, const int D, /* not const */ Position *const Xi, /* not const */ Velocity *const Vi, const double *const xmin, const double *const xmax, double *const Vmin, double *const Vmax);
-+void swarmActivity(const int S, const int D, const Position *const Xi, const int nb_eval, const int outlev);
-
- /*void printState( FILE *fp,
- State state,
-Index: autodocksuite-4.2.3/autodock/distdepdiel.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/distdepdiel.cc 2010-08-04 23:04:41.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/distdepdiel.cc 2010-08-04 23:04:56.000000000 +0200
-@@ -28,7 +28,7 @@
- #include "distdepdiel.h"
-
-
--double calc_ddd_Mehler_Solmajer( double distance, double approx_zero ) {
-+double calc_ddd_Mehler_Solmajer( const double distance, const double approx_zero ) {
- /*____________________________________________________________________________
- * Distance-dependent dielectric ewds: Mehler and Solmajer, Prot Eng 4, 903-910.
- *____________________________________________________________________________*/
-Index: autodocksuite-4.2.3/autodock/distdepdiel.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/distdepdiel.h 2010-08-04 23:04:41.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/distdepdiel.h 2010-08-04 23:05:04.000000000 +0200
-@@ -28,6 +28,6 @@
- #define _DISTDEPDIEL
-
-
--double calc_ddd_Mehler_Solmajer( double distance, double aprrox_zero );
-+double calc_ddd_Mehler_Solmajer( const double distance, const double aprrox_zero );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/parse_param_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_param_line.cc 2010-08-04 23:11:42.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_param_line.cc 2010-08-04 23:15:38.000000000 +0200
-@@ -36,7 +36,7 @@
- extern int debug;
- extern FILE *logFile;
-
--int parse_param_line( const char line[LINE_LEN] )
-+int parse_param_line( const char *const line)
-
- /******************************************************************************/
- /* Name: parse_param_line */
-@@ -76,7 +76,7 @@
- }; // 7 tokens // remember to set tokentablesize earlier
-
- c[0] = '\0';
-- for (j=0; ((line[j]!='\0')&&(line[j]!=' ')&&(line[j]!='\t')&&(line[j]!='\n')); j++) {
-+ for (j=0; ((line[j]!='\0')&&(line[j]!=' ')&&(line[j]!='\t')&&(line[j]!='\n')); j++) { //FIXME: check on j<LINE_LEN missing
- /* Ignore case */
- c[j] = (char)tolower((int)line[j]);
- if (debug > 0) {
-Index: autodocksuite-4.2.3/autodock/parse_param_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_param_line.h 2010-08-04 23:11:43.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_param_line.h 2010-08-04 23:14:37.000000000 +0200
-@@ -28,6 +28,6 @@
- #define PARSE_PAR_LINE
-
- #include "constants.h"
--int parse_param_line( const char line[LINE_LEN] );
-+int parse_param_line( const char *const line);
-
- #endif
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.cc 2010-08-04 23:07:50.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.cc 2010-08-04 23:32:10.000000000 +0200
-@@ -71,7 +71,8 @@
- // remember this filename for report_parameter_library()
- snprintf(parameter_library, sizeof parameter_library, "from file: \"%s\"", FN_parameter_library);
- while (fgets(parameter_library_line, sizeof(parameter_library_line), parameter_library_file) != NULL) {
-- param_keyword = parse_param_line( parameter_library_line );
-+ char *const s = parameter_library_line;
-+ param_keyword = parse_param_line("huhu");
- if (debug > 0) {
- pr(logFile, "DEBUG: parameter_library_line = %sDEBUG: param_keyword = %d\n", parameter_library_line, param_keyword);
- }
-@@ -209,7 +210,7 @@
- // so far we have param_string_4_0 and param_string_4_1
- // remember this choice for report_parameter_library()
-
-- char ** param_string;
-+ const char *const *param_string;
- //if (string_begins_with(version_num, "4.0")) param_string=param_string_4_0;
- if (unbound_model==Extended) {
- param_string=param_string_4_0;
-@@ -226,7 +227,8 @@
-
-
- while ( param_string[counter] != NULL) {
-- param_keyword = parse_param_line( param_string[counter] );
-+ const char* const s = param_string[counter];
-+ param_keyword = parse_param_line(s);
-
- (void)strcpy(parameter_library_line, param_string[counter]);
- counter++;
-Index: autodocksuite-4.2.3/autogrid/parse_param_line.cpp
-===================================================================
---- autodocksuite-4.2.3.orig/autogrid/parse_param_line.cpp 2010-08-04 23:36:23.000000000 +0200
-+++ autodocksuite-4.2.3/autogrid/parse_param_line.cpp 2010-08-04 23:36:34.000000000 +0200
-@@ -37,7 +37,7 @@
- extern int debug;
- extern FILE *logFile;
-
--int parse_param_line( char line[LINE_LEN] )
-+int parse_param_line( const char line[] )
-
- /******************************************************************************/
- /* Name: parse_param_line */
-Index: autodocksuite-4.2.3/autogrid/parse_param_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autogrid/parse_param_line.h 2010-08-04 23:36:06.000000000 +0200
-+++ autodocksuite-4.2.3/autogrid/parse_param_line.h 2010-08-04 23:36:20.000000000 +0200
-@@ -28,6 +28,6 @@
- #define PARSE_PAR_LINE
-
- #include "constants.h"
--int parse_param_line( char line[LINE_LEN] );
-+int parse_param_line( const char line[] );
-
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_90.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_90.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_90.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,333 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/alea.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/alea.cc 2010-08-05 01:23:23.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/alea.cc 2010-08-05 01:23:44.000000000 +0200
-@@ -3,7 +3,7 @@
- #include <sys/types.h>
- #include <time.h>
-
--double alea( double a, double b)
-+double alea( const double a, const double b)
- {
- //random number (uniform distribution) in [a b]
- double r ;
-@@ -13,7 +13,7 @@
- }
-
-
--int alea_integer(int a, int b)
-+int alea_integer(const int a, const int b)
- {
- // Integer random number in [a b]
- int ir;
-Index: autodocksuite-4.2.3/autodock/alea.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/alea.h 2010-08-05 01:23:12.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/alea.h 2010-08-05 01:23:53.000000000 +0200
-@@ -2,8 +2,8 @@
- #include <math.h>
- #include <stdlib.h>
-
--double alea( double a, double b);
--int alea_integer(int a, int b);
-+double alea( const double a, const double b);
-+int alea_integer(const int a, const int b);
-
-
-
-Index: autodocksuite-4.2.3/autodock/analysis.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/analysis.cc 2010-08-05 01:24:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/analysis.cc 2010-08-05 01:34:13.000000000 +0200
-@@ -56,46 +56,47 @@
- extern char *programname;
- extern int true_ligand_atoms;
-
--void analysis( int Nnb,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-- Real clus_rms_tol,
-- Real crdpdb[MAX_ATOMS][SPACE],
--
-- const EnergyTables *ptr_ad_energy_tables,
--
-- Real map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
-- Real econf[MAX_RUNS],
-- int irunmax,
-- int natom,
-- NonbondParam *nonbondlist,
-- int nconf,
-- int ntor,
-- State hist[MAX_RUNS],
-- char *smFileName,
-- Real sml_center[SPACE],
-- Boole B_symmetry_flag,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- char *FN_rms_ref_crds,
-- Real torsFreeEnergy,
-- Boole B_write_all_clusmem,
-- int ligand_is_inhibitor,
-- int outlev,
-- int ignore_inter[MAX_ATOMS],
-+void analysis( const int Nnb,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const Boole B_calcIntElec,
-+ const Real clus_rms_tol,
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+
-+ const EnergyTables *const ptr_ad_energy_tables,
-+
-+ //const
-+ #include "map_declare.h"
-+ const Real econf[MAX_RUNS],
-+ const int irunmax,
-+ const int natom,
-+ const NonbondParam *nonbondlist,
-+ const int nconf,
-+ const int ntor,
-+ const State hist[MAX_RUNS],
-+ const char *const smFileName,
-+ const Real sml_center[SPACE],
-+ const Boole B_symmetry_flag,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const char *const FN_rms_ref_crds,
-+ const Real torsFreeEnergy,
-+ const Boole B_write_all_clusmem,
-+ const int ligand_is_inhibitor,
-+ const int outlev,
-+ const int ignore_inter[MAX_ATOMS],
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Boole B_rms_atoms_ligand_only,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Boole B_rms_atoms_ligand_only,
-+ const Unbound_Model ad4_unbound_model
-
- )
-
-Index: autodocksuite-4.2.3/autodock/analysis.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/analysis.h 2010-08-05 01:24:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/analysis.h 2010-08-05 01:27:25.000000000 +0200
-@@ -41,46 +41,46 @@
- #ifndef ANALYSIS
- #define ANALYSIS
-
--void analysis( int Nnb,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Boole B_calcIntElec,
-- Real clus_rms_tol,
-- Real crdpdb[MAX_ATOMS][SPACE],
-+void analysis( const int Nnb,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const Boole B_calcIntElec,
-+ const Real clus_rms_tol,
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-
-- const EnergyTables *ptr_ad_energy_tables,
-+ const EnergyTables *const ptr_ad_energy_tables,
- #include "map_declare.h"
-- Real econf[MAX_RUNS],
-- int irunmax,
-- int natom,
-- NonbondParam *nonbondlist,
-- int nconf,
-- int ntor,
-- State hist[MAX_RUNS],
-- char *smFileName,
-- Real sml_center[SPACE],
-- Boole B_symmetry_flag,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- char *rms_ref_crds,
-- Real torsFreeEnergy,
-- Boole B_write_all_clusmem,
-- int ligand_is_inhibitor,
-- int outlev,
-- int ignore_inter[MAX_ATOMS],
-+ const Real econf[MAX_RUNS],
-+ const int irunmax,
-+ const int natom,
-+ const NonbondParam *nonbondlist,
-+ const int nconf,
-+ const int ntor,
-+ const State hist[MAX_RUNS],
-+ const char *const smFileName,
-+ const Real sml_center[SPACE],
-+ const Boole B_symmetry_flag,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const char *const rms_ref_crds,
-+ const Real torsFreeEnergy,
-+ const Boole B_write_all_clusmem,
-+ const int ligand_is_inhibitor,
-+ const int outlev,
-+ const int ignore_inter[MAX_ATOMS],
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Boole B_rms_atoms_ligand_only,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Boole B_rms_atoms_ligand_only,
-+ const Unbound_Model ad4_unbound_model
-
- );
- #endif
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.cc 2010-08-04 23:43:55.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.cc 2010-08-04 23:44:54.000000000 +0200
-@@ -277,10 +277,10 @@
- eb->deltaG = eb->e_inter + eb->e_intra + eb->e_torsFreeEnergy - eb->e_unbound_internal_FE;
- }
-
--void initialise_binding_energy_breakdown( EnergyBreakdown * eb,
-- Real torsFreeEnergy,
-- Real unbound_internal_FE ,
-- Unbound_Model ad4_unbound_model)
-+void initialise_binding_energy_breakdown( /* not const */ EnergyBreakdown *const eb,
-+ const Real torsFreeEnergy,
-+ const Real unbound_internal_FE ,
-+ const Unbound_Model ad4_unbound_model)
- {
- eb->e_inter_moving_fixed = 0.0; // (1) // trilinterp( 0, true_ligand_atoms, ...)
- eb->e_intra_moving_fixed_rec = 0.0; // (2) // trilinterp( true_ligand_atoms, natom, ...)
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.h 2010-08-04 23:43:56.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.h 2010-08-04 23:46:30.000000000 +0200
-@@ -65,11 +65,11 @@
-
- );
-
--void update_energy_breakdown( EnergyBreakdown * eb );
-+void update_energy_breakdown( EnergyBreakdown * eb ); //FIXME: Steffen: this misses the extra parameter const Unbound_Model ad4_unbound_model
-
--void initialise_energy_breakdown ( EnergyBreakdown * eb,
-- Real torsFreeEnergy,
-- Real unbound_internal_FE );
-+void initialise_energy_breakdown ( /* not const */ EnergyBreakdown *const eb,
-+ const Real torsFreeEnergy,
-+ const Real unbound_internal_FE );
-
- EnergyBreakdown calculateBindingEnergies(
- const int natom, // input number of atoms
-Index: autodocksuite-4.2.3/autodock/check_header_float.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_float.cc 2010-08-04 23:47:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_float.cc 2010-08-04 23:47:16.000000000 +0200
-@@ -37,7 +37,7 @@
- extern FILE *logFile;
-
-
--void check_header_float( Real f1, Real f2, char keyword[], char filename[] )
-+void check_header_float( const Real f1, const Real f2, const char keyword[], const char filename[] )
-
- {
- if ( f1 != f2 ) {
-Index: autodocksuite-4.2.3/autodock/check_header_float.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_float.h 2010-08-04 23:47:00.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_float.h 2010-08-04 23:47:22.000000000 +0200
-@@ -27,8 +27,8 @@
- #ifndef CHKHDFLOAT
- #define CHKHDFLOAT
-
--void check_header_float( Real f1,
-- Real f2,
-- char keyword[],
-- char filename[] );
-+void check_header_float( const Real f1,
-+ const Real f2,
-+ const char keyword[],
-+ const char filename[] );
- #endif
-Index: autodocksuite-4.2.3/autodock/check_header_int.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_int.cc 2010-08-04 23:47:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_int.cc 2010-08-04 23:47:56.000000000 +0200
-@@ -36,10 +36,10 @@
- extern FILE *logFile;
-
-
--void check_header_int( int i1,
-- int i2,
-- char axis,
-- char *filename )
-+void check_header_int( const int i1,
-+ const int i2,
-+ const char axis,
-+ const char *const filename )
-
- {
- char message[LINE_LEN];
-Index: autodocksuite-4.2.3/autodock/check_header_int.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_int.h 2010-08-04 23:47:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_int.h 2010-08-04 23:48:03.000000000 +0200
-@@ -31,8 +31,8 @@
- #include "print_2x.h"
- #include "stop.h"
-
--void check_header_int( int i1,
-- int i2,
-- char axis,
-- char * filename );
-+void check_header_int( const int i1,
-+ const int i2,
-+ const char axis,
-+ const char *const filename );
- #endif
-Index: autodocksuite-4.2.3/autodock/autodock4
-===================================================================
-Binary files autodocksuite-4.2.3.orig/autodock/autodock4 2010-08-05 01:30:06.000000000 +0200 and autodocksuite-4.2.3/autodock/autodock4 2010-08-10 00:20:08.000000000 +0200 differ
-Index: autodocksuite-4.2.3/autodock/call_glss.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/call_glss.cc 2010-08-10 00:30:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/call_glss.cc 2010-08-10 00:32:52.000000000 +0200
-@@ -260,9 +260,9 @@
- {
- register unsigned int i;
- register int j;
-- int num_generations = 0, allEnergiesEqual = 1, numTries = 0;
-+ unsigned int num_generations = 0, allEnergiesEqual = 1, numTries = 0;
- int indiv = 0; // Number of Individual in Population to set initial state variables for.
-- int max_numTries = 1000;
-+ const unsigned int max_numTries = 1000;
- double firstEnergy = 0.0;
- EvalMode localEvalMode = Normal_Eval;
- FILE *pop_fileptr;
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_FILEpointer.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_FILEpointer.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_FILEpointer.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,2575 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/banner.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/banner.cc 2010-07-22 21:22:20.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/banner.cc 2010-07-22 21:23:26.000000000 +0200
-@@ -33,7 +33,7 @@
-
- extern FILE *logFile;
-
--void banner( const char * version_num )
-+void banner( const char *const version_num )
- {
-
- /*----------------------------------------------------------------------------*/
-@@ -99,7 +99,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void show_copyright( FILE *fp )
-+void show_copyright( FILE *const fp )
- {
-
- (void) fprintf( fp, "GNU GENERAL PUBLIC LICENSE\n");
-@@ -361,7 +361,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void show_warranty( FILE *fp )
-+void show_warranty( FILE *const fp )
- {
-
- (void) fprintf( fp, "NO WARRANTY\n");
-Index: autodocksuite-4.2.3/autodock/banner.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/banner.h 2010-07-22 21:23:28.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/banner.h 2010-07-22 21:23:46.000000000 +0200
-@@ -27,7 +27,7 @@
- #ifndef BANNER
- #define BANNER
- #include "typedefs.h"
--void banner( const char * version_num );
--void show_copyright( FILE *fp );
--void show_warranty( FILE *fp );
-+void banner( const char *const version_num );
-+void show_copyright( FILE *const fp );
-+void show_warranty( FILE *const fp );
- #endif
-Index: autodocksuite-4.2.3/autodock/call_glss.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/call_glss.cc 2010-07-22 21:24:42.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/call_glss.cc 2010-07-23 20:40:39.000000000 +0200
-@@ -55,7 +55,7 @@
-
- Eval evaluate;
-
--Representation **generate_R(int num_torsions, GridMapSetInfo *info)
-+Representation **generate_R(const int num_torsions, GridMapSetInfo *info)
- {
- Representation **retval;
- Quat q;
-@@ -96,7 +96,7 @@
- return(retval);
- }
-
--Representation **generate_R_quaternion(int num_torsions, GridMapSetInfo *info)
-+Representation **generate_R_quaternion(const int num_torsions, const GridMapSetInfo *const info)
- {
- Representation **retval;
- Quat q;
-@@ -145,7 +145,7 @@
- return(retval);
- }
-
--Genotype generate_Gtype(int num_torsions, GridMapSetInfo *info)
-+Genotype generate_Gtype(const int num_torsions, const GridMapSetInfo *const info)
- {
- #ifdef DEBUG
- // (void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Gtype() about to call Genotype temp(5, generate_R())...\n");
-@@ -161,7 +161,7 @@
- return(temp);
- }
-
--Phenotype generate_Ptype(int num_torsions, GridMapSetInfo *info)
-+Phenotype generate_Ptype(const int num_torsions, const GridMapSetInfo *const info)
- {
- #ifdef DEBUG
- // (void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Ptype() about to call Phenotype temp(5, generate_R())...\n");
-@@ -177,7 +177,7 @@
- return(temp);
- }
-
--Individual random_ind(int num_torsions, GridMapSetInfo *info)
-+Individual random_ind(const int num_torsions, const GridMapSetInfo *const info)
- {
-
- #ifdef DEBUG
-@@ -204,7 +204,7 @@
- }
-
- #ifdef FALSE
--Individual set_ind(int num_torsions, GridMapSetInfo *info, State state)
-+Individual set_ind(const int num_torsions, const GridMapSetInfo *const info, const State state)
- {
- Genotype temp_Gtype;
- Phenotype temp_Ptype;
-@@ -251,12 +251,12 @@
-
- State call_glss(Global_Search *global_method, Local_Search *local_method,
- State sInit,
-- unsigned int num_evals, unsigned int pop_size,
-- int outlev,
-- unsigned int extOutputEveryNgens, Molecule *mol,
-- Boole B_RandomTran0, Boole B_RandomQuat0, Boole B_RandomDihe0,
-- GridMapSetInfo *info, char *FN_pop_file,
-- int end_of_branch[MAX_TORS])
-+ const unsigned int num_evals, const unsigned int pop_size,
-+ const int outlev,
-+ const unsigned int extOutputEveryNgens, Molecule *const mol,
-+ const Boole B_RandomTran0, const Boole B_RandomQuat0, const Boole B_RandomDihe0,
-+ const GridMapSetInfo *info, const char *const FN_pop_file,
-+ const int end_of_branch[MAX_TORS])
- {
- register unsigned int i;
- register int j;
-Index: autodocksuite-4.2.3/autodock/eval.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.cc 2010-07-22 21:31:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.cc 2010-07-22 21:31:24.000000000 +0200
-@@ -263,7 +263,7 @@
- return(retval);
- }
-
--int Eval::write(FILE *out_file, const Representation *const *const rep)
-+int Eval::write(FILE *const out_file, const Representation *const *const rep)
- {
- int i=0, retval=0;
- //char rec14[14];
-Index: autodocksuite-4.2.3/autodock/eval.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.h 2010-07-22 21:31:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.h 2010-07-22 21:31:36.000000000 +0200
-@@ -123,7 +123,7 @@
- double eval(const int); // GMM - allows calculation of a particular term of the total energy
- UnsignedFourByteLong evals(void);
- void reset(void);
-- int write(FILE *out_file, const Representation *const *const rep);
-+ int write(FILE *const out_file, const Representation *const *const rep);
- double evalpso(State *state);
- void compute_intermol_energy(Boole init_B_compute_intermol_energy); // for computing unbound state
- };
-Index: autodocksuite-4.2.3/autodock/input_state.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/input_state.cc 2010-07-22 21:31:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/input_state.cc 2010-07-22 21:44:12.000000000 +0200
-@@ -35,14 +35,14 @@
-
- #define LINELEN 132
-
--int input_state( State *S,
-- FILE *fp,
-+int input_state( State *const S,
-+ FILE *const fp,
- char line[LINE_LEN],
-- int ntor,
-- int *p_istep,
-- Real *p_energy,
-- Real *p_eint,
-- char *p_lastmove )
-+ const int ntor,
-+ int *const p_istep,
-+ Real *const p_energy,
-+ Real *const p_eint,
-+ char *const p_lastmove )
- {
- int i, istep, status;
- Real energy, eint;
-Index: autodocksuite-4.2.3/autodock/input_state.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/input_state.h 2010-07-22 21:44:17.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/input_state.h 2010-07-22 21:44:52.000000000 +0200
-@@ -30,11 +30,11 @@
- #include "qmultiply.h"
-
- int input_state( State *S,
-- FILE *fp,
-+ FILE *const fp,
- char line[LINE_LEN],
-- int ntor,
-- int *P_istep,
-- Real *P_energy,
-- Real *P_eint,
-- char *P_lastmove );
-+ const int ntor,
-+ int *const P_istep,
-+ Real *const P_energy,
-+ Real *const P_eint,
-+ char *const P_lastmove );
- #endif
-Index: autodocksuite-4.2.3/autodock/ls.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.cc 2010-07-22 21:45:02.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.cc 2010-07-22 21:46:43.000000000 +0200
-@@ -42,7 +42,7 @@
- extern FILE *logFile;
-
- // This function adds sign * (deviates + bias) to all the reals in the representation
--Phenotype genPh(const Phenotype &original, Real sign, Real *deviates, Real *bias)
-+Phenotype genPh(const Phenotype &original, const Real sign, const Real *const deviates, Real *const bias)
- {
- RepType genetype;
- register unsigned int i, index = 0;
-@@ -106,7 +106,7 @@
- #ifdef DEBUG
- //convenience function for debugging
- #define traceState(msg,vector) printDState(logFile,msg,vector,i,prevxyz,startxyz,prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates)
--void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-+void printDState(FILE *const logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
- Real startxyz[3], Quat prevQuat, Quat startQuat,
- unsigned int num_successes, unsigned int num_failures,
- Real temp_rho, Real * bias, Real * deviates);
-Index: autodocksuite-4.2.3/autodock/minmeanmax.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/minmeanmax.cc 2010-07-22 21:49:21.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/minmeanmax.cc 2010-07-22 21:51:07.000000000 +0200
-@@ -43,7 +43,7 @@
- #define which_bin(x, min, max, nbins) int((nbins)*((x)-(min))/((max)-(min)))
- #define clamp_range(x, min, max) ((x) < (min)) ? (min) : ((x) > (max)) ? (max) : (x)
-
--void minmeanmax( FILE *fp, Population &pop, int num_generations, GridMapSetInfo *info )
-+void minmeanmax( FILE *const fp, const Population &pop, const int num_generations, const GridMapSetInfo *const info )
- {
- #ifdef DEBUG
- fprintf( fp, "minmeanmax.cc/minmeanmax(); initialization\n" );
-Index: autodocksuite-4.2.3/autodock/nonbonds.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/nonbonds.cc 2010-07-22 21:51:21.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/nonbonds.cc 2010-07-22 21:51:52.000000000 +0200
-@@ -242,7 +242,7 @@
-
- /*----------------------------------------------------------------------------*/
-
--void print_1_4_message(FILE *file, Boole B_include_1_4_interactions, Real scale_1_4)
-+void print_1_4_message(FILE *const file, const Boole B_include_1_4_interactions, const Real scale_1_4)
- {
- if (B_include_1_4_interactions == FALSE) {
- pr(file, "1,4-interactions will be _ignored_ in the non-bonded internal energy calculation.\n\n");
-Index: autodocksuite-4.2.3/autodock/openfile.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/openfile.cc 2010-07-22 21:52:12.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/openfile.cc 2010-07-22 23:36:15.000000000 +0200
-@@ -51,13 +51,12 @@
- extern FILE *logFile;
- /*----------------------------------------------------------------------------*/
- /* fopen rewrite to either use BOINC api or normal system call */
--FILE *ad_fopen(const char *path, const char *mode)
-+FILE *ad_fopen(const char *const path, const char *const mode)
- {
- FILE *filep;
- #ifdef BOINC
-- int rc;
- char resolved_name[512];
-- rc = boinc_resolve_filename(path, resolved_name, sizeof(resolved_name));
-+ const int rc = boinc_resolve_filename(path, resolved_name, sizeof(resolved_name));
- if (rc){
- fprintf(stderr, "BOINC_ERROR: cannot open filename.%s\n",path);
- boinc_finish(rc); /* back to BOINC core */
-@@ -71,8 +70,8 @@
- }
-
- /*----------------------------------------------------------------------------*/
--int openfile( char *filename,
-- char mode[],
-+int openfile( const char *const filename,
-+ const char mode[],
- FILE **fp )
-
- {
-@@ -85,12 +84,12 @@
- }
-
- /*----------------------------------------------------------------------------*/
--int openFile( char *filename,
-- char mode[],
-- FILE **fp,
-- Clock start,
-- struct tms tms_start,
-- Boole mayExit)
-+int openFile( const char *const filename,
-+ const char mode[],
-+ FILE **fp,
-+ const Clock start,
-+ struct tms tms_start,
-+ const Boole mayExit)
-
- {
- Clock jobEnd;
-Index: autodocksuite-4.2.3/autodock/output_state.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/output_state.cc 2010-07-22 21:57:38.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/output_state.cc 2010-07-22 22:00:55.000000000 +0200
-@@ -43,18 +43,18 @@
- #define PERMS 0666 /* hexadecimal permissions for watch-file */
-
- /*----------------------------------------------------------------------------*/
--void output_state( FILE *fp,
-- State S,
-- int ntor,
-- int istep,
-- Real energy,
-- Real eint,
-- char lastmove,
-- Boole B_watch,
-- char *FN_watch,
-+void output_state( FILE *const fp,
-+ const State S,
-+ const int ntor,
-+ const int istep,
-+ const Real energy,
-+ const Real eint,
-+ const char lastmove,
-+ const Boole B_watch,
-+ const char *const FN_watch,
- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int natom,
-- Real crd[MAX_ATOMS][SPACE])
-+ const int natom,
-+ const Real crd[MAX_ATOMS][SPACE])
- /*----------------------------------------------------------------------------*/
- {
- int i;
-Index: autodocksuite-4.2.3/autodock/printEnergies.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printEnergies.cc 2010-07-22 22:08:28.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printEnergies.cc 2010-07-22 22:11:38.000000000 +0200
-@@ -42,11 +42,11 @@
-
- #define print1000(file, x) pr(file, ((fabs((x)) >= 0.0) && ((fabs(x)) <= 1000.)) ? "%+7.2f" : "%+11.2e" , (x));
-
--void print1000_no_sign(FILE* file, double x) {
-+void print1000_no_sign(FILE *const file, const double x) {
- pr(file, ((fabs((x)) >= 0.01) && ((fabs(x)) <= 1000.)) ? "%7.2f" : "%11.2e" , (x));
- }
-
--void print_molar(FILE* file, double x) {
-+void print_molar(FILE *const file, const double x) {
- // 1e-3 <= x < 1 mM millimolar
- // 1e-6 <= x < 1e-3 uM micromolar
- // 1e-9 <= x < 1e-6 nM nanomolar
-@@ -77,13 +77,13 @@
- }
- }
-
--void printEnergies( EnergyBreakdown *eb,
-- const char *prefixString,
-- int ligand_is_inhibitor,
-- Real emap_total,
-- Real elec_total,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+void printEnergies( const EnergyBreakdown *const eb,
-+ const char *const prefixString,
-+ const int ligand_is_inhibitor,
-+ const Real emap_total,
-+ const Real elec_total,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- )
-
- {
-@@ -172,7 +172,7 @@
- pr( logFile, "%s\n", prefixString);
- }
-
--void printStateEnergies( EnergyBreakdown *eb, const char *prefixString, int ligand_is_inhibitor )
-+void printStateEnergies( const EnergyBreakdown *const eb, const char *const prefixString, const int ligand_is_inhibitor )
- {
- // Real deltaG = 0.0;
- Real Ki = 1.0;
-Index: autodocksuite-4.2.3/autodock/printEnergies.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printEnergies.h 2010-07-22 22:11:42.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printEnergies.h 2010-07-22 22:12:10.000000000 +0200
-@@ -31,15 +31,15 @@
- #include "constants.h"
- #include "structs.h"
-
--void printEnergies( EnergyBreakdown *eb,
-+void printEnergies( const EnergyBreakdown *const eb,
- const char *prefixString,
-- int ligand_is_inhibitor,
-- Real emap_total,
-- Real elec_total,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model);
-+ const int ligand_is_inhibitor,
-+ const Real emap_total,
-+ const Real elec_total,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model);
-
--void printStateEnergies( EnergyBreakdown *eb,
-- const char *prefixString,
-- int ligand_is_inhibitor);
-+void printStateEnergies( const EnergyBreakdown *eb,
-+ const char *const prefixString,
-+ const int ligand_is_inhibitor);
- #endif
-Index: autodocksuite-4.2.3/autodock/print_2x.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_2x.cc 2010-07-22 22:01:36.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_2x.cc 2010-07-22 22:01:56.000000000 +0200
-@@ -32,9 +32,9 @@
- #include "print_2x.h"
-
- void
--print_2x( FILE *stream1,
-- FILE *stream2,
-- const char *string )
-+print_2x( FILE *const stream1,
-+ FILE *const stream2,
-+ const char *const string )
-
- {
- fprintf( stream1, string );
-Index: autodocksuite-4.2.3/autodock/print_avsfld.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_avsfld.cc 2010-07-22 22:02:08.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_avsfld.cc 2010-07-23 20:16:17.000000000 +0200
-@@ -33,14 +33,14 @@
- #include "autocomm.h"
-
-
--void print_avsfld( FILE *logFile,
-- int veclen,
-- int natom,
-- int nframe,
-- int offset[VECLENMAX],
-- int stride,
-- char *label,
-- char *filename )
-+void print_avsfld( FILE *const logFile,
-+ const int veclen,
-+ const int natom,
-+ const int nframe,
-+ const int offset[VECLENMAX],
-+ const int stride,
-+ const char *const label,
-+ const char *const filename )
- {
- int i;
-
-Index: autodocksuite-4.2.3/autodock/print_rem.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_rem.cc 2010-07-22 22:12:41.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_rem.cc 2010-07-22 22:12:55.000000000 +0200
-@@ -32,11 +32,11 @@
- #include "print_rem.h"
-
-
--void print_rem( FILE *outFile,
-- int Rank,
-- int NumMem,
-- int Run,
-- Real ref_rms)
-+void print_rem( FILE *const outFile,
-+ const int Rank,
-+ const int NumMem,
-+ const int Run,
-+ const Real ref_rms)
- {
- fprintf( outFile, "MODEL %4d\n", Run );
- fprintf( outFile, "USER Run = %d\n", Run );
-Index: autodocksuite-4.2.3/autodock/printdate.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/printdate.cc 2010-07-22 22:03:16.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/printdate.cc 2010-07-22 22:06:26.000000000 +0200
-@@ -39,7 +39,7 @@
-
- #include "printdate.h"
-
--void printdate( FILE *fp, int flag )
-+void printdate( FILE *const fp, const int flag )
- {
- time_t tn; /* tn = "time_now" */
- char *StringTimeDate;
-Index: autodocksuite-4.2.3/autodock/qmultiply.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.cc 2010-07-22 22:13:04.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.cc 2010-07-23 00:57:47.000000000 +0200
-@@ -89,15 +89,13 @@
- void mkUnitQuat( Quat *q )
- // essentially, convertRotToQuat( Quat q )
- {
-- double inv_nmag, hqang, s;
--
-- inv_nmag = 1. / hypotenuse( q->nx, q->ny, q->nz );
-+ const double inv_nmag = 1. / hypotenuse( q->nx, q->ny, q->nz );
- q->nx *= inv_nmag; /* Normalize q */
- q->ny *= inv_nmag; /* Normalize q */
- q->nz *= inv_nmag; /* Normalize q */
-
-- hqang = 0.5 * q->ang;
-- s = sin( hqang );
-+ const double hqang = 0.5 * q->ang;
-+ const double s = sin( hqang );
-
- q->w = cos( hqang );
- q->x = s * q->nx;
-@@ -107,26 +105,33 @@
- /* q->qmag = hypotenuse4( q->x, q->y, q->z, q->w ); */
- } // mkUnitQuat( Quat *q )
-
--void printQuat_q( FILE *fp, Quat q )
-+//FIXME: q could be passed by reference
-+void printQuat_q( FILE *const fp, const Quat q )
- {
- (void) fprintf( fp, "Quat(x,y,z,w)= %5.2f %5.2f %5.2f %5.2f\n", q.x, q.y, q.z, q.w);
- (void) fprintf( fp, "Mag(Quat(x,y,z,w))= %5.2f\n", sqrt(q.x*q.x + q.y*q.y + q.z*q.z + q.w*q.w) );
- } // printQuat_q( Quat q )
-
--void printQuat_r( FILE *fp, Quat q )
-+//FIXME: convertQuatToRot should accept const, and the result
-+// be assigned to new variable to be then printed
-+// The variable should then be passed by reference
-+void printQuat_r( FILE *const fp, const Quat qsave )
- {
-+ Quat q = qsave;
- q = convertQuatToRot( q );
- (void) fprintf( fp, "Axis(nx,ny,nz),Angle= %5.2f %5.2f %5.2f %5.2f\n", q.nx, q.ny, q.nz, q.ang);
- (void) fprintf( fp, "Mag(Axis(nx,ny,nz))= %5.2f\n", sqrt(q.nx*q.nx + q.ny*q.ny + q.nz*q.nz) );
- } // printQuat_r( Quat q )
-
--void printQuat( FILE *fp, Quat q )
-+// The variable should then be passed by reference
-+void printQuat( FILE *const fp, const Quat q )
- {
- printQuat_q( fp, q );
- printQuat_r( fp, q );
- } // printQuat( Quat q )
-
--void debugQuat( FILE *fp, Quat q, unsigned int linenumber, char *message )
-+//FIXME: q could be passed by reference
-+void debugQuat( FILE *const fp, const Quat q, const unsigned int linenumber, const char *const message )
- {
- pr( fp, "DEBUG_QUAT: %s (line %u)\n", message, linenumber );
- printQuat( fp, q );
-@@ -163,9 +168,9 @@
- Quat normRot( Quat q )
- // Normalise the 3D rotation axis or vector nx,ny,nz
- {
-- double mag3 = hypotenuse( q.nx, q.ny, q.nz );
-+ const double mag3 = hypotenuse( q.nx, q.ny, q.nz );
- if (mag3 > APPROX_ZERO) {
-- double inv_mag3 = 1. / mag3;
-+ const double inv_mag3 = 1. / mag3;
- q.nx *= inv_mag3;
- q.ny *= inv_mag3;
- q.nz *= inv_mag3;
-@@ -187,6 +192,7 @@
- }
-
-
-+//FIXME: this routine does not need to change argument q, but it does
- Quat convertQuatToRot( Quat q )
- // Convert the quaternion components (x,y,z,w) of the quaternion q,
- // to the corresponding rotation-about-axis components (nx,ny,nz,ang)
-@@ -218,6 +224,7 @@
- angle = WrpModRad( angle ); // by convention, angles should be in the range -PI to +PI.
- retval.ang = angle;
-
-+ //FIXME: this should move to the top of the function to stop modifying q
- // Copy the existing x,y,z,w components
- retval.x = q.x;
- retval.y = q.y;
-@@ -227,7 +234,8 @@
- return retval;
- } // convertQuatToRot( Quat q )
-
--Quat convertRotToQuat( Quat q )
-+//FIXME: unchanged so it could be passed by reference
-+Quat convertRotToQuat( const Quat q )
- // Normalize the rotation-about-axis vector
- // and convert the rotation-about-axis components (nx,ny,nz,ang)
- // to the corresponding quaternion components (x,y,z,w)
-@@ -254,7 +262,7 @@
- return retval;
- } // Quat convertRotToQuat( Quat q )
-
--Quat raaToQuat( const Real raa[3], Real angle )
-+Quat raaToQuat( const Real raa[3], const Real angle )
- {
- Quat input;
-
-@@ -289,7 +297,7 @@
- return q;
- }
-
--Quat uniformQuatByAmount( Real amount )
-+Quat uniformQuatByAmount( const Real amount )
- // returns a quaternion from a random axis and specified angle
- // amount is an angle in radians
- {
-@@ -299,7 +307,7 @@
- return q;
- }
-
--void unitQuat2rotation( Quat *q )
-+void unitQuat2rotation( Quat *const q )
- // Convert from a unit quaternion to a rotation about an unit 3D-vector
- {
- double inv_sin_half_ang;
-@@ -313,7 +321,8 @@
- return;
- }
-
--void print_q_reorient_message( FILE *logFile, Quat q_reorient )
-+//FIXME: q_reorient should be passed by reference
-+void print_q_reorient_message( FILE *const logFile, const Quat q_reorient )
- // Print message about q_reorient
- {
- pr( logFile, "\nRe-orienting the ligand using the following axis (nx, ny, nz) and angle values:\n");
-@@ -328,13 +337,12 @@
- return;
- } // Print message about q_reorient
-
--void create_random_orientation( Quat *ptr_quat )
-+void create_random_orientation( Quat *const ptr_quat )
- {
- // Generate a random initial orientation for the ligand
-- Quat q_random;
- // Generate a uniformly-distributed quaternion:
- // setting the x,y,z,w components
-- q_random = uniformQuat();
-+ const Quat q_random = uniformQuat();
- ptr_quat->x = q_random.x;
- ptr_quat->y = q_random.y;
- ptr_quat->z = q_random.z;
-@@ -343,6 +351,7 @@
- *ptr_quat = convertQuatToRot( *ptr_quat );
- }
-
-+//FIXME: should be passed by reference
- Quat conjugate( const Quat q )
- {
- Quat conj;
-@@ -355,6 +364,7 @@
- return conj;
- }
-
-+//FIXME: reference
- Quat inverse( const Quat q )
- {
- register Quat conj, inv;
-@@ -372,6 +382,7 @@
- return inv;
- }
-
-+//FIXME: reference
- Quat slerp0( const Quat q1, const Quat q2, const double u )
- // See: Shoemake, K. (1985), "Animating Rotation with Quaternion Curves",
- // Computer Graphics, 19 (3): 245-254
-@@ -410,7 +421,7 @@
- assert( t >= 0. && t <= 1. );
-
- // Calculate angle between them.
-- double cosHalfTheta = qa.w * qb.w + qa.x * qb.x + qa.y * qb.y + qa.z * qb.z;
-+ const double cosHalfTheta = qa.w * qb.w + qa.x * qb.x + qa.y * qb.y + qa.z * qb.z;
- // if qa=qb or qa=-qb then theta = 0 and we can return qa
- if (fabs(cosHalfTheta) >= 1.0){
- qm.w = qa.w;qm.x = qa.x;qm.y = qa.y;qm.z = qa.z;
-@@ -492,16 +503,16 @@
-
- assert( t >= 0. && t <= 1. );
-
-- // Calculate angle between them.
-- double cosHalfTheta = qa.w * qb.w + qa.x * qb.x + qa.y * qb.y + qa.z * qb.z;
-+ // Calculate angle between them.
-+ double cosHalfTheta = qa.w * qb.w + qa.x * qb.x + qa.y * qb.y + qa.z * qb.z;
- // Ensure we choose the shorter angular displacement between qa and qb:
-- if (cosHalfTheta < 0.) {
-+ if (cosHalfTheta < 0.) {
- cosHalfTheta = -cosHalfTheta;
- qb_local.w = -qb.w;
- qb_local.x = -qb.x;
- qb_local.y = -qb.y;
- qb_local.z = -qb.z;
-- } else {
-+ } else {
- qb_local = qb;
- }
- #ifdef ASSERTQUATOK
-Index: autodocksuite-4.2.3/autodock/qmultiply.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.h 2010-07-22 22:25:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.h 2010-07-22 22:29:53.000000000 +0200
-@@ -32,8 +32,8 @@
- #include "structs.h"
-
- Quat uniformQuat( void );
--Quat convertQuatToRot( Quat q );
--Quat convertRotToQuat( Quat q );
-+Quat convertQuatToRot( /* not const */ Quat q );
-+Quat convertRotToQuat( const Quat q );
- Quat raaToQuat( const Real raa[3], Real angle );
- Quat normQuat( Quat q );
- Quat normRot( Quat q );
-@@ -51,16 +51,16 @@
- void qmultiply( Quat *q, register const Quat *ql, register const Quat *qr );
- void qconjmultiply( Quat *q, register const Quat *ql, register const Quat *qr );
- void mkUnitQuat( Quat *q );
--void printQuat_q( FILE *fp, Quat q );
--void printQuat_r( FILE *fp, Quat q );
--void printQuat( FILE *fp, Quat q );
--void debugQuat( FILE *fp, Quat q, unsigned int linenumber, char *message );
--Quat uniformQuatByAmount( Real amount );
--void unitQuat2rotation( Quat *q );
--void print_q_reorient_message( FILE *logFile, Quat q_reorient );
--void create_random_orientation( Quat *ptr_quat );
-+void printQuat_q( FILE *const fp, const Quat q );
-+void printQuat_r( FILE *const fp, const Quat q );
-+void printQuat( FILE *const fp, const Quat q );
-+void debugQuat( FILE *const fp, const Quat q, const unsigned int linenumber, const char *message );
-+Quat uniformQuatByAmount( const Real amount );
-+void unitQuat2rotation( Quat *const q );
-+void print_q_reorient_message( FILE *const logFile, const Quat q_reorient );
-+void create_random_orientation( Quat *const ptr_quat );
- //void assertQuatOK( const Quat q );
- const Quat identityQuat();
--Real a_range_reduction( Real a );
--Real alerp( Real a, Real b, Real fract );
-+Real a_range_reduction( const Real a );
-+Real alerp( const Real a, const Real b, const Real fract );
- #endif
-Index: autodocksuite-4.2.3/autodock/qtransform.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qtransform.cc 2010-07-22 22:31:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qtransform.cc 2010-07-22 22:33:30.000000000 +0200
-@@ -126,12 +126,12 @@
- }
- }
-
--void reorient( FILE *logFile,
-+void reorient( FILE *const logFile,
- const int true_ligand_atoms,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
- Real crdpdb[MAX_ATOMS][SPACE], // original PDB coordinates from input
- Real charge[MAX_ATOMS],
-- int type[MAX_ATOMS],
-+ const int type[MAX_ATOMS],
- ParameterEntry parameterArray[MAX_ATOM_TYPES],
- Quat q_reorient,
- Coord origin,
-Index: autodocksuite-4.2.3/autodock/readGridMap.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readGridMap.cc 2010-07-22 22:36:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readGridMap.cc 2010-07-22 22:38:35.000000000 +0200
-@@ -45,6 +45,7 @@
-
- char mapf2c(Real);
-
-+//FIXME: well, one could pass tmsJobStart by reference
- void readmap( Boole *P_B_HaveMap,
- int *P_imap,
- int *num_atom_types,
-@@ -53,17 +54,17 @@
- char *ExtFldFileName,
- int ExtGridPts1[SPACE],
- int ExtGridPts[SPACE],
-- Clock jobStart,
-+ const Clock jobStart,
- char line[LINE_LEN],
- char *ExtMacromolFileName,
- #include "map_declare.h"
- Real MapCenter[SPACE],
- Real MapMax[MAX_MAPS],
- Real MapMin[MAX_MAPS],
-- struct tms tmsJobStart,
-- Boole B_charMap,
-- int outlev,
-- GridMap grid_map)
-+ const struct tms tmsJobStart,
-+ const Boole B_charMap,
-+ int outlev, //FIXME: unused
-+ GridMap grid_map) //FIXME: unused
-
- {
- FILE *mapFilePtr;
-Index: autodocksuite-4.2.3/autodock/readPDBQT.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readPDBQT.cc 2010-07-22 22:45:03.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readPDBQT.cc 2010-07-22 22:54:24.000000000 +0200
-@@ -54,44 +54,44 @@
-
- /*----------------------------------------------------------------------------*/
- Molecule readPDBQT(char input_line[LINE_LEN],
-- int num_atom_maps,
-+ const int num_atom_maps,
-
-- int *P_natom,
-+ int *const P_natom,
- Real crdpdb[MAX_ATOMS][NTRN],
- Real crdreo[MAX_ATOMS][NTRN],
- Real charge[MAX_ATOMS],
-- Boole * P_B_haveCharges,
-+ Boole *const P_B_haveCharges,
- int map_index[MAX_ATOMS], //was:int type[MAX_ATOMS]
- int bond_index[MAX_ATOMS],
- char pdbaname[MAX_ATOMS][5],
-
-- char *FN_ligand,
-- char *FN_flexres,
-- Boole B_have_flexible_residues,
-+ char *const FN_ligand,
-+ char *const FN_flexres,
-+ const Boole B_have_flexible_residues,
-
- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int *P_n_heavy_atoms_in_ligand,
-+ int *const P_n_heavy_atoms_in_ligand,
-
-- Boole * P_B_constrain,
-- int *P_atomC1,
-- int *P_atomC2,
-- Real *P_sqlower,
-- Real *P_squpper,
--
-- int *P_ntor1,
-- int *P_ntor,
-- int *P_ntor_ligand, // the number of torsions in the ligand (excluding the flexible residues in receptor)
-+ Boole *const P_B_constrain,
-+ int *const P_atomC1,
-+ int *const P_atomC2,
-+ Real *const P_sqlower,
-+ Real *const P_squpper,
-+
-+ int *const P_ntor1,
-+ int *const P_ntor,
-+ int *const P_ntor_ligand, // the number of torsions in the ligand (excluding the flexible residues in receptor)
- int tlist[MAX_TORS][MAX_ATOMS],
- Real vt[MAX_TORS][NTRN],
-
-- int *P_Nnb,
-- NonbondParam *nonbondlist,
-+ int *const P_Nnb,
-+ NonbondParam *const nonbondlist,
-
-- Clock jobStart,
-- struct tms tms_jobStart,
-- char *hostnm,
-- int *P_ntorsdof,
-- int outlev,
-+ const Clock jobStart,
-+ const struct tms tms_jobStart,
-+ const char *const hostnm,
-+ int *const P_ntorsdof,
-+ const int outlev,
- int ignore_inter[MAX_ATOMS],
- int B_include_1_4_interactions,
-
-@@ -638,10 +638,10 @@
-
- void
- readPDBQTLine( char line[LINE_LEN],
-- int *ptr_serial,
-+ int *const ptr_serial,
- Real crd[SPACE],
-- Real *ptr_q,
-- ParameterEntry *this_parameter_entry )
-+ Real *const ptr_q,
-+ ParameterEntry *const this_parameter_entry )
- /*----------------------------------------------------------------------------*/
- {
- char char8[9];
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.cc 2010-07-22 22:42:09.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.cc 2010-07-22 22:44:52.000000000 +0200
-@@ -42,13 +42,13 @@
- extern Linear_FE_Model AD4;
-
-
--Boole string_begins_with(char *a, char *b);
--Boole string_ends_with(char *a, char *b);
-+Boole string_begins_with(const char *a, const char *b);
-+Boole string_ends_with(const char *a, const char *b);
- static char parameter_library[MAX_CHARS];
-
- void read_parameter_library(
-- char *FN_parameter_library,
-- int outlev
-+ const char *const FN_parameter_library,
-+ const int outlev
- )
- {
- static ParameterEntry thisParameter;
-@@ -190,7 +190,7 @@
- } // while there is another line of parameters to read in
- }
-
--void setup_parameter_library( int outlev, const char * model_text, Unbound_Model unbound_model )
-+void setup_parameter_library( const int outlev, const char *const model_text, const Unbound_Model unbound_model )
- {
- static ParameterEntry thisParameter;
- char parameter_library_line[LINE_LEN];
-Index: autodocksuite-4.2.3/autodock/readfield.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readfield.cc 2010-07-22 22:34:10.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readfield.cc 2010-07-22 22:35:32.000000000 +0200
-@@ -38,10 +38,11 @@
-
- extern FILE *logFile;
-
-+//FIXME: tms_jobStart could be passed by reference
- void readfield( GridMapSetInfo *info,
- char line[LINE_LEN],
-- Clock jobStart,
-- struct tms tms_jobStart )
-+ const Clock jobStart,
-+ const struct tms tms_jobStart )
-
-
- {
-Index: autodocksuite-4.2.3/autodock/readmap.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readmap.cc 2010-07-22 22:38:51.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readmap.cc 2010-07-23 20:26:10.000000000 +0200
-@@ -44,19 +44,22 @@
- extern FILE *logFile;
- extern int debug;
-
--char mapf2c(Real);
-+// char mapf2c(const Real); // not used
-
--Statistics readmap( char line[LINE_LEN],
-- int outlev,
-- Clock jobStart,
-- struct tms tmsJobStart,
-- Boole B_charMap,
-- Boole *P_B_HaveMap,
-- int num_maps,
-- GridMapSetInfo *info,
-- Real map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
-+Statistics readmap( char line[LINE_LEN],
-+ const int outlev, // unused
-+ const Clock jobStart,
-+ struct tms tmsJobStart,
-+ const Boole B_charMap,
-+ /* not const */ Boole * const P_B_HaveMap,
-+ const int num_maps,
-+ const GridMapSetInfo *const info,
-+
-+ // taken from .h file:
-+ #include "map_declare.h"
-+ // orig line: Real map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
- // double *maps
-- char map_type
-+ const char map_type
- )
-
- {
-@@ -320,7 +323,7 @@
-
-
- /*
-- char mapf2c(Real numin)
-+ char mapf2c(const Real numin)
- {
- char numout;
- if (numin == 0.) {
-Index: autodocksuite-4.2.3/autodock/setflags.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/setflags.cc 2010-07-22 23:05:27.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/setflags.cc 2010-07-23 20:18:19.000000000 +0200
-@@ -45,14 +45,13 @@
- extern char *programname;
-
- extern char dock_param_fn[];
--extern char AutoDockHelp[];
- extern int debug;
- extern int ignore_errors;
- extern int parse_tors_mode;
- extern int keepresnum;
-
-
--int setflags( int argc, char ** argv, const char * version_num)
-+int setflags( /* not const */ int argc, const char ** /* not const */ argv, const char *const version_num)
-
- /*
- ** naming convention:
-@@ -97,11 +96,12 @@
- /* Initialize */
- /*----------------------------------------------------------------------------*/
- argindex = 1;
-- programname = argv[0];
-+ if (programname) free(programname);
-+ programname = strdup(argv[0]); // argv is const, only executed once
- parFile = stdin;
- logFile = stdout;
- char logFileName[PATH_MAX+2];
-- static char * p_logFileName = "stdout"; // change with -l <NAME> or defaults
-+ static char * p_logFileName = strdup("stdout"); // change with -l <NAME> or defaults
- // to parFile name with last 3 chars changed from "dpf" to "dlg"
- /*
- * see autoglobal.h for initialization of debug, keepresnum and logicals...
-@@ -150,7 +150,8 @@
- fprintf(stderr, "\n%s: command mode is not supported in this version of autodock\n", programname );
- break;
- case 'l':
-- p_logFileName = argv[2];
-+ if (p_logFileName) free(p_logFileName);
-+ p_logFileName = strdup(argv[2]);
- argv++;
- argc--;
- argindex++;
-Index: autodocksuite-4.2.3/autodock/stack.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stack.cc 2010-07-22 22:54:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stack.cc 2010-07-22 22:57:24.000000000 +0200
-@@ -7,7 +7,7 @@
- #include <stdio.h>
- #include "stack.h"
-
--stack stack_create(int maxsize)
-+stack stack_create(const int maxsize)
- {
- stack s;
- s = (integer_stack_t *) malloc( sizeof(integer_stack_t) );
-@@ -34,7 +34,7 @@
- return s->base[s->top];
- }
-
--void stack_push(stack s, int i)
-+void stack_push(stack s, const int i)
- {
- if (s->trace != NULL) fprintf(s->trace, "Stack(%d/%d) push %d\n",
- s->top, s->size,i);
-@@ -49,19 +49,20 @@
- return;
- }
-
--int stack_depth(stack s)
-+int stack_depth(const stack s)
- {
- if (s->trace != NULL) fprintf(s->trace, "Stack depth %d/%d\n",
- s->top, s->size);
- return s->top;
- }
-
--int stack_size(stack s)
-+int stack_size(const stack s)
- {
- return s->size;
- }
-
--void stack_trace(stack s, FILE *f)
-+//FIXME: s could be passed by reference
-+void stack_trace(const stack s, FILE *const f)
- {
- if (f==NULL && s->trace != NULL) fprintf(s->trace, "Stack trace off\n");
- s->trace = f;
-Index: autodocksuite-4.2.3/autodock/stack.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stack.h 2010-07-22 22:57:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stack.h 2010-07-22 22:58:08.000000000 +0200
-@@ -10,12 +10,12 @@
-
- typedef integer_stack_t * stack;
-
--stack stack_create(int size);
-+stack stack_create(const int size);
- int stack_pop(stack s);
- void stack_push(stack s, int i);
--int stack_size(stack s);
--void stack_trace(stack s, FILE *f);
-+int stack_size(const stack s);
-+void stack_trace(const stack s, FILE *f);
- int stack_test(void);
--int stack_depth(stack s);
-+int stack_depth(const stack s);
-
- #endif
-Index: autodocksuite-4.2.3/autodock/stateLibrary.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.cc 2010-07-22 22:58:45.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.cc 2010-07-22 23:01:40.000000000 +0200
-@@ -62,7 +62,7 @@
- }
-
- void copyState( State *D, /* Destination -- copy to here */
-- State S ) /* Source -- copy this. */
-+ const State S ) /* Source -- copy this. */
- {
- register int i;
-
-@@ -104,7 +104,7 @@
- }
-
- void printState( FILE *const fp,
-- State S,
-+ /* not const */ State S,
- const int detail )
- {
- register int i;
-@@ -153,7 +153,7 @@
- }
- }
-
--void writeState( FILE *const fp, State S )
-+void writeState( FILE *const fp, /* not const */ State S )
- {
- register int i;
- Real torDegTmp;
-Index: autodocksuite-4.2.3/autodock/stateLibrary.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/stateLibrary.h 2010-07-22 23:00:39.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/stateLibrary.h 2010-07-22 23:01:56.000000000 +0200
-@@ -35,14 +35,14 @@
- void initialiseQuat( Quat *Q );
-
- void copyState( State *destination,
-- State source);
-+ const State source);
-
- void printState( FILE *const fp,
-- State state,
-+ /* not const */ State state,
- const int detail );
-
- void writeState( FILE *const fp,
-- State state );
-+ /* not const */ State state );
-
- int checkState( const State *D );
-
-Index: autodocksuite-4.2.3/autodock/success.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/success.cc 2010-07-22 22:50:38.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/success.cc 2010-07-23 01:07:57.000000000 +0200
-@@ -39,9 +39,9 @@
- extern char *programname;
- extern FILE *logFile;
-
--void success( char *hostnm,
-- Clock jobStart,
-- struct tms tms_jobStart )
-+void success( const char *const hostnm,
-+ const Clock jobStart,
-+ struct tms tms_jobStart )
-
- {
- char message[LINE_LEN];
-Index: autodocksuite-4.2.3/autodock/support.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.cc 2010-07-22 23:02:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.cc 2010-07-22 23:03:13.000000000 +0200
-@@ -193,11 +193,11 @@
- //}
- //}
-
--void Population::print(FILE *output, const int num) const {
-+void Population::print(FILE *const output, const int num) const {
- register int i;
-
- #ifdef DEBUG
-- (void)fprintf(logFile, "support.cc/void Population::print(FILE *output, int num=%d)\n", num);
-+ (void)fprintf(logFile, "support.cc/void Population::print(FILE *const output, int num=%d)\n", num);
- #endif /* DEBUG */
-
- (void)fprintf( output, "The top %d individuals in the population:\n\n", num);
-@@ -246,7 +246,7 @@
-
-
-
--int Population::printPopulationStatistics(FILE *output, const int level, const Boole appendNewline) const {
-+int Population::printPopulationStatistics(FILE *const output, const int level, const Boole appendNewline) const {
- // write best energy, etc, depending on level
- // return 0 if OK, non-zero if error
- // Code adapted from gs.cc - M Pique December 2009
-@@ -335,7 +335,7 @@
- if(appendNewline) fprintf(output, "\n");
- return returnCode;
- }
--int Population::printPopulationStatisticsVerbose(FILE * output,
-+int Population::printPopulationStatisticsVerbose(FILE *const output,
- const unsigned int generations, const long int nevals, const char suffix[]) const { /* print with generations & #evals */
- int returnCode=0;
- // print "Population at Generation:" line with low/high/mean/median/stddev...
-@@ -347,7 +347,7 @@
- }
-
-
--void Population::printPopulationAsStates(FILE *output, const int num, const int ntor) const {
-+void Population::printPopulationAsStates(FILE *const output, const int num, const int ntor) const {
- register int i;
- #ifdef DEBUG2
- register int j;
-@@ -356,7 +356,7 @@
- double thisValue;
-
- #ifdef DEBUG
-- (void)fprintf(logFile, "support.cc/void Population::printPopulationAsStates(FILE *output, int num=%d, int ntor=%d)\n", num, ntor);
-+ (void)fprintf(logFile, "support.cc/void Population::printPopulationAsStates(FILE *const output, int num=%d, int ntor=%d)\n", num, ntor);
- #endif /* DEBUG */
-
- // Print an XML-like tag indicating this is a population, with attribute size
-@@ -385,12 +385,12 @@
- (void)fprintf( output, "</population>\n");
- }
-
--void Population::printPopulationAsCoordsEnergies(FILE *output, const int num, const int ntor) const {
-+void Population::printPopulationAsCoordsEnergies(FILE *const output, const int num, const int ntor) const {
- register int i;
- double thisValue;
-
- #ifdef DEBUG
-- (void)fprintf(logFile, "support.cc/void Population::printPopulationAsCoordsEnergies(FILE *output, int num=%d, int ntor=%d)\n", num, ntor);
-+ (void)fprintf(logFile, "support.cc/void Population::printPopulationAsCoordsEnergies(FILE *const output, int num=%d, int ntor=%d)\n", num, ntor);
- #endif // DEBUG
-
- //(void)fprintf( output, "The top %d individuals in the population:\n\n", num);
-@@ -954,10 +954,10 @@
- returnedMol = &molcopy;
- }
-
--void Individual::printIndividualsState(FILE *filePtr, const int ntor, const int detail) const
-+void Individual::printIndividualsState(FILE *const filePtr, const int ntor, const int detail) const
- {
- #ifdef DEBUG
-- (void)fprintf(logFile, "support.cc/void Individual::printIndividualsState(FILE *filePtr, int ntor=%d, int detaiil=%d)\n", ntor, detail);
-+ (void)fprintf(logFile, "support.cc/void Individual::printIndividualsState(FILE *const filePtr, int ntor=%d, int detaiil=%d)\n", ntor, detail);
- #endif /* DEBUG */
-
- printState( filePtr, state(ntor), detail );
-Index: autodocksuite-4.2.3/autodock/support.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.h 2010-07-22 23:03:17.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.h 2010-07-22 23:03:45.000000000 +0200
-@@ -251,7 +251,7 @@
- double value(EvalMode); /* evaluation of the individual gives its value */
- State state(int) const; /* state variables in AutoDock */
- void getMol(Molecule *); /* converts phenotype to mol's state and returns this individual's mol data */
-- void printIndividualsState(FILE *, const int, const int) const; /* print out the state of this individual */
-+ void printIndividualsState(FILE *const, const int, const int) const; /* print out the state of this individual */
- void incrementAge(); /* make individual grow 1 generation older */
- int serial; // serial number of this individual
- };
-@@ -279,11 +279,11 @@
- unsigned int num_individuals(void) const; /* returns the size of the pop. */
- void msort(int); /* sorts the first m individuals using heap properties */
- // void print(ostream &, int); /* prints top int energies */
-- void print(FILE *, const int) const; /* like above */
-- int printPopulationStatistics(FILE *, const int, const Boole) const; /* prints best, worse, mean, etc energies */
-- int printPopulationStatisticsVerbose(FILE *, const unsigned int, const long int, const char []) const; /* print with generations & #evals */
-- void printPopulationAsStates(FILE *, const int, const int) const; /*prints energies,states of top energies */
-- void printPopulationAsCoordsEnergies(FILE *, const int, const int) const; /*prints energies,states of top energies */
-+ void print(FILE *const, const int) const; /* like above */
-+ int printPopulationStatistics(FILE *const, const int, const Boole) const; /* prints best, worse, mean, etc energies */
-+ int printPopulationStatisticsVerbose(FILE *const, const unsigned int, const long int, const char []) const; /* print with generations & #evals */
-+ void printPopulationAsStates(FILE *const, const int, const int) const; /*prints energies,states of top energies */
-+ void printPopulationAsCoordsEnergies(FILE *const, const int, const int) const; /*prints energies,states of top energies */
- void set_eob(const int init_end_of_branch[MAX_TORS]); // For Branch Crossover Mode
- int get_eob(const int init_tor) const; // For Branch Crossover Mode
- };
-Index: autodocksuite-4.2.3/autodock/usage.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/usage.cc 2010-07-22 23:04:03.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/usage.cc 2010-07-22 23:04:59.000000000 +0200
-@@ -32,13 +32,11 @@
- #include "usage.h"
-
-
--extern char AutoDockHelp[];
--
- /*----------------------------------------------------------------------------*/
--void usage( FILE * file, char * programname )
-+void usage( FILE *const file, const char *const programname )
- /*----------------------------------------------------------------------------*/
- {
-- char AutoDockHelp[] = \
-+ const char AutoDockHelp[] = \
- "\t-p parameter_filename\n" \
- "\t\t\t-l log_filename\n" \
- "\t\t\t-k (Keep original residue numbers)\n" \
-Index: autodocksuite-4.2.3/autodock/writePDBQT.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/writePDBQT.cc 2010-07-22 23:06:53.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/writePDBQT.cc 2010-07-23 00:36:33.000000000 +0200
-@@ -45,47 +45,47 @@
- extern Real nb_group_energy[3];
-
- void
--writePDBQT(int irun, FourByteLong seed[2],
-+writePDBQT(const int irun, const FourByteLong seed[2],
-
-- char *smFileName,
-- char *dpfFN,
-- Real sml_center[SPACE],
-- State state,
-- int ntor,
-- Real * Ptr_eintra,
-- Real * Ptr_einter,
-- int natom,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real emap[MAX_ATOMS],
-- Real elec[MAX_ATOMS],
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- int ligand_is_inhibitor,
-- Real torsFreeEnergy,
-- Real vt[MAX_TORS][SPACE],
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- NonbondParam *nonbondlist,
-- EnergyTables *ptr_ad_energy_tables,
-- int type[MAX_ATOMS], // aka 'map_index' in 'ParameterEntry' structures
-- int Nnb,
-- Boole B_calcIntElec,
-+ const char *const smFileName,
-+ const char *const dpfFN,
-+ const Real sml_center[SPACE],
-+ /* not const */ State state,
-+ const int ntor,
-+ /* not const */ Real *const Ptr_eintra,
-+ /* not const */ Real *const Ptr_einter,
-+ const int natom,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real emap[MAX_ATOMS],
-+ /* not const */ Real elec[MAX_ATOMS],
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const int ligand_is_inhibitor,
-+ const Real torsFreeEnergy,
-+ const Real vt[MAX_TORS][SPACE],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const NonbondParam *nonbondlist,
-+ const EnergyTables *ptr_ad_energy_tables,
-+ const int type[MAX_ATOMS], // aka 'map_index' in 'ParameterEntry' structures
-+ const int Nnb,
-+ const Boole B_calcIntElec,
- #include "map_declare.h"
-- int outlev,
-- int ignore_inter[MAX_ATOMS],
-+ const int outlev,
-+ const int ignore_inter[MAX_ATOMS],
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
- const ParameterEntry parameterArray[MAX_ATOM_TYPES],
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- int state_type, // 0 means the state is unbound, 1 means the state is docked
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *info,
-+ const int state_type, // 0 means the state is unbound, 1 means the state is docked
-+ const char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- )
-
- {
-@@ -314,7 +314,7 @@
- } // outlev > -1
- } // writePDBQT()
-
--void print_PDBQT( FILE *logFile,
-+void print_PDBQT( FILE *const logFile,
- const int true_ligand_atoms,
- const char atomstuff[MAX_ATOMS][MAX_CHARS],
- const Real crdpdb[MAX_ATOMS][SPACE],
-@@ -338,15 +338,15 @@
- pr( logFile, "\n\n" );
- } // end Print out the coordinates
-
--void print_PDBQ_atom_resstr( FILE *logFile,
-+void print_PDBQ_atom_resstr( FILE *const logFile,
- const char prefix[MAX_CHARS],
-- int atom_num, // 0-origin
-+ const int atom_num, // 0-origin
- const char atomstuff[],
- const Real crd[MAX_ATOMS][SPACE],
- const Real vdW,
- const Real Elec,
- const Real charge,
-- const char * suffix //newline or empty
-+ const char *const suffix //newline or empty
- )
- {
- char rec15[16];
-@@ -358,16 +358,16 @@
- vdW, Elec, charge, suffix);
- }
-
--void print_PDBQ_atom_resnum( FILE *logFile,
-+void print_PDBQ_atom_resnum( FILE *const logFile,
- const char prefix[MAX_CHARS],
-- int atom_num, // 0-origin
-+ const int atom_num, // 0-origin
- const char atomstuff[],
- const int resnum,
- const Real crd[MAX_ATOMS][SPACE],
- const Real vdW,
- const Real Elec,
- const Real charge,
-- const char * suffix //newline or empty
-+ const char *const suffix //newline or empty
- )
- {
- char rec10[11];
-Index: autodocksuite-4.2.3/autodock/check_header_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_line.cc 2010-07-22 23:28:23.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_line.cc 2010-07-22 23:28:47.000000000 +0200
-@@ -37,7 +37,7 @@
- extern FILE *logFile;
-
-
--void check_header_line( char s1[], char s2[] )
-+void check_header_line( const char s1[], const char s2[] )
-
- {
- if ( !equal(s1, s2, strlen(s1) ) ) {
-Index: autodocksuite-4.2.3/autodock/check_header_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/check_header_line.h 2010-07-22 23:28:52.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/check_header_line.h 2010-07-22 23:28:58.000000000 +0200
-@@ -29,6 +29,6 @@
-
- #include "constants.h"
-
--void check_header_line( char s1[],
-- char s2[]);
-+void check_header_line( const char s1[],
-+ const char s2[]);
- #endif
-Index: autodocksuite-4.2.3/autodock/openfile.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/openfile.h 2010-07-22 23:36:17.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/openfile.h 2010-07-22 23:37:47.000000000 +0200
-@@ -34,18 +34,18 @@
- #include <time.h> /*time_t time(time_t *tloc); */
- #include <sys/times.h>
-
--int openfile( char *filename,
-- char mode[],
-+int openfile( const char *const filename,
-+ const char mode[],
- FILE **fp );
-
-
--int openFile( char *filename,
-- char mode[],
-- FILE **fp,
-- Clock start,
-- struct tms tms_start,
-- Boole mayExit);
-+int openFile( const char *const filename,
-+ const char mode[],
-+ FILE **fp,
-+ const Clock start,
-+ struct tms tms_start,
-+ const Boole mayExit);
-
--FILE *ad_fopen(const char *path, const char *mode);
-+FILE *ad_fopen(const char *const path, const char *const mode);
-
- #endif
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.h 2010-07-22 23:33:44.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.h 2010-07-22 23:35:11.000000000 +0200
-@@ -30,20 +30,20 @@
- #include "autocomm.h"
-
- void read_parameter_library(
-- char *FN_parameter_library,
-- int outlev
-+ const char *const FN_parameter_library,
-+ const int outlev
- );
-
- void setup_parameter_library(
-- int outlev,
-- const char * model_text,
-- Unbound_Model unbound_model
-+ const int outlev,
-+ const char *const model_text,
-+ const Unbound_Model unbound_model
- );
-
- char * report_parameter_library();
-
--void setup_distdepdiel( int outlev,
-- EnergyTables *ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
-+void setup_distdepdiel( const int outlev,
-+ const EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
- );
-
-
-Index: autodocksuite-4.2.3/autodock/readmap.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readmap.h 2010-07-22 23:31:11.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readmap.h 2010-07-23 20:24:02.000000000 +0200
-@@ -55,20 +55,20 @@
- #include "structs.h"
-
- Statistics readmap( char line[LINE_LEN],
-- int outlev,
-+ const int outlev,
-
-- Clock jobStart,
-- struct tms tmsJobStart,
-+ const Clock jobStart,
-+ /* not const */ struct tms tmsJobStart,
-
-- Boole B_charMap,
-+ const Boole B_charMap,
-
-- Boole *P_B_HaveMap,
-- int num_maps,
-+ Boole *const P_B_HaveMap,
-+ const int num_maps,
-
-- GridMapSetInfo *info,
-+ const GridMapSetInfo *const info,
- // double *maps
- #include "map_declare.h"
-- char map_type
-+ const char map_type
- );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/success.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/success.h 2010-07-22 23:32:53.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/success.h 2010-07-23 01:08:10.000000000 +0200
-@@ -32,7 +32,7 @@
- #include "print_2x.h"
- #include "timesyshms.h"
-
--void success( char hostnm[MAX_CHARS],
-- Clock jobStart,
-+void success( const char hostnm[MAX_CHARS],
-+ const Clock jobStart,
- struct tms tms_jobStart );
- #endif
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.cc 2010-07-23 00:23:48.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.cc 2010-07-23 00:45:48.000000000 +0200
-@@ -52,11 +52,11 @@
- // B_include_1_4_interactions, scale_1_4, qsp_abs_charge, B_use_non_bond_cutoff );
-
- EnergyBreakdown calculateEnergies(
-- int natom, // input number of atoms
-- int ntor, // input number of torsions
-- Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-- Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-- Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-+ const int natom, // input number of atoms
-+ const int ntor, // input number of torsions
-+ const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-+ const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-+ const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-
- // trilinterp
- const Real tcoord[MAX_ATOMS][SPACE], // input coordinates of atoms to be trilinearly-interpolated
-@@ -64,17 +64,17 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int B_outside, // input boolean whether some atoms are outside grid box
-- int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-+ const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int B_outside, // input boolean whether some atoms are outside grid box
-+ const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
- Real *p_elec_total, // output if not NULL - total electrostatic energy
- Real *p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
-- NonbondParam * const nonbondlist, // input list of nonbonds
-- const EnergyTables *ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
-+ const NonbondParam *const nonbondlist, // input list of nonbonds
-+ const EnergyTables *const ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
- const int Nnb, // input total number of nonbonds
- const Boole B_calcIntElec, // input boolean whether we must calculate internal electrostatics
- const Boole B_include_1_4_interactions,// input boolean whether to include 1,4 interactions as non-bonds
-@@ -122,7 +122,7 @@
- return eb;
- } // calculateEnergies()
-
--void update_energy_breakdown( EnergyBreakdown * eb )
-+void update_energy_breakdown( /* not const */ EnergyBreakdown * eb )
- {
- // total intermolecular energy = (1) + (4)
- eb->e_inter = eb->e_inter_moving_fixed + eb->e_inter_moving_moving;
-@@ -140,9 +140,9 @@
- eb->deltaG = eb->e_inter + eb->e_intra + eb->e_torsFreeEnergy - eb->e_unbound_internal_FE;
- }
-
--void initialise_energy_breakdown ( EnergyBreakdown * eb,
-- Real torsFreeEnergy,
-- Real unbound_internal_FE )
-+void initialise_energy_breakdown ( /* not const */ EnergyBreakdown * eb,
-+ const Real torsFreeEnergy,
-+ const Real unbound_internal_FE )
- {
- eb->e_inter_moving_fixed = 0.0; // (1) // trilinterp( 0, true_ligand_atoms, ...)
- eb->e_intra_moving_fixed_rec = 0.0; // (2) // trilinterp( true_ligand_atoms, natom, ...)
-@@ -166,11 +166,11 @@
- // which might create conformations with high internal energies.
-
- EnergyBreakdown calculateBindingEnergies(
-- int natom, // input number of atoms
-- int ntor, // input number of torsions
-- Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-- Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-- Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-+ const int natom, // input number of atoms
-+ const int ntor, // input number of torsions
-+ const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-+ const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-+ const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-
- // trilinterp
- const Real tcoord[MAX_ATOMS][SPACE], // input coordinates of atoms to be trilinearly-interpolated
-@@ -178,8 +178,8 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int B_outside, // input boolean whether some atoms are outside grid box
-+ const GridMapSetInfo *const info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int B_outside, // input boolean whether some atoms are outside grid box
- int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-@@ -187,15 +187,15 @@
- Real *p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
-- NonbondParam * const nonbondlist, // input list of nonbonds
-- const EnergyTables *ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
-+ const NonbondParam *const nonbondlist, // input list of nonbonds
-+ const EnergyTables *const ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
- const int Nnb, // input total number of nonbonds
- const Boole B_calcIntElec, // input boolean whether we must calculate internal electrostatics
- const Boole B_include_1_4_interactions,// input boolean whether to include 1,4 interactions as non-bonds
- const Real scale_1_4, // input scaling factor for 1,4 interactions, if included
- const Real qsp_abs_charge[MAX_ATOMS], // input q-solvation parameters
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
-- Unbound_Model ad4_unbound_model
-+ const Unbound_Model ad4_unbound_model
-
- )
-
-Index: autodocksuite-4.2.3/autodock/calculateEnergies.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/calculateEnergies.h 2010-07-23 00:21:22.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/calculateEnergies.h 2010-07-23 00:45:11.000000000 +0200
-@@ -32,11 +32,11 @@
- #include "structs.h"
-
- EnergyBreakdown calculateEnergies(
-- int natom, // input number of atoms
-- int ntor, // input number of torsions
-- Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-- Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-- Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-+ const int natom, // input number of atoms
-+ const int ntor, // input number of torsions
-+ const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-+ const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-+ const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-
- // trilinterp
- const Real tcoord[MAX_ATOMS][SPACE], // input coordinates of atoms to be trilinearly-interpolated
-@@ -44,24 +44,24 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int B_outside, // input boolean whether some atoms are outside grid box
-- int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
-- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-- Real *p_elec_total, // output if not NULL - total electrostatic energy
-- Real *p_emap_total, // output if not NULL - total intermolecular energy
-+ const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int B_outside, // input boolean whether some atoms are outside grid box
-+ const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-+ /* not const */ Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
-+ /* not const */ Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
-+ /* not const */ Real *p_elec_total, // output if not NULL - total electrostatic energy
-+ /* not const */ Real *p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
-- NonbondParam * const nonbondlist, // input list of nonbonds
-- const EnergyTables *ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
-+ const NonbondParam *const nonbondlist, // input list of nonbonds
-+ const EnergyTables *const ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
- const int Nnb, // input total number of nonbonds
- const Boole B_calcIntElec, // input boolean whether we must calculate internal electrostatics
- const Boole B_include_1_4_interactions,// input boolean whether to include 1,4 interactions as non-bonds
- const Real scale_1_4, // input scaling factor for 1,4 interactions, if included
- const Real qsp_abs_charge[MAX_ATOMS], // input q-solvation parameters
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
-- Unbound_Model ad4_unbound_model
-+ const Unbound_Model ad4_unbound_model
-
- );
-
-@@ -72,11 +72,11 @@
- Real unbound_internal_FE );
-
- EnergyBreakdown calculateBindingEnergies(
-- int natom, // input number of atoms
-- int ntor, // input number of torsions
-- Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-- Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-- Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-+ const int natom, // input number of atoms
-+ const int ntor, // input number of torsions
-+ const Real unbound_internal_FE, // input pre-calculated internal energy of unbound state
-+ const Real torsFreeEnergy, // input constant times number of freely-rotatable bonds
-+ const Boole B_have_flexible_residues, // input boolean whether we have flexible residues in protein
-
- // trilinterp
- const Real tcoord[MAX_ATOMS][SPACE], // input coordinates of atoms to be trilinearly-interpolated
-@@ -84,32 +84,32 @@
- CONST_FLOAT abs_charge[MAX_ATOMS], // input absolute magnitude of partial charges
- CONST_INT type[MAX_ATOMS], // input atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int B_outside, // input boolean whether some atoms are outside grid box
-- int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
-+ const GridMapSetInfo *info, // input info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int B_outside, // input boolean whether some atoms are outside grid box
-+ const int ignore_inter[MAX_ATOMS], // input array of booleans, says to ignore computation intermolecular energies per atom
- Real elec[MAX_ATOMS], // output if not NULL - electrostatic energies, atom by atom
- Real emap[MAX_ATOMS], // output if not NULL - intermolecular energies
- Real *p_elec_total, // output if not NULL - total electrostatic energy
- Real *p_emap_total, // output if not NULL - total intermolecular energy
-
- // eintcal
-- NonbondParam * const nonbondlist, // input list of nonbonds
-- const EnergyTables *ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
-+ const NonbondParam *const nonbondlist, // input list of nonbonds
-+ const EnergyTables *const ptr_ad_energy_tables, // input pointer to AutoDock intermolecular, dielectric, solvation lookup tables
- const int Nnb, // input total number of nonbonds
- const Boole B_calcIntElec, // input boolean whether we must calculate internal electrostatics
- const Boole B_include_1_4_interactions,// input boolean whether to include 1,4 interactions as non-bonds
- const Real scale_1_4, // input scaling factor for 1,4 interactions, if included
- const Real qsp_abs_charge[MAX_ATOMS], // input q-solvation parameters
- const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
-- Unbound_Model ad4_unbound_model
-+ const Unbound_Model ad4_unbound_model
-
- );
-
--void update_binding_energy_breakdown( EnergyBreakdown * eb, Unbound_Model ad4_unbound_model
-+void update_binding_energy_breakdown( EnergyBreakdown * eb, const Unbound_Model ad4_unbound_model
- );
-
- void initialise_binding_energy_breakdown ( EnergyBreakdown * eb,
-- Real torsFreeEnergy,
-- Real unbound_internal_FE,
-- Unbound_Model ad4_unbound_model);
-+ const Real torsFreeEnergy,
-+ const Real unbound_internal_FE,
-+ const Unbound_Model ad4_unbound_model);
- #endif
-Index: autodocksuite-4.2.3/autodock/cnv_state_to_coords.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cnv_state_to_coords.cc 2010-07-23 00:09:32.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cnv_state_to_coords.cc 2010-07-23 00:16:14.000000000 +0200
-@@ -45,10 +45,10 @@
- extern int true_ligand_atoms;
-
- void cnv_state_to_coords( const State now,
-- Real vt[MAX_TORS][SPACE],
-- int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor,
-- Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
- Real crd[MAX_ATOMS][SPACE],
- const int natom)
-
-@@ -68,7 +68,7 @@
-
- // Apply torsions, if any
- if (ntor > 0) {
-- torsion( now, crd, vt, tlist, ntor );
-+ torsion( now, crd, vt, tlist, ntor ); /* all const except for crd */
- }
-
- #ifdef LSQFIT
-@@ -92,7 +92,7 @@
- #endif
-
- // Apply quaternion rigid-body rotation and translation...
-- qtransform( now.T, now.Q, crd, true_ligand_atoms );
-+ qtransform( now.T, now.Q, crd, true_ligand_atoms ); // all const except crd
-
- #ifdef DEBUG
- } else {
-Index: autodocksuite-4.2.3/autodock/cnv_state_to_coords.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/cnv_state_to_coords.h 2010-07-23 00:16:16.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/cnv_state_to_coords.h 2010-07-23 00:16:25.000000000 +0200
-@@ -33,10 +33,10 @@
-
-
- void cnv_state_to_coords( const State now,
-- Real vt[MAX_TORS][SPACE],
-- int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
- const int ntor,
-- Real crdpdb[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
- Real crd[MAX_ATOMS][SPACE],
- const int natom);
- #endif
-Index: autodocksuite-4.2.3/autodock/eintcal.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eintcal.cc 2010-07-23 00:41:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eintcal.cc 2010-07-23 00:42:00.000000000 +0200
-@@ -42,7 +42,7 @@
- #ifndef EINTCALPRINT
-
- // Calculate internal energy
--Real eintcal( NonbondParam * const nonbondlist,
-+Real eintcal( const NonbondParam * const nonbondlist,
- const EnergyTables *ptr_ad_energy_tables,
- const Real tcoord[MAX_ATOMS][SPACE],
- const int Nnb,
-Index: autodocksuite-4.2.3/autodock/eintcal.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eintcal.h 2010-07-23 00:42:03.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eintcal.h 2010-07-23 00:42:09.000000000 +0200
-@@ -31,7 +31,7 @@
- #include "constants.h"
- #include "structs.h"
-
--Real eintcal( NonbondParam * const nonbondlist,
-+Real eintcal( const NonbondParam * const nonbondlist,
- const EnergyTables *ad_energy_tables,
- const Real tcoord[MAX_ATOMS][SPACE],
- const int Nnb,
-Index: autodocksuite-4.2.3/autodock/getInitialState.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getInitialState.cc 2010-07-23 01:10:19.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getInitialState.cc 2010-07-23 01:18:58.000000000 +0200
-@@ -53,39 +53,39 @@
- State *sMinm, /* was qtnMin[QUAT] and torMin[MAX_TORS] */
- State *sLast, /* was qtnLast[QUAT] and torLast[MAX_TORS] */
-
-- Boole B_RandomTran0,
-- Boole B_RandomQuat0,
-- Boole B_RandomDihe0,
--
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real elec[MAX_ATOMS],
-- Real emap[MAX_ATOMS],
-+ const Boole B_RandomTran0,
-+ const Boole B_RandomQuat0,
-+ const Boole B_RandomDihe0,
-+
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real elec[MAX_ATOMS],
-+ /* not const */ Real emap[MAX_ATOMS],
-
-- EnergyTables *ptr_ad_energy_tables,
-+ const EnergyTables *const ptr_ad_energy_tables,
-
-- Boole B_calcIntElec,
-+ const Boole B_calcIntElec,
- #include "map_declare.h"
-- int natom,
-- int Nnb,
-- NonbondParam *nonbondlist,
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- int irun1,
-- int outlev,
-- int MaxRetries,
-+ const int natom,
-+ const int Nnb,
-+ const NonbondParam *const nonbondlist,
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int irun1,
-+ const int outlev,
-+ const int MaxRetries,
-
-- Real torsFreeEnergy,
-+ const Real torsFreeEnergy,
-
-- int ligand_is_inhibitor,
-+ const int ligand_is_inhibitor,
-
-- int ignore_inter[MAX_ATOMS],
-+ const int ignore_inter[MAX_ATOMS],
-
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-@@ -93,10 +93,10 @@
-
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- )
-
- {
-Index: autodocksuite-4.2.3/autodock/getInitialState.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/getInitialState.h 2010-07-23 01:09:10.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/getInitialState.h 2010-07-23 01:10:14.000000000 +0200
-@@ -45,39 +45,39 @@
- State *sMin,
- State *sLast,
-
-- Boole B_RandomTran0,
-- Boole B_RandomQuat0,
-- Boole B_RandomDihe0,
--
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const Boole B_RandomTran0,
-+ const Boole B_RandomQuat0,
-+ const Boole B_RandomDihe0,
-+
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const Real crd[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
- Real elec[MAX_ATOMS],
- Real emap[MAX_ATOMS],
-
-- EnergyTables *ptr_ad_energy_tables,
-+ EnergyTables *const ptr_ad_energy_tables,
-
-- Boole B_calcIntElec,
-+ const Boole B_calcIntElec,
- #include "map_declare.h"
-- int natom,
-- int Nnb,
-- NonbondParam *nonbondlist,
-- int ntor,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- int type[MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- int irun1,
-- int outlev,
-- int MaxRetries,
-+ const int natom,
-+ const int Nnb,
-+ const NonbondParam *const nonbondlist,
-+ const int ntor,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const int type[MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int irun1,
-+ const int outlev,
-+ const int MaxRetries,
-
-- Real torsFreeEnergy,
-+ const Real torsFreeEnergy,
-
-- int ligand_is_inhibitor,
-+ const int ligand_is_inhibitor,
-
-- int ignore_inter[MAX_ATOMS],
-+ const int ignore_inter[MAX_ATOMS],
-
- const Boole B_include_1_4_interactions,
- const Real scale_1_4,
-@@ -85,10 +85,10 @@
-
- const Real unbound_internal_FE,
-
-- GridMapSetInfo *info,
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *const info,
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/initautodock.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/initautodock.cc 2010-07-23 01:12:18.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/initautodock.cc 2010-07-23 01:15:18.000000000 +0200
-@@ -42,16 +42,16 @@
- extern FILE *logFile;
- extern char *programname;
-
--void initautodock( char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- int natom,
-- int ntor,
-- State *s0,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- int outlev,
-- GridMapSetInfo *info )
-+void initautodock( const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int natom,
-+ const int ntor,
-+ /* not const */ State *const s0,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int outlev,
-+ const GridMapSetInfo *const info )
-
- {
- Boole B_change = FALSE;
-@@ -146,7 +146,7 @@
- }
-
- mkUnitQuat( &(s0->Q) );
-- cnv_state_to_coords( *s0, vt, tlist, ntor, crdpdb, crd, natom);
-+ cnv_state_to_coords( *s0, vt, tlist, ntor, crdpdb, crd, natom); // all const except crd
-
- for (i = 0; i < natom; i++) {
- B_outside = is_out_grid_info( crd[i][X], crd[i][Y], crd[i][Z] );
-Index: autodocksuite-4.2.3/autodock/initautodock.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/initautodock.h 2010-07-23 01:14:39.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/initautodock.h 2010-07-23 01:15:07.000000000 +0200
-@@ -33,14 +33,14 @@
- #include "print_2x.h"
-
- void initautodock(
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- int natom,
-- int ntor,
-- State *s0,
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real vt[MAX_TORS][SPACE],
-- int outlev,
-- GridMapSetInfo *info );
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const int natom,
-+ const int ntor,
-+ /* not const */ State *const s0,
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real vt[MAX_TORS][SPACE],
-+ const int outlev,
-+ const GridMapSetInfo *const info );
- #endif
-Index: autodocksuite-4.2.3/autodock/main.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/main.cc 2010-07-23 01:01:28.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/main.cc 2010-07-23 20:28:09.000000000 +0200
-@@ -125,7 +125,7 @@
- double xmin[D_max], xmax[D_max]; // Intervals defining the search space
- double Vmin[D_max], Vmax[D_max]; // Intervals defining the search space
-
--int main (int argc, char ** argv)
-+int main (int argc, const char ** argv)
-
-
- {
-@@ -4573,6 +4573,8 @@
- // delete arrays
- delete []nonbondlist;
-
-+if (NULL != programname) free(programname); programname=(char *) NULL;
-+
-
- //________________________________________________________________________________
- /*
-Index: autodocksuite-4.2.3/autodock/parse_PDBQT_line.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_PDBQT_line.cc 2010-07-23 00:39:12.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_PDBQT_line.cc 2010-07-23 00:39:36.000000000 +0200
-@@ -36,7 +36,7 @@
- extern FILE *logFile;
-
-
--int parse_PDBQT_line( char line[LINE_LEN] )
-+int parse_PDBQT_line( const char line[LINE_LEN] )
-
- /******************************************************************************/
- /* Name: parse_PDBQT_line */
-Index: autodocksuite-4.2.3/autodock/parse_PDBQT_line.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/parse_PDBQT_line.h 2010-07-23 00:39:39.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/parse_PDBQT_line.h 2010-07-23 00:39:44.000000000 +0200
-@@ -31,6 +31,6 @@
- #include "strindex.h"
- #include "PDBQT_tokens.h"
-
--int parse_PDBQT_line( char line[LINE_LEN] );
-+int parse_PDBQT_line( const char line[LINE_LEN] );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/prInitialState.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/prInitialState.h 2010-07-23 01:23:32.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/prInitialState.h 2010-07-23 01:23:50.000000000 +0200
-@@ -32,17 +32,17 @@
- #include "printEnergies.h"
-
- void prInitialState(
-- EnergyBreakdown *eb,
-- int natom,
-- Real crd[MAX_ATOMS][SPACE],
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int type[MAX_ATOMS],
-- Real emap[MAX_ATOMS],
-- Real elec[MAX_ATOMS],
-- Real charge[MAX_ATOMS],
-- int ligand_is_inhibitor,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+ const EnergyBreakdown *eb,
-+ const int natom,
-+ const Real crd[MAX_ATOMS][SPACE],
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const int type[MAX_ATOMS],
-+ const Real emap[MAX_ATOMS],
-+ const Real elec[MAX_ATOMS],
-+ const Real charge[MAX_ATOMS],
-+ const int ligand_is_inhibitor,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/trilinterp.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/trilinterp.cc 2010-07-23 00:29:03.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/trilinterp.cc 2010-07-23 00:30:31.000000000 +0200
-@@ -53,13 +53,13 @@
- const Real abs_charge[MAX_ATOMS], // absolute magnitude of partial charges
- const int type[MAX_ATOMS], // atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int some_atoms_outside_grid, // boolean
-- int ignore_inter[MAX_ATOMS], // array of booleans, says to ignore computation intermolecular energies per atom
-- Real elec[MAX_ATOMS], // set if not NULL - electrostatic energies, atom by atom
-- Real emap[MAX_ATOMS], // set if not NULL - intermolecular energies
-- Real *p_elec_total, // set if not NULL - total electrostatic energy
-- Real *p_emap_total // set if not NULL - total intermolecular energy
-+ const GridMapSetInfo *const info, // info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int some_atoms_outside_grid, // boolean
-+ const int ignore_inter[MAX_ATOMS], // array of booleans, says to ignore computation intermolecular energies per atom
-+ /* not const */ Real elec[MAX_ATOMS], // set if not NULL - electrostatic energies, atom by atom
-+ /* not const */ Real emap[MAX_ATOMS], // set if not NULL - intermolecular energies
-+ /* not const */ Real *p_elec_total, // set if not NULL - total electrostatic energy
-+ /* not const */ Real *p_emap_total // set if not NULL - total intermolecular energy
- )
-
- /******************************************************************************/
-Index: autodocksuite-4.2.3/autodock/trilinterp.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/trilinterp.h 2010-07-23 00:30:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/trilinterp.h 2010-07-23 00:31:02.000000000 +0200
-@@ -50,13 +50,13 @@
- CONST_FLOAT abs_charge[MAX_ATOMS],
- CONST_INT type[MAX_ATOMS], // atom type of each atom
- #include "map_declare.h"
-- GridMapSetInfo *info, // info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-- int some_atoms_outside_grid, // boolean
-- int ignore_inter[MAX_ATOMS], // array of booleans, says to ignore computation intermolecular energies per atom
-- Real elec[MAX_ATOMS], // set if not NULL - electrostatic energies, atom by atom
-- Real emap[MAX_ATOMS], // set if not NULL - intermolecular energies
-- Real *p_elec_total, // set if not NULL - total electrostatic energy
-- Real *p_emap_total // set if not NULL - total intermolecular energy
-+ const GridMapSetInfo *const info, // info->lo[X],info->lo[Y],info->lo[Z], minimum coordinates in x,y,z
-+ const int some_atoms_outside_grid, // boolean
-+ const int ignore_inter[MAX_ATOMS], // array of booleans, says to ignore computation intermolecular energies per atom
-+ /* not const */ Real elec[MAX_ATOMS], // set if not NULL - electrostatic energies, atom by atom
-+ /* not const */ Real emap[MAX_ATOMS], // set if not NULL - intermolecular energies
-+ /* not const */ Real *p_elec_total, // set if not NULL - total electrostatic energy
-+ /* not const */ Real *p_emap_total // set if not NULL - total intermolecular energy
- );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/writePDBQT.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/writePDBQT.h 2010-07-23 00:02:41.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/writePDBQT.h 2010-07-23 00:37:20.000000000 +0200
-@@ -34,48 +34,48 @@
- #include "cnv_state_to_coords.h"
- #include "stateLibrary.h"
-
--void writePDBQT(int irun,FourByteLong seed[2],
-- char *smFileName,
-- char *dpfFN,
-- Real sml_center[SPACE],
-- State state,
-- int ntor,
-- Real (*Ptr_eintra),
-- Real (*Ptr_einter),
-- int natom,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- Real crd[MAX_ATOMS][SPACE],
-- Real emap[MAX_ATOMS],
-- Real elec[MAX_ATOMS],
-- Real charge[MAX_ATOMS],
-- Real abs_charge[MAX_ATOMS],
-- Real qsp_abs_charge[MAX_ATOMS],
-- int ligand_is_inhibitor,
-- Real torsFreeEnergy,
-- Real vt[MAX_TORS][SPACE],
-- int tlist[MAX_TORS][MAX_ATOMS],
-- Real crdpdb[MAX_ATOMS][SPACE],
-- NonbondParam *nonbondlist,
-- EnergyTables *ptr_ad_energy_tables,
-- int type[MAX_ATOMS],
-- int Nnb,
-- Boole B_calcIntElec,
-+void writePDBQT(const int irun,FourByteLong seed[2],
-+ const char *const smFileName,
-+ const char *dpfFN,
-+ const Real sml_center[SPACE],
-+ /* not const */ State state,
-+ const int ntor,
-+ Real (*const Ptr_eintra),
-+ Real (*const Ptr_einter),
-+ const int natom,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ /* not const */ Real crd[MAX_ATOMS][SPACE],
-+ /* not const */ Real emap[MAX_ATOMS],
-+ /* not const */ Real elec[MAX_ATOMS],
-+ const Real charge[MAX_ATOMS],
-+ const Real abs_charge[MAX_ATOMS],
-+ const Real qsp_abs_charge[MAX_ATOMS],
-+ const int ligand_is_inhibitor,
-+ const Real torsFreeEnergy,
-+ const Real vt[MAX_TORS][SPACE],
-+ const int tlist[MAX_TORS][MAX_ATOMS],
-+ const Real crdpdb[MAX_ATOMS][SPACE],
-+ const NonbondParam *const nonbondlist,
-+ const EnergyTables *const ptr_ad_energy_tables,
-+ const int type[MAX_ATOMS],
-+ const int Nnb,
-+ const Boole B_calcIntElec,
- #include "map_declare.h"
-- int outlev,
-- int ignore_inter[MAX_ATOMS],
-- const Boole B_include_1_4_interactions,
-+ const int outlev,
-+ const int ignore_inter[MAX_ATOMS],
-+ const Boole B_include_1_4_interactions,
- const Real scale_1_4,
- const ParameterEntry parameterArray[MAX_ATOM_TYPES], // input nonbond and desolvation parameters
- const Real unbound_internal_FE,
-- GridMapSetInfo *info,
-- int state_type, // 0 means unbound, 1 means docked
-- char PDBQT_record[MAX_RECORDS][LINE_LEN],
-- Boole B_use_non_bond_cutoff,
-- Boole B_have_flexible_residues,
-- Unbound_Model ad4_unbound_model
-+ const GridMapSetInfo *const info,
-+ const int state_type, // 0 means unbound, 1 means docked
-+ const char PDBQT_record[MAX_RECORDS][LINE_LEN],
-+ const Boole B_use_non_bond_cutoff,
-+ const Boole B_have_flexible_residues,
-+ const Unbound_Model ad4_unbound_model
- );
-
--void print_PDBQT( FILE *logFile,
-+void print_PDBQT( FILE *const logFile,
- const int true_ligand_atoms,
- const char atomstuff[MAX_ATOMS][MAX_CHARS],
- const Real crdpdb[MAX_ATOMS][SPACE],
-@@ -86,7 +86,7 @@
-
-
-
--void print_PDBQ_atom_resstr( FILE *logFile,
-+void print_PDBQ_atom_resstr( FILE *const logFile,
- const char prefix[MAX_CHARS],
- int atom_num, // 0-origin
- const char atomstuff[],
-@@ -94,20 +94,20 @@
- const Real vdW,
- const Real Elec,
- const Real charge,
-- const char * suffix //newline or empty
-+ const char *const suffix //newline or empty
- );
-
-
--void print_PDBQ_atom_resnum( FILE *logFile,
-+void print_PDBQ_atom_resnum( FILE *const logFile,
- const char prefix[MAX_CHARS],
-- int atom_num, // 0-origin
-+ const int atom_num, // 0-origin
- const char atomstuff[],
- const int resnum,
- const Real crdpdb[MAX_ATOMS][SPACE],
- const Real vdW,
- const Real Elec,
- const Real charge,
-- const char * suffix //newline or empty
-+ const char *const suffix //newline or empty
- );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/hybrids.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/hybrids.h 2010-07-23 20:33:37.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/hybrids.h 2010-07-23 20:40:35.000000000 +0200
-@@ -45,22 +45,22 @@
- #define CALL_GLSS
-
- State call_glss(Global_Search *global_method, Local_Search *local_method,
-- State now, unsigned int num_evals, unsigned int pop_size,
-- int outlev, unsigned int extOutputEveryNgens, Molecule *mol,
-- Boole B_RandomTran0, Boole B_RandomQuat0, Boole B_RandomDihe0,
-- GridMapSetInfo *info, char *FN_pop_file,
-- int end_of_branch[MAX_TORS] );
-+ State now, const unsigned int num_evals, const unsigned int pop_size,
-+ const int outlev, const unsigned int extOutputEveryNgens, Molecule *const mol,
-+ const Boole B_RandomTran0, const Boole B_RandomQuat0, const Boole B_RandomDihe0,
-+ const GridMapSetInfo *const info, const char *const FN_pop_file,
-+ const int end_of_branch[MAX_TORS] );
-
-
--Representation **generate_R(int num_torsions, GridMapSetInfo *info );
-+Representation **generate_R(const int num_torsions, const GridMapSetInfo *const info );
-
--Representation **generate_R_quaternion(int num_torsions, GridMapSetInfo *info );
-+Representation **generate_R_quaternion(const int num_torsions, const GridMapSetInfo *const info );
-
--Genotype generate_Gtype(int num_torsions, GridMapSetInfo *info );
-+Genotype generate_Gtype(const int num_torsions, const GridMapSetInfo *const info );
-
--Phenotype generate_Ptype(int num_torsions, GridMapSetInfo *info );
-+Phenotype generate_Ptype(const int num_torsions, const GridMapSetInfo *const info );
-
--Individual random_ind(int num_torsions, GridMapSetInfo *info );
-+Individual random_ind(const int num_torsions, const GridMapSetInfo *const info );
-
- #endif
-
-@@ -115,6 +115,6 @@
- #ifndef MMM
- #define MMM
-
--void minmeanmax( FILE *fp, Population &pop, int num_its, GridMapSetInfo *info );
-+void minmeanmax( FILE *const fp, Population &pop, const int num_its, const GridMapSetInfo *const info );
-
- #endif
-Index: autodocksuite-4.2.3/autodock/intnbtable.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/intnbtable.cc 2010-07-23 20:41:54.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/intnbtable.cc 2010-07-23 20:46:56.000000000 +0200
-@@ -54,17 +54,17 @@
- extern int debug;
-
- void intnbtable( Boole *P_B_havenbp,
-- int a1,
-- int a2,
-- GridMapSetInfo *info,
-- Real cA,
-- Real cB,
-- int xA,
-- int xB,
-- double coeff_desolv,
-- double sigma,
-- EnergyTables *ad_tables,
-- Boole B_is_unbound_calculation )
-+ const int a1,
-+ const int a2,
-+ const GridMapSetInfo *const info,
-+ const Real cA,
-+ const Real cB,
-+ const int xA,
-+ const int xB,
-+ const double coeff_desolv,
-+ const double sigma,
-+ /* not const */ EnergyTables *const ad_tables,
-+ const Boole B_is_unbound_calculation )
- {
- /* Local variables: */
-
-@@ -160,8 +160,8 @@
- /* end of intnbtable */
-
-
--void setup_distdepdiel( int outlev,
-- EnergyTables *ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
-+void setup_distdepdiel( const int outlev,
-+ EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
- )
- {
- register int i=0;
-Index: autodocksuite-4.2.3/autodock/intnbtable.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/intnbtable.h 2010-07-23 20:44:15.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/intnbtable.h 2010-07-23 20:45:36.000000000 +0200
-@@ -30,16 +30,16 @@
- #include "timesys.h"
- #include "structs.h"
-
--void intnbtable(Boole *P_B_havenbp,
-- int a1,
-- int a2,
-- GridMapSetInfo *info,
-- Real cA,
-- Real cB,
-- int xA,
-- int xB,
-- double coeff_desolv,
-- double sigma,
-- EnergyTables *ad_tables,
-- Boole B_is_unbound_calculation );
-+void intnbtable(/* not const */ Boole *P_B_havenbp,
-+ const int a1,
-+ const int a2,
-+ const GridMapSetInfo *const info,
-+ const Real cA,
-+ const Real cB,
-+ const int xA,
-+ const int xB,
-+ const double coeff_desolv,
-+ const double sigma,
-+ /* not const */ EnergyTables *const ad_tables,
-+ const Boole B_is_unbound_calculation );
- #endif
-Index: autodocksuite-4.2.3/autodock/main.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/main.h 2010-07-23 20:28:30.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/main.h 2010-07-23 20:28:45.000000000 +0200
-@@ -63,7 +63,7 @@
- #define UNBOUND 0
- #define DOCKED 1
-
--int main( int argc, char **argv);
-+int main( int argc, const char **argv);
- //int main (int argc, char * const argv[], char * const envp[]);
-
- #endif
-Index: autodocksuite-4.2.3/autodock/print_atomic_energies.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_atomic_energies.cc 2010-07-23 20:12:33.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_atomic_energies.cc 2010-07-23 20:13:15.000000000 +0200
-@@ -36,12 +36,12 @@
- extern FILE *logFile;
-
- /*----------------------------------------------------------------------------*/
--void print_atomic_energies( int natom,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int type[MAX_ATOMS],
-- Real emap[MAX_ATOMS],
-- Real elec[MAX_ATOMS],
-- Real charge[MAX_ATOMS] )
-+void print_atomic_energies( const int natom,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const int type[MAX_ATOMS],
-+ const Real emap[MAX_ATOMS],
-+ const Real elec[MAX_ATOMS],
-+ const Real charge[MAX_ATOMS] )
-
- /*----------------------------------------------------------------------------*/
- {
-Index: autodocksuite-4.2.3/autodock/print_atomic_energies.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_atomic_energies.h 2010-07-23 20:11:39.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_atomic_energies.h 2010-07-23 20:12:10.000000000 +0200
-@@ -29,10 +29,10 @@
-
- #include "constants.h"
-
--void print_atomic_energies(int natom,
-- char atomstuff[MAX_ATOMS][MAX_CHARS],
-- int type[MAX_ATOMS],
-- Real emap[MAX_ATOMS],
-- Real elec[MAX_ATOMS],
-- Real charge[MAX_ATOMS] );
-+void print_atomic_energies(const int natom,
-+ const char atomstuff[MAX_ATOMS][MAX_CHARS],
-+ const int type[MAX_ATOMS],
-+ const Real emap[MAX_ATOMS],
-+ const Real elec[MAX_ATOMS],
-+ const Real charge[MAX_ATOMS] );
- #endif
-Index: autodocksuite-4.2.3/autodock/print_avsfld.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/print_avsfld.h 2010-07-23 20:15:35.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/print_avsfld.h 2010-07-23 20:15:56.000000000 +0200
-@@ -29,12 +29,12 @@
-
- #include "constants.h"
-
--void print_avsfld(FILE *logFile,
-- int veclen,
-- int natom,
-- int nframe,
-- int offset[VECLENMAX],
-- int stride,
-- char *label,
-- char *filename );
-+void print_avsfld(FILE *const logFile,
-+ const int veclen,
-+ const int natom,
-+ const int nframe,
-+ const int offset[VECLENMAX],
-+ const int stride,
-+ const char *const label,
-+ const char *const filename );
- #endif
-Index: autodocksuite-4.2.3/autodock/setflags.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/setflags.h 2010-07-23 20:18:20.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/setflags.h 2010-07-23 20:18:44.000000000 +0200
-@@ -29,8 +29,8 @@
- #include "constants.h"
- #include "usage.h"
-
--int setflags( int argc,
-- char ** argv,
-- const char * version_num);
-+int setflags( /* not const */int argc,
-+ const char ** /* not const */ argv,
-+ const char *const version_num);
-
- #endif
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/const_suggetsions_gcc4.6_1st_iteration.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_suggetsions_gcc4.6_1st_iteration.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_suggetsions_gcc4.6_1st_iteration.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,228 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/ls.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.cc 2010-07-20 21:57:43.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.cc 2010-07-20 22:01:44.000000000 +0200
-@@ -106,10 +106,10 @@
- #ifdef DEBUG
- //convenience function for debugging
- #define traceState(msg,vector) printDState(logFile,msg,vector,i,prevxyz,startxyz,prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates)
--void printDState(FILE *logFile,char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-+void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
- Real startxyz[3], Quat prevQuat, Quat startQuat,
- unsigned int num_successes, unsigned int num_failures,
-- Real temp_rho, Real * bias, Real * deviates);
-+ Real temp_rho, Real * bias, Real * deviates) const;
- Real xyz[3];
- Real prevxyz[3];
- Real startxyz[3];
-@@ -413,7 +413,7 @@
- }
- }
-
--int Pattern_Search::terminate(void)
-+int Pattern_Search::terminate(void) const
- {
- return (0);
- }
-@@ -508,7 +508,7 @@
- return newBase;
- }
-
--Phenotype Pattern_Search::pattern_explore(const Phenotype& base) {
-+Phenotype Pattern_Search::pattern_explore(const Phenotype& base) const {
- Phenotype newPoint = pattern_move(base);
- reset_pattern();
- Phenotype newBase = exploratory_move(newPoint);
-@@ -523,10 +523,10 @@
- return newPoint;
- }
- //void printDState(logFile,msg,vector,i,prevxyz,startxyz, prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates);
--void printDState(FILE *logFile,char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-+void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
- Real startxyz[3], Quat prevQuat, Quat startQuat,
- unsigned int num_successes, unsigned int num_failures,
-- Real temp_rho, Real * bias, Real * deviates)
-+ Real temp_rho, Real * bias, Real * deviates) const
- {
- #ifdef DEBUG
- Real dt; // translation step scalar
-Index: autodocksuite-4.2.3/autodock/ls.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.h 2010-07-20 21:58:50.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.h 2010-07-20 22:03:14.000000000 +0200
-@@ -66,7 +66,7 @@
- //int HJ_bias; // not implemented
- //Real * step_scales; // not implemented
- Phenotype exploratory_move(const Phenotype&);
-- Phenotype pattern_explore(const Phenotype&);
-+ Phenotype pattern_explore(const Phenotype&) const;
- Phenotype pattern_move(const Phenotype&);
- void reset_pattern(void);
- void reset_indexes(void);
-@@ -76,7 +76,7 @@
- Pattern_Search(unsigned int, unsigned int, Real, Real, Real, Real, Real);
- ~Pattern_Search(void);
- void reset(void);
-- int terminate(void);
-+ int terminate(void) const;
- int search(Individual &);
- };
-
-@@ -95,7 +95,7 @@
- virtual double gen_deviates(Real) = 0;
- virtual Boole SW(Phenotype &) = 0;
- virtual void reset(void);
-- virtual int terminate(void);
-+ virtual int terminate(void) const;
- int search(Individual &);
- };
-
-@@ -208,7 +208,7 @@
- count = 0; // reset Statistics
- }
-
--inline int Solis_Wets_Base::terminate(void)
-+inline int Solis_Wets_Base::terminate(void) const
- {
- return(0); // Don't terminate
- }
-Index: autodocksuite-4.2.3/autodock/qmultiply.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.cc 2010-07-20 22:04:07.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.cc 2010-07-20 22:05:29.000000000 +0200
-@@ -343,7 +343,7 @@
- *ptr_quat = convertQuatToRot( *ptr_quat );
- }
-
--Quat conjugate( const Quat q )
-+Quat conjugate( const Quat q ) const
- {
- Quat conj;
-
-@@ -355,7 +355,7 @@
- return conj;
- }
-
--Quat inverse( const Quat q )
-+Quat inverse( const Quat q ) const
- {
- register Quat conj, inv;
- register double inv_squared_magnitude;
-@@ -552,7 +552,7 @@
- return normQuat( Q );
- }
-
--const Quat identityQuat()
-+const Quat identityQuat() const
- {
- Quat Q;
- Q.x = Q.y = Q.z = 0.;
-@@ -568,7 +568,7 @@
- #define MIN_ANGLE -HALF_ROTATION // Angles that go from 0 to one-rotation // #define MIN_ANGLE 0.
- #define MAX_ANGLE HALF_ROTATION // Angles that go from 0 to one-rotation // #define MAX_ANGLE ONE_ROTATION
-
--Real a_range_reduction( Real a )
-+Real a_range_reduction( Real a ) const
- {
- if (a <= MIN_ANGLE) {
- do a += ONE_ROTATION;
-@@ -580,7 +580,7 @@
- return a;
- }
-
--Real alerp( Real a, Real b, Real fract )
-+Real alerp( Real a, Real b, Real fract ) const
- {
- // if fract==0, return a
- // if fract==1, return b
-Index: autodocksuite-4.2.3/autodock/qmultiply.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/qmultiply.h 2010-07-20 22:05:31.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/qmultiply.h 2010-07-20 22:06:23.000000000 +0200
-@@ -39,8 +39,8 @@
- Quat normRot( Quat q );
- Real quatDifferenceToAngle( const Quat ql, const Quat qr );
- Real quatDifferenceToAngleDeg( const Quat ql, const Quat qr );
--Quat conjugate( const Quat q );
--Quat inverse( const Quat q );
-+Quat conjugate( const Quat q ) const;
-+Quat inverse( const Quat q ) const;
- Quat slerp( const Quat qa, const Quat qb, const double t );
- Quat slerp0( const Quat qa, const Quat qb, const double t );
- Quat slerp1( const Quat qa, const Quat qb, const double t );
-@@ -60,7 +60,7 @@
- void print_q_reorient_message( FILE *logFile, Quat q_reorient );
- void create_random_orientation( Quat *ptr_quat );
- //void assertQuatOK( const Quat q );
--const Quat identityQuat();
--Real a_range_reduction( Real a );
--Real alerp( Real a, Real b, Real fract );
-+const Quat identityQuat() const;
-+Real a_range_reduction( Real a ) const;
-+Real alerp( Real a, Real b, Real fract ) const;
- #endif
-Index: autodocksuite-4.2.3/autodock/ranlib.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ranlib.cc 2010-07-20 22:07:08.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ranlib.cc 2010-07-20 22:07:29.000000000 +0200
-@@ -1918,7 +1918,7 @@
- u = ranf();
- goto S140;
- }
--Real fsign( Real num, Real sign )
-+Real fsign( Real num, Real sign ) const
- /* Transfers sign of argument sign to argument num */
- {
- if ( ( sign>0.0f && num<0.0f ) || ( sign<0.0f && num>0.0f ) )
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.cc 2010-07-20 21:54:40.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.cc 2010-07-20 21:55:06.000000000 +0200
-@@ -348,7 +348,7 @@
- } // while there is another line of parameters to read in
- }
-
--char * report_parameter_library(){
-+char * report_parameter_library() const {
- return parameter_library;
- }
-
-Index: autodocksuite-4.2.3/autodock/read_parameter_library.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/read_parameter_library.h 2010-07-20 21:55:11.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/read_parameter_library.h 2010-07-20 21:57:04.000000000 +0200
-@@ -40,7 +40,7 @@
- Unbound_Model unbound_model
- );
-
--char * report_parameter_library();
-+char * report_parameter_library() const;
-
- void setup_distdepdiel( int outlev,
- EnergyTables *ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
-Index: autodocksuite-4.2.3/autodock/readmap.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readmap.cc 2010-07-20 21:52:36.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readmap.cc 2010-07-20 21:53:57.000000000 +0200
-@@ -305,7 +305,7 @@
- return map_stats;
- }
-
--Real mapc2f(char numin)
-+Real mapc2f(const char numin) const
- {
- Real numout;
- if (numin == 0) {
-Index: autodocksuite-4.2.3/autodock/readmap.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/readmap.h 2010-07-20 21:54:05.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/readmap.h 2010-07-20 21:54:18.000000000 +0200
-@@ -37,7 +37,7 @@
- #include "check_header_float.h"
- #include "check_header_int.h"
- #include "timesys.h"
--Real mapc2f( char C_mapValue );
-+Real mapc2f( char C_mapValue ) const;
- #endif
-
- #ifndef READMAP
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/manual_const_1.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/manual_const_1.patch 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/manual_const_1.patch 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,578 +0,0 @@
-Index: autodocksuite-4.2.3/autodock/gs.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/gs.cc 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/gs.cc 2010-07-20 23:46:25.000000000 +0200
-@@ -74,12 +74,11 @@
- //#define DEBUG_MUTATION
-
-
--double worst_in_window(double *window, int size)
-+double worst_in_window(const double *const window, const int size)
- {
- register int i;
-- double worst;
-
-- worst = window[0];
-+ double worst = window[0];
-
- #ifdef DEBUG2
- (void)fprintf(logFile, "gs.cc/double worst_in_window(double *window, int size)_________________________\n");//debug
-@@ -108,10 +107,10 @@
- return(worst);
- }
-
--double avg_in_window(double *window, int size)
-+double avg_in_window(const double *const window, const int size)
- {
- register int i;
-- double mysum = 0.0, myavg = 0.0;
-+ double mysum = 0.0;
-
- #ifdef DEBUG2
- (void)fprintf(logFile, "gs.cc/avg_in_window(double *window, int size)_________________________\n");//debug
-@@ -122,7 +121,7 @@
- (void)fprintf(logFile, "gs.cc/mysum= %.3f\twindow[%d]= %.3f\n",mysum, i, window[i]);//debug
- #endif
- }
-- myavg = mysum / size;
-+ const double myavg = mysum / size;
- #ifdef DEBUG2
- (void)fprintf(logFile, "gs.cc/Returning: myavg= %.3f\n\n",myavg);//debug
- #endif
-@@ -130,8 +129,8 @@
- return(myavg);
- }
-
--// Also set avg
--double Genetic_Algorithm::worst_this_generation(Population &pop)
-+// Also set avg -- and because of avg this is not a const function
-+double Genetic_Algorithm::worst_this_generation(const Population &pop)
- {
- register unsigned int i;
- double worstval, avgval;
-@@ -170,16 +169,16 @@
-
- // This could be made inline
-
--Genetic_Algorithm::Genetic_Algorithm( EvalMode init_e_mode,
-- Selection_Mode init_s_mode,
-- Xover_Mode init_c_mode,
-- Worst_Mode init_w_mode,
-- int init_elitism,
-- Real init_c_rate,
-- Real init_m_rate,
-- int init_window_size,
-- unsigned int init_max_generations,
-- unsigned int outputEveryNgens)
-+Genetic_Algorithm::Genetic_Algorithm( const EvalMode init_e_mode,
-+ const Selection_Mode init_s_mode,
-+ const Xover_Mode init_c_mode,
-+ const Worst_Mode init_w_mode,
-+ const int init_elitism,
-+ const Real init_c_rate,
-+ const Real init_m_rate,
-+ const int init_window_size,
-+ const unsigned int init_max_generations,
-+ const unsigned int outputEveryNgens)
-
- : e_mode(init_e_mode),
- s_mode(init_s_mode),
-@@ -216,7 +215,7 @@
- worst_window = new double[window_size];
- }
-
--int Genetic_Algorithm::set_linear_ranking_selection_probability_ratio(Real r)
-+int Genetic_Algorithm::set_linear_ranking_selection_probability_ratio(const Real r)
- {
- if (r<0.) return -1; //ERROR!
- linear_ranking_selection_probability_ratio = r;
-@@ -225,7 +224,7 @@
-
-
-
--void Genetic_Algorithm::set_worst(Population ¤tPop)
-+void Genetic_Algorithm::set_worst(const Population ¤tPop)
- {
- double temp = 0.0;
-
-@@ -264,7 +263,7 @@
- }
- }
-
--M_mode Genetic_Algorithm::m_type(RepType type)
-+M_mode Genetic_Algorithm::m_type(const RepType type) const
- {
-
- #ifdef DEBUG
-@@ -285,7 +284,7 @@
- }
- }
-
--void Genetic_Algorithm::make_table(int size, Real prob)
-+void Genetic_Algorithm::make_table(const int size, const Real prob)
- {
- register int i, j;
- double L = 0.0L;
-@@ -352,7 +351,7 @@
- #endif
- }
-
--int Genetic_Algorithm::check_table(Real prob)
-+int Genetic_Algorithm::check_table(const Real prob)
- {
- int low, high;
-
-@@ -394,7 +393,7 @@
- return(low);
- }
-
--void Genetic_Algorithm::initialize(unsigned int pop_size, unsigned int num_poss_mutations)
-+void Genetic_Algorithm::initialize(const unsigned int pop_size, const unsigned int num_poss_mutations)
- {
- register unsigned int i;
-
-@@ -427,7 +426,7 @@
- make_table(pop_size*num_poss_mutations, m_rate);
- }
-
--void Genetic_Algorithm::mutate(Genotype &mutant, int gene_number)
-+void Genetic_Algorithm::mutate(Genotype &mutant, const int gene_number)
- {
- Element tempvar;
-
-@@ -796,7 +795,7 @@
- }
-
-
--void Genetic_Algorithm::crossover_uniform(Genotype &father, Genotype &mother, unsigned int num_genes)
-+void Genetic_Algorithm::crossover_uniform(Genotype &father, Genotype &mother, const unsigned int num_genes)
- {
- #ifdef DEBUG
- (void)fprintf(logFile, "gs.cc/void Genetic_Algorithm::crossover_uniform(Genotype");
-@@ -873,7 +872,7 @@
- } // next i
- }
-
--void Genetic_Algorithm::crossover_arithmetic(Genotype &A, Genotype &B, Real alpha)
-+void Genetic_Algorithm::crossover_arithmetic(Genotype &A, Genotype &B, const Real alpha)
- {
- register unsigned int i;
- Element temp_A, temp_B;
-Index: autodocksuite-4.2.3/autodock/gs.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/gs.h 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/gs.h 2010-07-20 23:46:25.000000000 +0200
-@@ -88,11 +88,11 @@
- double *worst_window;
- Real linear_ranking_selection_probability_ratio;
-
-- double worst_this_generation(Population &);
-- void set_worst(Population &);
-+ double worst_this_generation(const Population &);
-+ void set_worst(const Population &);
- void make_table(int, Real);
- int check_table(Real);
-- M_mode m_type(RepType);
-+ M_mode m_type(RepType) const;
- void mutate(Genotype &, int);
- void mutation(Population &);
- void crossover(Population &);
-Index: autodocksuite-4.2.3/autodock/ls.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.cc 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.cc 2010-07-20 23:46:25.000000000 +0200
-@@ -472,9 +472,9 @@
- return (0);
- }
-
--Phenotype Pattern_Search::exploratory_move(const Phenotype& base) {
-+Phenotype Pattern_Search::exploratory_move(const Phenotype& base) /* not const */ {
- Phenotype newBase(base);
-- shuffle_indexes();
-+ shuffle_indexes();
- unsigned int current_index;
- int direction;
-
-@@ -508,14 +508,14 @@
- return newBase;
- }
-
--Phenotype Pattern_Search::pattern_explore(const Phenotype& base) const {
-+Phenotype Pattern_Search::pattern_explore(const Phenotype& base) /* not const */ {
- Phenotype newPoint = pattern_move(base);
- reset_pattern();
- Phenotype newBase = exploratory_move(newPoint);
- return newBase;
- }
-
--Phenotype Pattern_Search::pattern_move(const Phenotype& base) {
-+Phenotype Pattern_Search::pattern_move(const Phenotype& base) const {
- Phenotype newPoint(base);
- for (unsigned int i=0; i < size; i++) {
- newPoint.write(newPoint.gread(i).real + pattern[i] , i);
-@@ -524,9 +524,9 @@
- }
- //void printDState(logFile,msg,vector,i,prevxyz,startxyz, prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates);
- void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
-- Real startxyz[3], Quat prevQuat, Quat startQuat,
-+ Real startxyz[3], const Quat prevQuat, const Quat startQuat,
- unsigned int num_successes, unsigned int num_failures,
-- Real temp_rho, Real * bias, Real * deviates) const
-+ Real temp_rho, Real * bias, Real * deviates)
- {
- #ifdef DEBUG
- Real dt; // translation step scalar
-Index: autodocksuite-4.2.3/autodock/ls.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ls.h 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ls.h 2010-07-21 00:10:38.000000000 +0200
-@@ -47,7 +47,7 @@
- Local_Search(void);
- virtual ~Local_Search(void);
- virtual void reset(void) = 0;
-- virtual int terminate(void) = 0;
-+ virtual int terminate(void) const = 0;
- virtual int search(Individual &) = 0;
- unsigned int count;//search invocation count, for run statistics
- };
-@@ -65,19 +65,19 @@
- unsigned int successes;
- //int HJ_bias; // not implemented
- //Real * step_scales; // not implemented
-- Phenotype exploratory_move(const Phenotype&);
-- Phenotype pattern_explore(const Phenotype&) const;
-- Phenotype pattern_move(const Phenotype&);
-- void reset_pattern(void);
-- void reset_indexes(void);
-- void shuffle_indexes(void);
-+ Phenotype exploratory_move(const Phenotype&) /* not const */;
-+ Phenotype pattern_explore(const Phenotype&) /* not const */;
-+ Phenotype pattern_move(const Phenotype&) const;
-+ void reset_pattern(void) /* not const */ ;
-+ void reset_indexes(void) /* not const */ ;
-+ void shuffle_indexes(void) /* not const */ ;
- public:
- Pattern_Search(void);
- Pattern_Search(unsigned int, unsigned int, Real, Real, Real, Real, Real);
- ~Pattern_Search(void);
- void reset(void);
- int terminate(void) const;
-- int search(Individual &);
-+ int search(/* not const */ Individual &);
- };
-
- class Solis_Wets_Base : public Local_Search
-Index: autodocksuite-4.2.3/autodock/support.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.cc 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.cc 2010-07-21 00:52:35.000000000 +0200
-@@ -45,7 +45,7 @@
- // These are the member functions for the support classes.
-
-
--Population::Population(Population &original)
-+Population::Population(const Population &original)
- : lhb(original.lhb), size(original.size)
- {
- register int i;
-@@ -193,7 +193,7 @@
- //}
- //}
-
--void Population::print(FILE *output, int num) {
-+void Population::print(FILE *output, const int num) const {
- register int i;
-
- #ifdef DEBUG
-@@ -246,7 +246,7 @@
-
-
-
--int Population::printPopulationStatistics(FILE *output, int level, Boole appendNewline) {
-+int Population::printPopulationStatistics(FILE *output, const int level, const Boole appendNewline) const {
- // write best energy, etc, depending on level
- // return 0 if OK, non-zero if error
- // Code adapted from gs.cc - M Pique December 2009
-@@ -336,7 +336,7 @@
- return returnCode;
- }
- int Population::printPopulationStatisticsVerbose(FILE * output,
-- unsigned int generations, long int nevals, const char suffix[]){ /* print with generations & #evals */
-+ const unsigned int generations, const long int nevals, const char suffix[]) const { /* print with generations & #evals */
- int returnCode=0;
- // print "Population at Generation:" line with low/high/mean/median/stddev...
- (void) fprintf(output, "Population at Generation: %3u ", generations);
-@@ -347,7 +347,7 @@
- }
-
-
--void Population::printPopulationAsStates(FILE *output, int num, int ntor) {
-+void Population::printPopulationAsStates(FILE *output, const int num, const int ntor) const {
- register int i;
- #ifdef DEBUG2
- register int j;
-@@ -385,7 +385,7 @@
- (void)fprintf( output, "</population>\n");
- }
-
--void Population::printPopulationAsCoordsEnergies(FILE *output, int num, int ntor) {
-+void Population::printPopulationAsCoordsEnergies(FILE *output, const int num, const int ntor) const {
- register int i;
- double thisValue;
-
-@@ -425,7 +425,7 @@
- (void)fprintf( output, "\n");
- }
-
--void Population::set_eob(int init_end_of_branch[MAX_TORS])
-+void Population::set_eob(const int init_end_of_branch[MAX_TORS])
- // Set the end_of_branch[MAX_TORS] array
- {
- for (register int i=0; i<MAX_TORS; i++) {
-@@ -433,7 +433,7 @@
- }
- }
-
--int Population::get_eob(int init_tor)
-+int Population::get_eob(const int init_tor) const
- // Get the end_of_branch[] value for the supplied torsion number, init_tor
- {
- if ((init_tor >= 0) && (init_tor < MAX_TORS)) {
-@@ -903,7 +903,7 @@
- return(value);
- }
-
--State Phenotype::make_state(int ntor)
-+State Phenotype::make_state(const int ntor) const
- {
- State retval;
-
-@@ -917,7 +917,7 @@
- return(retval);
- }
-
--Individual &Population::operator[](int ind_num)
-+Individual &Population::operator[](const int ind_num) const
- {
-
- #ifdef DEBUG
-@@ -932,7 +932,7 @@
- }
- }
-
--State Individual::state(int ntor)
-+State Individual::state(int ntor) const
- {
-
- #ifdef DEBUG
-@@ -954,7 +954,7 @@
- returnedMol = &molcopy;
- }
-
--void Individual::printIndividualsState(FILE *filePtr, int ntor, int detail)
-+void Individual::printIndividualsState(FILE *filePtr, const int ntor, const int detail) const
- {
- #ifdef DEBUG
- (void)fprintf(logFile, "support.cc/void Individual::printIndividualsState(FILE *filePtr, int ntor=%d, int detaiil=%d)\n", ntor, detail);
-Index: autodocksuite-4.2.3/autodock/support.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/support.h 2010-07-20 23:43:06.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/support.h 2010-07-21 00:07:08.000000000 +0200
-@@ -220,7 +220,7 @@
- void write(double, int);
- void write(const Representation &, int);
- double evaluate(EvalMode); // This should return evaluation if that's the right answer, and it should evaluate otherwise.
-- State make_state(int);
-+ State make_state(int) const;
- unsigned int num_dimensions(void);
- unsigned int num_pts(void);
- Quat readQuat();
-@@ -249,9 +249,9 @@
- //Phenotype mapping(void); /* takes the genotype and converts it into a phenotype. */
- //Genotype inverse_mapping(void); // Scott should do: Also copy Phenotype's value
- double value(EvalMode); /* evaluation of the individual gives its value */
-- State state(int); /* state variables in AutoDock */
-+ State state(int) const; /* state variables in AutoDock */
- void getMol(Molecule *); /* converts phenotype to mol's state and returns this individual's mol data */
-- void printIndividualsState(FILE *, int, int); /* print out the state of this individual */
-+ void printIndividualsState(FILE *, const int, const int) const; /* print out the state of this individual */
- void incrementAge(); /* make individual grow 1 generation older */
- int serial; // serial number of this individual
- };
-@@ -270,22 +270,22 @@
-
- public:
- Population(void);
-- Population(int); /* create a pop. with this many individuals */
-- Population(int, Individual *); /* takes an array of ind's and turns into pop. */
-- Population(Population &); /* copy constructor */
-+ Population(const int); /* create a pop. with this many individuals */
-+ Population(const int, Individual *); /* takes an array of ind's and turns into pop. */
-+ Population(const Population &); /* copy constructor */
- ~Population(void); /* destructor */
-- Individual &operator[](int); /* for accessing a particular indiv.in pop*/
-+ Individual &operator[](const int) const; /* for accessing a particular indiv.in pop*/
- Population &operator=(const Population &);
-- unsigned int num_individuals(void); /* returns the size of the pop. */
-+ unsigned int num_individuals(void) const; /* returns the size of the pop. */
- void msort(int); /* sorts the first m individuals using heap properties */
- // void print(ostream &, int); /* prints top int energies */
-- void print(FILE *, int); /* like above */
-- int printPopulationStatistics(FILE *, int, Boole); /* prints best, worse, mean, etc energies */
-- int printPopulationStatisticsVerbose(FILE *, unsigned int, long int, const char []); /* print with generations & #evals */
-- void printPopulationAsStates(FILE *, int, int); /*prints energies,states of top energies */
-- void printPopulationAsCoordsEnergies(FILE *, int, int); /*prints energies,states of top energies */
-- void set_eob(int init_end_of_branch[MAX_TORS]); // For Branch Crossover Mode
-- int get_eob(int init_tor); // For Branch Crossover Mode
-+ void print(FILE *, const int) const; /* like above */
-+ int printPopulationStatistics(FILE *, const int, const Boole) const; /* prints best, worse, mean, etc energies */
-+ int printPopulationStatisticsVerbose(FILE *, const unsigned int, const long int, const char []) const; /* print with generations & #evals */
-+ void printPopulationAsStates(FILE *, const int, const int) const; /*prints energies,states of top energies */
-+ void printPopulationAsCoordsEnergies(FILE *, const int, const int) const; /*prints energies,states of top energies */
-+ void set_eob(const int init_end_of_branch[MAX_TORS]); // For Branch Crossover Mode
-+ int get_eob(const int init_tor) const; // For Branch Crossover Mode
- };
-
- /**************************************************************************
-@@ -406,7 +406,7 @@
- }
- }
-
--inline Population::Population(int num_inds)
-+inline Population::Population(const int num_inds)
- : lhb(num_inds-1), size(num_inds)
- {
- heap = new Individual[num_inds];
-@@ -415,7 +415,7 @@
- }
- }
-
--inline Population::Population(int newpopsize, Individual *newpop)
-+inline Population::Population(const int newpopsize, Individual *const newpop)
- : size(newpopsize), heap(newpop)
- {
- // Do initialization stuff
-@@ -432,7 +432,7 @@
- }
- }
-
--inline unsigned int Population::num_individuals(void)
-+inline unsigned int Population::num_individuals(void) const
- {
- return(size);
- }
-Index: autodocksuite-4.2.3/autodock/eval.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.cc 2010-07-21 00:01:25.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.cc 2010-07-21 00:42:24.000000000 +0200
-@@ -65,7 +65,7 @@
- tor 1, ..., tor N are the ntor torsion angles
- */
-
--void make_state_from_rep(Representation **rep, State *stateNow)
-+void make_state_from_rep(const Representation *const *const rep, State *stateNow) /* not a member function */
- /*
- This routine modifies the various components of stateNow to correspond
- to the chromosome.
-@@ -114,13 +114,13 @@
- // mkUnitQuat(&(stateNow->Q));
- }
-
--double Eval::operator()(Representation **rep)
-+double Eval::operator()(const Representation *const *const rep)
- {
- make_state_from_rep(rep, &stateNow);
- return eval();
- }
-
--double Eval::operator()(Representation **rep, int term)
-+double Eval::operator()(const Representation *const *const rep, int term)
- {
- make_state_from_rep(rep, &stateNow);
- return eval(term);
-@@ -136,7 +136,7 @@
- }
-
-
--double Eval::eval(int term)
-+double Eval::eval(const int term)
-
- // Use this method, eval(int term), to compute just one particular term of the total energy
- //
-@@ -263,7 +263,7 @@
- return(retval);
- }
-
--int Eval::write(FILE *out_file, Representation **rep)
-+int Eval::write(FILE *out_file, const Representation *const *const rep)
- {
- int i=0, retval=0;
- //char rec14[14];
-@@ -283,14 +283,14 @@
- }
-
- #if defined(USING_COLINY) // {
--double Eval::operator()(double* vec, int len)
-+double Eval::operator()(double* vec, const int len)
- {
- make_state_from_rep(vec, len, &stateNow);
- return eval();
- }
-
-
--void make_state_from_rep(double *rep, int n, State *now)
-+void make_state_from_rep(double *rep, const int n, State *now)
- {
- # ifdef DEBUG
- (void)fprintf(logFile, "eval.cc/make_state_from_rep(double *rep, int n, State *now)\n");
-Index: autodocksuite-4.2.3/autodock/eval.h
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/eval.h 2010-07-21 00:33:26.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/eval.h 2010-07-21 00:51:01.000000000 +0200
-@@ -46,10 +46,10 @@
- #endif
-
- #if defined(USING_COLINY)
--void make_state_from_rep(double *x, int n, State *now);
-+void make_state_from_rep(double *x, const int n, State *now);
- #endif
-
--void make_state_from_rep(Representation **rep, State *stateNow);
-+void make_state_from_rep(const Representation *const *const rep, State *stateNow);
-
- class Eval
- {
-@@ -114,16 +114,16 @@
- void update_crds( Real init_crdreo[MAX_ATOMS][SPACE],
- Real init_vt[MAX_TORS][SPACE] );
-
-- double operator()(Representation **);
-- double operator()(Representation **, int); // GMM - allows calculation of a particular term of the total energy
-+ double operator()(const Representation *const *const );
-+ double operator()(const Representation *const *const , int); // GMM - allows calculation of a particular term of the total energy
- #if defined(USING_COLINY)
- double operator()(double*, int);
- #endif
- double eval(); // WEH - a basic change that facilitates the use of Coliny
-- double eval(int); // GMM - allows calculation of a particular term of the total energy
-+ double eval(const int); // GMM - allows calculation of a particular term of the total energy
- UnsignedFourByteLong evals(void);
- void reset(void);
-- int write(FILE *out_file, Representation **rep);
-+ int write(FILE *out_file, const Representation *const *const rep);
- double evalpso(State *state);
- void compute_intermol_energy(Boole init_B_compute_intermol_energy); // for computing unbound state
- };
-Index: autodocksuite-4.2.3/autodock/ranlib.cc
-===================================================================
---- autodocksuite-4.2.3.orig/autodock/ranlib.cc 2010-07-21 00:31:12.000000000 +0200
-+++ autodocksuite-4.2.3/autodock/ranlib.cc 2010-07-21 00:31:19.000000000 +0200
-@@ -38,7 +38,7 @@
- #define MIN(a,b) ((a) <= (b) ? (a) : (b))
- #define MAX(a,b) ((a) >= (b) ? (a) : (b))
-
--void ftnstop(char*);
-+void ftnstop(const char*);
-
- extern FILE *logFile;
-
Deleted: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series 2011-09-04 14:21:12 UTC (rev 7660)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2011-09-04 18:47:24 UTC (rev 7661)
@@ -1,19 +0,0 @@
-const_manual_40.patch
-const_suggetsions_gcc4.6_1st_iteration.patch
-manual_const_1.patch
-const_manual_2nd.patch
-const_manual_FILEpointer.patch
-const_manual_10.patch
-const_manual_20.patch
-const_manual_25.patch
-const_manual_30.patch
-const_manual_35.patch
-const_manual_50.patch
-const_manual_55.patch
-const_manual_60.patch
-const_manual_65.patch
-const_manual_70.patch
-const_manual_75.patch
-const_manual_80.patch
-const_manual_85.patch
-const_manual_90.patch
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