[med-svn] r5098 - trunk/packages/autodocksuite/trunk/debian/patches
Steffen Möller
moeller at alioth.debian.org
Tue Aug 3 22:20:56 UTC 2010
Author: moeller
Date: 2010-08-03 22:20:55 +0000 (Tue, 03 Aug 2010)
New Revision: 5098
Added:
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
Modified:
trunk/packages/autodocksuite/trunk/debian/patches/series
Log:
Further updates on patches to optimise autodock.
Added: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_65.patch 2010-08-03 22:20:55 UTC (rev 5098)
@@ -0,0 +1,183 @@
+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);
Added: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_70.patch 2010-08-03 22:20:55 UTC (rev 5098)
@@ -0,0 +1,328 @@
+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;
+ /*
Added: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_75.patch 2010-08-03 22:20:55 UTC (rev 5098)
@@ -0,0 +1,71 @@
+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,
Added: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_80.patch 2010-08-03 22:20:55 UTC (rev 5098)
@@ -0,0 +1,294 @@
+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
Modified: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series 2010-08-02 21:03:02 UTC (rev 5097)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2010-08-03 22:20:55 UTC (rev 5098)
@@ -11,3 +11,7 @@
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
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