[med-svn] r14635 - in trunk/packages/autodocksuite/trunk/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Mon Sep 9 18:40:56 UTC 2013
Author: moeller
Date: 2013-09-09 18:40:55 +0000 (Mon, 09 Sep 2013)
New Revision: 14635
Added:
trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch
trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch
Modified:
trunk/packages/autodocksuite/trunk/debian/changelog
trunk/packages/autodocksuite/trunk/debian/patches/series
Log:
Series of smallish optimisations and clarifications by introducing "const" to various function declarations and definitions.
Modified: trunk/packages/autodocksuite/trunk/debian/changelog
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/changelog 2013-09-09 07:40:10 UTC (rev 14634)
+++ trunk/packages/autodocksuite/trunk/debian/changelog 2013-09-09 18:40:55 UTC (rev 14635)
@@ -1,3 +1,9 @@
+autodocksuite (4.2.5.1-4) UNSTABLE; urgency=low
+
+ * created list of patches introducing more 'const' - not applied
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 09 Sep 2013 20:37:09 +0200
+
autodocksuite (4.2.5.1-3) unstable; urgency=low
* move package from experimental to unstable
Added: trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_1.patch 2013-09-09 18:40:55 UTC (rev 14635)
@@ -0,0 +1,92 @@
+Index: autodocksuite-4.2.5.1/autodock/eval.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/eval.cc
++++ autodocksuite-4.2.5.1/autodock/eval.cc
+@@ -63,7 +63,7 @@
+ tor 1, ..., tor N are the ntor torsion angles
+ */
+
+-void make_state_from_rep(const Representation *const *const rep, /* not const */ State *const stateNow, const int outlev, FILE *logFile) /* not a member function */
++void make_state_from_rep(const Representation *const *const rep, /* not const */ State *const stateNow, const int outlev, FILE *const logFile) /* not a member function */
+ /*
+ This routine modifies the various components of stateNow to correspond
+ to the chromosome.
+@@ -252,7 +252,7 @@
+ }
+
+ int Eval::write(const Representation *const *const rep,
+- const int true_ligand_atoms, const int outlev, FILE *logFile)
++ const int true_ligand_atoms, const int outlev, FILE *const logFile)
+ {
+ int i=0, retval=0;
+ //char rec14[14];
+@@ -272,14 +272,14 @@
+ }
+
+ #if defined(USING_COLINY) // {
+-double Eval::operator()(const double* const vec, const int len, const int outlev, FILE *logFile)
++double Eval::operator()(const double* const vec, const int len, const int outlev, FILE *const logFile)
+ {
+ make_state_from_rep(vec, len, &stateNow, outlev, logFile);
+ return eval();
+ }
+
+
+-void make_state_from_rep(const double *const rep, const int n, /* not const */ State *const now, const int outlev, FILE *logFile)
++void make_state_from_rep(const double *const rep, const int n, /* not const */ State *const now, const int outlev, FILE *const logFile)
+ {
+ # ifdef DEBUG
+ (void)fprintf(logFile, "eval.cc/make_state_from_rep(double *rep, int n, State *now)\n");
+Index: autodocksuite-4.2.5.1/autodock/eval.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/eval.h
++++ autodocksuite-4.2.5.1/autodock/eval.h
+@@ -49,7 +49,7 @@
+ 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 *const stateNow, int outlev, FILE *logFile);
++void make_state_from_rep(const Representation *const *const rep, State *const stateNow, int outlev, FILE *const logFile);
+
+ class Eval
+ {
+@@ -120,7 +120,7 @@
+ const Boole init_B_have_flexible_residues,
+ int init_true_ligand_atoms,
+ int init_outlev,
+- FILE *init_logFile
++ FILE *const init_logFile
+ );
+ void update_crds( Real init_crd[MAX_ATOMS][SPACE],
+ Real init_vt[MAX_TORS][SPACE] );
+@@ -134,7 +134,7 @@
+ double eval(const int); // GMM - allows calculation of a particular term of the total energy
+ UnsignedFourByteLong evals(void);
+ void reset(void);
+- int write(const Representation *const *const rep, const int true_ligand_atoms, const int outlev, FILE *logFile);
++ int write(const Representation *const *const rep, const int true_ligand_atoms, const int outlev, FILE *const logFile);
+ void compute_intermol_energy(const Boole init_B_compute_intermol_energy); // for computing unbound state
+ };
+
+@@ -182,7 +182,7 @@
+ const Boole init_B_have_flexible_residues,
+ int init_true_ligand_atoms,
+ int init_outlev,
+- FILE *init_logFile
++ FILE *const init_logFile
+ )
+
+ {
+Index: autodocksuite-4.2.5.1/autodock/qmultiply.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/qmultiply.cc
++++ autodocksuite-4.2.5.1/autodock/qmultiply.cc
+@@ -514,7 +514,7 @@
+ ratioB = sin(t * halfTheta) / sinHalfTheta;
+ } else {
+ // qa and qb (qb_local) are very close, so we can do a linear interpolation
+- ratioA = 1 - t ;
++ ratioA = 1. - t ;
+ ratioB = t;
+ }
+ // Calculate final values
Added: trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/MoreConst_2013_2.patch 2013-09-09 18:40:55 UTC (rev 14635)
@@ -0,0 +1,886 @@
+Index: autodocksuite-4.2.5.1/autodock/rep.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/rep.cc
++++ autodocksuite-4.2.5.1/autodock/rep.cc
+@@ -914,7 +914,7 @@
+
+ //______________________________________________________________________________
+ //
+-void BitVector::write(const FourByteLong& value, const int gene)
++void BitVector::write(const FourByteLong& value, const int gene)
+ {
+
+ #ifdef DEBUG
+Index: autodocksuite-4.2.5.1/autodock/conformation_sampler.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/conformation_sampler.cc
++++ autodocksuite-4.2.5.1/autodock/conformation_sampler.cc
+@@ -71,7 +71,7 @@
+ {ICO_Y, ICO_X, 0.}, {-ICO_Y, ICO_X, 0.}, {ICO_Y, -ICO_X, 0.}, {-ICO_Y, -ICO_X, 0.}};
+
+ ConformationSampler::ConformationSampler(const State& init_state,
+- int true_ligand_atoms, int outlev, FILE *logFile) {
++ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+ base_state = init_state;
+ base_ind = set_ind(info, init_state);
+ base_point = base_ind.phenotyp;
+@@ -116,11 +116,11 @@
+ }
+ }
+
+-void ConformationSampler::random_sample(int true_ligand_atoms, int outlev, FILE *logFile) {
++void ConformationSampler::random_sample(const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+ random_sample(1, true_ligand_atoms, outlev, logFile);
+ }
+
+-void ConformationSampler::random_sample(const int num_samples, int true_ligand_atoms, int outlev, FILE *logFile) {
++void ConformationSampler::random_sample(const int num_samples, const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+ Real multiplier;
+
+ for (int sample=0; sample < num_samples; sample++) {
+@@ -152,7 +152,7 @@
+
+ // NOTE: currently, the torsional free energy penalty is not included.
+ // Since this is an entropic term, I believe we can ignore it in this analysis.
+-Real ConformationSampler::current_energy(int true_ligand_atoms, int outlev, FILE *logFile) /* not const */ {
++Real ConformationSampler::current_energy(const int true_ligand_atoms, const int outlev, FILE *const logFile) /* not const */ {
+ evals++;
+ Real energy = probe_point.evaluate(Normal_Eval);
+ Real rmsd = current_rmsd(true_ligand_atoms, outlev, logFile);
+@@ -198,7 +198,7 @@
+ }
+
+ Real ConformationSampler::current_rmsd(
+- int true_ligand_atoms, int outlev, FILE *logFile) /* not const */ {
++ const int true_ligand_atoms, const int outlev, FILE *const logFile) /* not const */ {
+ probe_ind.phenotyp = probe_point;
+ probe_ind.inverse_mapping();
+ probe_state = probe_ind.state(base_state.ntor);
+@@ -245,7 +245,7 @@
+ }
+ }
+
+-void ConformationSampler::systematic_search(const int index, int true_ligand_atoms, int outlev, FILE *logFile) {
++void ConformationSampler::systematic_search(const int index, const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+
+ // for rotation axes, rotate using the pre-defined vertices
+ if ( is_axis_index( index ) ) {
+@@ -369,7 +369,7 @@
+ return RT_CONSTANT*log(Vtot*Vconf*Boltzmann_diff_sum);
+ }
+
+-void ConformationSampler::output_statistics(int outlev, FILE *logFile) const {
++void ConformationSampler::output_statistics(const int outlev, FILE *const logFile) const {
+ if(outlev<0) return;
+ fprintf(logFile, "Conformation starting energy: %.3f\n", base_energy);
+ fprintf(logFile, "RMSD from reference state: %.3f\n", reference_rmsd());
+@@ -391,7 +391,7 @@
+ }
+
+ void systematic_conformation_sampler(const State hist[MAX_RUNS], const int nconf, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
+- int true_ligand_atoms, int outlev, FILE *logFile) {
++ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+ vt = init_vt;
+ crdpdb = init_crdpdb;
+ tlist = init_tlist;
+@@ -415,7 +415,7 @@
+ }
+
+ void random_conformation_sampler(const State hist[MAX_RUNS], const int nconf, /* not const */ int num_samples, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
+- int true_ligand_atoms, int outlev, FILE *logFile) {
++ const int true_ligand_atoms, const int outlev, FILE *const logFile) {
+ vt = init_vt;
+ crdpdb = init_crdpdb;
+ tlist = init_tlist;
+@@ -442,7 +442,7 @@
+
+
+ /* copied (and slightly modified) from non-included code in call_glss.cc */
+-Individual set_ind(GridMapSetInfo *const info, const State state)
++Individual set_ind(const GridMapSetInfo *const info, const State& state) // ATTENTION: Steffen changed 2013 const State to const State &
+ {
+ Genotype temp_Gtype;
+ Phenotype temp_Ptype;
+@@ -500,7 +500,7 @@
+ Real angle_sin = sin(raa[3]);
+ Real t = 1.0 - angle_cos;
+
+- // make sure that input vecotr is a unit vector
++ // make sure that input vector is a unit vector
+ Real length = hypotenuse(raa[0], raa[1], raa[2]);
+ raa[0] /= length;
+ raa[1] /= length;
+Index: autodocksuite-4.2.5.1/autodock/conformation_sampler.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/conformation_sampler.h
++++ autodocksuite-4.2.5.1/autodock/conformation_sampler.h
+@@ -65,20 +65,20 @@
+ Real bin_Boltzmann_sum[NUM_BINS];
+
+ ConformationSampler(const State&,
+- int true_ligand_atoms, int outlev, FILE *logFile);
++ const int true_ligand_atoms, const int outlev, FILE *const logFile);
+ ~ConformationSampler(void);
+
+- void random_sample(int true_ligand_atoms, int outlev, FILE *logFile);
+- void random_sample(const int, int true_ligand_atoms, int outlev, FILE *logFile);
+- void systematic_search(const int index, int true_ligand_atoms, int outlev, FILE *logFile);
+- Real current_energy(int true_ligand_atoms, int outlev, FILE *logFile); /* not const */
+- Real current_rmsd(int true_ligand_atoms, int outlev, FILE *logFile); /* not const */
++ void random_sample(const int true_ligand_atoms, const int outlev, FILE *const logFile);
++ void random_sample(const int, const int true_ligand_atoms, const int outlev, FILE *const logFile);
++ void systematic_search(const int index, const int true_ligand_atoms, const int outlev, FILE *const logFile);
++ Real current_energy(const int true_ligand_atoms, const int outlev, FILE *const logFile); /* not const */
++ Real current_rmsd(const int true_ligand_atoms, const int outlev, FILE *const logFile); /* not const */
+ Real reference_rmsd(void) const;
+ Real fraction_favorable(void) const;
+ Real average_favorable_energy(void) const;
+ Real energy_volume(void) const;
+ Real RK_entropy(void) const;
+- void output_statistics(int outlev, FILE *logFile) const;
++ void output_statistics(const int outlev, FILE *const logFile) const;
+ Real partition_function(void) const;
+ Real partition_function(int bin) const;
+ Real entropy_estimate(void) const;
+@@ -93,16 +93,16 @@
+ const int nconf, Real init_vt[MAX_TORS][SPACE], Real init_crdpdb[MAX_ATOMS][SPACE],
+ int init_tlist[MAX_TORS+1][MAX_ATOMS], Real init_lig_center[SPACE],
+ const int init_natom, int init_type[MAX_ATOMS], GridMapSetInfo *const init_info,
+- int true_ligand_atoms, int outlev, FILE *logFile);
++ const int true_ligand_atoms, const int outlev, FILE *const logFile);
+
+ void random_conformation_sampler(const State hist[MAX_RUNS], const int nconf,
+ /* const */ int num_samples, Real init_vt[MAX_TORS][SPACE],
+ Real init_crdpdb[MAX_ATOMS][SPACE], int init_tlist[MAX_TORS+1][MAX_ATOMS],
+ Real init_lig_center[SPACE], const int init_natom, int init_type[MAX_ATOMS],
+ GridMapSetInfo *const init_info,
+- int true_ligand_atoms, int outlev, FILE *logFile);
++ const int true_ligand_atoms, const int outlev, FILE *const logFile);
+
+-Individual set_ind(GridMapSetInfo *const info, const State state);
++Individual set_ind(const GridMapSetInfo *const info, const State& state); // Attention, newly changed const State to State&
+ void raaEuler(const Real raa[4], /* not const */ Real euler[3]);
+ void testMatrix(void);
+ void raaMatrix(Real raa[4], Real matrix[3][3]);
+Index: autodocksuite-4.2.5.1/autodock/eintcal.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/eintcal.cc
++++ autodocksuite-4.2.5.1/autodock/eintcal.cc
+@@ -55,7 +55,7 @@
+ const Boole B_use_non_bond_cutoff,
+ const Boole B_have_flexible_residues, // if the receptor has flexibile residues, this will be set to TRUE
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+
+ #else
+@@ -80,7 +80,7 @@
+ const int type[],
+ char const atom_type_name[MAX_MAPS][3],
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+ // eintcalPrint ]
+
+Index: autodocksuite-4.2.5.1/autodock/eintcal.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/eintcal.h
++++ autodocksuite-4.2.5.1/autodock/eintcal.h
+@@ -46,6 +46,6 @@
+ const Boole B_use_non_bond_cutoff,
+ const Boole B_have_flexible_residues,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+
+ #endif /*!EINTCAL*/
+Index: autodocksuite-4.2.5.1/autodock/intnbtable.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/intnbtable.cc
++++ autodocksuite-4.2.5.1/autodock/intnbtable.cc
+@@ -51,8 +51,8 @@
+ #endif
+
+ extern int debug;
+-static void printminvalue( char *label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
+- const int neint, const int a1, const int a2, FILE *logFile); // see end of this file
++static void printminvalue(const char *const label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
++ const int neint, const int a1, const int a2, FILE *const logFile); // see end of this file
+
+
+ void intnbtable( Boole *const P_B_havenbp,
+@@ -69,7 +69,7 @@
+ ConstDouble sigma,
+ /* not const */ EnergyTables *const ad_tables,
+ const Boole B_is_unbound_calculation,
+- FILE *logFile,
++ FILE *const logFile,
+ const int outlev)
+ {
+ /* Local variables: */
+@@ -260,7 +260,7 @@
+ /* end of intnbtable */
+
+
+-void setup_distdepdiel( FILE *logFile,
++void setup_distdepdiel( FILE *const logFile,
+ const int outlev,
+ EnergyTables *const ptr_ad_energy_tables // Holds vdw+Hb, desolvation & dielectric lookup tables
+ )
+@@ -291,8 +291,8 @@
+ }
+ /* end of setup_distdepdiel */
+
+-static void printminvalue( char *label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
+- const int neint, const int a1, const int a2, FILE *logFile)
++static void printminvalue(const char *const label, const Real e_vdW_Hb[NEINT][MAX_ATOM_TYPES][MAX_ATOM_TYPES],
++ const int neint, const int a1, const int a2, FILE *const logFile)
+ {
+ /* report distance range over which minimum value appears - a 'smoothing' debug tool mostly */
+ int i;
+Index: autodocksuite-4.2.5.1/autodock/intnbtable.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/intnbtable.h
++++ autodocksuite-4.2.5.1/autodock/intnbtable.h
+@@ -44,6 +44,6 @@
+ ConstDouble sigma,
+ /* not const */ EnergyTables *const ad_tables,
+ const Boole B_is_unbound_calculation,
+- FILE *logFile,
++ FILE *const logFile,
+ const int outlev);
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/mkNewState.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkNewState.cc
++++ autodocksuite-4.2.5.1/autodock/mkNewState.cc
+@@ -50,7 +50,7 @@
+ const int N_con[MAX_TORS],
+ const int true_ligand_atoms,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ // Create a new state, based on the current state
+ {
+ register int i;
+Index: autodocksuite-4.2.5.1/autodock/mkNewState.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkNewState.h
++++ autodocksuite-4.2.5.1/autodock/mkNewState.h
+@@ -55,5 +55,5 @@
+ const int N_con[MAX_TORS],
+ const int true_ligand_atoms,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/mkRandomState.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkRandomState.cc
++++ autodocksuite-4.2.5.1/autodock/mkRandomState.cc
+@@ -34,10 +34,10 @@
+ #include "mkRandomState.h"
+
+
+-State mkRandomState( int ntor,
+- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
+- int N_con[MAX_TORS],
+- GridMapSetInfo *info)
++State mkRandomState( const int ntor,
++ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
++ const int N_con[MAX_TORS],
++ const GridMapSetInfo *const info)
+
+ {
+ State now;
+Index: autodocksuite-4.2.5.1/autodock/mkRandomState.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkRandomState.h
++++ autodocksuite-4.2.5.1/autodock/mkRandomState.h
+@@ -29,8 +29,8 @@
+
+ #include "constants.h"
+
+-State mkRandomState( int ntor,
+- Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
+- int N_con[MAX_TORS],
+- GridMapSetInfo *info);
++State mkRandomState( const int ntor,
++ const Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2],
++ const int N_con[MAX_TORS],
++ const GridMapSetInfo *const info);
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/mkTorTree.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkTorTree.cc
++++ autodocksuite-4.2.5.1/autodock/mkTorTree.cc
+@@ -58,9 +58,9 @@
+ /* not const */ Real *const P_squpper,
+ /* not const */ int *const P_ntorsdof,
+ /* not const */ int ignore_inter[MAX_ATOMS],
+- int true_ligand_atoms,
+- int outlev,
+- FILE *logFile)
++ const int true_ligand_atoms,
++ const int outlev,
++ FILE *const logFile)
+
+ {
+
+Index: autodocksuite-4.2.5.1/autodock/mkTorTree.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/mkTorTree.h
++++ autodocksuite-4.2.5.1/autodock/mkTorTree.h
+@@ -46,7 +46,7 @@
+ Real *const P_squpper,
+ int *const P_ntorsdof,
+ int ignore_inter[MAX_ATOMS],
+- int true_ligand_atoms,
+- int outlev,
+- FILE *logFile);
++ const int true_ligand_atoms,
++ const int outlev,
++ FILE *const logFile);
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/nonbonds.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/nonbonds.cc
++++ autodocksuite-4.2.5.1/autodock/nonbonds.cc
+@@ -50,9 +50,9 @@
+ const int bonded[MAX_ATOMS][MAX_NBONDS],
+ const int debug,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ {
+- int i,j,k,l;
++ int i,j,k,l;
+ int nonbond_type;
+ int errorcode = 0;
+
+@@ -137,7 +137,7 @@
+ /* not const */ int bonded[MAX_ATOMS][MAX_NBONDS],
+ const int debug,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+ {
+ int i,j;
+@@ -240,7 +240,7 @@
+ /*----------------------------------------------------------------------------*/
+
+ void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds,
+-const int outlev, FILE *logFile)
++const int outlev, FILE *const logFile)
+ {
+ pr(logFile, "%s", message);
+ for (int i = 0; i<natom; i++) { // loop over atoms, "i", from 1 to natom
+@@ -256,7 +256,7 @@
+
+ /*----------------------------------------------------------------------------*/
+
+-void print_1_4_message(const Boole B_include_1_4_interactions, const Real scale_1_4, const int outlev, FILE *logFile)
++void print_1_4_message(const Boole B_include_1_4_interactions, const Real scale_1_4, const int outlev, FILE *const logFile)
+ {
+ if (B_include_1_4_interactions == FALSE) {
+ if(outlev >= LOGBASIC)
+Index: autodocksuite-4.2.5.1/autodock/nonbonds.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/nonbonds.h
++++ autodocksuite-4.2.5.1/autodock/nonbonds.h
+@@ -37,7 +37,7 @@
+ const int bonded[MAX_ATOMS][MAX_NBONDS],
+ const int debug,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+ #endif
+
+ #ifndef GETBONDS
+@@ -52,13 +52,13 @@
+ /* not const */ int bonded[MAX_ATOMS][MAX_NBONDS],
+ const int debug,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+ #endif
+
+ #ifndef PRINTBONDS
+ #define PRINTBONDS
+ #include "constants.h"
+-void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds, const int outlev, FILE *logFile);
++void printbonds(const int natom, const int nbonds[MAX_ATOMS], const int bonded[MAX_ATOMS][MAX_NBONDS], const char *message, const int B_print_all_bonds, const int outlev, FILE *const logFile);
+ #endif
+
+ #ifndef PRINT14
+@@ -66,5 +66,5 @@
+ #include "constants.h"
+ #include <stdio.h>
+ void print_1_4_message(Boole B_include_1_4_interactions, Real scale_1_4,
+-const int outlev, FILE *logFile);
++const int outlev, FILE *const logFile);
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/readPDBQT.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/readPDBQT.cc
++++ autodocksuite-4.2.5.1/autodock/readPDBQT.cc
+@@ -96,7 +96,7 @@
+ /* not const */ int end_of_branch[MAX_TORS],
+ const int debug,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+
+ {
+@@ -667,7 +667,7 @@
+ Real *const ptr_q,
+ ParameterEntry *const this_parameter_entry,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ /*----------------------------------------------------------------------------*/
+ {
+ char char8[9];
+Index: autodocksuite-4.2.5.1/autodock/readPDBQT.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/readPDBQT.h
++++ autodocksuite-4.2.5.1/autodock/readPDBQT.h
+@@ -46,7 +46,7 @@
+ Real *const P_q,
+ ParameterEntry *thisparm,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+
+ Molecule readPDBQT( char line[LINE_LEN],
+
+@@ -98,6 +98,6 @@
+ /* not const */ int end_of_branch[MAX_TORS],
+ const int debug,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ );
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/torNorVec.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/torNorVec.cc
++++ autodocksuite-4.2.5.1/autodock/torNorVec.cc
+@@ -41,7 +41,7 @@
+ const int tlist[MAX_TORS][MAX_ATOMS],
+ /* not const */ Real vt[MAX_TORS][SPACE],
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ {
+
+ register int xyz = 0;
+@@ -99,7 +99,7 @@
+ /* not const */ Molecule *ligand,
+ const int debug,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ { // Update the unit vectors for the torsion rotations
+ register int i=0, j=0;
+ if (debug > 0) {
+Index: autodocksuite-4.2.5.1/autodock/torNorVec.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/torNorVec.h
++++ autodocksuite-4.2.5.1/autodock/torNorVec.h
+@@ -36,7 +36,7 @@
+ const int tlist[MAX_TORS+1][MAX_ATOMS],
+ /* not const */ Real vt[MAX_TORS][SPACE],
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+
+ void update_torsion_vectors( const Real crdpdb[MAX_ATOMS][SPACE],
+ const int ntor,
+@@ -45,6 +45,6 @@
+ /* not const */ Molecule *ligand,
+ const int debug,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/weedbonds.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/weedbonds.cc
++++ autodocksuite-4.2.5.1/autodock/weedbonds.cc
+@@ -48,7 +48,7 @@
+ const int type[MAX_ATOMS],
+ const int debug,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+
+ {
+ int a11=0;
+@@ -246,7 +246,7 @@
+ const NonbondParam *const nonbondlist,
+ const int type[MAX_ATOMS],
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+
+ {
+ register int i = 0;
+Index: autodocksuite-4.2.5.1/autodock/weedbonds.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/weedbonds.h
++++ autodocksuite-4.2.5.1/autodock/weedbonds.h
+@@ -44,7 +44,7 @@
+ const int type[MAX_ATOMS],
+ const int debug,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+ #endif
+
+
+@@ -66,6 +66,6 @@
+ const NonbondParam *nonbondlist,
+ const int type[MAX_ATOMS],
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+ #endif
+
+Index: autodocksuite-4.2.5.1/autodock/analysis.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/analysis.cc
++++ autodocksuite-4.2.5.1/autodock/analysis.cc
+@@ -102,7 +102,7 @@
+ const Boole B_rms_heavy_atoms_only,
+ const int h_index,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+
+ )
+
+Index: autodocksuite-4.2.5.1/autodock/analysis.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/analysis.h
++++ autodocksuite-4.2.5.1/autodock/analysis.h
+@@ -87,6 +87,6 @@
+ const Boole B_rms_heavy_atoms_only,
+ const int h_index,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ );
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/calculateEnergies.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/calculateEnergies.cc
++++ autodocksuite-4.2.5.1/autodock/calculateEnergies.cc
+@@ -72,7 +72,7 @@
+ 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 int outlev,
+- FILE *logFile
++ FILE *const logFile
+
+ )
+
+@@ -189,7 +189,7 @@
+ const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+
+ )
+
+Index: autodocksuite-4.2.5.1/autodock/calculateEnergies.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/calculateEnergies.h
++++ autodocksuite-4.2.5.1/autodock/calculateEnergies.h
+@@ -61,7 +61,7 @@
+ const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+
+ );
+
+@@ -103,7 +103,7 @@
+ const Boole B_use_non_bond_cutoff, // input boolean whether to use a nonbond distance cutoff
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+
+ );
+
+Index: autodocksuite-4.2.5.1/autodock/call_gs.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/call_gs.cc
++++ autodocksuite-4.2.5.1/autodock/call_gs.cc
+@@ -47,11 +47,11 @@
+
+ extern Eval evaluate;
+
+-State call_gs(Global_Search *global_method, State& now, unsigned int num_evals, unsigned int pop_size,
+- Molecule *mol,
+- Output_pop_stats& extOutput_pop_stats,
+- GridMapSetInfo *info,
+- int end_of_branch[MAX_TORS], int outlev, FILE * logFile)
++State call_gs(Global_Search *const global_method, const State& now, const unsigned int num_evals, const unsigned int pop_size,
++ Molecule *const mol,
++ const Output_pop_stats& extOutput_pop_stats,
++ const GridMapSetInfo *const info,
++ const int end_of_branch[MAX_TORS], const int outlev, FILE *const logFile)
+ {
+ register unsigned int i;
+
+Index: autodocksuite-4.2.5.1/autodock/clmode.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/clmode.cc
++++ autodocksuite-4.2.5.1/autodock/clmode.cc
+@@ -55,7 +55,7 @@
+ const Boole B_rms_heavy_atoms_only,
+ const int h_index,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+
+ {
+ FILE *clusFile;
+Index: autodocksuite-4.2.5.1/autodock/clmode.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/clmode.h
++++ autodocksuite-4.2.5.1/autodock/clmode.h
+@@ -54,6 +54,6 @@
+ const Boole B_rms_heavy_atoms_only,
+ const int h_index,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ );
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/cnv_state_to_coords.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/cnv_state_to_coords.cc
++++ autodocksuite-4.2.5.1/autodock/cnv_state_to_coords.cc
+@@ -50,7 +50,7 @@
+ const int natom,
+ const int true_ligand_atoms,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+
+ {
+ #ifdef DEBUG
+Index: autodocksuite-4.2.5.1/autodock/getInitialState.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/getInitialState.cc
++++ autodocksuite-4.2.5.1/autodock/getInitialState.cc
+@@ -99,7 +99,7 @@
+ const Boole B_have_flexible_residues,
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+
+ {
+Index: autodocksuite-4.2.5.1/autodock/getInitialState.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/getInitialState.h
++++ autodocksuite-4.2.5.1/autodock/getInitialState.h
+@@ -92,7 +92,7 @@
+ const Boole B_have_flexible_residues,
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ );
+
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/gs.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/gs.cc
++++ autodocksuite-4.2.5.1/autodock/gs.cc
+@@ -1415,7 +1415,7 @@
+ //
+ // This is where the action is... SEARCH!
+ //
+-int Genetic_Algorithm::search(Population &solutions, int outlev, FILE *logFile)
++int Genetic_Algorithm::search(Population &solutions, const int outlev, FILE *const logFile)
+ {
+ register unsigned int i;
+
+@@ -1516,8 +1516,8 @@
+ }
+ return(0);
+ }
+-int Genetic_Algorithm::localsearch(Population &thisPop, Local_Search *local_method,
+- int outlev, FILE *logFile)
++int Genetic_Algorithm::localsearch(Population &thisPop, Local_Search *const local_method,
++ const int outlev, FILE *const logFile)
+ {
+ // apply local search (if not NULL) to population with
+ // frequency search_freq
+Index: autodocksuite-4.2.5.1/autodock/gs.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/gs.h
++++ autodocksuite-4.2.5.1/autodock/gs.h
+@@ -46,8 +46,8 @@
+ public:
+ Global_Search(unsigned int init_max_evals, unsigned int init_max_generations);
+ virtual ~Global_Search(void);
+- virtual int search(Population &, int, FILE *) = 0;
+- virtual int localsearch(Population &, Local_Search *, int, FILE *) = 0;
++ virtual int search(Population &, const int, FILE *const) = 0;
++ virtual int localsearch(Population &, Local_Search *const, int, FILE *) = 0;
+ virtual int terminate(void) = 0;
+ virtual void reset(void) = 0;
+ virtual void reset(const Output_pop_stats&) = 0;
+@@ -137,8 +137,8 @@
+ char * shortname(void);
+ char * longname(void);
+ int terminate(void);
+- int search(Population &, int, FILE *);
+- int localsearch(Population &, Local_Search *, int, FILE *);
++ int search(Population &, const int, FILE *const);
++ int localsearch(Population &, Local_Search *, const int, FILE *const);
+ int set_linear_ranking_selection_probability_ratio(ConstReal );
+
+ };
+Index: autodocksuite-4.2.5.1/autodock/investigate.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/investigate.cc
++++ autodocksuite-4.2.5.1/autodock/investigate.cc
+@@ -94,7 +94,7 @@
+ const int h_index,
+ const int true_ligand_atoms,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+
+ {
+ Boole B_outside = FALSE;
+Index: autodocksuite-4.2.5.1/autodock/pso.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/pso.cc
++++ autodocksuite-4.2.5.1/autodock/pso.cc
+@@ -35,7 +35,7 @@
+ * Caution: do not reorder the Pop array outside of these functions. MP/RH
+ * Packaged algorithm options into a structure to simplify signatures.
+ ***********************************************************************/
+-int ParticleSwarmGS::search(Population &Pop, int outlev, FILE * logFile)
++int ParticleSwarmGS::search(Population &Pop, const int outlev, FILE *const logFile)
+ {
+ int j;
+ double curVal;
+@@ -371,7 +371,7 @@
+ return (0);
+ }
+
+-int ParticleSwarmGS::localsearch(Population &Pop, Local_Search *local_method, int outlev, FILE * logFile)
++int ParticleSwarmGS::localsearch(Population &Pop, Local_Search *const local_method, const int outlev, FILE *const logFile)
+ {
+ // does local search (unconditonally) on "best" (index) indiv, which may not be historic best
+
+Index: autodocksuite-4.2.5.1/autodock/pso.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/pso.h
++++ autodocksuite-4.2.5.1/autodock/pso.h
+@@ -92,8 +92,8 @@
+ void reset(void);
+ void reset(const Output_pop_stats&);
+ int terminate(void);
+- int search(Population &, int outlev, FILE * logFile);
+- int localsearch(Population &, Local_Search *, int outlev, FILE * logFile);
++ int search(Population &, const int outlev, FILE *const logFile);
++ int localsearch(Population &, Local_Search *const, const int outlev, FILE *const logFile);
+ };
+
+ inline char * ParticleSwarmGS::shortname(void)
+Index: autodocksuite-4.2.5.1/autodock/read_parameter_library.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/read_parameter_library.cc
++++ autodocksuite-4.2.5.1/autodock/read_parameter_library.cc
+@@ -48,7 +48,7 @@
+ static char parameter_library[MAX_CHARS];
+
+ void read_parameter_library(
+- FILE *logFile,
++ FILE *const logFile,
+ const int outlev,
+ const char *const FN_parameter_library,
+ Linear_FE_Model *AD4
+Index: autodocksuite-4.2.5.1/autodock/readfield.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/readfield.cc
++++ autodocksuite-4.2.5.1/autodock/readfield.cc
+@@ -41,7 +41,7 @@
+ const Clock& jobStart,
+ const struct tms& tms_jobStart,
+ const int outlev,
+- FILE *logFile)
++ FILE *const logFile)
+ {
+ FILE *fldFile;
+ char rec9[9], inputline[LINE_LEN];
+Index: autodocksuite-4.2.5.1/autodock/readfield.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/readfield.h
++++ autodocksuite-4.2.5.1/autodock/readfield.h
+@@ -37,7 +37,7 @@
+ const Clock& jobStart,
+ const struct tms& tms_jobStart,
+ const int outlev,
+- FILE *logFile);
++ FILE *const logFile);
+
+
+ #endif
+Index: autodocksuite-4.2.5.1/autodock/simanneal.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/simanneal.cc
++++ autodocksuite-4.2.5.1/autodock/simanneal.cc
+@@ -145,7 +145,7 @@
+ const char PDBQT_record[MAX_RECORDS][LINE_LEN],
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+
+ {
+Index: autodocksuite-4.2.5.1/autodock/writePDBQT.cc
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/writePDBQT.cc
++++ autodocksuite-4.2.5.1/autodock/writePDBQT.cc
+@@ -84,7 +84,7 @@
+ const Boole B_have_flexible_residues,
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ )
+
+ {
+Index: autodocksuite-4.2.5.1/autodock/writePDBQT.h
+===================================================================
+--- autodocksuite-4.2.5.1.orig/autodock/writePDBQT.h
++++ autodocksuite-4.2.5.1/autodock/writePDBQT.h
+@@ -75,7 +75,7 @@
+ const Boole B_have_flexible_residues,
+ const Unbound_Model ad4_unbound_model,
+ const int outlev,
+- FILE *logFile
++ FILE *const logFile
+ );
+
+ void print_PDBQT( FILE *const logFile,
Modified: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series 2013-09-09 07:40:10 UTC (rev 14634)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2013-09-09 18:40:55 UTC (rev 14635)
@@ -1 +1,3 @@
-make.patch
+#does not work?!?#make.patch
+#MoreConst_2013_1.patch
+#MoreConst_2013_2.patch
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