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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
