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/*
$Id: call_glss.cc,v 1.75 2014/06/12 01:44:07 mp Exp $
AutoDock
Copyright (C) 2009 The Scripps Research Institute. All rights reserved.
All Rights Reserved.
AutoDock is a Trade Mark of The Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
/********************************************************************
Call_glss: Invokes either GA-only or a GA-LS hybrid to try and solve the
docking problem.
rsh 9/95
********************************************************************/
#include <string.h>
#include "gs.h"
#include "ls.h"
#include "support.h"
#include "eval.h"
#include "hybrids.h"
#include "constants.h"
#include "structs.h"
#include "openfile.h"
#include "qmultiply.h"
#include <sys/types.h> /*time_t time(time_t *tloc); */
#include <time.h> /*time_t time(time_t *tloc); */
#include "timesyshms.h"
extern char *programname;
extern int debug;
Representation **generate_R(const int num_torsions, GridMapSetInfo *const info, FILE *logFile)
{
Representation **retval;
Quat q;
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Representation **generate_R() about to create a new Representation with 5 elements, retval...\n");
#endif
retval = new Representation *[5];
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Representation **generate_R() done creating a new Representation with 5 elements, retval...\n");
#endif
// Set the x-translation
retval[0] = new RealVector( 1, info->lo[X], info->hi[X] );
// Set the y-translation
retval[1] = new RealVector( 1, info->lo[Y], info->hi[Y] );
// Set the z-translation
retval[2] = new RealVector( 1, info->lo[Z], info->hi[Z] );
// Generate a uniformly-distributed random quaternion for a random rotation (UDQ)
q = randomQuat();
#ifdef DEBUG
printQuat( logFile, q );
#endif
// Set the unit vector components (the "axis"), for the rotation about axis
retval[3] = new RealVector( 4, -1., 1., q.x, q.y, q.z, q.w ); // uniformly-distributed quaternion (UDQ)
// Set the angle for any torsion angles
retval[4] = new RealVector( num_torsions, -PI, PI ); // torsion angle is uniformly distributed, -PI to PI
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Representation **generate_R() done assigning each of the retval[0-4] elements...\n");
#endif
return(retval);
}
Representation **generate_R_quaternion(const int num_torsions, const GridMapSetInfo *const info, FILE *logFile)
{
Representation **retval;
Quat q;
#ifdef DEBUG
(void)fprintf(logFile,"\ncall_glss.cc/Representation **generate_R_quaternion() about to create a new Representation with 5 elements, retval...\n");
#endif
retval = new Representation *[5];
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Representation **generate_R_quaternion() done creating a new Representation with 5 elements, retval...\n");
#endif
// Set the x-translation
retval[0] = new RealVector( 1, info->lo[X], info->hi[X] );
// Set the y-translation
retval[1] = new RealVector( 1, info->lo[Y], info->hi[Y] );
// Set the z-translation
retval[2] = new RealVector( 1, info->lo[Z], info->hi[Z] );
// Generate a uniformly-distributed random quaternion for a random rotation (UDQ)
q = randomQuat();
#ifdef DEBUG
printQuat( logFile, q );
#endif
#ifdef DEBUG_QUAT
#ifdef DEBUG_QUAT_PRINT
pr( logFile, "DEBUG_QUAT: generate_R_quaternion()\n" );
(void) fflush(logFile);
#endif
// Make sure the quaternion is suitable for 3D rotation
assertQuatOK( q );
#endif
// Set the quaternion (x,y,z,w) genes
retval[3] = new RealVector( 4, -1., 1., q.x, q.y, q.z, q.w ); // uniformly-distributed quaternion (UDQ)
// TODO retval[3] = new ConstrainedRealVector( 4, -1., 1., q.x, q.y, q.z, q.w ); // uniformly-distributed quaternion (UDQ)
// Set the torsion angles
retval[4] = new RealVector( num_torsions, -PI, PI );
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Representation **generate_R_quaternion() done assigning each of the retval[0-5] elements...\n\n");
#endif
return(retval);
}
Genotype generate_Gtype(const int num_torsions, const GridMapSetInfo *const info, int outlev, FILE *logFile)
{
#ifdef DEBUG
// (void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Gtype() about to call Genotype temp(5, generate_R())...\n");
(void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Gtype() about to call Genotype temp(5, generate_R_quaternion())...\n");
#endif
// Genotype temp((unsigned int)5, generate_R(num_torsions, info));
Genotype temp((unsigned int)5, generate_R_quaternion(num_torsions, info, logFile));
#ifdef DEBUG
// (void)fprintf(logFile,"call_glss.cc/Genotype generate_Gtype() done calling Genotype temp(5, generate_R())...\n\n");
(void)fprintf(logFile,"call_glss.cc/Genotype generate_Gtype() done calling Genotype temp(5, generate_R_quaternion())...\n\n");
#endif
return(temp);
}
Phenotype generate_Ptype(const int num_torsions, const GridMapSetInfo *const info, Eval *evaluate, int outlev, FILE *logFile)
{
#ifdef DEBUG
// (void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Ptype() about to call Phenotype temp(5, generate_R())...\n");
(void)fprintf(logFile,"\ncall_glss.cc/Genotype generate_Ptype() about to call Phenotype temp(5, generate_R_quaternion())...\n");
#endif
// Phenotype temp((unsigned int)5, generate_R(num_torsions, info));
Phenotype temp((unsigned int)5, generate_R_quaternion(num_torsions, info, logFile), evaluate);
#ifdef DEBUG
// (void)fprintf(logFile,"call_glss.cc/Genotype generate_Ptype() done calling Phenotype temp(5, generate_R())...\n\n");
(void)fprintf(logFile,"call_glss.cc/Genotype generate_Ptype() done calling Phenotype temp(5, generate_R_quaternion())...\n\n");
#endif
return(temp);
}
Individual random_ind(const int num_torsions, const GridMapSetInfo *const info, Eval *evaluate, int outlev, FILE *logFile)
{
#ifdef DEBUG
(void)fprintf(logFile,"\ncall_glss.cc/Individual random_ind() About to generate_Gtype()...\n");
#endif
Genotype temp_Gtype = generate_Gtype(num_torsions, info, outlev, logFile);
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Individual random_ind() About to generate_Ptype()...\n");
#endif
Phenotype temp_Ptype = generate_Ptype(num_torsions, info, evaluate, outlev, logFile);
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Individual random_ind() About to Individual temp(temp_Gtype, temp_Ptype)...\n");
#endif
//shotgun wedding: does not map genotype to phenotype
Individual temp(temp_Gtype, temp_Ptype);
temp.mapping();
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/Individual random_ind() Done Individual temp(temp_Gtype, temp_Ptype)...\n\n");
#endif
return(temp);
}
#ifdef MOVEDTOCONFORMATIONSAMPLER
// this block moved to conformation_sampler.cc
Individual set_ind(const int num_torsions, const GridMapSetInfo *const info, const State state, FILE *logFile)
{
Genotype temp_Gtype;
Phenotype temp_Ptype;
Quat q;
int i;
temp_Gtype = generate_Gtype(num_torsions, info, logFile);
temp_Ptype = generate_Ptype(num_torsions, info, logFile);
// use the state to generate a Genotype
temp_Gtype.write(state.T.x, 0);
temp_Gtype.write(state.T.y, 1);
temp_Gtype.write(state.T.z, 2);
#ifdef DEBUG_QUAT
#ifdef DEBUG_QUAT_PRINT
pr( logFile, "DEBUG_QUAT: set_ind()\n" );
(void) fflush(logFile);
#endif
// Make sure the quaternion is suitable for 3D rotation
assertQuatOK( q );
#endif
temp_Gtype.write( q.x, 3);
temp_Gtype.write( q.y, 4);
temp_Gtype.write( q.z, 5);
temp_Gtype.write( q.w, 6);
for (i=0;i<state.ntor; i++) {
temp_Gtype.write(state.tor[i], 7+i);
};
Individual temp(temp_Gtype, temp_Ptype);
// use mapping to generate a Phenotype
//temp.phenotyp = temp.mapping();
temp.mapping();
return(temp);
}
#endif
State call_glss(/* not const */ Global_Search *global_method,
/* not const */ Local_Search *local_method,
const State& sInit,
const unsigned int num_evals, const unsigned int pop_size,
const int outlev, FILE *logFile,
const Output_pop_stats& output_pop_stats,
Molecule * const mol,
Eval *evaluate,
const Boole B_RandomTran0, const Boole B_RandomQuat0, const Boole B_RandomDihe0,
const GridMapSetInfo *info, const char *const FN_pop_file,
/* not const */ int end_of_branch[MAX_TORS])
{
register unsigned int i;
register int j;
int allEnergiesEqual = 1, numTries = 0;
int indiv = 0; // Number of Individual in Population to set initial state variables for.
int max_numTries = 1000;
double firstEnergy = 0.0;
EvalMode localEvalMode = Normal_Eval;
static FILE *pop_fileptr = NULL;
if(outlev>=LOGRUNV) \
(void)fprintf(logFile, "call_glss: global_method %s local_method %s\n",
global_method?global_method->shortname():"NULL",
local_method?local_method->shortname():"NULL");
if (global_method) global_method->reset(output_pop_stats);
if (local_method) local_method->reset();
evaluate->reset();
if(outlev>=LOGRUNV) \
(void)fprintf( logFile, "Creating an initial population of %u individuals.\n", pop_size);
Population thisPop(pop_size, evaluate);
// Pass in the end_of_branch tree for Branch Crossover Mode.
thisPop.set_eob( end_of_branch );
thisPop.nevals_last_pop_stats = 0; // reset last time stats were printed
#ifdef DEBUG
(void)fprintf(logFile,"\ncall_glss.cc/State call_glss(): {\n");
#endif
do {
++numTries;
// Create a population of pop_size random individuals...
for (i=0; i<pop_size; i++) {
#ifdef DEBUG
(void)fprintf(logFile,"\ncall_glss.cc/State call_glss(): Creating individual thisPop[i=%d] using random_ind(%d,info)...\n", i, sInit.ntor);
#endif
thisPop[i] = random_ind( sInit.ntor, info, evaluate, outlev, logFile);
#ifdef DEBUG
(void)fprintf(logFile,"call_glss.cc/State call_glss(): Created individual i= %d in thisPop[i]\n\n", i);
#endif
thisPop[i].mol = mol;
thisPop[i].age = 0L;
}
// If initial values were supplied, put them in thisPop[0] and remap
if (!B_RandomTran0) {
if (outlev >= LOGRUNVV) (void)fprintf(logFile, "Setting the initial translation (tran0) for individual number %d to %.2lf %.2lf %.2lf\n\n", indiv+1, sInit.T.x, sInit.T.y, sInit.T.z);
thisPop[indiv].genotyp.write( sInit.T.x, 0 );
thisPop[indiv].genotyp.write( sInit.T.y, 1 );
thisPop[indiv].genotyp.write( sInit.T.z, 2 );
// Remember to keep the phenotype up-to-date
thisPop[indiv].mapping();
}
if (!B_RandomQuat0) {
if (outlev >= LOGRUNVV) {
AxisAngle aa = QuatToAxisAngle(sInit.Q);
(void)fprintf(logFile,
"Setting the initial orientation using quaterion values (x,y,z,w) for individual number %d to %.6lf %.6lf %.6lf %.6lf\n\n",
indiv+1, sInit.Q.x, sInit.Q.y, sInit.Q.z, sInit.Q.w);
(void) fprintf(logFile,
"which corresponds to the axis-angle (x,y,z,degree) values: %.2lf %.2lf %.2lf %.2lf\n\n",
aa.nx, aa.ny, aa.nz, aa.ang);
}
thisPop[indiv].genotyp.write( sInit.Q.x, 3 );
thisPop[indiv].genotyp.write( sInit.Q.y, 4 );
thisPop[indiv].genotyp.write( sInit.Q.z, 5 );
thisPop[indiv].genotyp.write( sInit.Q.w, 6 );
// Remember to keep the phenotype up-to-date
thisPop[indiv].mapping();
}
if (sInit.ntor > 0) {
if (!B_RandomDihe0) {
if (outlev >= LOGRUNVV)
(void)fprintf(logFile, "Setting the initial torsions (dihe0) for individual number %d to ", indiv+1);
for (j=0; j<sInit.ntor; j++) {
thisPop[indiv].genotyp.write( sInit.tor[j], 7+j );
if (outlev >=LOGRUNVV) (void)fprintf(logFile, "%.2lf ", RadiansToDegrees(sInit.tor[j]));
};
if (outlev >= LOGRUNVV) (void)fprintf(logFile, " deg\n\n");
// Remember to keep the phenotype up-to-date
thisPop[indiv].mapping();
}
}
#ifdef DEBUG
(void)fprintf(logFile,"\n\ncall_glss.cc // ensuring there is variation in the energies\n\n");
#endif
// Now ensure that there is some variation in the energies...
firstEnergy = thisPop[0].value(localEvalMode);
#ifdef DEBUG
(void)fprintf(logFile,"\n\ncall_glss.cc // ensuring there is variation in the energies, firstEnergy=%lf\n\n", firstEnergy);
#endif
for (i=1; i<pop_size; i++) {
#ifdef DEBUG
(void)fprintf(logFile,"\n\ncall_glss.cc // ensuring there is variation in the energies, i=%d, thisPop[i].value=%lf\n\n", i, thisPop[i].value(localEvalMode));
#endif
allEnergiesEqual = allEnergiesEqual && (thisPop[i].value(localEvalMode) == firstEnergy);
}
if ( pop_size>1 && allEnergiesEqual) {
(void)fprintf(logFile,"NOTE: All energies are equal in population; re-initializing. (Try Number %d)\n", numTries);
}
if (numTries > max_numTries) {
(void)fprintf(logFile,"WARNING: the number of tries has exceeded the maximum number of tries permitted.\nWARNING: AutoDock will attempt continue with the currently-generated random population.\n");
break;
}
} while (pop_size>1 && allEnergiesEqual);
#ifdef DEBUG
(void)fprintf(logFile,"\ncall_glss.cc/State call_glss(): }\n");
if (outlev > 2) {
thisPop.printPopulationAsCoordsEnergies( logFile, pop_size, sInit.ntor );
}
#endif
if (outlev >= LOGRUNVV ) {
(void)fprintf( logFile, "The initial population consists of the following %d individuals:\n\n", pop_size);
(void)fprintf( logFile, "<generation t=\"%d\" after_performing=\"initialisation of population\">\n", 0);
(void)fprintf( logFile, "</generation>\n\n\n");
}
// We now have a mapped and evaluated population suitable for search
// next line will resemble "Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with .."
if(outlev >= LOGFORADT )
(void)fprintf( logFile, "Beginning %s%s (%s%s), with a maximum of %u energy evaluations.\n\n",
local_method?"LAMARCKIAN ":"",
global_method?global_method->longname():"NULL",
local_method?"L":"",
global_method?global_method->shortname():"NULL",
num_evals);
// major loop over generations - terminated by logic within
// generation 0 is searchless and is used to print initial population statistics
//
// skeleton is:
// while ( ! terminate ) increment generation 0 to ...
// if ( generation > 0 ) { search population globally and locally }
// if ( search is terminating or generation is "due" ) print stats
// if ( search is terminating ) break
// end while
Boole terminate = FALSE;
for(int generation=0; ! terminate ; generation++) {
struct tms tms_genStart;
struct tms tms_genEnd;
Clock genEnd;
Clock genStart = times( &tms_genStart );
if (outlev >= LOGRUNVV ) (void)fprintf( logFile, "Global-Local Search Iteration: %d\n", generation);
if(generation>0) {
if (outlev >= LOGRUNVV) (void)fprintf( logFile, "Performing Global Search.\n");
global_method->search(thisPop, evaluate, outlev, logFile);
if (outlev >= LOGRUNVVV) {
(void)fprintf( logFile, "<generation t=\"%d\" after_performing=\"global search\">\n", generation);
thisPop.printPopulationAsStates( logFile, pop_size, sInit.ntor );
(void)fprintf( logFile, "</generation>\n\n\n");
}
if (pop_size > 1 && outlev >= LOGRUNVVV) minmeanmax( logFile, thisPop, generation, info );
// call the global method's local search method if any
if(local_method != NULL) {
if (outlev >= LOGRUNVV ) (void)fprintf( logFile, "Performing Local Search.\n");
if (outlev >= LOGRUNVVV ) for (i=0; i<pop_size; i++) {
(void)fprintf( logFile, "LS: %d",generation);
(void)fprintf( logFile, " %d",i+1);
(void)fprintf( logFile, " %f",thisPop[i].value(localEvalMode));
}
global_method->localsearch(thisPop, local_method, evaluate, outlev, logFile);
if (outlev >= LOGRUNVVV ) for (i=0; i<pop_size; i++) {
(void)fprintf( logFile, " %f",thisPop[i].value(localEvalMode));
(void)fprintf( logFile, " \n");
}
if (outlev >= LOGRUNVV ) {
(void)fprintf( logFile, "<generation t=\"%d\" after_performing=\"local search\">\n", generation);
thisPop.printPopulationAsStates( logFile, pop_size, sInit.ntor );
(void)fprintf( logFile, "</generation>\n\n\n");
}
} // if a local_method is active
if (pop_size > 1 && outlev >= LOGRUNVVV ) minmeanmax( logFile, thisPop, generation, info );
} // end if generation > 0
// note we terminate without searching if num_evals is 0
// current global methods' "terminate()" are generation count or convergence based
terminate = global_method->terminate() || evaluate->evals() >= num_evals;
genEnd = times( &tms_genEnd );
if(pop_size>0 && generation==0 && outlev >= LOGRUNV) {
// print initial best energy for statistics
// M Pique 28 Oct 2009 - adding a (harmless...) thisPop.msort(1) here
// broke the unbound-extended test. Investigating why
// Conclusion: the test is sensitive to population order since it does
// only one generation of glss. So I'm removing the msort(1) and doing
// the search for lowest-energy individual by hand.
double bestenergy = thisPop[0].value(Normal_Eval);
for (i=1; i<pop_size; i++) if(bestenergy>thisPop[i].value(Normal_Eval)) \
bestenergy=thisPop[i].value(Normal_Eval);
(void)fprintf(logFile,"Initial-Value: %.3f\n", bestenergy);
}
// Print basic generation statistics
// (code moved here from gs.cc search() May 2011 MP)
if (debug > 0) {
(void)fprintf(logFile,
"DEBUG: Generation: %3u, output_pop_stats.everyNgens = %3d, generation%%output_pop_stats.everyNgens = %u\n",
generation, output_pop_stats.everyNgens,
output_pop_stats.everyNgens>0?generation%output_pop_stats.everyNgens:0);
}
/* Only output statistics if the output level is not 0. */
if (output_pop_stats.everyNgens != 0
&& generation%output_pop_stats.everyNgens == 0) {
// print "Generation:" line (basic info, no mean/median/stddev...
(void)fprintf(logFile,"Generation: %3u ", generation);
#ifdef DEBUG3
// medium (with age/pop info) output level, no newline at end
(void) thisPop.printPopulationStatistics(logFile, 2, "");
#else
// lowest output level, no newline at end
(void) thisPop.printPopulationStatistics(logFile, 1, "");
#endif /* DEBUG3 */
(void)fprintf(logFile," Num.evals.: %d Timing: ",
evaluate->evals() );
timesyshms( genEnd - genStart, &tms_genStart, &tms_genEnd, logFile);
}
// Print extended generational population statistics, when "due" :
//
// at generation 0
// or..
// upon search termination
// or..
// every generation 0 to 20
// every tenth generation 20 to output_pop_stats.everyNgens (typically 100)
// every "output_pop_stats.everyNgens" (typically 100) if greater than that
//
// or..
// every "output_pop_stats.everyNevals" (typically 1,000,000)
// The number of evals when last printed is kept in 'thisPop'.
//
// This is purely for studying population convergence and is
// controlled by the "output_population_statistics" DPF keyword. - M Pique 2010
if (outlev>= LOGRUNV && output_pop_stats.level > 0 && (
generation==0
||
terminate
||
(output_pop_stats.everyNgens != 0 && (
(generation <= 20) ||
(generation <= (int)output_pop_stats.everyNgens
&& generation%10 == 0) ||
(generation%output_pop_stats.everyNgens == 0 ) ) )
|| (output_pop_stats.everyNevals != 0 &&
evaluate->evals() - thisPop.nevals_last_pop_stats
>= output_pop_stats.everyNevals)
)
) {
// print "Population at Generation:" line
// with low/high/mean/median/stddev/state_of_best_indiv...
// followed by GA global search stats (crossover count, mutation count)
// and local search stats (invocation count)
(void) thisPop.printPopulationStatisticsVerbose(logFile,
generation, evaluate->evals(), sInit.ntor, "");
if (global_method) {
fprintf(logFile, " cg_count: %u", global_method->cg_count);
fprintf(logFile, " ci_count: %u", global_method->ci_count);
fprintf(logFile, " mg_count: %u", global_method->mg_count);
fprintf(logFile, " mi_count: %u", global_method->mi_count);
}
if (local_method) fprintf(logFile, " ls_count: %u", local_method->ls_count);
fprintf(logFile, "\n");
thisPop.nevals_last_pop_stats = evaluate->evals();
}
if (strlen(FN_pop_file) > 0) { // YES, do print!
if (pop_fileptr==NULL) {
// attempt open
if ((pop_fileptr = ad_fopen( FN_pop_file, "w", logFile)) == NULL) {
char msg[PATH_MAX+200];
sprintf(msg, "%s: ERROR: I'm sorry, I cannot create\"%s\".", programname, FN_pop_file);
stop(msg);
} else {
fprintf(logFile, "Opened population file \"%s\" for writing.\n",FN_pop_file);
fprintf(pop_fileptr, "Opened from call_glss\n");
fflush(pop_fileptr);
}
} else {
fprintf(pop_fileptr, "Generation %d\n", generation);
fflush( pop_fileptr ); // debug
// MP TODO FAILS 2012-08-17 thisPop.printPopulationAsCoordsEnergies( pop_fileptr, pop_size, sInit.ntor);
fflush( pop_fileptr );
}
}
(void)fflush(logFile);
} // end while not terminating loop over generation
if (pop_size>1) thisPop.msort(1);
(void)fprintf(logFile,"Final-Value: %.3f\n", thisPop[0].value(Normal_Eval));
return( thisPop[0].state(sInit.ntor) );
}
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