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/*
$Id: getInitialState.cc,v 1.42 2014/07/02 00:01:21 mp Exp $
AutoDock
Copyright (C) 2009 The Scripps Research Institute. 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
#include <math.h>
#include <stdio.h>
#include <sys/types.h>
#include <sys/param.h>
#include <time.h>
#include "timesys.h"
#include "getInitialState.h"
#include "trilinterp.h"
#include "calculateEnergies.h"
extern char *programname;
void getInitialState(
/* not const */ Real *const Addr_e0total,
ConstReal e0max,
/* not const */ State *const sInit, /* was qtn0[QUAT] and tor0[MAX_TORS] */
/* not const */ State *const sMinm, /* was qtnMin[QUAT] and torMin[MAX_TORS] */
/* not const */ State *const sLast, /* was qtnLast[QUAT] and torLast[MAX_TORS] */
const Boole B_RandomTran0,
const Boole B_RandomQuat0,
const Boole B_RandomDihe0,
const Real charge[MAX_ATOMS],
const Real abs_charge[MAX_ATOMS],
const Real qsp_abs_charge[MAX_ATOMS],
/* not const */ Real crd[MAX_ATOMS][SPACE],
const Real crdpdb[MAX_ATOMS][SPACE],
const char atomstuff[MAX_ATOMS][MAX_CHARS],
/* not const */ EnergyComponent *peratomE, // output if not NULL - intermolecular energies
const EnergyTables *const ptr_ad_energy_tables,
const Boole B_calcIntElec,
#include "map_declare.h"
const int natom,
const int Nnb,
int Nnb_array[3],
GroupEnergy *group_energy,
const int true_ligand_atoms,
const NonbondParam *const nonbondlist,
const int ntor,
const int tlist[MAX_TORS+1][MAX_ATOMS],
const int type[MAX_ATOMS],
const Real vt[MAX_TORS][SPACE],
const int irun, // 0-origin, includes nconf
const int MaxRetries,
ConstReal torsFreeEnergy,
const int ligand_is_inhibitor,
const int ignore_inter[MAX_ATOMS],
const Boole B_include_1_4_interactions,
ConstReal scale_1_4,
ConstReal scale_eintermol, // input scaling factor for intermolecular energies
ConstReal unbound_internal_FE,
const GridMapSetInfo *const info,
const Boole B_use_non_bond_cutoff,
const Boole B_have_flexible_residues,
const Unbound_Model ad4_unbound_model,
const int outlev,
FILE *logFile
)
{
Real e0total = 0.;
Real e0inter = 0.;
Real e0intra = 0.;
Real e0min = BIG;
int retries = 0;
register int i = 0;
Clock initStart;
Clock initEnd;
struct tms tms_initStart;
struct tms tms_initEnd;
EnergyBreakdown eb;
/* Store time at start of initialization process... */
initStart = times( &tms_initStart );
retries = 0;
if ((B_RandomTran0) || (B_RandomQuat0) || (B_RandomDihe0)) {
do {
/*
** while e0total, initial energy, is too high,
*/
/*
** Initialize all state variables...
*/
if (B_RandomTran0) {
sInit->T.x = random_range( info->lo[X], info->hi[X] );
sInit->T.y = random_range( info->lo[Y], info->hi[Y] );
sInit->T.z = random_range( info->lo[Z], info->hi[Z] );
if (outlev >= LOGRUNV) {
pr( logFile, "Random initial translation, tran0 %.3f %.3f %.3f\n", sInit->T.x, sInit->T.y, sInit->T.z);
}
}/*if*/
if (B_RandomQuat0) {
sInit->Q = randomQuat(); // generate a uniformly-distributed quaternion
if (outlev >= LOGRUNV ) {
pr( logFile, "Random initial quaternion, quaternion0 %.3f %.3f %.3f %.3f\n", sInit->Q.x, sInit->Q.y, sInit->Q.z, sInit->Q.w );
// convert from qx,qy,qz,qw to axis-angle (nx,ny,nz,ang)
AxisAngle aa = QuatToAxisAngle(sInit->Q);
pr( logFile, "Random initial axis-angle, axisangle0 %.3f %.3f %.3f %.1f\n", aa.nx, aa.ny, aa.nz, RadiansToDegrees( aa.ang ) );
}
}/*if*/
if ( B_RandomDihe0 && (ntor > 0) ) {
if (outlev >= LOGRUNV ) {
pr( logFile, "Random initial torsions, ndihe = %d\ndihe0 = ", ntor);
}
sInit->ntor = ntor;
for (i=0; i<ntor; i++) {
sInit->tor[i] = random_range(-180.,180.);
if (outlev >= LOGRUNV ) {
pr( logFile, "%7.2f ", sInit->tor[i] ); /*in degrees*/
}
sInit->tor[i] = DegreesToRadians( sInit->tor[i] ); /*now in radians*/
}
if (outlev >= LOGRUNV ) {
pr( logFile, "\n");
}
}/*if*/
copyState( sMinm, *sInit );
copyState( sLast, *sInit );
/* _________________________________________________________________________
**
** Initialize the automated docking simulation,
** _________________________________________________________________________
*/
initautodock( atomstuff, crd, crdpdb,
natom, ntor, sInit, tlist, vt, true_ligand_atoms,outlev, info);
e0inter = scale_eintermol * trilinterp( 0, natom, crd, charge, abs_charge, type, map,
info, ignore_inter, peratomE, NULL,
NULL_ENERGY_BREAKDOWN);
e0intra = eintcal( nonbondlist, ptr_ad_energy_tables, crd,
Nnb, Nnb_array, group_energy,
B_calcIntElec, B_include_1_4_interactions,
scale_1_4, qsp_abs_charge,
B_use_non_bond_cutoff, B_have_flexible_residues,
outlev, logFile);
e0total = e0inter + e0intra;
if (e0total < e0min) {
/*
** This energy is lower so update
** the initialization minimum-energy state variables,
*/
e0min = e0total;
copyState( sMinm, *sInit );
}
/*
if ( (e0total > e0max) && ((!B_RandomTran0)||(!B_RandomQuat0)) ) {
B_RandomTran0 = TRUE;
B_RandomQuat0 = TRUE;
}
*/
++retries;
if ((retries > 0) && (retries < MaxRetries) &&
(e0total > e0max) && (outlev >= LOGRUNVV)) {
pr(logFile, "Initial total energy, e0total = %.3f, too high!\n", e0total);
pr(logFile, "Number of attempts = %d (run %d)\n\n", retries, irun+1);
pr(logFile, "Will try again...\n");
} else if (retries >= MaxRetries) {
if(outlev >= LOGRUNVV)
pr( logFile, "Sorry, too many retries (%d). Continuing...\n\nWill use the state with the lowest energy found, %.2f\n\n", MaxRetries, e0min);
e0total = e0min;
copyState( sInit, *sMinm );
break;
}
fflush( logFile );
} while ( e0total > e0max );
} // endif
cnv_state_to_coords( *sInit, vt, tlist, ntor, crdpdb, crd, natom,
true_ligand_atoms, outlev, logFile);
eb = calculateBindingEnergies( natom, ntor, unbound_internal_FE, torsFreeEnergy, B_have_flexible_residues,
crd, charge, abs_charge, type, map, info,
ignore_inter, peratomE, NULL,
nonbondlist, ptr_ad_energy_tables,
Nnb, Nnb_array, group_energy, true_ligand_atoms,
B_calcIntElec, B_include_1_4_interactions, scale_1_4, qsp_abs_charge, B_use_non_bond_cutoff, ad4_unbound_model,
outlev, logFile);
copyState( sMinm, *sInit );
copyState( sLast, *sInit );
if(outlev>=LOGRUNVV) {
prInitialState( &eb, natom, true_ligand_atoms, crd, atomstuff, type, peratomE, charge,
ligand_is_inhibitor, B_have_flexible_residues, ad4_unbound_model,
outlev, logFile);
initEnd = times( &tms_initEnd );
pr(logFile, "Number of initialization attempts = %d (run %d)\n", retries, irun+1);
pr(logFile, "Time spent initializing: (Real, CPU, System): ");
timesys( initEnd - initStart, &tms_initStart, &tms_initEnd, logFile);
}
*Addr_e0total = eb.e_inter + eb.e_intra;
}
/* EOF */
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