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init.c
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init.c
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#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <string.h>
#include <math.h>
#include "mcce.h"
ENV env;
int init()
{ FILE *fp;
float kscale;
time_t now;
printf(" Load run control file \"%s\"...\n", FN_RUNPRM); fflush(stdout);
if (get_env()) {printf(" FATAL: init(): \"failed initializing.\"\n"); return USERERR;}
else {printf(" Done\n\n"); fflush(stdout);}
printf(" Tentatively load local param file \"%s\"...", env.new_tpl); fflush(stdout);
if (env.do_premcce) remove(env.new_tpl);
if ((fp=fopen(env.new_tpl, "r"))) {
fclose(fp);
if (load_param(env.new_tpl)) {
printf("\n FATAL: init(): Failed loading file \"%s\".\n", env.new_tpl);
return USERERR;
}
printf(" File loaded.\n");
}
else printf(" No such file, ignore.\n");
printf(" Done\n\n");
fflush(stdout);
printf(" Load parameters from directory \"%s\" ... \n", env.param); fflush(stdout);
if (load_all_param(env.param)) {printf(" FATAL: init(): \"failed.\"\n"); return USERERR;}
else {printf(" Done\n\n"); fflush(stdout);}
printf(" Load linear free energy correction parameters from \"%s\"...", env.extra);fflush(stdout);
if ((fp=fopen(env.extra, "r"))) {
printf("%s\n", env.extra);
fclose(fp);
if (load_param(env.extra)) {
printf("\n FATAL: init(): Failed loading file \"%s\".\n", env.extra);
return USERERR;
}
printf(" File loaded.\n");
}
else printf(" No such file, ignore.\n");
printf(" Done\n\n");
fflush(stdout);
/* Order of scale values (highest has priority):
* 1. values from (SCALE_VDW), (SCALE_VDW0), (SCALE_VDW1) options in run.prm
* 2. tpl file (usually extra.tpl)
* 3. default value from env.epsilon_prot
*/
kscale = 1.0; /*/env.epsilon_prot;*/ /* scaling factor based on dielectric constant */
if (env.scale_vdw0 < 0) {
if (param_get("SCALING", "VDW0", "", &env.scale_vdw0)) env.scale_vdw0 = 1.0*kscale;
}
if (env.scale_vdw1 < 0) {
if (param_get("SCALING", "VDW1", "", &env.scale_vdw1)) env.scale_vdw1 = 1.0*kscale;
}
if (env.scale_vdw < 0) {
if (param_get("SCALING", "VDW", "", &env.scale_vdw)) env.scale_vdw = 1.0*kscale;
}
if (param_get("SCALING", "TORS", "", &env.scale_tor)) env.scale_tor = 1.0*kscale;
if (param_get("SCALING", "ELE", "", &env.scale_ele)) env.scale_ele = 1.0;
if (param_get("SCALING", "DSOLV", "", &env.scale_dsolv)) env.scale_dsolv = 1.0;
remove(env.debug_log);
remove(env.progress_log);
now = time(NULL);
if (env.test_seed < 0) srand(now); //allows random numbers to be fixed for testing
else srand(env.test_seed);
return 0;
}
int get_env()
{ FILE *fp;
char sbuff[256];
char delphiexe_home[256];
char *str1;
/* vars related to run.trace */
time_t now;
struct tm *time_ptr;
int dotrace = 0;
FILE *tr;
char trbuff[256];
FILE *ent;
memset(&env, 0, sizeof(ENV));
// All of the default vlaues used by mcce, one can change these values in run.prm (comment by Salah 11/2015)
// Default values
env.test_seed = -1;
env.minimize_size = 0;
env.PI = 4.*atan(1.);
env.d2r = env.PI/180.;
strcpy(env.debug_log, "debug.log");
strcpy(env.new_tpl, "new.tpl");
strcpy(env.progress_log, "progress.log");
strcpy(env.extra, "extra.tpl");
env.reassign = 0;
env.pbe_start = 0;
env.pbe_end = 999999;
strcpy(env.pbe_solver, "delphi");
strcpy(env.rxn_method, "self"); //surface or self energies
env.rot_specif = 0;
env.prune_thr = 0.01;
env.ngh_vdw_thr = 0.1;
env.repack_e_thr_exposed = 0.5;
env.repack_e_thr_buried = 4.;
env.repack_fav_vdw_off = 0;
env.nconf_limit = 0;
env.n_hv_conf_limit = 20;
env.relax_wat = 1;
env.trans_dist = 0.5;
env.hdirected = 0;
env.hdirdiff = 1.0;
env.hdirlimt = 36;
env.water_relax_thr = 2.4;
env.n_initial_relax = 0;
//env.initial_relax_rebuild = 0;
env.hv_relax_ncycle = 0;
env.hv_relax_niter = 50;
env.hv_relax_vdw_thr = 5;
env.hv_relax_hv_vdw_thr = 5;
env.hv_relax_elec_thr = -2.0;
env.hv_relax_elec_crg_thr = 0.1;
env.hv_relax_elec_dist_thr = 2.4;
env.hv_relax_dt = 1;
env.hv_tors_scale = 1;
env.hv_relax_constraint = 1.;
env.hv_relax_constraint_frc = 10.;
env.hv_relax_n_shake = 3000;
env.hv_relax_shake_tol = 1e-4; /* Ratio to constraint distance */
env.hv_relax_include_ngh = 0;
env.hv_relax_ngh_thr = 4.;
env.prune_rmsd = 2.0;
env.prune_ele = 2.0;
env.prune_vdw = 2.0;
env.relax_n_hyd = 6;
env.relax_clash_thr = 10.;
env.recalc_tors = 0;
env.default_radius = 1.7;
env.factor_14lj = 0.5;
env.epsilon_coulomb = 6.;
env.sas2vdw = -0.06;
env.warn_pairwise = 20.0;
env.big_pairwise = 5.0;
env.do_gaussian_smooth = 0;
env.monte_adv_opt = 0;
env.anneal_temp_start = ROOMT;
env.anneal_nstep = 1;
env.monte_tsx = 0;
env.anneal_niter_step = 30;
env.monte_niter_max = -1;
env.adding_conf = 0;
env.monte_old_input = 0;
env.monte_niter_chk = 100;
env.monte_converge = 1e-4;
env.monte_do_energy = 0;
env.monte_print_nonzero = 1;
strcpy(env.pbe_folder, "/tmp");
env.delphi_clean = 1;
env.ionrad = 0.0;
env.salt =0.00;
/* default value for IPECE */
memset(&env.ipece,0,sizeof(IPECE));
env.ipece.grid_space = 1.0;
env.ipece.mem_position_defined = 0;
env.ipece.probe_radius = 1.40;
env.ipece.surface_exp_dist = 5.;
env.ipece.boundary_extention = 5.;
env.ipece.half_mem_thickness = 15.;
env.ipece.mem_separation = 3.;
env.ipece.membrane_size = 10.;
strcpy(env.ipece.mem_resName, "MEM");
env.ipece.mem_chainID = 'X';
env.ipece.mem_atom_radius = 1.7;
env.ipece.beta = 0.2;
env.ipece.n_iteration = 500;
env.ipece.translation_max = 3.;
env.ipece.rotation_max = 10.*env.d2r;
env.mfe_cutoff = 0.0;
env.mfe_point = 0.0;
env.mfe_flag = 0;
env.scale_vdw0=-1.0;
env.scale_vdw1=-1.0;
env.scale_vdw=-1.0;
// apbs
env.fg_scale = 1.5;
env.grids_apbs = 129;
strcpy(env.apbs_method, "mg-auto");
strcpy(env.srfm, "mol"); /*model used to construct the dielectric and ion-accessibility coefficients*/
strcpy(env.chgm, "spl0"); /*method by which the biomolecular point charges are mapped to the grid*/
strcpy(env.bcfl, "sdh"); /*specify the type of boundry condition used -"Single Debye-Hückel" boundary condition*/
strcpy(env.apbs_exe, "apbs");
env.ignore_input_h = 1;
env.do_corrections = 1;
/* open "run.prm" to read in mcce environment variables */
if ((fp=fopen(FN_RUNPRM, "r")) == NULL) {
printf(" FATAL: get_env(): \"No run control file %s.\"\n", FN_RUNPRM);
return USERERR;
}
// This while loop reads all the values from run.prm (comment by Salah 11/2015)
// user values
while (fgets(sbuff, sizeof(sbuff), fp)) {
if (sbuff[0] == '#') {
continue;
}
if (strstr(sbuff, "(DO_TRACE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't') dotrace = 1;
}
else if (strstr(sbuff, "(TEST_SEED)")) {
env.test_seed = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(IGNORE_INPUT_H)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.ignore_input_h = 1;
else env.ignore_input_h = 0;
}
else if (strstr(sbuff, "(INPDB)")) {
strcpy(env.inpdb, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MCCE_HOME)")) {
strcpy(env.mcce_home, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(DEBUG_LOG)")) {
strcpy(env.debug_log, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PROGRESS_LOG)")) {
strcpy(env.progress_log, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(NEWTPL)")) {
strcpy(env.new_tpl, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(EXTRA)")) {
strcpy(env.extra, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MINIMIZE_SIZE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.minimize_size = 1;
else env.minimize_size = 0;
}
else if (strstr(sbuff, "(DO_PREMCCE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.do_premcce = 1;
}
else env.do_premcce = 0;
}
else if (strstr(sbuff, "(TERMINALS)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.terminals = 1;
}
else env.terminals = 0;
}
else if (strstr(sbuff, "(DO_ROTAMERS)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.do_rotamers = 1;
else env.do_rotamers = 0;
}
else if (strstr(sbuff, "(DO_ENERGY)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.do_energies = 1;
else env.do_energies = 0;
}
else if (strstr(sbuff, "(DO_MONTE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.do_monte = 1;
else env.do_monte = 0;
}
else if (strstr(sbuff, "(REBUILD_SC)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.rebuild_sc = 1;
else env.rebuild_sc = 0;
}
else if (strstr(sbuff, "(ROT_SWAP)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.rot_swap = 1;
else env.rot_swap = 0;
}
else if (strstr(sbuff, "(DEFAULT_RADIUS)")) {
env.default_radius = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(FACTOR_14LJ)")) {
env.factor_14lj = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(EPSILON_COULOMB)")) {
env.epsilon_coulomb = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SAS2VDW)")) {
env.sas2vdw = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(CLASH_DISTANCE)")) {
env.clash_distance = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(H2O_SASCUTOFF)")) {
env.h2o_sascutoff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RENAME_RULES)")) {
strcpy(env.rename_rules, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ROT_SPECIF)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.rot_specif = 1;
else env.rot_specif = 0;
}
else if (strstr(sbuff, "(SWING)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.swing = 1;
else env.swing = 0;
}
else if (strstr(sbuff, "(HDIRECTED)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.hdirected = 1;
else env.hdirected = 0;
}
else if (strstr(sbuff, "(HDIRDIFF)")) {
env.hdirdiff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HDIRLIMT)")) {
env.hdirlimt = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PACK)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.pack = 1;
else env.pack = 0;
}
else if (strstr(sbuff, "(N_TRANS)")) {
env.n_trans = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TRANS_DIST)")) {
env.trans_dist = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PRUNE_THR)")) {
env.prune_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SAS_CUTOFF)")) {
env.sas_cutoff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(VDW_CUTOFF)")) {
env.vdw_cutoff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(REPACK_CUTOFF)")) {
env.repack_cutoff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(REPACK_FAV_VDW_OFF)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.repack_fav_vdw_off = 1;
else env.repack_fav_vdw_off = 0;
}
else if (strstr(sbuff, "(REPACK_E_THR_EXPOSED)")) {
env.repack_e_thr_exposed = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(REPACK_E_THR_BURIED)")) {
env.repack_e_thr_buried = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(NGH_VDW_THR)")) {
env.ngh_vdw_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PHI_SWING)")) {
env.phi_swing = atof(strtok(sbuff, " ")) * env.d2r;
}
else if (strstr(sbuff, "(ROTATIONS)")) {
env.rotations = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ROTAMER_LIMIT)")) {
env.rotamer_limit = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(REPACKS)")) {
env.repacks = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(NCONF_LIMIT)")) {
env.nconf_limit = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(N_HV_CONF_LIMIT)")) {
env.n_hv_conf_limit = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_WAT)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.relax_wat = 1;
else env.relax_wat = 0;
}
else if (strstr(sbuff, "(WATER_RELAX_THR)")) {
env.water_relax_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(N_INITIAL_RELAX)")) {
env.n_initial_relax = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_NCYCLE)")) {
env.hv_relax_ncycle = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_NITER)")) {
env.hv_relax_niter = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_VDW_THR)")) {
env.hv_relax_vdw_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_HV_VDW_THR)")) {
env.hv_relax_hv_vdw_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_ELEC_THR)")) {
env.hv_relax_elec_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_ELEC_CRG_THR)")) {
env.hv_relax_elec_crg_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_ELEC_DIST_THR)")) {
env.hv_relax_elec_dist_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_DT)")) {
env.hv_relax_dt = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_TORS_SCALE)")) {
env.hv_tors_scale = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_CONSTRAINT)")) {
env.hv_relax_constraint = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_CONSTRAINT_FRC)")) {
env.hv_relax_constraint_frc = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_N_SHAKE)")) {
env.hv_relax_n_shake = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_SHAKE_TOL)")) {
env.hv_relax_shake_tol = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(HV_RELAX_INCLUDE_NGH)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.hv_relax_include_ngh = 1;
else env.hv_relax_include_ngh = 0;
}
else if (strstr(sbuff, "(HV_RELAX_NGH_THR)")) {
env.hv_relax_ngh_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_H)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.relax_h = 1;
else env.relax_h = 0;
}
else if (strstr(sbuff, "(RELAX_E_THR)")) {
env.relax_e_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_NSTATES)")) {
env.relax_nstates = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_N_HYD)")) {
env.relax_n_hyd = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_CLASH_THR)")) {
env.relax_clash_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_PHI)")) {
env.relax_phi = 3.1415926/180.0 * atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_NITER)")) {
env.relax_niter = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RELAX_TORQ_THR)")) {
env.relax_torq_thr = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PRUNE_RMSD)")) {
env.prune_rmsd = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PRUNE_ELE)")) {
env.prune_ele = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PRUNE_VDW)")) {
env.prune_vdw = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(REASSIGN)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.reassign = 1;
}
else env.average_pairwise = 0;
}
else if (strstr(sbuff, "(EPSILON_PROT)")) {
env.epsilon_prot = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(EPSILON_SOLV)")) {
env.epsilon_solv = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GRIDS_DELPHI)")) {
env.grids_delphi = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GRIDS_PER_ANG)")) {
env.grids_per_ang = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(RADIUS_PROBE)")) {
env.radius_probe = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(IONRAD)")) {
env.ionrad = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SALT)")) {
env.salt = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(DELPHI_EXE)")) {
if (strstr(sbuff, "delphi1") || strstr(sbuff, "Delphi1")) {
strcpy(env.delphi_exe_home, "delphi1");
sprintf(delphiexe_home, "%s", strtok(sbuff, " "));
} // delphi2 is the new delphi, made in Nov. 2015, by Salah
if(strstr(sbuff, "delphi2") || strstr(sbuff, "Delphi2")){
strcpy(env.delphi_exe_home, "delphi2");
sprintf(delphiexe_home, "%s", strtok(sbuff, " "));
}
strcpy(env.delphi_exe, delphiexe_home);
}
else if (strstr(sbuff, "(GAUSSIAN_SMOOTH)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.do_gaussian_smooth = 1;
}
else env.do_gaussian_smooth = 0;
}
else if (strstr(sbuff, "(DELPHI_FAILS)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 'd' || str1[0] == 'D') {
env.delphi_fails = 'd';
}
else env.delphi_fails = 's';
}
else if (strstr(sbuff, "(RECALC_TORS)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.recalc_tors = 1;
}
else env.recalc_tors = 0;
}
else if (strstr(sbuff, "(AVERAGE_PAIRWISE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.average_pairwise = 1;
}
else env.average_pairwise = 0;
}
else if (strstr(sbuff, "(WARN_PAIRWISE)")) {
env.warn_pairwise = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_ADV_OPT)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.monte_adv_opt = 1;
else env.monte_adv_opt = 0;
}
else if (strstr(sbuff, "(MONTE_SEED)")) {
env.monte_seed = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_T)")) {
env.monte_temp = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_RUNS)")) {
env.monte_runs = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NSTART)")) {
env.monte_nstart = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NEQ)")) {
env.monte_neq = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NITER)")) {
env.monte_niter = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_FLIPS)")) {
env.monte_flips = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_TRACE)")) {
env.monte_trace = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_TSX)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.monte_tsx = 1;
}
else env.monte_tsx = 0;
}
else if (strstr(sbuff, "(MONTE_N_REDUCE)")) {
env.monte_n_red = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_REDUCE)")) {
env.monte_reduce = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(NSTATE_MAX)")) {
env.nstate_max = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ADDING_CONF)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.adding_conf = 1;
}
else env.adding_conf = 0;
}
else if (strstr(sbuff, "(MONTE_OLD_INPUT)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.monte_old_input = 1;
}
else env.monte_old_input = 0;
}
else if (strstr(sbuff, "(MONTE_NITER_CYCLE)")) {
env.monte_niter_cycle = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NITER_MIN)")) {
env.monte_niter_min = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NITER_MAX)")) {
env.monte_niter_max = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_NITER_CHK)")) {
env.monte_niter_chk = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_CONVERGE)")) {
env.monte_converge = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MONTE_DO_ENERGY)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.monte_do_energy = 1;
}
else env.monte_do_energy = 0;
}
else if (strstr(sbuff, "(MONTE_PRINT_NONZERO)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') {
env.monte_print_nonzero = 1;
}
else env.monte_print_nonzero = 0;
}
else if (strstr(sbuff, "(ANNEAL_TEMP_START)")) {
env.anneal_temp_start = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ANNEAL_NSTEP)")) {
env.anneal_nstep = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ANNEAL_NITER_STEP)")) {
env.anneal_niter_step = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TITR_TYPE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 'p' || str1[0] == 'P') env.titr_type = 'p';
else env.titr_type = 'e';
}
else if (strstr(sbuff, "(TITR_PH0)")) {
env.titr_ph0 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TITR_EH0)")) {
env.titr_eh0 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TITR_PHD)")) {
env.titr_phd = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TITR_EHD)")) {
env.titr_ehd = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(TITR_STEPS)")) {
env.titr_steps = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(BIG_PAIRWISE)")) {
env.big_pairwise = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(VDWF1)")) {
env.vdwf1 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(VDWF2)")) {
env.vdwf2 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(ROTATE_RES)")) {
strcpy(env.rotate_res, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PBE_START)")) {
env.pbe_start = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(PBE_END)")) {
env.pbe_end = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SCALE_VDW)")) {
env.scale_vdw = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SCALE_VDW0)")) {
env.scale_vdw0 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SCALE_VDW1)")) {
env.scale_vdw1 = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SCALE_ELE)")) {
env.scale_ele = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SKIP_ELE)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.skip_ele = 1;
else env.skip_ele = 0;
}
else if (strstr(sbuff, "(PBE_FOLDER)")) {
strcpy(env.pbe_folder, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(DELPHI_CLEAN)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.delphi_clean = 1;
else env.delphi_clean = 0;
}
else if (strstr(sbuff, "(PBE_SOLVER)")) {
strcpy(sbuff, strtok(sbuff, " "));
if (strstr(sbuff, "apbs") || strstr(sbuff, "APBS")) {
strcpy(env.pbe_solver, "apbs");
}
else if (strstr(sbuff, "delphi") || strstr(sbuff, "DELPHI")) {
strcpy(env.pbe_solver, "delphi");
}
else if (strstr(sbuff, "zap") || strstr(sbuff, "ZAP")) {
strcpy(env.pbe_solver, "zap");
}
else {
printf("\n Not known PBE solver: \"%s\". Using delphi in step 3...\n", sbuff);
strcpy(env.pbe_solver, "delphi");
}
}
else if (strstr(sbuff, "(RXN_METHOD)")) {
strcpy(sbuff, strtok(sbuff, " "));
if (strstr(sbuff, "self") || strstr(sbuff, "SELF")) {
strcpy(env.rxn_method, "self");
}
else if (strstr(sbuff, "ntsurface") || strstr(sbuff, "NTSURFACE")) {
strcpy(env.rxn_method, "ntsurface");
}
else if (strstr(sbuff, "surface") || strstr(sbuff, "SURFACE")) {
strcpy(env.rxn_method, "surface");
}
else {
printf("\n Not known RXN method: \"%s\". Using self energies in step 3...\n", sbuff);
strcpy(env.rxn_method, "self");
}
}
/* apbs*/
else if (strstr(sbuff, "(GRIDS_APBS)")) {
env.grids_apbs = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(SURFACE_APBS)")) {
strcpy(env.srfm, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(CHARGES_APBS)")) {
strcpy(env.chgm, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(BOUND_COND_APBS)")) {
strcpy(env.bcfl, strtok(sbuff, " "));
}
else if (strstr(sbuff, "(FINE_SCALE)")) {
env.fg_scale = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(APBS_EXE)")) {
strcpy(env.apbs_exe, strtok(sbuff, " "));
}
/* IPECE */
else if (strstr(sbuff, "(IPECE_GRID_SPACE)")) {
env.ipece.grid_space = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(IPECE_ADD_MEM)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 't' || str1[0] == 'T') env.ipece.add_mem = 1;
else env.ipece.add_mem = 0;
}
else if (strstr(sbuff, "(IPECE_MEM_THICKNESS)")) {
env.ipece.half_mem_thickness = 0.5 * atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(IPECE_MEM_CHAINID)")) {
env.ipece.mem_chainID = *strtok(sbuff, " "); /* first character of the line */
}
else if (strstr(sbuff, "(IPECE_MEM_ATOM_RADIUS)")) {
env.ipece.grid_space = atof(strtok(sbuff, " "));
}
/*Pascal's MSC Ga Parameters*/
else if (strstr(sbuff, "(GA_POP_SIZE")) {
env.pop_size = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_MUTATION_RATE)")) {
env.mutation_rate = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_MIGRATION_RATE)")) {
env.migration_rate = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_CROSSOVER_RATE)")) {
env.xover_rate = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_RANDOM_CUT_POINTS)")) {
env.rand_cut_points = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_SEED)")) {
env.ga_seed = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_GENERATIONS)")) {
env.generations = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_PHASE)")) {
env.ga_phase = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_SHIFT)")) {
env.ga_shift = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_DIST_CENTER)")) {
env.ga_dist_center = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_DIST_CENTER_EPS)")) {
env.ga_dist_center_eps = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_MAX_BUCKET_POP)")) {
env.pop_bucket = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_RESIDUE_MIN_ENERGY_CUTOFF)")) {
env.residue_check = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_OCCUPANCY_CUTOFF)")) {
env.occupancy = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_DELTA_E)")) {
env.ga_deltaE = atof(strtok(sbuff, " "));
}
else if(strstr(sbuff,"(SIDECHAIN_OPT)")) {
env.sidechain_opt = atoi(strtok(sbuff, " "));
if (env.sidechain_opt == 2) {
env.sidechain_opt = 1;
env.rot_mhd_prune = 1;
}
}
else if(strstr(sbuff,"(GA_OUTPUT)")) {
env.output = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_SPHERE_FOCUS_RESID)")) {
env.ga_focus_resid = atoi(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(GA_SPHERE_PROBE_RADIUS)")) {
env.ga_focus_probe_radius = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MFE_CUTOFF)")) {
env.mfe_cutoff = atof(strtok(sbuff, " "));
}
else if (strstr(sbuff, "(MFE_POINT)")) {
if (!(strchr(strtok(sbuff, " "), 'f'))) {
env.mfe_flag = 1;
env.mfe_point = atof(strtok(sbuff, " "));
}
}
else if (strstr(sbuff, "(DO_CORRECTIONS)")) {
str1 = strtok(sbuff, " ");
if (str1[0] == 'f' || str1[0] == 'F') {
env.do_corrections = 0;
}
else env.do_corrections = 1;
}
}
fclose(fp);
if (env.monte_niter_cycle <= 0) env.monte_niter_cycle = 1000;
if (env.repack_e_thr_exposed <= 0) env.repack_e_thr_exposed = 1e-4;
if (env.repack_e_thr_buried <= 0) env.repack_e_thr_buried = 1e-4;
if (env.ipece.boundary_extention <= env.ipece.probe_radius*4.)
env.ipece.boundary_extention = env.ipece.probe_radius*4.;
/* round the dielectric constant to the nearest integer number */
sprintf(env.param, "%s/param%02d", env.mcce_home, (int) (env.epsilon_prot));
/* sets env.ga_seed and env.monte_seed equal to env.test_seed if env.test_seed has been set to a
non random value, eliminating all randomness from MCCE */
if (env.test_seed >= 1) {
env.monte_seed = env.test_seed;
env.ga_seed = env.test_seed;
}
// adds in the default behavior of the run.trace output
// This if statment is only to load all of the used values from run.prm to run.trace (comment by Salah 11/2015)
if (dotrace == 1) {
if ((fp=fopen(FN_RUNPRM, "r")) == NULL) {
printf(" FATAL: get_env(): \"No run control file %s.\"\n", FN_RUNPRM);
return USERERR;
}
if ((tr=fopen("run.trace", "a")) == NULL) {
printf(" FATAL: get_env(): \"Cannot create run.trace file.\"\n");
return USERERR;
}
/* this block grabs the subversion revision number from .svn/entries */
if ((ent=fopen("/home/mcce/mcce2.5.1/.svn/entries", "r")) != NULL) {
int i;
for (i = 0; i < 4; ++i) {
fgets(trbuff, sizeof(trbuff), ent);
}
fprintf(tr, "The MCCE directory revision number is: %s", trbuff);
fclose(ent);
}
else {
fprintf(tr, "%s\n", "can't open entries file");
}
/* this block prints a timestamp */
now = time(NULL);
time_ptr = localtime(&now);
fprintf(tr, "%s\n", asctime(time_ptr));
/* this block prints headers for all of the columns */
fprintf(tr, "%31s%31s\t%31s%31s\n", "run.prm var name", "run.prm var value", "init.c var name", "init.c var value");
while (fgets(trbuff, sizeof(trbuff), fp)) {
if (strstr(trbuff, "(ADDING_CONF)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(ADDING_CONF)", strtok(trbuff, " "), "env.adding_conf", env.adding_conf);
}
else if (strstr(trbuff, "(ANNEAL_NITER_STEP)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(ANNEAL_NITER_STEP)", strtok(trbuff, " "), "env.anneal_niter_step", env.anneal_niter_step);
}
else if (strstr(trbuff, "(ANNEAL_NSTEP)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(ANNEAL_NSTEP)", strtok(trbuff, " "), "env.anneal_nstep", env.anneal_nstep);
}
else if (strstr(trbuff, "(ANNEAL_TEMP_START)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(ANNEAL_TEMP_START)", strtok(trbuff, " "), "env.anneal_temp_start", env.anneal_temp_start);
}
else if (strstr(trbuff, "(APBS_EXE)")) {
fprintf(tr, "%31s%31s\t%31s%31s\n", "(APBS_EXE)", strtok(trbuff, " "), "env.apbs_exe", env.apbs_exe);
}
else if (strstr(trbuff, "(AVERAGE_PAIRWISE)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(AVERAGE_PAIRWISE)", strtok(trbuff, " "), "env.average_pairwise", env.average_pairwise);
}
else if (strstr(trbuff, "(BIG_PAIRWISE)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(BIG_PAIRWISE)", strtok(trbuff, " "), "env.big_pairwise", env.big_pairwise);
}
else if (strstr(trbuff, "(BOUND_COND_APBS)")) {
fprintf(tr, "%31s%31s\t%31s%31s\n", "(BOUND_COND_APBS)", strtok(trbuff, " "), "env.bcfl", env.bcfl);
}
else if (strstr(trbuff, "(CHARGES_APBS)")) {
fprintf(tr, "%31s%31s\t%31s%31s\n", "(CHARGES_APBS)", strtok(trbuff, " "), "env.chgm", env.chgm);
}
else if (strstr(trbuff, "(CLASH_DISTANCE)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(CLASH_DISTANCE)", strtok(trbuff, " "), "env.clash_distance", env.clash_distance);
}
else if (strstr(trbuff, "(DEBUG_LOG)")) {
fprintf(tr, "%31s%31s\t%31s%31s\n", "(DEBUG_LOG)", strtok(trbuff, " "), "env.debug_log", env.debug_log);
}
else if (strstr(trbuff, "(DEFAULT_RADIUS)")) {
fprintf(tr, "%31s%31s\t%31s%31f\n", "(DEFAULT_RADIUS)", strtok(trbuff, " "), "env.default_radius", env.default_radius);
}
else if (strstr(trbuff, "(DELPHI_CLEAN)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(DELPHI_CLEAN)", strtok(trbuff, " "), "env.delphi_clean", env.delphi_clean);
}
else if (strstr(trbuff, "(DELPHI_EXE)")) {
fprintf(tr, "%31s%31s\t%31s%31s\n", "(DELPHI_EXE)", strtok(trbuff, " "), "env.delphi_exe", env.delphi_exe);
}
else if (strstr(trbuff, "(DELPHI_FAILS)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(DELPHI_FAILS)", strtok(trbuff, " "), "env.delphi_fails", env.delphi_fails);
}
else if (strstr(trbuff, "(DO_ENERGY)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(DO_ENERGY)", strtok(trbuff, " "), "env.do_energies", env.do_energies);
}
else if (strstr(trbuff, "(DO_MONTE)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(DO_MONTE)", strtok(trbuff, " "), "env.do_monte", env.do_monte);
}
else if (strstr(trbuff, "(DO_PREMCCE)")) {
fprintf(tr, "%31s%31s\t%31s%31d\n", "(DO_PREMCCE)", strtok(trbuff, " "), "env.do_premcce", env.do_premcce);
}