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  1. /*
  2.  
  3.  $Id: main.cc,v 1.69 2007/05/01 02:40:12 garrett Exp $
  4.  
  5.  AutoDock
  6.  
  7.  Copyright (C) 1989-2007,  Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson, Scott Halliday, Max Chang, Bill Hart, Richard Belew
  8.  All Rights Reserved.
  9.  
  10.  AutoDock is a Trade Mark of The Scripps Research Institute.
  11.  
  12.  This program is free software; you can redistribute it and/or
  13.  modify it under the terms of the GNU General Public License
  14.  as published by the Free Software Foundation; either version 2
  15.  of the License, or (at your option) any later version.
  16.  
  17.  This program is distributed in the hope that it will be useful,
  18.  but WITHOUT ANY WARRANTY; without even the implied warranty of
  19.  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20.  GNU General Public License for more details.
  21.  
  22.  You should have received a copy of the GNU General Public License
  23.  along with this program; if not, write to the Free Software
  24.  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  25.  
  26.  */
  27.  
  28. #ifdef HAVE_CONFIG_H
  29. #include <config.h>
  30. #endif
  31.  
  32. #include <math.h>
  33. #include <sys/types.h> // time_t time(time_t *tloc);
  34. #include <time.h>      // time_t time(time_t *tloc);
  35. #include <sys/times.h>
  36. #include <stdlib.h>
  37. #include <string.h>
  38. #include <sys/param.h>
  39. #include <ctype.h> // tolower
  40. #include <unistd.h> // sysconf
  41.  
  42. /* the BOINC API header file */
  43. #ifdef BOINC
  44. #include "diagnostics.h"
  45. #include "boinc_api.h"
  46. #include "filesys.h"                 // boinc_fopen(), etc... */
  47. #endif
  48.  
  49. #include "coliny.h"
  50. #include "hybrids.h"
  51. #include "ranlib.h"
  52. #include "gs.h"
  53. #include "ls.h"
  54. #include "rep.h"
  55. #include "support.h"
  56. #include "distdepdiel.h"
  57. #include "calculateEnergies.h"
  58. #include "conformation_sampler.h"
  59. #include "main.h"
  60.  
  61. extern int debug;
  62. extern int keepresnum;
  63. extern Real idct;
  64. extern Eval evaluate;
  65. extern Linear_FE_Model AD4;
  66. extern Real nb_group_energy[3]; ///< total energy of each nonbond group (intra-ligand, inter, and intra-receptor)
  67. extern int Nnb_array[3];  ///< number of nonbonds in the ligand, intermolecular and receptor groups
  68.  
  69. static const char* const ident[] = {ident[1], "@(#)$Id: main.cc,v 1.69 2007/05/01 02:40:12 garrett Exp $"};
  70.  
  71.  
  72. int sel_prop_count = 0;
  73.  
  74.  
  75. int main (int argc, char * const argv[], char * const envp[])
  76.  
  77. /*******************************************************************************
  78. **      Name: main  (AutoDock)                                                **
  79. **  Function: Performs Automated Docking of Small Molecule into Macromolecule **
  80. ** Copyright: (C) 1994-2005 TSRI, Arthur J. Olson's Labortatory.              **
  81. **____________________________________________________________________________**
  82. **   Authors: Garrett Matthew Morris, Current C/C++ version 4.0               **
  83. **                                       e-mail: garrett@scripps.edu          **
  84. **                                                                            **
  85. **            David Goodsell, Orignal FORTRAN version 1.0                     **
  86. **                                       e-mail: goodsell@scripps.edu         **
  87. **                                                                            **
  88. **            The Scripps Research Institute                                  **
  89. **            Department of Molecular Biology, MB5                            **
  90. **            10550 North Torrey Pines Road                                   **
  91. **            La Jolla, CA 92037.                                             **
  92. **                                                                            **
  93. **      Date: 02/10/04                                                        **
  94. **____________________________________________________________________________**
  95. **    Inputs: Control file, Small Molecule PDBQT file, macromolecular grid map**
  96. **            files.                                                          **
  97. **   Returns: Autodock Log File, includes docked conformation clusters (PDBQT)**
  98. **   Globals: X, Y, Z, SPACE, MAX_GRID_PTS, NEINT, MAX_ATOMS,                 **
  99. **            MAX_MAPS, ATOM_MAPS, A_DIVISOR, LINE_LEN,TRUE,FALSE             **
  100. **            programname, command_mode,                                      **
  101. **            command_in_fp, command_out_fp, parFile, logFile.                **
  102. **____________________________________________________________________________**
  103. ** Modification Record                                                        **
  104. ** Date     Inits   Comments                                                  **
  105. ** 09/06/95 RSH     Added code to handle GA/LS stuff                          **
  106. **          DSG     Quaternion rotations                                      **
  107. **          DSG     Generates torsions from annotated pdb list                **
  108. **          DSG     Generates internal energies                               **
  109. **          DSG     Performs a limited Cluster analysis of conformations      **
  110. ** 05/07/92 GMM     C translation                                             **
  111. ** 05/14/92 GMM     Time-dependent seed in random-number generation           **
  112. ** 10/29/92 GMM     Application Visualization System (AVS) readable grid      **
  113. **                  display file input.                                       **
  114. **                  [AVS is a trademark of Stardent Computer Inc.]            **
  115. **                  Also added the 'total_charge' check.                      **
  116. ** 11/19/93 GMM     #ifdef NOSQRT, with non-square-rooting acceleration.      **
  117. ** 09/26/94 GMM     Cluster analysis now outputs RMS deviations.              **
  118. ** 09/28/94 GMM     Modularized code.                                         **
  119. ** 10/02/94 GMM     Distance constraints added, for Ed Moret. Accelerated.    **
  120. ** 09/06/95 RSH     Incorporation of GA/SW tokens                             **
  121. *******************************************************************************/
  122.  
  123. {
  124. //   ATOM_MAPS
  125. //
  126. char            atm_typ_str[ATOM_MAPS]; //  "atm_typ_str" (in AD3) used to serve a similar role to "atom_type_name" (in AD4).
  127.  
  128. //   MAX_MAPS
  129. //
  130. char            *ligand_atom_type_ptrs[MAX_MAPS]; /* array of ptrs used to parse input line of atom type names */
  131. ParameterEntry  parameterArray[MAX_MAPS];
  132.  
  133. //   MAX_GRID_PTS & MAX_MAPS
  134. //
  135. static Real map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS];
  136. // double *map;  // Use this with malloc...
  137.  
  138. GridMapSetInfo *info;  // this information is from the AVS field file
  139.  
  140. //   MAX_ATOMS
  141. //
  142. char atomstuff[MAX_ATOMS][MAX_CHARS];
  143. char pdbaname[MAX_ATOMS][5];
  144. Real crdpdb[MAX_ATOMS][SPACE];  // original PDB coordinates from input
  145. Real crdreo[MAX_ATOMS][SPACE];  // reoriented coordinates
  146. Real crd[MAX_ATOMS][SPACE];     // current coordinates
  147. Real charge[MAX_ATOMS];
  148. Real abs_charge[MAX_ATOMS];
  149. Real qsp_abs_charge[MAX_ATOMS];
  150. Real elec[MAX_ATOMS];
  151. Real emap[MAX_ATOMS];
  152. int type[MAX_ATOMS];
  153. int bond_index[MAX_ATOMS];
  154. int ignore_inter[MAX_ATOMS];
  155. Atom atoms[MAX_ATOMS];
  156.  
  157. //   MAX_TORS
  158. //
  159. int  tlist[MAX_TORS][MAX_ATOMS];
  160. Real vt[MAX_TORS][SPACE];
  161. Real F_TorConRange[MAX_TORS][MAX_TOR_CON][2];
  162. unsigned short  US_TorE[MAX_TORS];
  163. Boole B_isTorConstrained[MAX_TORS];
  164. int N_con[MAX_TORS];
  165. unsigned short US_torProfile[MAX_TORS][NTORDIVS];
  166.  
  167. //   MAX_NONBONDS
  168. //
  169. NonbondParam *nonbondlist = new NonbondParam[MAX_NONBONDS];
  170.  
  171. //   LINE_LEN
  172. //
  173. char error_message[LINE_LEN];
  174. char message[LINE_LEN];
  175. char line[LINE_LEN];
  176. char torfmt[LINE_LEN];
  177.  
  178. //   MAX_CHARS
  179. //
  180. char FN_clus[MAX_CHARS];
  181. char FN_watch[MAX_CHARS];
  182. //char FN_gdfld[MAX_CHARS]  // now part of the GridMapSetInfo structure;
  183. //char FN_gpf[MAX_CHARS];  // now part of the GridMapSetInfo structure
  184. char FN_ligand[MAX_CHARS];
  185. char dummy_FN_ligand[MAX_CHARS];
  186. char FN_trj[MAX_CHARS];
  187. //char FN_receptor[MAX_CHARS];// now part of the GridMapSetInfo structure
  188. char FN_rms_ref_crds[MAX_CHARS];
  189. char FN_parameter_library[MAX_CHARS];
  190. char hostnm[MAX_CHARS];
  191. char param[2][MAX_CHARS];
  192. char c_mode_str[MAX_CHARS];
  193. char FN_pop_file[MAX_CHARS];
  194. char FN_flexres[MAX_CHARS];
  195. char rms_atoms_cmd[MAX_CHARS];
  196. char confsampler_type[MAX_CHARS];
  197.  
  198. //   MAX_RECORDS
  199. //
  200. char PDBQT_record[MAX_RECORDS][LINE_LEN];
  201.  
  202. //   SPACE
  203. //
  204. Real lig_center[SPACE];
  205. //Real map_center[SPACE];
  206.  
  207. //   MAX_RUNS
  208. //
  209. Real econf[MAX_RUNS];  // this is the list of energies printed in the histogram in "analysis"
  210. State sHist[MAX_RUNS];  /* qtnHist[MAX_RUNS][QUAT],torHist[MAX_RUNS][MAX_TORS];*/
  211. State sUnbound; // State of the unbound ligand's conformation
  212. State sUnbound_ext; // State of the unbound ligand's conformation after extended-conformation search
  213. //// UNCOMMENT if using Step 2 in unbound calculation ---> State sUnbound_ls; // State of the unbound ligand's conformation after a local search
  214. State sUnbound_ad; // State of the unbound ligand's conformation after an AutoDock search
  215.  
  216. char out_acc_rej = '?';
  217. char timeSeedIsSet[2];
  218. char selminpar = 'm';
  219. char S_contype[8];
  220.  
  221. static ParameterEntry * foundParameter;
  222.  
  223. Real cA;
  224. Real cB;
  225. Real cA_unbound = 392586.8;  // repulsive
  226. Real cB_unbound = 0.0; // attractive
  227. Real epsij;
  228. Real F_A;
  229. Real F_Aova;
  230. Real F_tor;
  231. Real F_torPref;
  232. Real F_torHWdth;
  233. Real Rij;
  234. Real sqlower;
  235. Real squpper;
  236. Real tmpconst;
  237.  
  238. // Distance-dependence in Desolvation Term
  239. const double sigma = 3.6L;
  240. const double qsolpar = 0.01097L;
  241.  
  242. // ELECSCALE converts between CGS units and SI units;
  243. // see, e.g. p 254, "Molecular Modeling and Simulation", by Tamar Schlick, Springer.
  244. //
  245. // Units of ELECSCALE are (Kcal/mol ) * (Angstrom / esu^2)
  246. // and this allows us to use distances in  Angstroms and charges in esu...
  247. const Real ELECSCALE = 332.06363;  
  248.  
  249. // const Real ELECSCALE = 83.0159075;   this ELECSCALE (corresponding to eps(r) = 1/4r) gives -7.13 kcal/mol for 1pgp Tests/test_autodock4.py
  250.  
  251. // i
  252. double Ri, epsi, Ri_hb, epsi_hb;
  253. hbond_type hbondi;
  254.  
  255. // j
  256. double Rj, epsj, Rj_hb, epsj_hb;
  257. hbond_type hbondj;
  258.  
  259. Real scale_1_4 = 0.5;
  260. Real c=0.0;
  261. Real clus_rms_tol = 0.0;
  262. Real e0max = BIG;
  263. Real eintra = 0.0;  // sum of intramolecular energy for the ligand plus that of the protein
  264. Real einter = 0.0; // intermolecular energy between the ligand and the protein
  265. Real etotal = 0.0;
  266. Real AD3_FE_coeff_estat   = 1.000;
  267. Real qtwFac = 1.0;
  268. Real qtwStep0 = DegreesToRadians( 5.0 );
  269. Real qtwStepFinal = DegreesToRadians( 0.5 );
  270. Real maxrad = -1.0;
  271. Real r2sum=0.0;
  272. // Real RJ = 8.31441;     // in J/K/mol, Gas Constant, Atkins Phys.Chem., 2/e
  273. // Real Rcal = 1.9871917; // in cal/K/mol, Gas Constant, RJ/4.184
  274. // Real T0K = 273.15;        // 0 degrees Celsius, in K
  275. Real RTreduc = 1.0;
  276. // Real spacing = 0.0;// now part of the GridMapSetInfo structure
  277. Real RT0 = 616.0;
  278. Real RTFac = 0.95;
  279. Real torsdoffac = 0.3113;
  280. Real torsFreeEnergy = 0.0;
  281. Real torFac = 1.0;
  282. Real torStep0 = 5.0;
  283. Real torStepFinal = 5.0;
  284. Real trnFac = 1.0;
  285. Real trnStep0 = 0.2;
  286. Real trnStepFinal = 0.2;
  287. Real WallEnergy = 1.0e8; /* Energy barrier beyond walls of gridmaps. */
  288. //  The GA Stuff
  289. Real m_rate = 0.02;
  290. Real c_rate = 0.80;
  291. Real alpha = 0;
  292. Real beta = 1;
  293. Real search_freq = 0.06;
  294. Real rho = 1.0;
  295. Real lb_rho = 0.01;
  296. Real *rho_ptr = NULL;
  297. Real *lb_rho_ptr = NULL;
  298. Real unbound_internal_FE = 0.0;
  299. Real unbound_ext_internal_FE = 0.0;
  300. Real unbound_ad_internal_FE = 0.0;
  301. Real unbound_internal_FE_saved = 0.0;
  302. Real emap_total = 0.;
  303. Real elec_total = 0.;
  304. Real charge_total = 0.;
  305. Real etot = 0.;
  306.  
  307. EnergyBreakdown eb;
  308.  
  309. initialise_energy_breakdown(&eb, 0, 0);
  310.  
  311. unsigned int outputEveryNgens = 100;
  312.  
  313. Boole B_atom_types_found = FALSE;
  314. Boole B_isGaussTorCon = FALSE;
  315. Boole B_constrain_dist;
  316. Boole B_either = FALSE;
  317. Boole B_calcIntElec = FALSE;
  318. Boole B_calcIntElec_saved = FALSE;
  319. Boole B_write_trj = FALSE;
  320. Boole B_watch = FALSE;
  321. Boole B_acconly = FALSE;
  322. Boole B_cluster_mode = FALSE;
  323. Boole B_havemap = FALSE;
  324. Boole B_havenbp = FALSE;
  325. Boole B_haveCharges;
  326. Boole B_linear_schedule = FALSE;
  327. Boole B_qtwReduc = FALSE;
  328. Boole B_selectmin = FALSE;
  329. Boole B_symmetry_flag = TRUE;
  330. Boole B_tempChange = TRUE;
  331. Boole B_torReduc = FALSE;
  332. Boole B_trnReduc = FALSE;
  333. Boole B_write_all_clusmem = FALSE;
  334. Boole B_ShowTorE = FALSE;
  335. Boole B_RandomTran0 = FALSE;
  336. Boole B_RandomQuat0 = FALSE;
  337. Boole B_RandomDihe0 = FALSE;
  338. Boole B_CalcTrnRF = FALSE;
  339. Boole B_CalcQtwRF = FALSE;
  340. Boole B_CalcTorRF = FALSE;
  341. Boole B_charMap = FALSE;
  342. Boole B_include_1_4_interactions = FALSE;  // This was the default behaviour in previous AutoDock versions (1 to 3).
  343. Boole B_found_move_keyword = FALSE;
  344. Boole B_found_ligand_types = FALSE;
  345. Boole B_found_elecmap = FALSE;
  346. Boole B_found_desolvmap = FALSE;
  347. Boole B_use_non_bond_cutoff = TRUE;
  348. Boole B_have_flexible_residues = FALSE;  // if the receptor has flexible residues, this will be set to TRUE
  349. Boole B_rms_atoms_ligand_only = TRUE;  // cluster on the ligand atoms only
  350. Boole B_reorient_random = FALSE; // if true, create a new random orientation before docking
  351. int atm1=0;
  352. int atm2=0;
  353. int a1=0;
  354. int a2=0;
  355. int atomC1;
  356. int atomC2;
  357. int dpf_keyword = -1;
  358. //int gridpts1[SPACE];  // now part of the GridMapSetInfo structure
  359. //int gridpts[SPACE];  // now part of the GridMapSetInfo structure
  360. int Htype = 0;
  361. int ncycles = -1;
  362. int iCon=0;
  363. int indcom = 0;
  364. int ligand_is_inhibitor = 1;
  365. int ltorfmt = 4;
  366. int nruns = 0;
  367. int nstepmax = -1;
  368. int naccmax = 0;
  369. int natom = 0;
  370. int nconf = 0;
  371. int ncycm1 = 1;
  372. int ndihed = 0;
  373. int nlig = 0;
  374. int nres = 0;
  375. int nmol = 0;
  376. int Nnb = 0;
  377. int nrejmax = 0;
  378. int ntor = 0;
  379. int ntor1 = 1;
  380. int ntor_ligand = 0;
  381. int ntorsdof = 0;
  382. int num_maps = 0;
  383. int num_atom_types = 0;
  384. int nval = 0;
  385. int outlev = -1;
  386. int retval = 0;
  387. int status = 0;
  388. int trj_end_cyc = 0;
  389. int trj_begin_cyc = 0;
  390. int trj_freq = 0;
  391. int xA = 12;
  392. int xB = 6;
  393. int xA_unbound = 12;
  394. int xB_unbound = 6;
  395. int I_tor;
  396. int I_torBarrier;
  397. int MaxRetries = 1000; /* Default maximum number of retries for ligand init. */
  398. int OutputEveryNTests = 1000;
  399. int NumLocalTests = 10;
  400. int maxTests = 10000;
  401. int parameter_library_found = 0;
  402. /* int beg; */
  403. /* int end; */
  404. /* int imol = 0; */
  405. int outside = FALSE;
  406. int atoms_outside = FALSE;
  407. // unsigned int min_evals_unbound =  250000;
  408. unsigned int max_evals_unbound = 1000000;
  409. int saved_sInit_ntor = 0;
  410. int confsampler_samples = 0;
  411.  
  412. unsigned short US_energy;
  413. unsigned short US_tD;
  414. unsigned short US_torBarrier = TORBARMAX;
  415. unsigned short US_min = TORBARMAX;
  416.  
  417. register int i = 0;
  418. register int j = 0;
  419. register int k = 0;
  420. //register int m = 0;
  421. register int xyz = 0;
  422. int j1 = 1;
  423.  
  424. State sInit;            /* Real qtn0[QUAT], tor0[MAX_TORS]; */
  425.  
  426. Quat q_reorient;
  427.  
  428. Molecule ligand;        /* ligand */
  429.  
  430. static Real F_A_from;
  431. static Real F_A_to;
  432. static Real F_lnH;
  433. static Real F_W;
  434. static Real F_hW;
  435. static FourByteLong clktck = 0;
  436.  
  437. static Real version_num = 4.00;
  438.  
  439. struct tms tms_jobStart;
  440. struct tms tms_gaStart;
  441. struct tms tms_gaEnd;
  442.  
  443. Clock  jobStart;
  444. Clock  gaStart;
  445. Clock  gaEnd;
  446.  
  447. time_t time_seed;
  448.  
  449. EnergyTables *ad_energy_tables;  // Holds vdw+Hb, desolvation & dielectric lookup tables
  450. EnergyTables *unbound_energy_tables;  // Use for computing unbound energy & conformation
  451.  
  452. Statistics map_stats;
  453.  
  454. //  The GA Stuff
  455. FourByteLong seed[2];
  456. unsigned int pop_size = 200;
  457. unsigned int num_generations = 0;  //  Don't terminate on the basis of number of generations
  458. unsigned int num_evals = 250000;
  459. unsigned int num_evals_unbound = num_evals;
  460. unsigned int max_its = 300;
  461. unsigned int max_succ = 4;
  462. unsigned int max_fail = 4;
  463. int window_size = 10;
  464. int low = 0;
  465. int high = 100;
  466. int elitism = 1;
  467.  
  468.  
  469. Selection_Mode s_mode = Proportional;
  470. Xover_Mode c_mode = TwoPt;  //  can be: OnePt, TwoPt, Uniform or Arithmetic
  471. Worst_Mode w_mode = AverageOfN;
  472. EvalMode e_mode = Normal_Eval;
  473. Global_Search *GlobalSearchMethod = NULL;
  474. Local_Search *LocalSearchMethod = NULL;
  475. //// Local_Search *UnboundLocalSearchMethod = NULL;
  476.  
  477. info = (GridMapSetInfo *) malloc( sizeof(GridMapSetInfo) );
  478. ad_energy_tables = (EnergyTables *) malloc( sizeof(EnergyTables) );
  479. unbound_energy_tables = (EnergyTables *) malloc( sizeof(EnergyTables) );
  480.  
  481. // Create a coordinate at the origin:
  482. Coord origin;
  483. origin.x = 0.;
  484. origin.y = 0.;
  485. origin.z = 0.;
  486.  
  487. //______________________________________________________________________________
  488. /*
  489. ** Get the time at the start of the run...
  490. */
  491.  
  492. jobStart = times( &tms_jobStart );
  493.  
  494.  
  495. //_____________________________________________________________________________
  496. /*
  497. ** Boinc initialization
  498. */
  499. #ifdef BOINC
  500.     int flags = 0;
  501.     int rc;
  502.     flags =
  503.       BOINC_DIAG_DUMPCALLSTACKENABLED |
  504.       BOINC_DIAG_HEAPCHECKENABLED |
  505.       BOINC_DIAG_REDIRECTSTDERR |
  506.       BOINC_DIAG_REDIRECTSTDOUT ;
  507.     boinc_init_diagnostics(flags);
  508.  
  509. #ifdef BOINCCOMPOUND
  510.     BOINC_OPTIONS options;
  511.     options.main_program = false;
  512.     options.check_heartbeat = false; // monitor does check heartbeat
  513.     options.handle_trickle_ups = false;
  514.     options.handle_trickle_downs = false;
  515.     options.handle_process_control = false;
  516.     options.send_status_msgs = true;// only the worker programs (i.e. model) sends status msgs
  517.     options.direct_process_action = true;// monitor handles suspend/quit, but app/model doesn't
  518.     // Initialisation of Boinc
  519.     rc =  boinc_init_options(options); //return 0 for success
  520.     if( rc ){
  521.       fprintf(stderr,"BOINC_ERROR: boinc_init_options() failed \n");
  522.       exit(rc);
  523.     }
  524.  
  525. #else
  526.     // All BOINC applications must initialize the BOINC interface:
  527.     rc = boinc_init();
  528.     if (rc){
  529.       fprintf(stderr, "BOINC_ERROR: boinc_init() failed.\n");
  530.       exit(rc);
  531.     }
  532. #endif
  533. #endif
  534.  
  535.  
  536. //______________________________________________________________________________
  537. /*
  538. ** Parse the arguments in the command line...
  539. */
  540.  
  541. if ( setflags(argc,argv) == -1) {
  542.     exit(-1);
  543. } /* END PROGRAM */
  544.  
  545.  
  546. //______________________________________________________________________________
  547. /*
  548. ** Initialize torsion arrays and constants.
  549. */
  550.  
  551. (void) strcpy( torfmt, "%*s\0" ); /* len(torfmt) is 4 chars */
  552.  
  553. for (j = 0;  j < MAX_ATOMS;  j++ ) {
  554.     type[j] = 0;
  555.     ignore_inter[j] = 0;
  556. }
  557.  
  558. for (i = 0; i  < MAX_TORS;  i++ ) {
  559.     for (j = 0;  j < MAX_ATOMS;  j++ ) {
  560.         tlist[i][j] = 0;
  561.     }
  562. }
  563.  
  564. for (i = 0; i  < MAX_TORS;  i++ ) {
  565.     B_isTorConstrained[i] = 0;
  566.     US_torProfile[i][0] = 0;
  567.     N_con[i] = 0;
  568. }
  569.  
  570. initialiseState( &sInit );
  571. initialiseState( &(ligand.S) );
  572.  
  573. initialiseQuat( &q_reorient );
  574.  
  575. F_W      =  360.0 / NTORDIVS;
  576. F_hW     =  F_W  / 2.0;
  577. F_A_from = -360.0 + F_hW;
  578. F_A_to   =  360.0 + F_hW;
  579.  
  580. for (k = 0; k < MAX_RUNS; k++) {
  581.     for (i = 0; i  < MAX_TORS;  i++ ) {
  582.         sHist[k].tor[i] = 0.0;
  583.     }
  584. }
  585.  
  586. for (i = 0; i < MAX_TORS;  i++ ) {
  587.     if ( (ltorfmt += 4) > LINE_LEN ) {
  588.         prStr( error_message, "%s:  ERROR: MAX_TORS = %d torsions declared in \"constants.h\";\n\t LINE_LEN = %d, Therefore you must change \"LINE_LEN\" to exceed %d...\n", programname, MAX_TORS, LINE_LEN, 4+4*MAX_TORS );
  589.         stop( error_message );
  590.         exit( -1 );
  591.     } else {
  592.         (void) strcat( torfmt, " %lf\0" );  /* add on 4 chars  for each new torsion... */
  593.     }
  594. } /* len(torfmt) is 4+4*MAX_TORS chars */
  595.  
  596. for (j = 0; j < MAX_NONBONDS; j++) {
  597.     nonbondlist[j].a1 = nonbondlist[j].a2 = 0;
  598. }
  599.  
  600. for (j = 0; j < MAX_RUNS; j++) {
  601.     // isort[j] = j;
  602.     econf[j] = 0.0;
  603. }
  604.  
  605. B_constrain_dist = B_haveCharges = FALSE;
  606. ntor1 = ntor = atomC1 = atomC2 = 0;
  607. sqlower = squpper = 0.0;
  608.  
  609. timeSeedIsSet[0] = 'F';
  610. timeSeedIsSet[1] = 'F';
  611.  
  612. if (clktck == 0) {        /* fetch clock ticks per second first time */
  613.     if ( (clktck = sysconf(_SC_CLK_TCK)) < (FourByteLong)0L) {
  614.         stop("\"sysconf(_SC_CLK_TCK)\" command failed in \"main.c\"\n");
  615.         exit( -1 );
  616.     } else {
  617.         idct = (Real)1.0 / (Real)clktck;
  618.         if (debug) {
  619.             pr(logFile, "N.B. debug is on and set to %d\n\n", debug);
  620.             pr(logFile, "\n\nFYI:  Number of clock ticks per second = %d\n", (int)clktck);
  621.             pr(logFile, "FYI:  Elapsed time per clock tick = %.3e milli-seconds\n\n\n\n", idct * 1000. );
  622.         }
  623.     }
  624. }
  625.  
  626. (void) strcpy(FN_rms_ref_crds,"unspecified filename\0");
  627.  
  628.  
  629. //______________________________________________________________________________
  630. /*
  631. ** log(x): compute the natural (base e) logarithm of x,
  632. */
  633.  
  634. F_lnH = ((Real)log(0.5));
  635.  
  636. //______________________________________________________________________________
  637. /*
  638. ** Determine output level before we ouput anything.  
  639. ** We must parse the entire DPF -- silently -- for any outlev settings.
  640. */
  641.  
  642. while( fgets(line, LINE_LEN, parFile) != NULL ) { /* PARSING-DPF parFile */
  643.     dpf_keyword = parse_dpf_line( line );
  644.  
  645.     switch( dpf_keyword ) {
  646.     case DPF_OUTLEV:
  647.         /*
  648.         **  outlev
  649.         **  Output level,
  650.         */
  651.         retval = sscanf( line, "%*s %d", &outlev );
  652.         switch ( outlev ) {
  653.         case -1:
  654.             outputEveryNgens = (unsigned int) OUTLEV0_GENS;
  655.             break;
  656.         case 0:
  657.             outputEveryNgens = (unsigned int) OUTLEV0_GENS;
  658.             break;
  659.         case 1:
  660.             outputEveryNgens = (unsigned int) OUTLEV1_GENS;
  661.             break;
  662.         case 2:
  663.         default:
  664.             outputEveryNgens = (unsigned int) OUTLEV2_GENS;
  665.             break;
  666.         }
  667.         break;
  668.  
  669.     case DPF_FLEXRES:
  670.         // The DPF specifies a flexible residues file
  671.         // -- set a flag
  672.         // -- get the filename
  673.         B_have_flexible_residues = TRUE;
  674.         (void) sscanf( line, "%*s %s", FN_flexres );
  675.         break;
  676.  
  677.     default:
  678.         break;
  679.     } // switch( dpf_keyword )
  680. } // while
  681.  
  682. // Rewind DPF, so we can resume normal parsing
  683. (void) rewind( parFile );
  684.  
  685. //______________________________________________________________________________
  686. /*
  687. ** Output banner...
  688. */
  689.  
  690. banner( version_num );
  691.  
  692. (void) fprintf(logFile, "                           $Revision: 1.69 $\n\n");
  693. (void) fprintf(logFile, "                   Compiled on %s at %s\n\n\n", __DATE__, __TIME__);
  694.  
  695.  
  696. //______________________________________________________________________________
  697. /*
  698. ** Print the time and date when the file was created...
  699. */
  700.  
  701. pr( logFile, "This file was created at:\t\t\t" );
  702. printdate( logFile, 1 );
  703.  
  704. (void) strcpy(hostnm, "unknown host\0");
  705.  
  706. if (gethostname( hostnm, MAX_CHARS ) == 0) {
  707.     pr( logFile, "                   using:\t\t\t\"%s\"\n", hostnm );
  708. }
  709.  
  710. pr( logFile, "\nNOTE: \"rus\" stands for:\n\n      r = Real, wall-clock or elapsed time;\n      u = User or cpu-usage time;\n      s = System time\n\nAll timings are in seconds, unless otherwise stated.\n\n\n" );
  711.  
  712. //______________________________________________________________________________
  713.  
  714. (void) fprintf(logFile, "\n      ________________________________________________________________\n\n");
  715. (void) fprintf(logFile, "                   SETTING UP DEFAULT PARAMETER LIBRARY\n");
  716. (void) fprintf(logFile, "      ________________________________________________________________\n\n\n");
  717.  
  718. //______________________________________________________________________________
  719. //
  720. // Read in default parameters
  721. //
  722. setup_parameter_library(outlev);
  723.  
  724. //
  725. // Compute the look-up table for the distance-dependent dielectric function
  726. //
  727. (void) fprintf(logFile, "\n\nPreparing Energy Tables for Bound Calculation:\n\n");
  728. setup_distdepdiel(outlev, ad_energy_tables);
  729. (void) fprintf(logFile, "Preparing Energy Tables for Unbound Calculation:\n\n");
  730. setup_distdepdiel(outlev, unbound_energy_tables);
  731.  
  732. //______________________________________________________________________________
  733.  
  734. (void) fprintf(logFile, "\n      ___________________________________________________\n\n");
  735. (void) fprintf(logFile,   "             PARSING INPUT DOCKING PARAMETER FILE\n");
  736. (void) fprintf(logFile,   "      ___________________________________________________\n\n");
  737.  
  738. //______________________________________________________________________________
  739. /*
  740. ** (Note: "dock_param_fn" set in "setflags.c"...)
  741. */
  742. pr( logFile, "Docking parameter file (DPF) used for this docking:\t\t%s\n\n", dock_param_fn );
  743.  
  744. //______________________________________________________________________________
  745. /*
  746. ** Start reading in the DPF parameter/run-control file,
  747. */
  748.  
  749. while( fgets(line, LINE_LEN, parFile) != NULL ) { /* PARSING-DPF parFile */
  750.     // "line" is a string containing the current line of the input DPF.
  751.  
  752.     dpf_keyword = parse_dpf_line( line );
  753.  
  754.     switch( dpf_keyword ) {
  755.         case -1:
  756.             pr( logFile, "DPF> %s", line );
  757.             prStr( error_message,"%s: WARNING: Unrecognized keyword in docking parameter file.\n", programname );
  758.             pr_2x( logFile, stderr, error_message );
  759.             continue;
  760.             /* break; */
  761.  
  762.         case DPF_NULL:
  763.         case DPF_COMMENT:
  764.             pr( logFile, "DPF> %s", line );
  765.             (void) fflush(logFile);
  766.             break;
  767.  
  768.         default:
  769.             pr( logFile, "\n\nDPF> %s\n", line );
  770.             indcom = strindex( line, "#" );
  771.             if (indcom != -1) {
  772.                 line[ indcom ] = '\0'; /* Truncate "line" at the comment */
  773.             }
  774.             (void) fflush(logFile);
  775.             break;
  776.     } /* switch */
  777.  
  778.     switch( dpf_keyword ) {
  779.  
  780. //______________________________________________________________________________
  781.  
  782.     case DPF_NULL:
  783.     case DPF_COMMENT:
  784.         break;
  785.  
  786. //______________________________________________________________________________
  787.  
  788.     case DPF_OUTLEV:
  789.         /*
  790.         **  outlev
  791.         **  Output level,
  792.         */
  793.         retval = sscanf( line, "%*s %d", &outlev );
  794.         switch ( outlev ) {
  795.         case -1:
  796.             pr( logFile, "Output Level = -1.  ONLY STATE VARIABLES OUTPUT, NO COORDINATES.\n" );
  797.             outputEveryNgens = (unsigned int) OUTLEV0_GENS;
  798.             break;
  799.         case 0:
  800.             pr( logFile, "Output Level = 0.\n" );
  801.             outputEveryNgens = (unsigned int) OUTLEV0_GENS;
  802.             break;
  803.         case 1:
  804.             pr( logFile, "Output Level = 1.  MINIMUM OUTPUT DURING DOCKING.\n" );
  805.             outputEveryNgens = (unsigned int) OUTLEV1_GENS;
  806.             break;
  807.         case 2:
  808.         default:
  809.             pr( logFile, "Output Level = 2.  FULL OUTPUT DURING DOCKING.\n" );
  810.             outputEveryNgens = (unsigned int) OUTLEV2_GENS;
  811.             break;
  812.         }
  813.         pr( logFile, "\n\tOutput every %u generations.\n", outputEveryNgens );
  814.         (void) fflush(logFile);
  815.         break;
  816.  
  817. /*____________________________________________________________________________*/
  818.  
  819.     case DPF_PARAMETER_LIBRARY:
  820.         /*
  821.         ** parameter_file AD4_parameters.dat
  822.         **  or
  823.         ** parameter_library AD4_parameters.dat
  824.         **
  825.         ** initial implementation based on hsearch was suggested by Mike Pique
  826.         */
  827.  
  828.         parameter_library_found = sscanf( line, "%*s %s", FN_parameter_library );
  829.         (void) fflush(logFile);
  830.  
  831.         read_parameter_library(FN_parameter_library, outlev);
  832.  
  833.         break;
  834.  
  835. /*____________________________________________________________________________*/
  836.  
  837.     case DPF_INCLUDE_1_4_INTERACTIONS:
  838.         /*
  839.          * include_1_4_interactions 0.5
  840.          *
  841.          * Set the Boolean variable, B_include_1_4_interactions, to TRUE.
  842.          *
  843.          * NOTE:  You must use this command _before_ the "move ligand.pdbqt"
  844.          *        command, since "include_1_4_interactions" affects how the Ligand
  845.          *        PDBQT specified by the "move" command will be interpreted.
  846.          */
  847.         if (B_found_move_keyword == TRUE) {
  848.             // If we have found the move keyword already, warn the user
  849.             // that this command ("include_1_4_interactions 0.5") should have
  850.             // been given before this!
  851.             pr(logFile, "\nWARNING:  This command will be ignored.\n\nYou must put this command _before_ the \"move ligand.pdbqt\" command, since this command affects how the PDBQT file will be interpreted.\n\n");
  852.         }
  853.         (void) sscanf( line, "%*s " FDFMT, &scale_1_4 );
  854.         B_include_1_4_interactions = TRUE;
  855.         print_1_4_message(logFile, B_include_1_4_interactions, scale_1_4);
  856.         break;
  857.  
  858. //______________________________________________________________________________
  859.  
  860.     case DPF_INTELEC:
  861.         /*
  862.         **  intelec
  863.         **  Calculate internal electrostatic energies...
  864.         */
  865.         B_calcIntElec = TRUE;
  866.         if (outlev >= 0) {
  867.             pr( logFile, "Electrostatic energies will be calculated for all non-bonds between moving atoms.\n\n");
  868.         }
  869.         retval = sscanf( line, "%*s " FDFMT, &AD3_FE_coeff_estat );
  870.         if (retval == 1) {
  871.             if (outlev >= 0) {
  872.                 pr(logFile, "NOTE!  Internal electrostatics will NOT be scaled by the factor specified by this command,  %.4f -- the coefficient set by this command is ignored in AutoDock 4;\n", AD3_FE_coeff_estat);
  873.                 pr(logFile, "       the coefficient that will actually be used should be set in the parameter library file.\n");
  874.                 pr(logFile, "       The coefficient for the electrostatic energy term is %.4f", AD4.coeff_estat);
  875.                 if (parameter_library_found == 1) {
  876.                     pr( logFile, " as specified in parameter library \"%s\".\n", FN_parameter_library );
  877.                 } else {
  878.                     pr( logFile, ", the factory default value.\n");
  879.                 }
  880.             }
  881.         } else {
  882.             AD3_FE_coeff_estat = 1.0;
  883.         }
  884.  
  885.         (void) fflush(logFile);
  886.         break;
  887.  
  888. //______________________________________________________________________________
  889.  
  890.     case DPF_SEED:
  891.         /*
  892.         **  seed
  893.         **  Set the random-number gerator's seed value,
  894.         */
  895.         retval = (int)sscanf( line, "%*s %s %s", param[0], param[1]);
  896.         timeSeedIsSet[0] = 'F';
  897.         timeSeedIsSet[1] = 'F';
  898.         pr(logFile, "%d seed%c found.\n", retval, ((retval==1)? ' ' : 's'));
  899.         for (j=0; j<retval; j++) {
  900.             for (i=0; i<(int)strlen(param[j]); i++) {
  901.                 param[j][i] = (char)tolower( (int)param[j][i] );
  902.             }
  903.             pr(logFile, "argument \"%s\" found\n", param[j]);
  904.         }
  905.         if ((retval==2) || (retval==1)) {
  906.             for (i=0; i<retval ; i++ ) {
  907.                 if (equal(param[i], "tim", 3)) {
  908.                     timeSeedIsSet[i] = 'T';
  909.                     seed[i] = (FourByteLong)time( &time_seed );
  910.                     seed_random(seed[i]);
  911.                     pr(logFile,"Random number generator was seeded with the current time, value = %ld\n",seed[i]);
  912.                 } else if (equal(param[i], "pid", 3)) {
  913.                     timeSeedIsSet[i] = 'F';
  914.                     seed[i] = getpid();
  915.                     seed_random(seed[i]);
  916.                     pr(logFile,"Random number generator was seeded with the process ID, value   = %ld\n",seed[i]);
  917.                 } else {
  918.                     timeSeedIsSet[i] = 'F';
  919.                     seed[i] = atol(param[i]);
  920.                     seed_random(seed[i]);
  921.                     pr(logFile,"Random number generator was seeded with the user-specified value  %ld\n",seed[i]);
  922.                 }
  923.             }/*i*/
  924.             pr(logFile, "\n");
  925.             if (retval==2) {
  926.                 setall(seed[0], seed[1]);
  927.                 initgn(-1);  // Reinitializes the state of the current random number generator
  928.                 pr(logFile,"Portable random number generator was seeded with the user-specified values  %ld, %ld\n", seed[0], seed[1]);
  929.             }
  930.         } else {
  931.             pr(logFile, "Error encountered reading seeds!\n");
  932.         }
  933.  
  934.         (void) fflush(logFile);
  935.         break;
  936.  
  937. /*____________________________________________________________________________*/
  938.  
  939.     case DPF_LIGAND_TYPES:
  940.         /*
  941.          *  Read in the ligand atom type names, e.g.
  942.          *
  943.          *  ligand_types C HD OA P               # ligand atom type names
  944.          *
  945.          *  The order of the arguments is the index that will
  946.          *  be used for look up in the grid maps, "map_index".
  947.          */
  948.        
  949.         //  Use the function "parsetypes" to read in the atom types;
  950.         //  
  951.         //  The array "ligand_atom_type_ptrs" is returned, having been filled with pointers
  952.         //  to the beginning of each "atom type word" (not atom type characters);
  953.         //  In AutoDock 4, an atom type can be either 1 or 2 characters long.
  954.         //
  955.         //  Note: "atm_typ_str" (in AD3) served a similar role to "atom_type_name" (now used in AD4).
  956.         num_atom_types = parsetypes(line, ligand_atom_type_ptrs, MAX_ATOM_TYPES);
  957.  
  958.         B_found_ligand_types = TRUE;
  959.  
  960.         // This is not necessary if we increment num_maps one-at-a-time as we read each atom map in
  961.         // num_maps += num_atom_types;
  962.         info->num_atom_types = num_atom_types;
  963.  
  964.         for (i=0; i<num_atom_types; i++) {
  965.             strcpy(info->atom_type_name[i], ligand_atom_type_ptrs[i]);
  966. #ifdef DEBUG
  967.             (void) fprintf(logFile, "%d %s ->%s\n",i, ligand_atom_type_ptrs[i], info->atom_type_name[i]);
  968. #endif
  969.         }
  970.  
  971.         if (num_atom_types > 0) {
  972.             B_atom_types_found = TRUE;
  973.         } else {
  974.             prStr( error_message, "%s:  ERROR! No atom types have been found; we cannot continue without this information!\n\n", programname );
  975.             pr_2x( logFile, stderr, error_message );
  976.             prStr( error_message, "%s:  ERROR! Are you trying to use an AutoDock 3 DPF with AutoDock 4?\n\n", programname );
  977.             pr_2x( logFile, stderr, error_message );
  978.             exit(-1);
  979.         }
  980.  
  981.         if (debug > 0) {
  982.             for (i=0; i<num_atom_types; i++) {
  983.                 (void) fprintf(logFile, "info->atom_type_name[%d] = %s\n", i, info->atom_type_name[i] );
  984.             }
  985.         }
  986.  
  987.         // For all ligand atom types... set up the map_index
  988.         // "ligand_types"
  989.         for (i=0; i<num_atom_types; i++) {
  990.             foundParameter = apm_find(info->atom_type_name[i]);
  991.             if (foundParameter != NULL ) {
  992.                 // Not NULL means we have found this atom type's parameters.
  993.                 // Set the ParameterEntry's "map_index" member to the
  994.                 // 0-based index it had in the list of ligand types supplied in the DPF "types" line:
  995.                 foundParameter->map_index = i;
  996.                 parameterArray[i] = *(foundParameter);
  997.                 if (outlev > 0) {
  998.                     (void) fprintf( logFile, "Parameters found for ligand type \"%s\" (grid map index = %d, weighted well depth, epsilon = %6.4f)", foundParameter->autogrid_type, foundParameter->map_index, foundParameter->epsij );
  999.                     if (parameter_library_found == 1) {
  1000.                         pr( logFile, " in parameter library \"%s\".\n", FN_parameter_library );
  1001.                     } else {
  1002.                         pr( logFile, "\n");
  1003.                     }
  1004.                 }
  1005.             } else {
  1006.                 // We could not find this parameter -- return error here
  1007.                 prStr( error_message,"%s: ERROR:  Unknown ligand atom type \"%s\"; add parameters for it to the parameter library first!\n", programname, info->atom_type_name[i]);
  1008.                 pr_2x( logFile, stderr, error_message );
  1009.                 if (parameter_library_found == 1) {
  1010.                     prStr( error_message,"%s:         Edit the parameter library file \"%s\" and try again.\n", programname, FN_parameter_library );
  1011.                     pr_2x( logFile, stderr, error_message );
  1012.                 }
  1013.                 exit(-1);
  1014.             } // if / else apm_find
  1015.         } // for i
  1016.         pr( logFile, "\n\n");
  1017.  
  1018.         (void) fflush( logFile);
  1019.  
  1020.         // Calculate the internal energy table
  1021.  
  1022.         // loop over atom types, i, from 1 to number of atom types
  1023.         for (i=0; i<num_atom_types; i++) {
  1024.  
  1025.             //  Find internal energy parameters, i.e.  epsilon and r-equilibrium values...
  1026.             //  Lennard-Jones and Hydrogen Bond Potentials
  1027.  
  1028.             Ri = parameterArray[i].Rij;
  1029.             epsi = parameterArray[i].epsij;
  1030.             Ri_hb = parameterArray[i].Rij_hb;
  1031.             epsi_hb = parameterArray[i].epsij_hb;
  1032.             hbondi = parameterArray[i].hbond;
  1033.  
  1034.             // loop over atom types, j, from i to number of atom types
  1035.             for (j=i; j<num_atom_types; j++) {
  1036.                
  1037.                 //  Find internal energy parameters, i.e.  epsilon and r-equilibrium values...
  1038.                 //  Lennard-Jones and Hydrogen Bond Potentials
  1039.  
  1040.                 Rj = parameterArray[j].Rij;
  1041.                 epsj = parameterArray[j].epsij;
  1042.                 Rj_hb = parameterArray[j].Rij_hb;
  1043.                 epsj_hb = parameterArray[j].epsij_hb;
  1044.                 hbondj = parameterArray[j].hbond;
  1045.  
  1046.                 // we need to determine the correct xA and xB exponents
  1047.                 xA = 12; // for both LJ, 12-6 and HB, 12-10, xA is 12
  1048.                 xB =  6; // assume we have LJ, 12-6
  1049.  
  1050.                 if ( ((hbondi == DS) || (hbondi == D1)) && ((hbondj == AS) || (hbondj == A1) || (hbondj == A2)) ) {
  1051.                     // i is a donor and j is an acceptor.
  1052.                     // i is a hydrogen, j is a heteroatom
  1053.                     // we need to calculate the arithmetic mean of Ri_hb and Rj_hb  // not in this Universe...  :-(
  1054.                     //Rij = arithmetic_mean(Ri_hb, Rj_hb);// not in this Universe...  :-(
  1055.                     Rij = Rj_hb;
  1056.                     // we need to calculate the geometric mean of epsi_hb and epsj_hb  // not in this Universe...  :-(
  1057.                     //epsij = geometric_mean(epsi_hb, epsj_hb);// not in this Universe...  :-(
  1058.                     epsij = epsj_hb;
  1059.                     xB = 10;
  1060.                 } else if ( ((hbondi == AS) || (hbondi == A1) || (hbondi == A2)) && ((hbondj == DS) || (hbondj == D1))) {
  1061.                     // i is an acceptor and j is a donor.
  1062.                     // i is a heteroatom, j is a hydrogen
  1063.                     // we need to calculate the arithmetic mean of Ri_hb and Rj_hb// not in this Universe...  :-(
  1064.                     //Rij = arithmetic_mean(Ri_hb, Rj_hb);// not in this Universe...  :-(
  1065.                     Rij = Ri_hb;
  1066.                     // we need to calculate the geometric mean of epsi_hb and epsj_hb// not in this Universe...  :-(
  1067.                     //epsij = geometric_mean(epsi_hb, epsj_hb);// not in this Universe...  :-(
  1068.                     epsij = epsi_hb;
  1069.                     xB = 10;
  1070.                 } else {
  1071.                     // we need to calculate the arithmetic mean of Ri and Rj
  1072.                     Rij = arithmetic_mean(Ri, Rj);
  1073.                     // we need to calculate the geometric mean of epsi and epsj
  1074.                     epsij = geometric_mean(epsi, epsj);
  1075.                 }
  1076.  
  1077.                 /* Check that the Rij is reasonable */
  1078.                 if ((Rij < RIJ_MIN) || (Rij > RIJ_MAX)) {
  1079.                     (void) fprintf( logFile,
  1080.                     "WARNING: pairwise distance, Rij, %.2f, is not a very reasonable value for the equilibrium separation of two atoms! (%.2f Angstroms <= Rij <= %.2f Angstroms)\n\n", Rij, RIJ_MIN, RIJ_MAX);
  1081.                     (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
  1082.                     /* gmm commented out for dave goodsell, mutable atoms
  1083.                      * exit(-1); */
  1084.                 }
  1085.                 /* Check that the epsij is reasonable */
  1086.                 if ((epsij < EPSIJ_MIN) || (epsij > EPSIJ_MAX)) {
  1087.                     (void) fprintf( logFile,
  1088.                     "WARNING: well-depth, epsilon_ij, %.2f, is not a very reasonable value for the equilibrium potential energy of two atoms! (%.2f kcal/mol <= epsilon_ij <= %.2f kcal/mol)\n\n", epsij, EPSIJ_MIN, EPSIJ_MAX);
  1089.                     (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
  1090.                     /* gmm commented out for dave goodsell, mutable atoms
  1091.                      * exit(-1); */
  1092.                 }
  1093.                 /* Defend against division by zero... */
  1094.                 if (xA != xB) {
  1095.                     cA = (tmpconst = epsij / (Real)(xA - xB)) * pow( (double)Rij, (double)xA ) * (Real)xB;
  1096.                     cB = tmpconst * pow( (double)Rij, (double)xB ) * (Real)xA;
  1097.                     pr(logFile, "\nCalculating internal non-bonded interaction energies for docking calculation;\n");
  1098.                     intnbtable( &B_havenbp, a1, a2, info, cA, cB, xA, xB, AD4.coeff_desolv, sigma, ad_energy_tables, BOUND_CALCULATION );
  1099.                     pr(logFile, "\nCalculating internal non-bonded interaction energies for unbound conformation calculation;\n");
  1100.                     intnbtable( &B_havenbp, a1, a2, info, cA_unbound, cB_unbound, xA_unbound, xB_unbound, AD4.coeff_desolv, sigma, unbound_energy_tables, UNBOUND_CALCULATION );
  1101.                     // Increment the atom type numbers, a1 and a2, for the internal non-bond table
  1102.                     a2++;
  1103.                     if (a2 >= info->num_atom_types) {
  1104.                         a1++;
  1105.                         a2 = a1;
  1106.                     }
  1107.                    
  1108.                 } else {
  1109.                     pr(logFile,"WARNING: Exponents must be different, to avoid division by zero!\n\tAborting...\n");
  1110.                     exit(-1);
  1111.                 }
  1112.                 (void) fflush(logFile);
  1113.  
  1114.             } // for j
  1115.         } // for i
  1116.         break;
  1117.  
  1118. //______________________________________________________________________________
  1119.  
  1120.     case DPF_FLD:
  1121.         /*
  1122.         ** fld
  1123.         ** GRID_DATA_FILE
  1124.         ** Read the (AVS-format) grid data file, .fld
  1125.         */
  1126.         // TO DO: add outlev
  1127.         readfield( info, line, jobStart, tms_jobStart );
  1128.  
  1129.         /*
  1130.         // Dynamically allocate memory for the maps
  1131.         map = NewGridMapSet(info);
  1132.            
  1133.         if (map == NULL) {
  1134.             prStr(error_message, "%s:  Sorry, there is not enough memory to store the grid maps.  Please use smaller maps and/or fewer atom types.\n", programname);
  1135.             stop(error_message);
  1136.             exit(1);
  1137.         }
  1138.         // Initialise the maps
  1139.         for (i=0; i<num_map_values; i++) {
  1140.             map[i] = 0.0L;
  1141.         }
  1142.         */
  1143.         (void) fflush(logFile);
  1144.         break;
  1145.  
  1146. //______________________________________________________________________________
  1147.  
  1148.     case DPF_MAP:
  1149.         /*
  1150.         ** map
  1151.         ** ATOMIC AFFINITY, ELECTROSTATIC POTENTIAL OR DESOLVATION ENERGY GRID MAP
  1152.         ** Read in active site grid map...
  1153.         */
  1154.         B_charMap = FALSE;
  1155.         if (B_atom_types_found == TRUE) {
  1156.             // Read in the AutoGrid atomic affinity map
  1157.             // map_index could be incremented here if we had the atom_type stored in each map...
  1158.             map_stats = readmap( line, outlev, jobStart, tms_jobStart, B_charMap, &B_havemap, num_maps, info, map, 'a' );
  1159.             pr(logFile, "Min= %.3lf Mean= %.3lf Max= %.3lf\n\n",
  1160.                     map_stats.minimum, map_stats.mean, map_stats.maximum);
  1161.             num_maps++;
  1162.  
  1163.         } else {
  1164.             prStr( error_message, "%s:  ERROR! No atom types have been found; we cannot continue without this information!\n\n", programname );
  1165.             pr_2x( logFile, stderr, error_message );
  1166.             prStr( error_message, "%s:  ERROR! Are you trying to use an AutoDock 3 DPF with AutoDock 4?\n\n", programname );
  1167.             pr_2x( logFile, stderr, error_message );
  1168.             exit(-1);
  1169.         }
  1170.         (void) fflush(logFile);
  1171.         break;
  1172.  
  1173. //______________________________________________________________________________
  1174.  
  1175.     case DPF_ELECMAP:
  1176.         /*
  1177.          *  elecmap file.e.map
  1178.          */
  1179.         map_stats = readmap( line, outlev, jobStart, tms_jobStart, B_charMap, &B_havemap, num_maps, info, map, 'e' );
  1180.         pr(logFile, "Min= %.3lf Mean= %.3lf Max= %.3lf\n\n",
  1181.                 map_stats.minimum, map_stats.mean, map_stats.maximum);
  1182.         ElecMap = num_maps;
  1183.         B_found_elecmap = TRUE;
  1184.         num_maps++;
  1185.         (void) fflush(logFile);
  1186.         break;
  1187.  
  1188. //______________________________________________________________________________
  1189.  
  1190.     case DPF_DESOLVMAP:
  1191.         /*
  1192.          *  desolvmap file.d.map
  1193.          */
  1194.         map_stats = readmap( line, outlev, jobStart, tms_jobStart, B_charMap, &B_havemap, num_maps, info, map, 'd' );
  1195.         pr(logFile, "Min= %.3lf Mean= %.3lf Max= %.3lf\n\n",
  1196.                 map_stats.minimum, map_stats.mean, map_stats.maximum);
  1197.         DesolvMap = num_maps;
  1198.         B_found_desolvmap = TRUE;
  1199.         num_maps++;
  1200.         (void) fflush(logFile);
  1201.         break;
  1202.  
  1203. //______________________________________________________________________________
  1204.  
  1205.     case DPF_CHARMAP:
  1206.         /*
  1207.         ** charmap
  1208.         ** ATOMIC AFFINITY, ELECTROSTATIC POTENTIAL OR DESOLVATION ENERGY GRID MAP
  1209.         ** Read in active site grid map...
  1210.         */
  1211.         B_charMap = TRUE;
  1212.         if (B_atom_types_found == TRUE) {
  1213.             // map_index could be incremented here if we had the atom_type stored in each map...
  1214.             map_stats = readmap( line, outlev, jobStart, tms_jobStart, B_charMap, &B_havemap, num_maps, info, map, 'c' );
  1215.             pr(logFile, "Min= %.3lf Mean= %.3lf Max= %.3lf\n\n",
  1216.                     map_stats.minimum, map_stats.mean, map_stats.maximum);
  1217.             num_maps++;
  1218.         } else {
  1219.             prStr( error_message, "%s:  ERROR! No atom types have been found; we cannot continue without this information!\n\n", programname );
  1220.             pr_2x( logFile, stderr, error_message );
  1221.             prStr( error_message, "%s:  ERROR! Are you trying to use an AutoDock 3 DPF with AutoDock 4?\n\n", programname );
  1222.             pr_2x( logFile, stderr, error_message );
  1223.             exit(-1);
  1224.         }
  1225.         (void) fflush(logFile);
  1226.         break;
  1227.  
  1228. //______________________________________________________________________________
  1229.  
  1230.     case DPF_MOVE:
  1231.         /*
  1232.         ** move ligand_file.pdbqt
  1233.         ** Specify the movable ligand,
  1234.         */
  1235.         //
  1236.         // Initialisations that must be done before reading in a new ligand...
  1237.         //
  1238.         nconf = 0;
  1239.         for (k = 0; k < MAX_RUNS; k++) {
  1240.             for (i = 0; i  < MAX_TORS;  i++ ) {
  1241.                 sHist[k].tor[i] = 0.0;
  1242.             }
  1243.         }
  1244.         for (j = 0; j < MAX_RUNS; j++) {
  1245.             // isort[j] = j;
  1246.             econf[j] = 0.0;
  1247.         }
  1248.         for (j = 0;  j < MAX_ATOMS;  j++ ) {
  1249.             type[j] = 0;
  1250.             ignore_inter[j] = 0;
  1251.         }
  1252.         for (i = 0; i  < MAX_TORS;  i++ ) {
  1253.             for (j = 0;  j < MAX_ATOMS;  j++ ) {
  1254.                 tlist[i][j] = 0;
  1255.             }
  1256.         }
  1257.         for (i = 0; i  < MAX_TORS;  i++ ) {
  1258.             B_isTorConstrained[i] = 0;
  1259.             US_torProfile[i][0] = 0;
  1260.             N_con[i] = 0;
  1261.         }
  1262.         initialiseState( &sInit );
  1263.         initialiseState( &(ligand.S) );
  1264.         initialiseQuat( &q_reorient );
  1265.         B_constrain_dist = B_haveCharges = FALSE;
  1266.         ntor1 = ntor = atomC1 = atomC2 = 0;
  1267.         sqlower = squpper = 0.0;
  1268.         strcpy( FN_pop_file, "");  // means don't print pop_file
  1269.         //
  1270.         // end of initialization
  1271.         //
  1272.  
  1273.         // this is the DPF_MOVE section...
  1274.         B_found_move_keyword = TRUE;
  1275.  
  1276.         print_1_4_message(logFile, B_include_1_4_interactions, scale_1_4);
  1277.  
  1278.         natom=0;
  1279.         ligand = readPDBQT( line,
  1280.                             num_atom_types,
  1281.                             &natom,
  1282.                             crdpdb, crdreo, charge, &B_haveCharges,
  1283.                             type, bond_index,
  1284.                             pdbaname, FN_ligand, FN_flexres, B_have_flexible_residues, atomstuff, Htype,
  1285.                             &B_constrain_dist, &atomC1, &atomC2,
  1286.                             &sqlower, &squpper,
  1287.                             &ntor1, &ntor, &ntor_ligand,
  1288.                             tlist, vt,
  1289.                             &Nnb, nonbondlist,
  1290.                             jobStart, tms_jobStart, hostnm, &ntorsdof, outlev,
  1291.                             ignore_inter,
  1292.                             B_include_1_4_interactions,
  1293.                             atoms, PDBQT_record );
  1294.  
  1295.         // pre-calculate some values we will need later in computing the desolvation energy
  1296.         //
  1297.         for (i=0; i<natom; i++) {
  1298.             abs_charge[i] = fabs(charge[i]);
  1299.             qsp_abs_charge[i] = qsolpar * abs_charge[i];
  1300.         }
  1301.         pr(logFile, "Number of atoms in ligand:  %d\n\n", true_ligand_atoms);
  1302.  
  1303.         pr(logFile, "Number of vibrational degrees of freedom of ligand:  %d\n\n\n", (3 * true_ligand_atoms) - 6 );
  1304.         pr( logFile, "Number of torsional degrees of freedom = %d\n", ntorsdof);
  1305.  
  1306.         torsFreeEnergy = (Real)ntorsdof * AD4.coeff_tors;
  1307.  
  1308.         pr( logFile, "Estimated loss of torsional free energy upon binding = %+.4f kcal/mol\n\n", torsFreeEnergy);
  1309.  
  1310.         for (i=0;i<natom;i++) {
  1311.             if (ignore_inter[i] == 1) {
  1312.                 pr(logFile, "Special Boundary Conditions:\n");
  1313.                 pr(logFile, "____________________________\n\n");
  1314.                 pr(logFile, "AutoDock will ignore the following atoms in the input PDBQT file \nin intermolecular energy calculations:\n");
  1315.                 pr(logFile, "\n(This is because these residue atoms are at the boundary between \nflexible and rigid, and since they cannot move \nthey will not affect the total energy.)\n\n");
  1316.                 break;
  1317.             }
  1318.         }
  1319.         for (i=0;i<natom;i++) {
  1320.             if (ignore_inter[i] == 1) {
  1321.                 pr(logFile, "Atom number %d:  %s\n", i+1, atomstuff[i] );
  1322.             }
  1323.         }
  1324.         pr(logFile, "\n");
  1325.  
  1326.         if (!B_haveCharges) {
  1327.             pr( logFile, "%s: WARNING! No partial atomic charges have been supplied yet.\n\n",programname);
  1328.         } else {
  1329.             if (Nnb > 0) {
  1330.             pr(logFile,"Calculating the product of the partial atomic charges, q1*q2, for all %d non-bonded pairs...\n\n", Nnb);
  1331.             pr(logFile," -- Scaled q1*q2 means multiplied by both  %.1lf (for conversion later on to kcal/mol)\n", (double)ELECSCALE);
  1332.             pr(logFile,"    and by the AD4 FF electrostatics coefficient, %.4lf\n\n", (double)AD4.coeff_estat);
  1333.             if (outlev >= 0) {
  1334.                 pr(logFile,"Non-bonded                           Scaled\n");
  1335.                 pr(logFile,"   Pair     Atom1-Atom2    q1*q2      q1*q2\n");
  1336.                 pr(logFile,"__________  ___________  _________  _________\n");
  1337.                 for (i = 0;  i < Nnb;  i++) {
  1338.                     atm1 = nonbondlist[i].a1;
  1339.                     atm2 = nonbondlist[i].a2;
  1340.                     int t1 = nonbondlist[i].t1;
  1341.                     int t2 = nonbondlist[i].t2;
  1342.                     nonbondlist[i].desolv =
  1343.                            ( parameterArray[t2].vol * (parameterArray[t1].solpar + qsp_abs_charge[atm1])
  1344.                            + parameterArray[t1].vol * (parameterArray[t2].solpar + qsp_abs_charge[atm2]) );
  1345.                     nonbondlist[i].q1q2 = charge[atm1] * charge[atm2];
  1346.                     pr(logFile,"   %4d     %5d-%-5d    %5.2f",i+1,atm1+1,atm2+1,nonbondlist[i].q1q2);
  1347.                     nonbondlist[i].q1q2 *= ELECSCALE * AD4.coeff_estat;
  1348.                     pr(logFile,"     %6.2f\n",nonbondlist[i].q1q2);
  1349.                 }
  1350.                 pr(logFile,"\n");
  1351.                 } // if outlev > 0
  1352.             } // if NNb > 0
  1353.         } // else
  1354.  
  1355.         sInit.ntor = ligand.S.ntor;
  1356.         ++nmol;
  1357.         ++nlig;
  1358.  
  1359.         (void) fflush(logFile);
  1360.         break;
  1361.  
  1362. /*____________________________________________________________________________*/
  1363.  
  1364.     case DPF_FLEXRES:
  1365.         /*
  1366.          * flexible_residues file.pdbqt
  1367.          */
  1368.         (void) fflush(logFile);
  1369.         pr(logFile, "\nThe flexible residues will be read in from \"%s\".\n", FN_flexres);
  1370.         break;
  1371.  
  1372.  
  1373. #ifdef USING_COLINY
  1374. /*____________________________________________________________________________*/
  1375.  
  1376.     case DPF_COLINY:
  1377.     {
  1378.         //ostdiostream fstr(logFile);
  1379.         //ostdiostream fstr(logFile->_file);
  1380.         //CommonIO::set_streams(&fstr,&fstr,&cin);
  1381.  
  1382.         struct tms tms_colinyStart;
  1383.         struct tms tms_colinyEnd;
  1384.  
  1385.         Clock  colinyStart;
  1386.         Clock  colinyEnd;
  1387.  
  1388.         int coliny_seed;
  1389.         char algname[64];
  1390.         char nruns_str[64];
  1391.         (void) sscanf(line, "%*s %s %d", algname, &nruns);
  1392.         (void) sscanf(line, "%*s %s %s", algname, nruns_str);
  1393.  
  1394.         if (strcmp(algname,"help")==0) {
  1395.             std::vector<double> initvec;
  1396.             coliny_init(algname, "");
  1397.             prStr(error_message, "%s:  ERROR:  no optimizer type specified.", programname);
  1398.             stop(error_message);
  1399.             exit(-1);
  1400.         }
  1401.         else if (strcmp(nruns_str,"help")==0) {
  1402.             std::vector<double> initvec;
  1403.             coliny_init(algname, nruns_str);
  1404.             prStr(error_message, "%s:  ERROR:  no optimizer type specified.", programname);
  1405.             stop(error_message);
  1406.             exit(-1);
  1407.         }
  1408.  
  1409.         if (!command_mode) {
  1410.             if (nruns>MAX_RUNS) {
  1411.                 prStr(error_message, "%s:  ERROR:  %d runs requested, but only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", programname, nruns, MAX_RUNS);
  1412.                 stop(error_message);
  1413.                 exit(-1);
  1414.             } else if (!B_found_elecmap) {
  1415.                 prStr(error_message, "%s:  ERROR:  no \"elecmap\" command has been specified!\n", programname);
  1416.                 stop(error_message);
  1417.                 exit(-1);
  1418.             } else if (!B_found_desolvmap) {
  1419.                 prStr(error_message, "%s:  ERROR:  no \"desolvmap\" command has been specified!\n", programname);
  1420.                 stop(error_message);
  1421.                 exit(-1);
  1422.             }
  1423.  
  1424.             evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom,
  1425.                             map, elec, emap, nonbondlist, ad_energy_tables,
  1426.                             Nnb, B_calcIntElec, B_isGaussTorCon, B_isTorConstrained, B_ShowTorE,
  1427.                             US_TorE, US_torProfile,
  1428.                             vt, tlist,
  1429.                             crdpdb, crdreo, sInit, ligand, ignore_inter, B_include_1_4_interactions, scale_1_4,
  1430.                             parameterArray, unbound_internal_FE, info,
  1431.                             B_use_non_bond_cutoff, B_have_flexible_residues);
  1432.  
  1433.             evaluate.compute_intermol_energy(TRUE);
  1434.  
  1435.             char domain[1024];
  1436.             // NOTE: Coliny enforces the bound constraints, but since the
  1437.             // torsion angles are periodic, we simply prevent the optimizer
  1438.             // from going too far.
  1439.             if (sInit.ntor > 0) {
  1440.                 sprintf(domain,"[%f,%f] [%f,%f] [%f,%f] [-1000.0,1000.0]^3 [-3.1416,3.1416] [-3.1416,3.1416]^%d",(double)info->lo[X], (double)info->hi[X], (double)info->lo[Y], (double)info->hi[Y], (double)info->lo[Z], (double)info->hi[Z], sInit.ntor);
  1441.                 //sprintf(domain,"[%f,%f] [%f,%f] [%f,%f] [-1.0,1.1]^3 [-6.2832,12.5664] [-6.2832,12.5664]^%d",(double)info->lo[X], (double)info->hi[X], (double)info->lo[Y], (double)info->hi[Y], (double)info->lo[Z], (double)info->hi[Z], sInit.ntor);
  1442.             } else {
  1443.                 sprintf(domain,"[%f,%f] [%f,%f] [%f,%f] [-1000.0,1000.0]^3 [-3.1416,3.1416]",(double)info->lo[X], (double)info->hi[X], (double)info->lo[Y], (double)info->hi[Y], (double)info->lo[Z], (double)info->hi[Z]);
  1444.             }
  1445.             pr(logFile, "Number of Coliny %s dockings = %d run%c\n", algname, nruns, (nruns>1)?'s':' ');
  1446.             pr(logFile, "Search Domain: %s\n", domain);
  1447.  
  1448.             //
  1449.             // COLINY-SPECIFIC LOGIC - BEGIN
  1450.             //
  1451.  
  1452.             try {
  1453.  
  1454.                 std::vector<double> initvec, finalpt;
  1455.                 // set up initial point
  1456.                 initvec.resize(7+sInit.ntor);
  1457.                 initvec[0] = sInit.T.x;
  1458.                 initvec[1] = sInit.T.y;
  1459.                 initvec[2] = sInit.T.z;
  1460.                 /*
  1461.                  * axis-angle (nx,ny,nz,ang) suffers from bias
  1462.                 initvec[3] = sInit.Q.nx;
  1463.                 initvec[4] = sInit.Q.ny;
  1464.                 initvec[5] = sInit.Q.nz;
  1465.                 initvec[6] = DegreesToRadians( sInit.Q.ang );
  1466.                 */
  1467.                 sInit.Q = convertRotToQuat( sInit.Q );
  1468.                 initvec[3] = sInit.Q.x;
  1469.                 initvec[4] = sInit.Q.y;
  1470.                 initvec[5] = sInit.Q.z;
  1471.                 initvec[6] = sInit.Q.w;
  1472.                 for (j=0; j < sInit.ntor ; j++) {
  1473.                   initvec[j+7] = DegreesToRadians(sInit.tor[j]);
  1474.                 }
  1475.                 coliny_init(algname, domain);
  1476.  
  1477.                 for (j=0; j<nruns; j++) {
  1478.                   fprintf( logFile, "\n\n\tBEGINNING Coliny %s DOCKING\n",algname);
  1479.                   pr(logFile, "\nDoing %s run:  %d/%d.\n", algname, j+1, nruns);
  1480.  
  1481.                   //coliny uses a single seed
  1482.                   coliny_seed = seed[0]+seed[1]+j;
  1483.                   pr(logFile, "Seed: %d [%ld+%ld+%d]\n", coliny_seed, seed[0], seed[1], j);
  1484.                   //pr(logFile, "Seeds:  %ld %ld\n", seed[0], seed[1]);
  1485.                   (void) fflush(logFile);
  1486.  
  1487.                   colinyStart = times(&tms_colinyStart);
  1488.  
  1489.                   finalpt.resize( initvec.size() );
  1490.                   int neval, niters;
  1491.                   coliny_minimize( coliny_seed, initvec, finalpt, neval, niters );
  1492.                   //fstr.flush();
  1493.  
  1494.                   make_state_from_rep( (double *)&(finalpt[0]), int(finalpt.size()), &sHist[nconf]);
  1495.  
  1496.                   pr(logFile, "\nTotal Num Evals: %d\n", neval);
  1497.                   printState(logFile, sHist[nconf], 2);
  1498.  
  1499.                   colinyEnd = times(&tms_colinyEnd);
  1500.                   pr(logFile, "Time taken for this %s run:\n", algname);
  1501.                   timesyshms(colinyEnd-colinyStart, &tms_colinyStart, &tms_colinyEnd);
  1502.                   pr(logFile, "\n");
  1503.  
  1504.                   pr(logFile, "Total number of Energy Evaluations: %d\n", (int)evaluate.evals() );
  1505.                   //pr(logFile, "Total number of Iterations:        %d\n", (int)niters);
  1506.  
  1507.                   pr(logFile, "\nFinal docked state:\n");
  1508.                   pr( logFile, UnderLine );
  1509.                   pr( logFile, "\n\n\tFINAL Coliny %s DOCKED STATE\n",algname );
  1510.                   pr( logFile,     "\t____________________________________\n\n\n" );
  1511.                   (void) fflush(logFile);
  1512.  
  1513.                   writePDBQT( j, seed, FN_ligand, dock_param_fn, lig_center,
  1514.                               sHist[nconf], ntor, &eintra, &einter, natom, atomstuff,
  1515.                               crd, emap, elec,
  1516.                               charge, abs_charge, qsp_abs_charge,
  1517.                               ligand_is_inhibitor,
  1518.                               torsFreeEnergy,
  1519.                               vt, tlist, crdpdb, nonbondlist,
  1520.                               ad_energy_tables,
  1521.                               type, Nnb, B_calcIntElec,
  1522.                               map,
  1523.                               outlev,
  1524.                               ignore_inter,
  1525.                               B_include_1_4_interactions, scale_1_4, parameterArray, unbound_internal_FE,
  1526.                               info, DOCKED, PDBQT_record, B_use_non_bond_cutoff, B_have_flexible_residues);
  1527.  
  1528.                   econf[nconf] = eintra + einter + torsFreeEnergy - unbound_internal_FE;
  1529.                   evaluate.reset();
  1530.                  
  1531.                   ++nconf;
  1532.  
  1533.                 } // Next run
  1534.                 if(write_stateFile){
  1535.                   fprintf(stateFile,"\t</runs>\n");
  1536.                   (void) fflush(stateFile);
  1537.                 }
  1538.                 (void) fflush(logFile);
  1539.             }
  1540.             catch (std::exception& err) {
  1541.               (void)fprintf(logFile, "Caught Exception: %s\n", err.what());
  1542.               exit(1);
  1543.             }
  1544.  
  1545.         } else {
  1546.             (void)fprintf(logFile, "NOTE: Command mode has been set, so optimization cannot be performed.\n\n");
  1547.         }
  1548.     }
  1549.     break;
  1550. #endif
  1551.  
  1552.  
  1553. //______________________________________________________________________________
  1554.  
  1555.     case DPF_ABOUT:
  1556.         /*
  1557.         **  about
  1558.         **  Rotation center for current ligand,
  1559.         */
  1560.         (void) sscanf( line, "%*s " FDFMT3, &lig_center[X], &lig_center[Y], &lig_center[Z]);
  1561.         pr( logFile, "Small molecule center of rotation =\t" );
  1562.         pr( logFile, "(%+.3f, %+.3f, %+.3f)\n\n", lig_center[X], lig_center[Y], lig_center[Z]);
  1563.         /*
  1564.         **  Center the ligand,
  1565.         */
  1566.         if ( nmol == 0 ) {
  1567.             pr( logFile, "Must specify a ligand PDBQT file, using the \"move\" command.\n");
  1568.         } else {
  1569.             if (outlev >= 0) {
  1570.                 pr( logFile, "Translating small molecule by:\t" );
  1571.                 pr( logFile, "(%+.3f, %+.3f, %+.3f)\n\n", -lig_center[X], -lig_center[Y], -lig_center[Z]);
  1572.             }
  1573.             /*
  1574.             **  Zero-out on central point...
  1575.             */
  1576.             maxrad = -1.0;
  1577.             for ( i=0; i<true_ligand_atoms; i++ ) { /*new, gmm, 6-23-1998*/
  1578.                 r2sum=0.0;
  1579.                 for (xyz = 0;  xyz < SPACE;  xyz++) {
  1580.                     c = crd[i][xyz] = (crdpdb[i][xyz] -= lig_center[xyz]);
  1581.                     r2sum += c*c;
  1582.                 } /* xyz */
  1583.                 maxrad = max(maxrad,sqrt(r2sum));
  1584.             } /* i */
  1585.             if (outlev >= 0) {
  1586.                 pr( logFile, "Furthest ligand atom from \"about\" center is %.3f Angstroms (maxrad).\n\n",maxrad);
  1587.             }
  1588.         }
  1589.         (void) fflush(logFile);
  1590.         break;
  1591.  
  1592. /*____________________________________________________________________________*/
  1593.  
  1594.     case DPF_REORIENT:
  1595.         /*
  1596.          *  reorient random
  1597.          *      # applies a random rotation to the input ligand
  1598.          * -OR-
  1599.          *  reorient standard
  1600.          *      # moves the ligand such that
  1601.          *      # the first three atoms lie parallel to the xy-plane, and
  1602.          *      # the first two atoms lie parallel to the x-axis
  1603.          * -OR-
  1604.          *  reorient <axis-x> <axis-y> <axis-z> <angle>
  1605.          *      # applies the specified rotation to the input ligand
  1606.          */
  1607.         (void) sscanf( line, "%*s %s", param[0] );
  1608.         { // Parse the reorient command
  1609.             for (i=0; i<6; i++) {
  1610.                 param[0][i] = (char)tolower( (int)param[0][i] );
  1611.             }
  1612.             if (equal(param[0],"random",6)) {
  1613.                 // reorient random
  1614.                 B_reorient_random = TRUE; // create a new random orientation before docking
  1615.  
  1616.                 create_random_orientation( &q_reorient );
  1617.  
  1618.             } else if (equal(param[0],"standard",8)) {
  1619.                 { // reorient standard
  1620.                 B_reorient_random = FALSE; // do not create a new random orientation before docking
  1621.  
  1622.                 if (true_ligand_atoms >= 3 ) {
  1623.                     // Move the ligand such that
  1624.                     // the first three atoms lie parallel to the xy-plane, and
  1625.                     // the first two atoms lie parallel to the x-axis
  1626.                     Vector vec_01,     // vector between ligand atoms 0 and 1
  1627.                            vec_12,     // vector between ligand atoms 1 and 2
  1628.                            vec_normal, // vector perpendicular to plane of vec_01 and vec_12
  1629.                            vec_x_axis, // vector along the X-axis
  1630.                            vec_z_axis, // vector along the Z-axis
  1631.                            vec_reorient_axis; // vector describing the axis about which to reorient
  1632.                     // Set the X and Z axes:
  1633.                     vec_x_axis[X] = 1.;
  1634.                     vec_x_axis[Y] = 0.;
  1635.                     vec_x_axis[Z] = 0.;
  1636.                     vec_z_axis[X] = 0.;
  1637.                     vec_z_axis[Y] = 0.;
  1638.                     vec_z_axis[Z] = 1.;
  1639.                     for (xyz = 0;  xyz < SPACE;  xyz++) {
  1640.                         vec_01[xyz] = (double)( crdpdb[1][xyz] - crdpdb[0][xyz] );
  1641.                         vec_12[xyz] = (double)( crdpdb[2][xyz] - crdpdb[1][xyz] );
  1642.                     }
  1643.                     // Compute the normal to vec_01 and vec_12
  1644.                     Cross_product( vec_normal, vec_01, vec_12 );
  1645.                     Print_vector( logFile, "vec_01", vec_01 );
  1646.                     Print_vector( logFile, "vec_12", vec_12 );
  1647.                     Print_vector( logFile, "vec_normal", vec_normal );
  1648.                     Print_vector( logFile, "vec_z_axis", vec_z_axis );
  1649.                     // Compute the angle between vec_01 and vec_12
  1650.                     double angle_012 = 0.;
  1651.                     angle_012 = Angle_between( vec_01, vec_12 );
  1652.                     pr( logFile, "Angle between vectors 01 and 12 = %.2f degrees\n", RadiansToDegrees( angle_012 ) );
  1653.                     if ( ( fabs(angle_012) < APPROX_ZERO ) || ( ( fabs(angle_012) > (PI - APPROX_ZERO) ) && ( fabs(angle_012) < (PI + APPROX_ZERO) ) ) ) {
  1654.                         // angle is too small or "too linear" to align the molecule into the xy-plane
  1655.                         pr( logFile, "%s:  WARNING!  The angle between the first three atoms is not suitable (%6.3f degrees) to align them with the xy-plane.\n", programname, RadiansToDegrees( angle_012 ) );
  1656.                     } else {
  1657.                         // Calculate angle between vec_normal and the z-axis
  1658.                         double angle_n1z = 0.;  // Angle between vec_normal and the z-axis
  1659.                         angle_n1z = Angle_between( vec_normal, vec_z_axis );
  1660.                         pr( logFile, "Angle between vec_normal and vec_z_axis = %.2f degrees\n", RadiansToDegrees( angle_n1z ) );
  1661.                         //
  1662.                         // We need to rotate the molecule about the normal to vec_normal and vec_z_axis
  1663.                         Cross_product( vec_reorient_axis, vec_normal, vec_z_axis );
  1664.                         //
  1665.                         // Set the rotation axis for reorientation
  1666.                         q_reorient.nx = vec_reorient_axis[X];
  1667.                         q_reorient.ny = vec_reorient_axis[Y];
  1668.                         q_reorient.nz = vec_reorient_axis[Z];
  1669.                         //
  1670.                         // Normalise the vector defining the axis of rotation:
  1671.                         q_reorient = normRot( q_reorient );
  1672.                         //
  1673.                         // Set the angle for reorientation of the first 3 atoms
  1674.                         // into the xy-plane
  1675.                         q_reorient.ang = -angle_n1z;
  1676.                         //
  1677.                         // Convert the rotation-about-axis components (nx,ny,nz,ang)
  1678.                         // to a rotation-quaternion (x,y,z,w):
  1679.                         q_reorient = convertRotToQuat( q_reorient );
  1680.  
  1681.                         // Rotate ligand into the xy-plane...
  1682.                         // qtransform( origin, q_reorient, crdreo, true_ligand_atoms );
  1683.                         qtransform( origin, q_reorient, crdpdb, true_ligand_atoms );
  1684.  
  1685.                         // Compute the updated vec_01, the vector between atom 0 and atom 1,
  1686.                         // since the preceding "qtransform" changed the coordinates.
  1687.                         for (xyz = 0;  xyz < SPACE;  xyz++) {
  1688.                             // vec_01[xyz] = (double)( crdreo[1][xyz] - crdreo[0][xyz] );
  1689.                             vec_01[xyz] = (double)( crdpdb[1][xyz] - crdpdb[0][xyz] );
  1690.                         }
  1691.                         //
  1692.                         // Compute the angle between vec_01 and the x-axis:
  1693.                         double angle_01x = 0.;
  1694.                         angle_01x = Angle_between( vec_01, vec_x_axis );
  1695.                         //
  1696.                         pr( logFile, "Angle between vector 01 and the x-axis = %.2f degrees\n", RadiansToDegrees( angle_01x ) );
  1697.                         //
  1698.                         // The rotation axis to rotate the first two atoms, 0 and 1,
  1699.                         // to be parallel to the x-axis, will be
  1700.                         // perpendicular to the xy-plane, i.e. the z-axis,
  1701.                         // since the molecule's first 3 atoms are now in the xy-plane.
  1702.                         q_reorient.nx = vec_z_axis[X];
  1703.                         q_reorient.ny = vec_z_axis[Y];
  1704.                         q_reorient.nz = vec_z_axis[Z];
  1705.                         //
  1706.                         // Set the rotation angle:
  1707.                         q_reorient.ang = angle_01x;
  1708.                         //
  1709.                         // Build the quaternion from the axis-angle rotation values:
  1710.                         q_reorient = convertRotToQuat( q_reorient );
  1711.                     } // angle_012 is appropriate to align into xy-plane
  1712.  
  1713.                 } else {
  1714.                     prStr( error_message, "%s: ERROR! Insufficient atoms in the ligand.  There must be at least three atoms in the ligand to use this command.\n", programname );
  1715.                     stop( error_message );
  1716.                     exit( -1 );
  1717.                 }
  1718.                 } // reorient standard
  1719.             } else {
  1720.                 { // reorient <nx> <ny> <nz> <angle>
  1721.                     B_reorient_random = FALSE; // do not create a new random orientation before docking
  1722.  
  1723.                     // Read the specified initial orientation for the ligand
  1724.                     retval = (int)sscanf( line,"%*s %lf %lf %lf %lf", &(q_reorient.nx), &(q_reorient.ny), &(q_reorient.nz), &(q_reorient.ang) );
  1725.                     if ( retval == 4 ) {
  1726.                         // Normalise the vector defining the axis of rotation:
  1727.                         q_reorient = normRot( q_reorient );
  1728.                         // Make sure angle is in radians, and ranges from -PI to PI
  1729.                         q_reorient.ang = DegreesToRadians( q_reorient.ang ); // convert from degrees to radians
  1730.                         q_reorient.ang = ModRad( q_reorient.ang ); // wrap to range (0, 2*PI) using modulo 2*PI
  1731.                         q_reorient.ang = WrpRad( q_reorient.ang ); // wrap to range (-PI, PI)
  1732.                         pr( logFile, "After normalising the vector, and converting the angle to radians, the axis-angle rotation becomes ((%.3f, %.3f, %.3f), %.2f radians)\n",
  1733.                                 q_reorient.nx, q_reorient.ny, q_reorient.ny, q_reorient.ang);
  1734.                         // Convert the rotation-about-axis components (nx,ny,nz,ang)
  1735.                         // to a rotation-quaternion (x,y,z,w):
  1736.                         q_reorient = convertRotToQuat( q_reorient );
  1737.                     } else {
  1738.                         prStr( error_message, "%s: ERROR! Please specify the vector and rotation angle using four real numbers.\n", programname );
  1739.                         stop( error_message );
  1740.                         exit( -1 );
  1741.                     }
  1742.                 } // reorient <nx> <ny> <nz> <angle>
  1743.             } // endif
  1744.         } // end parsing reorient command line
  1745.  
  1746.         // reorient( logFile, true_ligand_atoms, atomstuff, crdreo, charge, type,
  1747.         reorient( logFile, true_ligand_atoms, atomstuff, crdpdb, charge, type,
  1748.                   parameterArray, q_reorient, origin, ntor, tlist, vt, &ligand, debug );
  1749.  
  1750.         (void) fflush(logFile);
  1751.         break;
  1752.  
  1753.  
  1754. //______________________________________________________________________________
  1755.  
  1756.     case DPF_TRAN0:
  1757.         /*
  1758.         **  tran0
  1759.         **  Initial_translation,
  1760.         */
  1761.         (void) sscanf( line, "%*s %s", param[0]);
  1762.         for (i=0; i<6; i++) {
  1763.             param[0][i] = (char)tolower( (int)param[0][i] );
  1764.         }
  1765.         if (equal(param[0],"random",6)) {
  1766.             B_RandomTran0 = TRUE;
  1767.             ligand.S.T.x = sInit.T.x = random_range( info->lo[X], info->hi[X] );
  1768.             ligand.S.T.y = sInit.T.y = random_range( info->lo[Y], info->hi[Y] );
  1769.             ligand.S.T.z = sInit.T.z = random_range( info->lo[Z], info->hi[Z] );
  1770.         } else {
  1771.             B_RandomTran0 = FALSE;
  1772.             (void) sscanf( line,"%*s %lf %lf %lf", &(sInit.T.x), &(sInit.T.y), &(sInit.T.z));
  1773.             ligand.S.T.x = sInit.T.x;
  1774.             ligand.S.T.y = sInit.T.y;
  1775.             ligand.S.T.z = sInit.T.z;
  1776.             if (outlev >= 0) {
  1777.                 pr( logFile, "Initial translation =\t\t\t(%.3f, %.3f, %.3f) Angstroms\n", sInit.T.x, sInit.T.y, sInit.T.z );
  1778.             }
  1779.             (void) fflush(logFile);
  1780.         }
  1781.         break;
  1782.  
  1783. //______________________________________________________________________________
  1784.  
  1785.     case DPF_AXISANGLE0:
  1786.     case DPF_QUATERNION0:
  1787.         /*
  1788.          * Handles both axisangle0 and quaternion0
  1789.          *
  1790.          *  axisangle0 1. 0. 0. 0.
  1791.          *  axisangle0 random
  1792.          *  ( quat0 <--- deprecated )
  1793.          *  Initial_quaternion, specified as an axis and angle
  1794.          *
  1795.          *  quaternion0 0. 0. 0. 1.
  1796.          *  quaternion0 random
  1797.          *  Initial_quaternion, specified as the four components (qx, qy, qz, qw)
  1798.          */
  1799.         {
  1800.         // Local Block...
  1801.         double a, b, c, d;
  1802.         (void) sscanf( line, "%*s %s", param[0]);
  1803.         for (i=0; i<6; i++) {
  1804.             param[0][i] = (char)tolower( (int)param[0][i] );
  1805.         }
  1806.         if (equal(param[0],"random",6)) {
  1807.             // Make a random initial quaternion,
  1808.             // and set the boolean B_RandomQuat0 to true,
  1809.             // so we can generate random quaternions in population-based methods.
  1810.             B_RandomQuat0 = TRUE;
  1811.             create_random_orientation( &(sInit.Q) );
  1812.             if (outlev >= 0) {
  1813.                 pr( logFile, "Each run will begin with a new, random initial orientation.\n");
  1814.             }
  1815.         } else {
  1816.             // Read in the user-defined axis-angle values for the initial quaternion
  1817.             // and set the boolean B_RandomQuat0 to false,
  1818.             B_RandomQuat0 = FALSE;
  1819.             (void) sscanf( line, "%*s %lf %lf %lf %lf", &a, &b, &c, &d);
  1820.             sInit.Q = (dpf_keyword == DPF_QUATERNION0) ?
  1821.                       quatComponentsToQuat(a,b,c,d) :
  1822.                       axisDegreeToQuat(a,b,c,d);
  1823.         }
  1824.         ligand.S.Q = sInit.Q;
  1825.         if (outlev >= 0) {
  1826.             if (dpf_keyword == DPF_QUATERNION0) {
  1827.                 pr( logFile, "Initial quaternion,  (x,y,z,w) =\t( %.3f, %.3f, %.3f, %.3f ),\n", sInit.Q.x, sInit.Q.y, sInit.Q.z, sInit.Q.w);
  1828.             } else {
  1829.                 pr( logFile, "Initial axis-angle,  (nx,ny,nz,ang) =\t( %.3f, %.3f, %.3f, %.1f deg ),\n", a, b, c, d );
  1830.                 pr( logFile, "Normalized axis,     (nx,ny,nz)     =\t( %.3f %.3f %.3f )\n", sInit.Q.nx, sInit.Q.ny, sInit.Q.nz );
  1831.             }
  1832. #ifdef DEBUG
  1833.             pr( logFile, "Initial Quaternion sInit.Q:\n\n");
  1834.             printQuat( logFile, sInit.Q );
  1835.             pr( logFile, "Initial Quaternion ligand.S.Q:\n\n");
  1836.             printQuat( logFile, ligand.S.Q );
  1837. #endif
  1838.         }
  1839.         (void) fflush(logFile);
  1840.         }
  1841.         break;
  1842.  
  1843. //______________________________________________________________________________
  1844.  
  1845.     case DPF_NDIHE:
  1846.         /*
  1847.         **  ndihe
  1848.         **  Number of dihedral angles to be specified by "dihe0"
  1849.         */
  1850.         (void) sscanf( line, "%*s %d", &ndihed );
  1851.         if ( nmol == 0 ) {
  1852.             if (outlev >= 0) {
  1853.                 pr( logFile, "Must specify a ligand PDBQT file, using the \"move\" command.\n");
  1854.             }
  1855.         } else {
  1856.             if (outlev >= 0) {
  1857.                 pr( logFile, "%s: WARNING!  The \"ndihe\" command is no longer supported.  The number of torsions in the PDBQT file(s) is the number that will be used (i.e. %d)\n", programname, ntor);
  1858.             }
  1859.             if ( ndihed != ntor ) {
  1860.                 pr( logFile, "%s: WARNING!  You requested %d torsions, but I found %d in PDBQT-file specifications.\n", programname, ndihed, ntor );
  1861.             } /* if */
  1862.         }
  1863.         (void) fflush(logFile);
  1864.         break;
  1865.  
  1866. //______________________________________________________________________________
  1867.  
  1868.     case DPF_DIHE0:
  1869.         /*
  1870.         **  dihe0
  1871.         **  Initial dihedral angles, input in degrees,
  1872.         */
  1873.         (void) sscanf( line, "%*s %s", param[0]);
  1874.         for (i=0; i<6; i++) {
  1875.             param[0][i] = (char)tolower( (int)param[0][i] );
  1876.         }
  1877.         if (equal(param[0],"random",6)) {
  1878.             B_RandomDihe0 = TRUE;
  1879.             sInit.ntor = nval = ntor;
  1880.             for ( i=0; i<nval; i++ ) {
  1881.                 sInit.tor[i] = random_range( -180.0, 180.0 );
  1882.             }
  1883.         } else {
  1884.             B_RandomDihe0 = FALSE;
  1885.             retval = (int)sscanf( line, torfmt, TOR_ARG_LIST );
  1886.             if (retval == 0) {
  1887.                 pr( logFile, "WARNING!  AutoDock could not read any torsions!\n" );
  1888.             } else if (retval == EOF) {
  1889.                 pr( logFile, "WARNING!  End of file encountered while reading dihe0 line\n");
  1890.             } else if (retval < ntor) {
  1891.                 pr( logFile, "WARNING!  Only %d initial torsion angles were detected on input line.\n",retval);
  1892.                 pr( logFile, "WARNING!  I am sorry, the number of torsions detected in the PDBQT files was %d torsions.\n", ntor);
  1893.             } else {
  1894.                 if (outlev >= 0) {
  1895.                     pr( logFile, "%d initial torsion angles were detected on input line.\n", retval );
  1896.                 }
  1897.             }
  1898.             nval = retval;
  1899.         }
  1900.         for ( i=0; i<nval; i++ ) {
  1901.             if (outlev >= 0) {
  1902.                 pr( logFile, "\tInitial torsion %2d = %7.2f deg\n", (i+1), sInit.tor[i] ); /* sInit.tor is in degrees */
  1903.                 /* Convert sInit.tor[i] into radians */
  1904.             }
  1905.             ligand.S.tor[i] = sInit.tor[i] = DegreesToRadians( sInit.tor[i] ); /* sInit.tor is now in radians  Added:05-01-95 */
  1906.         }
  1907.         (void) fflush(logFile);
  1908.         break;
  1909.  
  1910. //______________________________________________________________________________
  1911.  
  1912.     case DPF_TSTEP:
  1913.         /*
  1914.         **  tstep
  1915.         **  Translation_step,
  1916.         */
  1917.         retval = (int)sscanf( line, "%*s " FDFMT2, &trnStep0, &trnStepFinal );
  1918.         if (retval == 0) {
  1919.             pr( logFile, "WARNING!  AutoDock could not read any arguments!\n" );
  1920.         } else if (retval == EOF) {
  1921.             pr( logFile, "WARNING!  End of file encountered!\n");
  1922.         } else if (retval > 0) {
  1923.             pr( logFile, "Initial cycle, maximum translation step = +/- %-.1f Angstroms\n", trnStep0);
  1924.         }
  1925.         if (retval == 2) {
  1926.             B_CalcTrnRF = TRUE;
  1927.             if (outlev >= 0) {
  1928.                 pr( logFile, "Final cycle,   maximum translation step = +/- %-.1f Angstroms\n", trnStepFinal);
  1929.                 pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
  1930.             }
  1931.         }
  1932.         (void) fflush(logFile);
  1933.         break;
  1934.  
  1935. //______________________________________________________________________________
  1936.  
  1937.     case DPF_QSTEP:
  1938.         /*
  1939.         **  qstep
  1940.         **  Quaternion_step,
  1941.         */
  1942.         retval = (int)sscanf( line, "%*s " FDFMT2, &qtwStep0, &qtwStepFinal );
  1943.         if (retval == 0) {
  1944.             pr( logFile, "WARNING!  AutoDock could not read any arguments!\n" );
  1945.         } else if (retval == EOF) {
  1946.             pr( logFile, "WARNING!  End of file encountered!\n");
  1947.         } else if (retval > 0) {
  1948.             if (outlev >= 0) {
  1949.                 pr( logFile, "Initial cycle, maximum quaternion angle step = +/- %-.1f deg\n", qtwStep0);
  1950.             }
  1951.             /* convert to radians */
  1952.             qtwStep0 = DegreesToRadians( qtwStep0 );
  1953.         }
  1954.         if (retval == 2) {
  1955.             B_CalcQtwRF = TRUE;
  1956.             if (outlev >= 0) {
  1957.                 pr( logFile, "Final cycle,   maximum quaternion angle step = +/- %-.1f deg\n", qtwStepFinal);
  1958.                 pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
  1959.             }
  1960.             /* convert to radians */
  1961.             qtwStepFinal = DegreesToRadians( qtwStepFinal );
  1962.         }
  1963.         (void) fflush(logFile);
  1964.         break;
  1965.  
  1966. //______________________________________________________________________________
  1967.  
  1968.     case DPF_DSTEP:
  1969.         /*
  1970.         **  dstep
  1971.         **  Torsion_step,
  1972.         */
  1973.         retval = (int)sscanf( line, "%*s " FDFMT2, &torStep0, &torStepFinal );
  1974.         if (retval == 0) {
  1975.             pr( logFile, "WARNING!  AutoDock could not read any arguments!\n" );
  1976.         } else if (retval == EOF) {
  1977.             pr( logFile, "WARNING!  End of file encountered!\n");
  1978.         } else if (retval > 0) {
  1979.             if (outlev >= 0) {
  1980.                 pr( logFile, "Initial cycle, maximum torsion angle step = +/- %-.1f deg\n", torStep0);
  1981.             }
  1982.             /* convert to radians */
  1983.             torStep0 = DegreesToRadians( torStep0 );
  1984.         }
  1985.         if (retval == 2) {
  1986.             B_CalcTorRF = TRUE;
  1987.             if (outlev >= 0) {
  1988.                 pr( logFile, "Final cycle,   maximum torsion angle step = +/- %-.1f deg\n", torStepFinal);
  1989.                 pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
  1990.             }
  1991.             /* convert to radians */
  1992.             torStepFinal = DegreesToRadians( torStepFinal );
  1993.         }
  1994.         (void) fflush(logFile);
  1995.         break;
  1996.  
  1997. //______________________________________________________________________________
  1998.  
  1999.     case DPF_TRNRF:
  2000.         /*
  2001.         **  trnrf
  2002.         **  Translation reduction factor,
  2003.         */
  2004.         (void) sscanf( line, "%*s " FDFMT, &trnFac );
  2005.         if (outlev >= 0) {
  2006.             pr( logFile, "Reduction factor for translations =\t%-.3f /cycle\n", trnFac );
  2007.         }
  2008.         B_trnReduc = (trnFac != 1.);
  2009.         (void) fflush(logFile);
  2010.         break;
  2011.  
  2012. //______________________________________________________________________________
  2013.  
  2014.     case DPF_QUARF:
  2015.         /*
  2016.         **  quarf
  2017.         **  Quaternion reduction factor,
  2018.         */
  2019.         (void) sscanf( line, "%*s " FDFMT, &qtwFac );
  2020.         if (outlev >= 0) {
  2021.             pr( logFile, "Reduction factor for quaternion angle =\t%-.3f /cycle\n", qtwFac );
  2022.         }
  2023.         B_qtwReduc = (qtwFac != 1.);
  2024.         (void) fflush(logFile);
  2025.         break;
  2026.  
  2027. //______________________________________________________________________________
  2028.  
  2029.     case DPF_DIHRF:
  2030.         /*
  2031.         **  dihrf
  2032.         **  Torsion reduction factor,
  2033.         */
  2034.         (void) sscanf( line, "%*s " FDFMT, &torFac );
  2035.         if (outlev >= 0) {
  2036.             pr( logFile, "Reduction factor for torsion angles =\t%-.3f /cycle\n", torFac );
  2037.         }
  2038.         B_torReduc = (torFac != 1.);
  2039.         (void) fflush(logFile);
  2040.         break;
  2041.  
  2042. //______________________________________________________________________________
  2043.  
  2044.     case DPF_FLEX:
  2045.         /*
  2046.         **  flex
  2047.         **  Flexible side-chains, cannot translate:
  2048.         */
  2049.         nmol++;
  2050.         nres++;
  2051.         (void) fflush(logFile);
  2052.         break;
  2053.  
  2054. //______________________________________________________________________________
  2055.  
  2056.     case DPF_INTNBP_REQM_EPS:
  2057.         /*
  2058.         **  intnbp_r_eps
  2059.         **  Read internal energy parameters:
  2060.         **  Lennard-Jones and Hydrogen Bond Potentials,
  2061.         **  Using epsilon and r-equilibrium values...
  2062.         */
  2063.         (void) sscanf( line, "%*s " FDFMT2 " %d %d", &Rij, &epsij, &xA, &xB );
  2064.         /* check that the Rij is reasonable */
  2065.         if ((Rij < RIJ_MIN) || (Rij > RIJ_MAX)) {
  2066.             (void) fprintf( logFile,
  2067.             "WARNING: pairwise distance, Rij, %.2f, is not a very reasonable value for the equilibrium separation of two atoms! (%.2f Angstroms <= Rij <= %.2f Angstroms)\n\n", Rij, RIJ_MIN, RIJ_MAX);
  2068.             (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
  2069.             /* GMM COMMENTED OUT FOR DAVE GOODSELL, MUTABLE ATOMS
  2070.              * exit(-1); */
  2071.         }
  2072.         /* check that the epsij is reasonable */
  2073.         if ((epsij < EPSIJ_MIN) || (epsij > EPSIJ_MAX)) {
  2074.             (void) fprintf( logFile,
  2075.             "WARNING: well-depth, epsilon_ij, %.2f, is not a very reasonable value for the equilibrium potential energy of two atoms! (%.2f kcal/mol <= epsilon_ij <= %.2f kcal/mol)\n\n", epsij, EPSIJ_MIN, EPSIJ_MAX);
  2076.             (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
  2077.             /* GMM COMMENTED OUT FOR DAVE GOODSELL, MUTABLE ATOMS
  2078.              * exit(-1); */
  2079.         }
  2080.         /* Defend against division by zero... */
  2081.         if (xA != xB) {
  2082.             // Calculate the coefficients from Rij and epsij
  2083.             cA = (tmpconst = epsij / (Real)(xA - xB)) * pow( (double)Rij, (double)xA ) * (Real)xB;
  2084.             cB = tmpconst * pow( (double)Rij, (double)xB ) * (Real)xA;
  2085.             pr(logFile, "\nCalculating internal non-bonded interaction energies for docking calculation;\n");
  2086.             intnbtable( &B_havenbp, a1, a2, info, cA, cB, xA, xB, AD4.coeff_desolv, sigma, ad_energy_tables, BOUND_CALCULATION );
  2087.             pr(logFile, "\nCalculating internal non-bonded interaction energies for unbound conformation calculation;\n");
  2088.             intnbtable( &B_havenbp, a1, a2, info, cA_unbound, cB_unbound, xA_unbound, xB_unbound, AD4.coeff_desolv, sigma, unbound_energy_tables, UNBOUND_CALCULATION );
  2089.             // Increment the atom type numbers, a1 and a2, for the internal non-bond table
  2090.             a2++;
  2091.             if (a2 >= info->num_atom_types) {
  2092.                 a1++;
  2093.                 a2 = a1;
  2094.             }
  2095.         } else {
  2096.             pr(logFile,"WARNING: Exponents must be different, to avoid division by zero!\n\tAborting...\n");
  2097.             exit(-1);
  2098.         }
  2099.         (void) fflush(logFile);
  2100.         break;
  2101.  
  2102. //______________________________________________________________________________
  2103.  
  2104.     case DPF_INTNBP_COEFFS:
  2105.         /*
  2106.         **  intnbp_coeffs
  2107.         **  Read internal energy parameters:
  2108.         **  Lennard-Jones and Hydrogen Bond Potentials,
  2109.         **  Using coefficients...
  2110.         */
  2111.         (void) sscanf( line, "%*s " FDFMT2 " %d %d", &cA, &cB, &xA, &xB );
  2112.  
  2113.         /* Defend against division by zero... */
  2114.         if (xA != xB) {
  2115.             pr(logFile, "\nCalculating internal non-bonded interaction energies for docking calculation;\n");
  2116.             intnbtable( &B_havenbp, a1, a2, info, cA, cB, xA, xB, AD4.coeff_desolv, sigma, ad_energy_tables, BOUND_CALCULATION );
  2117.             pr(logFile, "\nCalculating internal non-bonded interaction energies for unbound conformation calculation;\n");
  2118.             intnbtable( &B_havenbp, a1, a2, info, cA_unbound, cB_unbound, xA_unbound, xB_unbound, AD4.coeff_desolv, sigma, unbound_energy_tables, UNBOUND_CALCULATION );
  2119.             // Increment the atom type numbers, a1 and a2, for the internal non-bond table
  2120.             a2++;
  2121.             if (a2 >= info->num_atom_types) {
  2122.                 a1++;
  2123.                 a2 = a1;
  2124.             }
  2125.         } else {
  2126.             pr(logFile,"WARNING: Exponents must be different. Aborting...\n");
  2127.             exit(-1);
  2128.         }
  2129.  
  2130.         (void) fflush(logFile);
  2131.         break;
  2132.  
  2133. //______________________________________________________________________________
  2134.  
  2135.     case DPF_UNBOUND_INTNBP_COEFFS:
  2136.         /*
  2137.         **  unbound_intnbp_coeffs
  2138.         **  Read internal energy parameters for unbound extended state calculation:
  2139.         */
  2140.         (void) sscanf( line, "%*s " FDFMT2 " %d %d", &cA_unbound, &cB_unbound, &xA_unbound, &xB_unbound );
  2141.  
  2142.         pr(logFile, "\nSetting the internal non-bonded interaction energy parameters for the\nunbound docking calculation, E = %.1f / r^%d - %.1f / r^%d\n\n", cA_unbound, xA_unbound, cB_unbound, xB_unbound);
  2143.         (void) fflush(logFile);
  2144.         break;
  2145.  
  2146. //______________________________________________________________________________
  2147.  
  2148.     case DPF_RT0:
  2149.         /*
  2150.         **  rt0
  2151.         **  Initial Temperature,
  2152.         */
  2153.         (void) sscanf( line, "%*s " FDFMT, &RT0 );
  2154.         if (RT0 <= 0.) {
  2155.             pr( logFile, "\nWARNING!  Negative temperatures not allowed! Will default to RT = 616 cal mol.\n" );
  2156.             RT0 = 616.0;
  2157.         }
  2158.         if (outlev >= 0) {
  2159.             pr( logFile, "\n\t\tTEMPERATURE SCHEDULE INFORMATION\n" );
  2160.             pr( logFile, "\t\t________________________________\n\n" );
  2161.             pr( logFile, "               -1 -1                 -1 -1\n" );
  2162.             pr( logFile, "R = %5.3f J mol  K    = %5.3f cal mol  K  \n\n", RJ, Rcal );
  2163.             pr( logFile, "                                        -1\n" );
  2164.             pr( logFile, "Initial R*Temperature = %8.2f cal mol\n", RT0 );
  2165.             pr( logFile, "      (=> Temperature = %8.2f K\n", RT0/Rcal );
  2166.             pr( logFile, "                   or = %8.2f C)\n\n", RT0/Rcal - T0K );
  2167.         }
  2168.         break;
  2169.  
  2170. //______________________________________________________________________________
  2171.  
  2172.     case DPF_RTRF:
  2173.         /*
  2174.         **  rtrf
  2175.         **  Temperature reduction factor,
  2176.         */
  2177.         (void) sscanf( line, "%*s " FDFMT, &RTFac);
  2178.         if (outlev >= 0) {
  2179.             pr( logFile, "R*Temperature reduction factor = %8.2f\t/cycle\n", RTFac );
  2180.         }
  2181.         if (RTFac >= 1.) {
  2182.             stop("Cooling is impossible with a reduction\n\tfactor greater than or equal to 1.0!" );
  2183.             exit( -1 );
  2184.         } else if (RTFac == 0.0 ) {
  2185.             stop("Cooling is impossible with a ZERO reduction factor!" );
  2186.             exit( -1 );
  2187.         } else if (RTFac < 0.0 ) {
  2188.             stop("Cooling is impossible with a NEGATIVE reduction factor!" );
  2189.             exit( -1 );
  2190.         }
  2191.         (void) fflush(logFile);
  2192.         B_tempChange = ( RTFac != 1.0 );
  2193.         break;
  2194.  
  2195. //______________________________________________________________________________
  2196.  
  2197.     case DPF_RUNS:
  2198.         /*
  2199.         **  runs
  2200.         **  Number of docking runs,
  2201.         */
  2202.         (void) sscanf( line, "%*s %d", &nruns );
  2203.         if ( nruns > MAX_RUNS ) {
  2204.             prStr( error_message, "%s:  ERROR: %d runs were requested, but AutoDock is only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", programname, nruns, MAX_RUNS);
  2205.             stop( error_message );
  2206.             exit( -1 );
  2207.         }
  2208.         pr( logFile, "Number of runs =\t\t\t\t%8d run%c\n", nruns, (nruns > 1)?'s':' ');
  2209.         (void) fflush(logFile);
  2210.         break;
  2211.  
  2212. //______________________________________________________________________________
  2213.  
  2214.     case DPF_CYCLES:
  2215.         /*
  2216.         **  cycles
  2217.         **  Number of constant temperature SA cycles,
  2218.         */
  2219.         (void) sscanf( line, "%*s %d", &ncycles );
  2220.         if (ncycles < 0) {
  2221.             pr( logFile, "WARNING!  Negative number of cycles found!  Using default value.\n");
  2222.             ncycles = 50;
  2223.         }
  2224.         pr( logFile, "Maximum number of cycles =\t\t\t%8d cycles\n\n", ncycles);
  2225.         if (B_linear_schedule) {
  2226.             RTreduc = RT0 / ncycles;
  2227.             if (outlev >= 0) {
  2228.                 pr( logFile, "\nA linear temperature reduction schedule was requested...\n" );
  2229.                 pr( logFile, "Annealing temperature will be reduced by %.3f cal mol per cycle.\n\n", RTreduc );
  2230.             }
  2231.         }
  2232.         (void) fflush(logFile);
  2233.         break;
  2234.  
  2235. //______________________________________________________________________________
  2236.  
  2237.     case DPF_ACCS:
  2238.         /*
  2239.         **  accs
  2240.         **  Maximum number of steps accepted,
  2241.         */
  2242.         (void) sscanf( line, "%*s %d", &naccmax );
  2243.         if (naccmax < 0) {
  2244.             naccmax = 100;
  2245.             pr( logFile, "WARNING!  Negative number of accepted moves found!  Using default value.\n");
  2246.         }
  2247.         if (outlev >= 0) {
  2248.             pr( logFile, "Maximum number accepted per cycle =\t\t%8d steps\n", naccmax);
  2249.         }
  2250.         if (nrejmax != 0) {
  2251.             nstepmax = naccmax + nrejmax;
  2252.             if (outlev >= 0) {
  2253.                 pr( logFile, "                                           \t_________\n" );
  2254.                 pr( logFile, "Maximum possible number of steps per cycle =\t%8d\tsteps\n\n", nstepmax);
  2255.             }
  2256.         }
  2257.         (void) fflush(logFile);
  2258.         break;
  2259.  
  2260. //______________________________________________________________________________
  2261.  
  2262.     case DPF_REJS:
  2263.         /*
  2264.         **  rejs
  2265.         **  Maximum number of steps rejected,
  2266.         */
  2267.         (void) sscanf( line, "%*s %d", &nrejmax );
  2268.         if (nrejmax < 0) {
  2269.             nrejmax = 100;
  2270.             pr( logFile, "WARNING!  Negative number of rejected moves found!  Using default value.\n");
  2271.         }
  2272.         if (outlev >= 0) {
  2273.             pr( logFile, "Maximum number rejected per cycle =\t\t%8d steps\n", nrejmax);
  2274.         }
  2275.         if (naccmax != 0) {
  2276.             nstepmax = naccmax + nrejmax;
  2277.             if (outlev >= 0) {
  2278.                 pr( logFile, "                                           \t_________\n" );
  2279.                 pr( logFile, "Maximum possible number of steps per cycle =\t%8d steps\n\n", nstepmax);
  2280.             }
  2281.         }
  2282.         (void) fflush(logFile);
  2283.         break;
  2284.  
  2285. //______________________________________________________________________________
  2286.  
  2287.     case DPF_SELECT:
  2288.         /*
  2289.         **  select
  2290.         **  Select either minimum or last state from previous cycle,
  2291.         */
  2292.         (void) sscanf( line, "%*s %1s", &selminpar );
  2293.         B_selectmin = (selminpar == 'm');
  2294.         if ( B_selectmin ) {
  2295.             if (outlev >= 0) {
  2296.                 pr( logFile, "%s will begin each new cycle\nwith the state of minimum energy from the previous annealing cycle.\n", programname);
  2297.             }
  2298.         } else {
  2299.             if (outlev >= 0) {
  2300.                 pr( logFile, "%s will begin each new cycle\nwith the last state from the previous annealing cycle.\n", programname);
  2301.             }
  2302.         }
  2303.         (void) fflush(logFile);
  2304.         break;
  2305.  
  2306. //______________________________________________________________________________
  2307.  
  2308.     case DPF_RMSTOL:
  2309.         /*
  2310.         **  rmstol
  2311.         **  Cluster tolerance,
  2312.         */
  2313.         (void) sscanf( line, "%*s " FDFMT, &clus_rms_tol);
  2314.         if (outlev >= 0) {
  2315.             pr( logFile, "Maximum RMS tolerance for conformational cluster analysis = %.2f Angstroms\n", clus_rms_tol);
  2316.         }
  2317.         (void) fflush(logFile);
  2318.         break;
  2319.  
  2320. //______________________________________________________________________________
  2321.  
  2322.     case DPF_RMSREF:
  2323.         /*
  2324.         **  rmsref
  2325.         **  RMS Reference Coordinates:
  2326.         */
  2327.         (void) sscanf( line, "%*s %s", FN_rms_ref_crds);
  2328.         if (outlev >= 0) {
  2329.             pr( logFile, "RMS reference coordinates will taken from \"%s\"\n", FN_rms_ref_crds );
  2330.         }
  2331.         (void) fflush(logFile);
  2332.         break;
  2333.  
  2334. //______________________________________________________________________________
  2335.  
  2336.     case DPF_RMSATOMS:
  2337.         /*
  2338.         **  rmsatoms ligand_only
  2339.         **  rmsatoms all
  2340.         **
  2341.         **  Set the atoms to compute the RMSD values for cluster analysis
  2342.         **  either "ligand_only" (the default) or "all" moving atoms (ligand + receptor)
  2343.         */
  2344.         retval = sscanf( line, "%*s %s", rms_atoms_cmd);
  2345.         if (retval != 1) {
  2346.             pr( logFile, "%s:  ERROR: please specify an argument (either \"ligand_only\" or \"all\").  By default, only the ligand atoms will be used for the cluster analysis.\n", programname );
  2347.             B_rms_atoms_ligand_only = TRUE;  // cluster on the ligand atoms only
  2348.         } else {
  2349.             if ( strncmp( rms_atoms_cmd, "ligand_only", 11 ) == 0 ) {
  2350.                 if (outlev >= 0) {
  2351.                     pr( logFile, "RMS clustering will be performed on the ligand atoms only.\n" );
  2352.                 }
  2353.                 B_rms_atoms_ligand_only = TRUE;  // cluster on the ligand atoms only
  2354.             } else if ( strncmp( rms_atoms_cmd, "all", 3 ) == 0 ) {
  2355.                 if (outlev >= 0) {
  2356.                     pr( logFile, "RMS clustering will be performed on the moving atoms of the receptor plus all the ligand atoms.\n" );
  2357.                 }
  2358.                 B_rms_atoms_ligand_only = FALSE;  // cluster on the ligand atoms plus moving receptor atoms
  2359.             } else {
  2360.                 if (outlev >= 0) {
  2361.                     pr( logFile, "RMS clustering will be performed on the ligand atoms only.\n" );
  2362.                 }
  2363.                 B_rms_atoms_ligand_only = TRUE;  // cluster on the ligand atoms only
  2364.             }
  2365.         }
  2366.         (void) fflush(logFile);
  2367.         break;
  2368.  
  2369. //______________________________________________________________________________
  2370.  
  2371.     case DPF_TRJFRQ:
  2372.         /*
  2373.         **  trjfrq
  2374.         **  Trajectory frequency,
  2375.         */
  2376.         (void) sscanf( line, "%*s %d", &trj_freq);
  2377.         B_write_trj = (trj_freq > 0);
  2378.         if (outlev >= 0) {
  2379.             pr( logFile, UnderLine );
  2380.             pr( logFile, "\t\tTRAJECTORY INFORMATION\n" );
  2381.             pr( logFile, "\t\t______________________\n\n\n" );
  2382.         }
  2383.         if (B_write_trj) {
  2384.             if (outlev >= 0) {
  2385.                 pr( logFile, "Output frequency for trajectory frames =\tevery %d step%s\n", trj_freq, (trj_freq > 1)?"s.":"." );
  2386.             }
  2387.         } else {
  2388.             if (outlev >= 0) {
  2389.                 pr( logFile, "No trajectory of states will be written.\n\n" );
  2390.                 pr( logFile, "Subsequent \"trjbeg\", \"trjend\", \"trjout\" and \"trjsel\" parameters will be ignored.\n\n" );
  2391.             }
  2392.         }
  2393.         (void) fflush(logFile);
  2394.         break;
  2395.  
  2396. //______________________________________________________________________________
  2397.  
  2398.     case DPF_TRJBEG:
  2399.         /*
  2400.         **  trjbeg
  2401.         **  Trajectory begin cycle,
  2402.         */
  2403.         (void) sscanf( line, "%*s %d", &trj_begin_cyc );
  2404.         if (outlev >= 0) {
  2405.             pr( logFile, "Begin outputting trajectory of states at cycle:\t%d\n", trj_begin_cyc );
  2406.         }
  2407.         if (trj_begin_cyc < 0) {
  2408.             trj_begin_cyc = 0;
  2409.         } else if (trj_begin_cyc > ncycles) {
  2410.             trj_begin_cyc = trj_end_cyc = ncycles;
  2411.         }
  2412.         --trj_begin_cyc;
  2413.         (void) fflush(logFile);
  2414.         break;
  2415.  
  2416. //______________________________________________________________________________
  2417.  
  2418.     case DPF_TRJEND:
  2419.         /*
  2420.         **  trjend
  2421.         **  Trajectory end cycle,
  2422.         */
  2423.         (void) sscanf( line, "%*s %d", &trj_end_cyc );
  2424.         if (outlev >= 0) {
  2425.             pr( logFile, "Cease outputting trajectory of states at cycle:\t%d\n", trj_end_cyc );
  2426.         }
  2427.         if (trj_end_cyc > ncycles) {
  2428.             trj_end_cyc = ncycles;
  2429.         } else if (trj_end_cyc < 0) {
  2430.             trj_end_cyc = 1;
  2431.         }
  2432.         --trj_end_cyc;
  2433.         (void) fflush(logFile);
  2434.         break;
  2435.  
  2436. //______________________________________________________________________________
  2437.  
  2438.     case DPF_TRJOUT:
  2439.         /*
  2440.         **  trjout
  2441.         **  Trajectory file,
  2442.         */
  2443.         (void) sscanf( line, "%*s %s", FN_trj );
  2444.         if (outlev >= 0) {
  2445.             pr( logFile, "\nWrite trajectory of state variables to file: \"%s\"\n", FN_trj);
  2446.         }
  2447.         (void) fflush(logFile);
  2448.         break;
  2449.  
  2450. //______________________________________________________________________________
  2451.  
  2452.     case DPF_TRJSEL:
  2453.         /*
  2454.         **  trjsel
  2455.         **  Trajectory select,
  2456.         */
  2457.         (void) sscanf( line, "%*s %1s", &out_acc_rej );
  2458.         B_acconly = (out_acc_rej == 'A');
  2459.         B_either  = (out_acc_rej == 'E');
  2460.         if (B_acconly) {
  2461.             if (outlev >= 0) {
  2462.                 pr( logFile, "Output *accepted* states only.\n" );
  2463.             }
  2464.         } else if (B_either) {
  2465.             if (outlev >= 0) {
  2466.                 pr( logFile, "Output *either* accepted or rejected states.\n" );
  2467.             }
  2468.         } else {
  2469.             pr( logFile, "WARNING: Missing or unknown accepted/rejected output flag.\n" );
  2470.         }
  2471.         (void) fflush(logFile);
  2472.         break;
  2473.  
  2474. //______________________________________________________________________________
  2475.  
  2476.     case DPF_EXTNRG:
  2477.         /*
  2478.         **  extnrg
  2479.         **  Wall Energy,
  2480.         */
  2481.         (void) sscanf( line, "%*s " FDFMT, &WallEnergy );
  2482.         if (outlev >= 0) {
  2483.             pr( logFile, "External grid energy (beyond grid map walls) = %.2f\n\n", WallEnergy );
  2484.         }
  2485.         (void) fflush(logFile);
  2486.         break;
  2487.  
  2488. //______________________________________________________________________________
  2489.  
  2490.     case DPF_CLUSTER:
  2491.         /*
  2492.         **  cluster
  2493.         **  Cluster mode,
  2494.         */
  2495.         (void) sscanf( line, "%*s %s", FN_clus );
  2496.         B_cluster_mode = TRUE;
  2497.         if (outlev >= 0) {
  2498.             pr( logFile, "Cluster mode is now set.\n\n" );
  2499.         }
  2500.         clmode( num_atom_types, clus_rms_tol,
  2501.                 hostnm, jobStart, tms_jobStart,
  2502.                 B_write_all_clusmem, FN_clus, crdpdb, lig_center,
  2503.                 B_symmetry_flag, FN_rms_ref_crds );
  2504.         (void) fflush(logFile);
  2505.         break;
  2506.  
  2507. //______________________________________________________________________________
  2508.  
  2509.     case DPF_CLUSALL:
  2510.         /*
  2511.         ** write_all_clusmem
  2512.         ** Write all cluster members...
  2513.         */
  2514.         B_write_all_clusmem = TRUE;
  2515.         if (outlev >= 0) {
  2516.             pr( logFile, "All members of each cluster will be written out after the clustering histogram.\n(This is instead of outputting just the lowest energy member in each.)\n\n" );
  2517.         }
  2518.         break;
  2519.  
  2520. //______________________________________________________________________________
  2521.  
  2522.     case DPF_RMSNOSYM:
  2523.         /*
  2524.         **  rmsnosym
  2525.         **  Calculate RMS values in the normal way,
  2526.         **  ignoring any atom-type equivalences...
  2527.         */
  2528.         B_symmetry_flag = FALSE;
  2529.         if (outlev >= 0) {
  2530.             pr( logFile, "Symmetry will be ignored in RMS calculations.\n\n" );
  2531.         }
  2532.         (void) fflush(logFile);
  2533.         break;
  2534.  
  2535. //______________________________________________________________________________
  2536.  
  2537.     case DPF_SCHEDLIN:
  2538.         /*
  2539.         **  linear_schedule
  2540.         **  Use a linear (arithmetic) temperature
  2541.         **  reduction schedule.  This is necessary for
  2542.         **  more accurate entropy estimations...
  2543.         */
  2544.         B_linear_schedule = TRUE;
  2545.         if (outlev >= 0) {
  2546.             pr( logFile, "A linear temperature reduction schedule will be used...\n\n" );
  2547.         }
  2548.         if (ncycles == -1) {
  2549.             pr( logFile, "\nWARNING!  Please specify the number of cycles first!\n\n" );
  2550.         } else {
  2551.             RTreduc = RT0 / ncycles;
  2552.             if (outlev >= 0) {
  2553.                 pr( logFile, "Annealing temperature will be reduced by %.3f cal mol per cycle.\n\n", RTreduc );
  2554.             }
  2555.         }
  2556.         (void) fflush(logFile);
  2557.         break;
  2558.  
  2559. //______________________________________________________________________________
  2560.  
  2561.     case DPF_WATCH:
  2562.         /*
  2563.         **  watch
  2564.         **  for watching a job's progress PDBQT file in AVS,
  2565.         */
  2566.         (void) sscanf( line, "%*s %s", FN_watch);
  2567.         if (B_write_trj) {
  2568.             pr(logFile,"\nAutoDock will create the watch-file \"%s\", for real-time monitoring of runs.\n\n", FN_watch);
  2569.             pr(logFile,"\nThe watch-file will be updated every %d moves, in accordance with the trajectory parameters..\n\n", trj_freq);
  2570.             B_watch = TRUE;
  2571.         } else {
  2572.             pr(logFile,"\nYou must set \"trjfrq\" to be greater than zero. No watch-file will be created.\n\n");
  2573.             B_watch = FALSE;
  2574.         }
  2575.         (void) fflush(logFile);
  2576.         break;
  2577.  
  2578. //______________________________________________________________________________
  2579.  
  2580.     case DPF_GAUSSTORCON:
  2581.     case DPF_HARDTORCON:
  2582.         /*
  2583.         ** "gausstorcon" Add Gaussian torsion contraints,
  2584.         ** "hardtorcon"  Add Hard torsion contraints,
  2585.         */
  2586.         (void) sscanf( line, "%*s %d " FDFMT2, &I_tor, &F_torPref, &F_torHWdth);
  2587.         if (I_tor <= 0) {
  2588.             pr( logFile, "\nTorsion IDs less than 1 (%d) are not allowed!\n\n", I_tor);
  2589.         } else if (I_tor > ntor) {
  2590.             pr( logFile, "\nRequested torsion ID (%d) is larger than the number of torsions found (%d)!\n\n", I_tor, ntor);
  2591.         } else { /* torsion-ID accepted */
  2592.             --I_tor;    /* Because humans start at 1, and C at 0... */
  2593.             if ( B_isTorConstrained[I_tor] == 0 ) {
  2594.  
  2595.                 if (dpf_keyword ==  DPF_GAUSSTORCON) {
  2596.                     B_isGaussTorCon = TRUE;
  2597.                     B_isTorConstrained[I_tor] = 1;
  2598.                     /*
  2599.                     ** Initialize... Torsion Energy Profile...
  2600.                     ** Set energies at every torsion division
  2601.                     ** to the user-defined (maximum) barrier energy,
  2602.                     */
  2603.                     for (US_tD = 0;  US_tD < NTORDIVS;  US_tD++) {
  2604.                         US_torProfile[I_tor][US_tD] = US_torBarrier;
  2605.                     }
  2606.                 } else {
  2607.                     /*
  2608.                     ** DPF_HARDTORCON
  2609.                     */
  2610.                     B_isTorConstrained[I_tor] = 2;
  2611.                 }
  2612.             }
  2613.             if (dpf_keyword ==  DPF_GAUSSTORCON) {
  2614.                 (void) strcpy( S_contype, " half-" );
  2615.             } else {
  2616.                 (void) strcpy( S_contype, " " );
  2617.             }
  2618.                 /*
  2619.             ** F_torPref ranges from -180.0 to +180.0 degrees...
  2620.             */
  2621.             F_torPref = WrpDeg(ModDeg(F_torPref));
  2622.             if (F_torHWdth < 0.) {
  2623.                 pr(logFile,"\nI'm sorry, negative%swidths (%.1f) are not allowed. I will use the default (%.1f) instead.\n\n", S_contype, F_torHWdth, DEFHWDTH);
  2624.                 F_torHWdth = DEFHWDTH;
  2625.             } else if (F_torHWdth > 90.) {
  2626.                 pr(logFile,"\nI'm sorry, your requested%swidth (%.1f) is too large. I will use the default (%.1f) instead.\n\n", S_contype, F_torHWdth, DEFHWDTH);
  2627.                 F_torHWdth = DEFHWDTH;
  2628.             }
  2629.             pr( logFile, "For torsion %d, Adding a constrained-torsion zone centered on %.1f degrees;\n%swidth = %.1f degrees.\n\n", 1+I_tor, F_torPref, S_contype, F_torHWdth);
  2630.  
  2631.             if (dpf_keyword == DPF_GAUSSTORCON) {
  2632.                 /*
  2633.                 ** Calculate the torsion energy profile;
  2634.                 ** combine this with previous profile without
  2635.                 ** losing any information.
  2636.                 */
  2637.                 for (F_A = F_A_from;  F_A <= F_A_to;  F_A += F_W) {
  2638.                     F_Aova = (F_A - F_torPref) / F_torHWdth;
  2639.                     US_energy = (unsigned short) (((Real)US_torBarrier) * (1.0 - exp(F_lnH * F_Aova*F_Aova)));
  2640.                     /*
  2641.                     ** if F_A(<-180.or>180), wrap to -180to180,
  2642.                     */
  2643.                     F_tor = WrpDeg(ModDeg(F_A));
  2644.                     /*
  2645.                     ** Convert from F_tor to US_tD
  2646.                     */
  2647.                     US_tD = (unsigned short) ((F_tor - F_hW + 180.)/F_W);
  2648.                     US_torProfile[I_tor][US_tD] = min(US_energy,US_torProfile[I_tor][US_tD]);
  2649.                 }/* for F_A */
  2650.                 /*
  2651.                 ** Ensure that the lowest point(s) in the profile are
  2652.                 ** zero...
  2653.                 */
  2654.                 US_min = TORBARMAX;
  2655.                 for (US_tD = 0;  US_tD < NTORDIVS;  US_tD++) {
  2656.                     US_min = min(US_min,US_torProfile[I_tor][US_tD]);
  2657.                 }
  2658.                 for (US_tD = 0;  US_tD < NTORDIVS;  US_tD++) {
  2659.                     US_torProfile[I_tor][US_tD] -= US_min;
  2660.                 }
  2661.             } else { /*DPF_HARDTORCON*/
  2662.  
  2663.                 iCon = N_con[I_tor] + 1;
  2664.                 if (iCon < MAX_TOR_CON) {
  2665.                     F_TorConRange[I_tor][N_con[I_tor]][LOWER] = F_torPref - 0.5* F_torHWdth;
  2666.                     F_TorConRange[I_tor][N_con[I_tor]][UPPER] = F_torPref + 0.5* F_torHWdth;
  2667.                     N_con[I_tor] = iCon;
  2668.                 } else {
  2669.                     pr(logFile,"\n\n I'm sorry, you can only have %d (=MAX_TOR_CON) torsion constraints.\nIf you need more, change the \"#define MAX_TOR_CON\" line in \"constants.h\".\n\n",MAX_TOR_CON);
  2670.                 }/* Still room to add another constraint. */
  2671.             } /*DPF_HARDTORCON*/
  2672.         }/* torsion-ID accepted */
  2673.         (void) fflush(logFile);
  2674.         break;
  2675.  
  2676. //______________________________________________________________________________
  2677.  
  2678.     case DPF_BARRIER:
  2679.         /*
  2680.         **  barrier
  2681.         **  Define torsion-barrier energy...
  2682.         */
  2683.         (void) sscanf( line, "%*s %d", &I_torBarrier);
  2684.         US_torBarrier = (unsigned short)I_torBarrier;
  2685.         US_torBarrier = min(US_torBarrier, TORBARMAX);
  2686.         pr(logFile,"\nTorsion barrier energy is set to %uhd\n\n", US_torBarrier);
  2687.         (void) fflush(logFile);
  2688.         break;
  2689.  
  2690. //______________________________________________________________________________
  2691.  
  2692.     case DPF_SHOWTORPEN:
  2693.         /*
  2694.         **  showtorpen
  2695.         **  Show torsion's penalty energy.
  2696.         */
  2697.         B_ShowTorE = TRUE;
  2698.         pr(logFile,"\nConstrained torsion penalty energies will be stored during docking, and output after each run\n\n");
  2699.         (void) fflush(logFile);
  2700.         break;
  2701.  
  2702. //______________________________________________________________________________
  2703.  
  2704.     case DPF_E0MAX:
  2705.         /*
  2706.         **  e0max
  2707.         **  Set maximum initial energy,
  2708.         */
  2709.         retval = sscanf( line, "%*s " FDFMT " %d", &e0max, &MaxRetries );
  2710.         if (retval == 0) {
  2711.             pr( logFile, "Could not read any arguments!\n" );
  2712.         } else if (retval == EOF) {
  2713.             pr( logFile, "End of file encountered!\n");
  2714.         } else if (retval == 1) {
  2715.             pr(logFile,"Using the default maximum number of retries for initialization, %d retries.\n\n", MaxRetries);
  2716.         } else if (retval == 2) {
  2717.             pr(logFile,"Using user-specified maximum number of retries for initialization, %d retries.\n\n", MaxRetries);
  2718.         }
  2719.         if (e0max < 0.) {
  2720.             e0max = 1000.0;
  2721.         }
  2722.         pr(logFile,"\nIf the initial energy is greater than e0max, %.3f,\nthen a new, random initial state will be created.\n\n",e0max);
  2723.         (void) fflush(logFile);
  2724.         break;
  2725.  
  2726. //______________________________________________________________________________
  2727.  
  2728.     case DPF_SIMANNEAL:
  2729.         /*
  2730.         ** simanneal
  2731.         */
  2732.         /*
  2733.         ** Calculate reduction factor based on initial and final step values,
  2734.         ** and number of cycles...
  2735.         */
  2736.         if (!command_mode) {
  2737.             ncycm1 = ncycles - 1;
  2738.             if (ncycm1 < 0) {
  2739.                 ncycm1 = 1;
  2740.             }
  2741.             if (B_CalcTrnRF) {
  2742.                 trnFac = RedFac(trnStep0, trnStepFinal, ncycm1);
  2743.                 pr( logFile, "Calculated reduction factor for translations     = %-.3f /cycle\n", trnFac);
  2744.                 B_trnReduc = (trnFac != 1.);
  2745.             }
  2746.             if (B_CalcQtwRF) {
  2747.                 qtwFac = RedFac(qtwStep0, qtwStepFinal, ncycm1);
  2748.                 pr( logFile, "Calculated reduction factor for quaternion angle = %-.3f /cycle\n", qtwFac );
  2749.                 B_qtwReduc = (qtwFac != 1.);
  2750.             }
  2751.             if (B_CalcTorRF) {
  2752.                 torFac    = RedFac(torStep0, torStepFinal, ncycm1);
  2753.                 pr( logFile, "Calculated reduction factor for torsion angles   = %-.3f /cycle\n", torFac );
  2754.                 B_torReduc = (torFac != 1.);
  2755.             }
  2756.             pr(logFile, "\n");
  2757.             /*
  2758.             ** Number of ligands read in...
  2759.             */
  2760.             if (nlig > 0) {
  2761.                 pr( logFile, "\nTotal number of ligands read in by the DPF \"move\" command = %d\n\n", nlig );
  2762.             }
  2763.             if (nres > 0) {
  2764.                 pr( logFile, "\nTotal number of residues read in by the DPF \"flex\" command = %d\n\n", nres );
  2765.             }
  2766.             pr(logFile, "\n");
  2767.             if (B_havenbp) {
  2768.                 nbe( info, ad_energy_tables, num_atom_types );
  2769.             }
  2770.             if (B_cluster_mode) {
  2771.                 clmode( num_atom_types, clus_rms_tol,
  2772.                         hostnm, jobStart, tms_jobStart,
  2773.                         B_write_all_clusmem, FN_clus, crdpdb, lig_center,
  2774.                         B_symmetry_flag, FN_rms_ref_crds );
  2775.             }
  2776.             for (j = 0; j < MAX_RUNS; j++) {
  2777.                 econf[j] = torsFreeEnergy - unbound_internal_FE;
  2778.             }
  2779.             /* ___________________________________________________________________
  2780.             **
  2781.             ** Begin the automated docking simulation,
  2782.             ** ___________________________________________________________________
  2783.             */
  2784.             simanneal( &nconf, Nnb, WallEnergy, atomstuff, charge, abs_charge, qsp_abs_charge, B_calcIntElec,
  2785.                         crd, crdpdb, dock_param_fn,
  2786.                         ad_energy_tables,
  2787.                         econf, B_either,
  2788.                         elec, emap,
  2789.                         ncycles, nruns, jobStart,
  2790.                         map,
  2791.                         naccmax, natom, nonbondlist, nrejmax, ntor1, ntor, outlev,
  2792.                         sInit, sHist,   qtwFac, B_qtwReduc, qtwStep0,
  2793.                         B_selectmin, FN_ligand, lig_center, RT0, B_tempChange, RTFac,
  2794.                         tms_jobStart, tlist, torFac, B_torReduc, torStep0,
  2795.                         FN_trj, trj_end_cyc, trj_begin_cyc, trj_freq, trnFac,
  2796.                         B_trnReduc, trnStep0, type, vt, B_write_trj,
  2797.                         B_constrain_dist, atomC1, atomC2, sqlower, squpper,
  2798.                         B_linear_schedule, RTreduc,
  2799.                         /*maxrad,*/
  2800.                         B_watch, FN_watch,
  2801.                         B_isGaussTorCon, US_torProfile, B_isTorConstrained,
  2802.                         B_ShowTorE, US_TorE, F_TorConRange, N_con,
  2803.                         B_RandomTran0, B_RandomQuat0, B_RandomDihe0,
  2804.                         e0max, torsFreeEnergy, MaxRetries, ligand_is_inhibitor,
  2805.                         ignore_inter,
  2806.                         B_include_1_4_interactions, scale_1_4,
  2807.                         parameterArray, unbound_internal_FE,
  2808.                         info, B_use_non_bond_cutoff,
  2809.                         B_have_flexible_residues,
  2810.                         PDBQT_record);
  2811.  
  2812.             (void) fflush(logFile);
  2813.         } else {
  2814.             (void)fprintf(logFile, "NOTE: Command mode has been set, so simulated annealing cannot be performed.\n\n");
  2815.             (void) fflush(logFile);
  2816.         }
  2817.         break;
  2818.  
  2819. //______________________________________________________________________________
  2820.  
  2821.     case DPF_SET_GA:
  2822.  
  2823.       if (GlobalSearchMethod != NULL) {
  2824.           pr(logFile, "Deleting the previous settings for the Genetic Algorithm.\n");
  2825.           (void) fflush(logFile);
  2826.           delete GlobalSearchMethod;
  2827.           GlobalSearchMethod = NULL;
  2828.       }
  2829.  
  2830.       if (debug > 0) {
  2831.           pr( logFile, "\n\tOutput every %u generations.\n", outputEveryNgens );
  2832.       }
  2833.       GlobalSearchMethod = new Genetic_Algorithm(e_mode, s_mode, c_mode, w_mode, elitism, c_rate, m_rate,
  2834.                                                  window_size, num_generations, outputEveryNgens );
  2835.       ((Genetic_Algorithm *)GlobalSearchMethod)->mutation_values( low, high, alpha, beta, trnStep0, qtwStep0, torStep0  );
  2836.       ((Genetic_Algorithm *)GlobalSearchMethod)->initialize(pop_size, 7+sInit.ntor);
  2837.  
  2838.       (void) fflush(logFile);
  2839.       break;
  2840. //______________________________________________________________________________
  2841.  
  2842.     case DPF_SET_SW1:
  2843.  
  2844.       if (LocalSearchMethod != NULL) {
  2845.           pr(logFile, "Deleting the previous settings for the local search Solis-Wets algorithm (SW1 object).\n");
  2846.           delete LocalSearchMethod;
  2847.           LocalSearchMethod = NULL;
  2848.       }
  2849.  
  2850.       pr(logFile, "Creating a new Local Search object using the Solis-Wets algorithm (SW1) with the current settings.\n\n");
  2851.       LocalSearchMethod = new Solis_Wets1(7+sInit.ntor, max_its, max_succ, max_fail, rho, lb_rho, 2.0, 0.5, search_freq);
  2852.  
  2853.       (void) fflush(logFile);
  2854.       break;
  2855. //______________________________________________________________________________
  2856.  
  2857.     case DPF_SET_PSW1:
  2858.  
  2859.       if (LocalSearchMethod != NULL) {
  2860.           pr(logFile, "Deleting the previous settings for the local search pseudo-Solis-Wets algorithm (pSW1 object).\n");
  2861.           delete LocalSearchMethod;
  2862.           LocalSearchMethod = NULL;
  2863.       }
  2864.  
  2865.       pr(logFile, "Creating a new Local Search object using the pseudo-Solis-Wets algorithm (pSW1) with the current settings.\n\n");
  2866.  
  2867.       //  Allocate space for the variable rho's
  2868.       rho_ptr = new Real[7+sInit.ntor];
  2869.       lb_rho_ptr = new Real[7+sInit.ntor];
  2870.  
  2871.       //  Initialize the rho's corresponding to the translation
  2872.       //  0,1,2   x,y,z
  2873.       //  3,4,5,6 qx,qy,qz,qw
  2874.       //  7,...   tor1
  2875.       for (j=0; j<3; j++) {
  2876.          // j=0,1,2
  2877.          rho_ptr[j] = trnStep0;
  2878.          // lb_rho_ptr[j] = trnStepFinal;
  2879. #define LB_RHO_FRACTION 0.10 // fraction of step size for Solis & Wets local search
  2880.          lb_rho_ptr[j] = LB_RHO_FRACTION * trnStep0;
  2881.       }
  2882.  
  2883.       //  Initialize the rho's corresponding to the quaterion
  2884.       for (; j<7; j++) {
  2885.          // j=3,4,5,6
  2886.          // rho_ptr[j] = qtwStep0;
  2887.          rho_ptr[j] = 1.0; // 4D normalized quaternion's components
  2888.          // lb_rho_ptr[j] = qtwStepFinal;
  2889.          // lb_rho_ptr[j] = LB_RHO_FRACTION * qtwStep0;
  2890.          lb_rho_ptr[j] = LB_RHO_FRACTION * 1.0;
  2891.       }
  2892.  
  2893.       //  Initialize the rho's corresponding to the torsions
  2894.       for (; j<7+sInit.ntor; j++) {
  2895.          // j=7,...
  2896.          rho_ptr[j] = torStep0;
  2897.          // lb_rho_ptr[j] = torStepFinal;
  2898.          lb_rho_ptr[j] = LB_RHO_FRACTION * torStep0;
  2899.       }
  2900.  
  2901.       LocalSearchMethod = new Pseudo_Solis_Wets1(7+sInit.ntor, max_its, max_succ, max_fail, 2.0, 0.5, search_freq, rho_ptr, lb_rho_ptr);
  2902.  
  2903.       (void) fflush(logFile);
  2904.       break;
  2905.  
  2906. //______________________________________________________________________________
  2907.  
  2908.     case DPF_SET_PATTERN:
  2909.  
  2910.       if (LocalSearchMethod != NULL) {
  2911.           pr(logFile, "Deleting the previous settings for the local search Pattern Search algorithm (PS object).\n");
  2912.           delete LocalSearchMethod;
  2913.           LocalSearchMethod = NULL;
  2914.       }
  2915.  
  2916.  
  2917.       pr(logFile, "Creating a new Local Search object using the Pattern Search algorithm (PS) with the current settings.\n\n");
  2918.       LocalSearchMethod = new Pattern_Search(7+sInit.ntor, max_succ, rho, lb_rho, 2.0, 0.5, search_freq);
  2919.  
  2920.       (void) fflush(logFile);
  2921.       break;
  2922.  
  2923. //______________________________________________________________________________
  2924.  
  2925.     case DPF_GALS:
  2926.         (void) fflush( logFile );
  2927.         /*
  2928.         ** Genetic Algorithm-Local search,  a.k.a. Lamarckian Genetic Algorithm
  2929.         */
  2930.         if (!command_mode) {
  2931.             (void) sscanf( line, "%*s %d", &nruns );
  2932.             if ( nruns > MAX_RUNS ) {
  2933.                 prStr( error_message, "%s:  ERROR: %d runs requested, but only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", programname, nruns, MAX_RUNS);
  2934.                 stop( error_message );
  2935.                 exit( -1 );
  2936.             } else if ((GlobalSearchMethod==NULL)||(LocalSearchMethod==NULL)) {
  2937.                 prStr(error_message, "%s:  ERROR:  You must use \"set_ga\" to allocate both Global Optimization object AND Local Optimization object.\n", programname);
  2938.                 stop(error_message);
  2939.                 exit(-1);
  2940.             } else if (!B_found_elecmap) {
  2941.                 prStr(error_message, "%s:  ERROR:  no \"elecmap\" command has been specified!\n", programname);
  2942.                 stop(error_message);
  2943.                 exit(-1);
  2944.             } else if (!B_found_desolvmap) {
  2945.                 prStr(error_message, "%s:  ERROR:  no \"desolvmap\" command has been specified!\n", programname);
  2946.                 stop(error_message);
  2947.                 exit(-1);
  2948.             }
  2949.  
  2950.             pr( logFile, "Number of requested LGA dockings = %d run%c\n", nruns, (nruns > 1)?'s':' ');
  2951.  
  2952. #ifdef DEBUG
  2953.             pr( logFile, "\nAbout to call evaluate.setup(), sInit:\n\n");
  2954.             printState( logFile, sInit, 2 );
  2955. #endif
  2956.  
  2957.             evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  2958.                             elec, emap, nonbondlist, ad_energy_tables, Nnb,
  2959.                             B_calcIntElec, B_isGaussTorCon, B_isTorConstrained,
  2960.                             B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  2961.                             ignore_inter,
  2962.                             B_include_1_4_interactions, scale_1_4,
  2963.                             parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  2964.  
  2965.             evaluate.compute_intermol_energy(TRUE);
  2966.  
  2967.             if(write_stateFile){
  2968.               fprintf(stateFile,"\t<run_requested>%d</run_requested>\n",nruns);
  2969.               fprintf(stateFile,"\t<runs>\n");
  2970.             }
  2971.             for (j=0; j<nruns; j++) {
  2972.                 j1=j+1;
  2973.  
  2974.                 (void) fprintf( logFile, "\n\n\tBEGINNING LAMARCKIAN GENETIC ALGORITHM DOCKING\n");
  2975.                 (void) fflush( logFile );
  2976.                 pr( logFile, "\nRun:\t%d / %d\n", j1, nruns );
  2977.  
  2978.                 pr(logFile, "Date:\t");
  2979.                 printdate( logFile, 2 );
  2980.                 (void) fflush( logFile );
  2981.  
  2982.                 gaStart = times( &tms_gaStart );
  2983.  
  2984.                 if (B_reorient_random == TRUE) {
  2985.                     // create a new random orientation before docking
  2986.                     create_random_orientation( &q_reorient );
  2987.                     // reorient the ligand
  2988.                     reorient( logFile, true_ligand_atoms, atomstuff, crdpdb, charge, type,
  2989.                               parameterArray, q_reorient, origin, ntor, tlist, vt, &ligand, debug );
  2990.                     // update the evaluate object
  2991.                     evaluate.update_crds( crdpdb, vt );
  2992.                 }
  2993.  
  2994.                 //  Can get rid of the following line
  2995.                 ((Genetic_Algorithm *)GlobalSearchMethod)->initialize(pop_size, 7+sInit.ntor);
  2996.  
  2997.                 // Reiterate output level...
  2998.                 pr(logFile, "Output level is set to %d.\n\n", outlev);
  2999.  
  3000.                 // Start Lamarckian GA run -- Bound simulation
  3001.                 sHist[nconf] = call_glss( GlobalSearchMethod, LocalSearchMethod,
  3002.                                           sInit,
  3003.                                           num_evals, pop_size,
  3004.                                           outlev,
  3005.                                           outputEveryNgens, &ligand,
  3006.                                           B_RandomTran0, B_RandomQuat0, B_RandomDihe0,
  3007.                                           info, FN_pop_file );
  3008.                 // State of best individual at end of GA-LS run is returned.
  3009.                 // Finished Lamarckian GA run
  3010.  
  3011.                 gaEnd = times( &tms_gaEnd );
  3012.                 pr( logFile, "\nRun completed;  time taken for this run:\n");
  3013.                 timesyshms( gaEnd - gaStart, &tms_gaStart, &tms_gaEnd );
  3014.                 pr( logFile, "\n");
  3015.                 printdate( logFile, 1 );
  3016.                 (void) fflush( logFile );
  3017.  
  3018.                 pr(logFile, "Total number of Energy Evaluations: %lu\n", evaluate.evals() );
  3019.                 pr(logFile, "Total number of Generations:        %u\n", ((Genetic_Algorithm *)GlobalSearchMethod)->num_generations());
  3020.  
  3021.                 pr( logFile, "\n\n\tFINAL LAMARCKIAN GENETIC ALGORITHM DOCKED STATE\n" );
  3022.                 pr( logFile,     "\t_______________________________________________\n\n\n" );
  3023.  
  3024.                 writePDBQT( j, seed,  FN_ligand, dock_param_fn, lig_center,
  3025.                             sHist[nconf], ntor, &eintra, &einter, natom, atomstuff,
  3026.                             crd, emap, elec,
  3027.                             charge, abs_charge, qsp_abs_charge,
  3028.                             ligand_is_inhibitor,
  3029.                             torsFreeEnergy,
  3030.                             vt, tlist, crdpdb, nonbondlist,
  3031.                             ad_energy_tables,
  3032.                             type, Nnb, B_calcIntElec,
  3033.                             map,
  3034.                             outlev, ignore_inter,
  3035.                             B_include_1_4_interactions, scale_1_4, parameterArray, unbound_internal_FE,
  3036.                             info, DOCKED, PDBQT_record, B_use_non_bond_cutoff, B_have_flexible_residues);
  3037.  
  3038.                 econf[nconf] = eintra + einter + torsFreeEnergy - unbound_internal_FE;
  3039.  
  3040.                 ++nconf;
  3041.  
  3042.                 pr( logFile, UnderLine );
  3043.             } // Next LGA run
  3044.             if(write_stateFile){
  3045.                fprintf(stateFile,"\t</runs>\n");
  3046.                (void) fflush(stateFile);
  3047.             }
  3048.             (void) fflush(logFile);
  3049.         } else {
  3050.             (void)fprintf(logFile, "NOTE: Command mode has been set.  Sorry, genetic algorithm-local search cannot be performed.\n\n");
  3051.         }
  3052.         break;
  3053.  
  3054. //______________________________________________________________________________
  3055.  
  3056.     case DPF_LS:
  3057.        // do_local_only
  3058.        (void) sscanf(line, "%*s %d", &nruns);
  3059.  
  3060.         if (!command_mode) {
  3061.             if ( nruns > MAX_RUNS ) {
  3062.  
  3063.                prStr( error_message, "%s:  ERROR: %d runs requested, but only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", programname, nruns, MAX_RUNS);
  3064.                stop( error_message );
  3065.                exit( -1 );
  3066.  
  3067.            } else if (LocalSearchMethod==NULL) {
  3068.  
  3069.                prStr(error_message, "%s:  ERROR:  You must use \"set_sw1\", \"set_psw1\" or \"set_pattern\" to create a Local Optimization object.\n", programname);
  3070.                stop(error_message);
  3071.                exit(-1);
  3072.            } else if (!B_found_elecmap) {
  3073.                prStr(error_message, "%s:  ERROR:  no \"elecmap\" command has been specified!\n", programname);
  3074.                stop(error_message);
  3075.                exit(-1);
  3076.            } else if (!B_found_desolvmap) {
  3077.                prStr(error_message, "%s:  ERROR:  no \"desolvmap\" command has been specified!\n", programname);
  3078.                stop(error_message);
  3079.                exit(-1);
  3080.            }
  3081.  
  3082.  
  3083.            pr( logFile, "Number of Local Search (LS) only dockings = %d run%c\n", nruns, (nruns > 1)?'s':' ');
  3084.            evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  3085.                            elec, emap,
  3086.                            nonbondlist,
  3087.                            ad_energy_tables,
  3088.                            Nnb, B_calcIntElec, B_isGaussTorCon,B_isTorConstrained,
  3089.                            B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  3090.                            ignore_inter,
  3091.                            B_include_1_4_interactions, scale_1_4,
  3092.                            parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  3093.  
  3094.             evaluate.compute_intermol_energy(TRUE);
  3095.  
  3096.            if(write_stateFile){
  3097.              fprintf(stateFile,"\t<run_requested>%d</run_requested>\n",nruns);
  3098.              fprintf(stateFile,"\t<runs>\n");
  3099.            }
  3100.  
  3101.            for (j=0; j<nruns; j++) {
  3102.  
  3103.                (void) fprintf( logFile, "\n\n\tBEGINNING SOLIS & WETS LOCAL SEARCH DOCKING\n");
  3104.                pr( logFile, "\nRun:\t%d / %d\n", j+1, nruns );
  3105.                (void) fflush( logFile );
  3106.  
  3107.                pr(logFile, "Date:\t");
  3108.                printdate( logFile, 2 );
  3109.                (void) fflush( logFile );
  3110.  
  3111.                gaStart = times( &tms_gaStart );
  3112.  
  3113.                sHist[nconf] = call_ls(LocalSearchMethod, sInit, pop_size, &ligand);
  3114.  
  3115.                pr(logFile, "There were %lu Energy Evaluations.\n", evaluate.evals());
  3116.  
  3117.                gaEnd = times( &tms_gaEnd );
  3118.                pr( logFile, "Time taken for this Local Search (LS) run:\n");
  3119.                timesyshms( gaEnd - gaStart, &tms_gaStart, &tms_gaEnd );
  3120.                pr( logFile, "\n");
  3121.                (void) fflush( logFile );
  3122.  
  3123.                pr( logFile, "\n\n\tFINAL LOCAL SEARCH DOCKED STATE\n" );
  3124.                pr( logFile,     "\t_______________________________\n\n\n" );
  3125.  
  3126.                writePDBQT( j, seed, FN_ligand, dock_param_fn, lig_center,
  3127.                            sHist[nconf], ntor, &eintra, &einter, natom, atomstuff,
  3128.                            crd, emap, elec,
  3129.                            charge, abs_charge, qsp_abs_charge,
  3130.                            ligand_is_inhibitor,
  3131.                            torsFreeEnergy,
  3132.                            vt, tlist, crdpdb, nonbondlist,
  3133.                            ad_energy_tables,
  3134.                            type, Nnb, B_calcIntElec,
  3135.                            map,
  3136.                            outlev,
  3137.                            ignore_inter,
  3138.                            B_include_1_4_interactions, scale_1_4, parameterArray, unbound_internal_FE,
  3139.                            info, DOCKED, PDBQT_record, B_use_non_bond_cutoff, B_have_flexible_residues);
  3140.  
  3141.                econf[nconf] = eintra + einter + torsFreeEnergy - unbound_internal_FE;
  3142.  
  3143.                ++nconf;
  3144.  
  3145.                pr( logFile, UnderLine );
  3146.  
  3147.            } // Next run
  3148.            if(write_stateFile){
  3149.              fprintf(stateFile,"\t</runs>\n");
  3150.              (void) fflush(stateFile);
  3151.            }
  3152.            (void) fflush(logFile);
  3153.        } else {
  3154.             (void)fprintf(logFile, "NOTE: Command mode has been set, so local search cannot be performed.\n\n");
  3155.        }
  3156.        break;
  3157.  
  3158. //______________________________________________________________________________
  3159.  
  3160.     case DPF_GS:
  3161.       (void) sscanf(line, "%*s %d", &nruns);
  3162.  
  3163.       if (!command_mode) {
  3164.           if (nruns>MAX_RUNS) {
  3165.  
  3166.               prStr(error_message, "%s:  ERROR:  %d runs requested, but only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", programname, nruns, MAX_RUNS);
  3167.               stop(error_message);
  3168.               exit(-1);
  3169.  
  3170.           } else if (GlobalSearchMethod==NULL) {
  3171.               prStr(error_message, "%s:  ERROR:  You must use \"set_ga\" to allocate a Global Optimization object.\n", programname);
  3172.               stop(error_message);
  3173.               exit(-1);
  3174.           } else if (!B_found_elecmap) {
  3175.                prStr(error_message, "%s:  ERROR:  no \"elecmap\" command has been specified!\n", programname);
  3176.                stop(error_message);
  3177.                exit(-1);
  3178.            }
  3179.            else if (!B_found_desolvmap) {
  3180.                prStr(error_message, "%s:  ERROR:  no \"desolvmap\" command has been specified!\n", programname);
  3181.                stop(error_message);
  3182.                exit(-1);
  3183.            }
  3184.  
  3185.  
  3186.           pr(logFile, "Number of Genetic Algorithm (GA) only dockings = %d run%c\n", nruns, (nruns>1)?'s':' ');
  3187.  
  3188.  
  3189.           evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  3190.                           elec, emap,
  3191.                           nonbondlist,
  3192.                           ad_energy_tables,
  3193.                           Nnb, B_calcIntElec, B_isGaussTorCon,B_isTorConstrained,
  3194.                           B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  3195.                           ignore_inter,
  3196.                           B_include_1_4_interactions, scale_1_4,
  3197.                           parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  3198.  
  3199.             evaluate.compute_intermol_energy(TRUE);
  3200.  
  3201.           if(write_stateFile){
  3202.             fprintf(stateFile,"\t<run_requested>%d</run_requested>\n",nruns);
  3203.             fprintf(stateFile,"\t<runs>\n");
  3204.           }
  3205.           for (j=0; j<nruns; j++) {
  3206.  
  3207.               fprintf( logFile, "\n\n\tBEGINNING GENETIC ALGORITHM DOCKING\n");
  3208.               pr(logFile, "\nDoing Genetic Algorithm run:  %d/%d.\n", j+1, nruns);
  3209.               (void) fflush( logFile );
  3210.  
  3211.               pr(logFile, "Date:\t");
  3212.               printdate( logFile, 2 );
  3213.               (void) fflush( logFile );
  3214.  
  3215.               gaStart = times(&tms_gaStart);
  3216.  
  3217.               sHist[nconf] = call_gs( GlobalSearchMethod, sInit, num_evals, pop_size,
  3218.                                       &ligand, outputEveryNgens, info);
  3219.  
  3220.               pr(logFile, "\nFinal docked state:\n");
  3221.               printState(logFile, sHist[nconf], 2);
  3222.  
  3223.               gaEnd = times(&tms_gaEnd);
  3224.               pr(logFile, "Time taken for this Genetic Algorithm (GA) run:\n");
  3225.               timesyshms(gaEnd-gaStart, &tms_gaStart, &tms_gaEnd);
  3226.               pr(logFile, "\n");
  3227.               (void) fflush(logFile);
  3228.  
  3229.               pr(logFile, "Total number of Energy Evaluations: %lu\n", evaluate.evals() );
  3230.               pr(logFile, "Total number of Generations:        %u\n", ((Genetic_Algorithm *)GlobalSearchMethod)->num_generations());
  3231.  
  3232.  
  3233.               pr( logFile, "\n\n\tFINAL GENETIC ALGORITHM DOCKED STATE\n" );
  3234.               pr( logFile,     "\t____________________________________\n\n\n" );
  3235.  
  3236.               writePDBQT( j, seed, FN_ligand, dock_param_fn, lig_center,
  3237.                           sHist[nconf], ntor, &eintra, &einter, natom, atomstuff,
  3238.                           crd, emap, elec,
  3239.                           charge, abs_charge, qsp_abs_charge,
  3240.                           ligand_is_inhibitor,
  3241.                           torsFreeEnergy,
  3242.                           vt, tlist, crdpdb, nonbondlist,
  3243.                           ad_energy_tables,
  3244.                           type, Nnb, B_calcIntElec,
  3245.                           map,
  3246.                           outlev,
  3247.                           ignore_inter,
  3248.                           B_include_1_4_interactions, scale_1_4, parameterArray, unbound_internal_FE,
  3249.                           info, DOCKED, PDBQT_record, B_use_non_bond_cutoff, B_have_flexible_residues);
  3250.  
  3251.               econf[nconf] = eintra + einter + torsFreeEnergy - unbound_internal_FE;
  3252.  
  3253.               ++nconf;
  3254.  
  3255.               pr( logFile, UnderLine );
  3256.  
  3257.           } // Next run
  3258.           if(write_stateFile){
  3259.             fprintf(stateFile,"\t</runs>\n");
  3260.             (void) fflush(stateFile);
  3261.           }
  3262.           (void) fflush(logFile);
  3263.       } else {
  3264.             (void)fprintf(logFile, "NOTE: Command mode has been set, so global search cannot be performed.\n\n");
  3265.       }
  3266.       break;
  3267.  
  3268. //______________________________________________________________________________
  3269.  
  3270.     case GA_pop_size:
  3271.        (void) sscanf(line, "%*s %u", &pop_size);
  3272.        pr(logFile, "A population of %u individuals will be used\n", pop_size);
  3273.         (void) fflush(logFile);
  3274.        break;
  3275.  
  3276. //______________________________________________________________________________
  3277.  
  3278.     case GA_num_generations:
  3279.        (void) sscanf(line, "%*s %u", &num_generations);
  3280.        pr(logFile, "The GA will run for at most %u generations.\n", num_generations);
  3281.         (void) fflush(logFile);
  3282.        break;
  3283.  
  3284. //______________________________________________________________________________
  3285.  
  3286.     case GA_num_evals:
  3287.        (void) sscanf(line, "%*s %u", &num_evals);
  3288.        pr(logFile, "There will be at most %u function evaluations used.\n", num_evals);
  3289.         (void) fflush(logFile);
  3290.        break;
  3291.  
  3292. //______________________________________________________________________________
  3293.  
  3294.     case GA_window_size:
  3295.        (void) sscanf(line, "%*s %d", &window_size);
  3296.        pr(logFile, "The GA's selection window is %d generations.\n", window_size);
  3297.         (void) fflush(logFile);
  3298.        break;
  3299.  
  3300. //______________________________________________________________________________
  3301.  
  3302.     case GA_low:
  3303.        (void) sscanf(line, "%*s %d", &low);
  3304.        pr(logFile, "Setting low to %d.\n", low);
  3305.         (void) fflush(logFile);
  3306.        break;
  3307.  
  3308. //______________________________________________________________________________
  3309.  
  3310.     case GA_high:
  3311.        (void) sscanf(line, "%*s %d", &high);
  3312.        pr(logFile, "Setting high to %d.\n", high);
  3313.         (void) fflush(logFile);
  3314.        break;
  3315.  
  3316. //______________________________________________________________________________
  3317.  
  3318.     case GA_elitism:
  3319.        (void) sscanf(line, "%*s %d", &elitism);
  3320.        pr(logFile, "The %d best will be preserved each generation.\n", elitism);
  3321.         (void) fflush(logFile);
  3322.        break;
  3323.  
  3324. //______________________________________________________________________________
  3325.  
  3326.     case GA_mutation_rate:
  3327.        (void) sscanf(line, "%*s " FDFMT, &m_rate);
  3328.        pr(logFile, "The mutation rate is %f.\n", m_rate);
  3329.         (void) fflush(logFile);
  3330.        break;
  3331.  
  3332. //______________________________________________________________________________
  3333.  
  3334.     case GA_crossover_rate:
  3335.        (void) sscanf(line, "%*s " FDFMT, &c_rate);
  3336.        pr(logFile, "The crossover rate is %f.\n", c_rate);
  3337.         (void) fflush(logFile);
  3338.        break;
  3339.  
  3340. //______________________________________________________________________________
  3341.  
  3342.     case GA_Cauchy_alpha:
  3343.        (void) sscanf(line, "%*s " FDFMT, &alpha);
  3344.        pr(logFile, "The alpha parameter (for the Cauchy distribution) is being set to %f.\n",
  3345.           alpha);
  3346.         (void) fflush(logFile);
  3347.        break;
  3348.  
  3349. //______________________________________________________________________________
  3350.  
  3351.     case GA_Cauchy_beta:
  3352.        (void) sscanf(line, "%*s " FDFMT, &beta);
  3353.        pr(logFile, "The beta parameter (for the Cauchy distribution) is being set to %f.\n",
  3354.           beta);
  3355.         (void) fflush(logFile);
  3356.        break;
  3357.  
  3358. //______________________________________________________________________________
  3359.  
  3360.     case SW_max_its:
  3361.        (void) sscanf(line, "%*s %u", &max_its);
  3362.        pr(logFile, "Solis & Wets algorithms will perform at most %u iterations.\n", max_its);
  3363.         (void) fflush(logFile);
  3364.        break;
  3365.  
  3366. //______________________________________________________________________________
  3367.  
  3368.     case SW_max_succ:
  3369.        (void) sscanf(line, "%*s %u", &max_succ);
  3370.        pr(logFile, "Solis & Wets algorithms expand rho every %u in a row successes.\n", max_succ);
  3371.         (void) fflush(logFile);
  3372.       break;
  3373.  
  3374. //______________________________________________________________________________
  3375.  
  3376.     case SW_max_fail:
  3377.        (void) sscanf(line, "%*s %u", &max_fail);
  3378.        pr(logFile, "Solis & Wets algorithms contract rho every %u in a row failures.\n", max_fail);
  3379.         (void) fflush(logFile);
  3380.       break;
  3381.  
  3382. //______________________________________________________________________________
  3383.  
  3384.     case SW_rho:
  3385.        (void) sscanf(line, "%*s " FDFMT, &rho);
  3386.        pr(logFile, "rho is set to %f.\n", rho);
  3387.         (void) fflush(logFile);
  3388.       break;
  3389.  
  3390. //______________________________________________________________________________
  3391.  
  3392.     case SW_lb_rho:
  3393.         (void) sscanf(line, "%*s " FDFMT, &lb_rho);
  3394.         pr(logFile, "rho will never get smaller than %f.\n", lb_rho);
  3395.         (void) fflush(logFile);
  3396.         break;
  3397.  
  3398. //______________________________________________________________________________
  3399.  
  3400.     case LS_search_freq:
  3401.         (void) sscanf(line, "%*s " FDFMT, &search_freq);
  3402.         pr(logFile, "Local search will be performed with frequency %f.\n", search_freq);
  3403.         (void) fflush(logFile);
  3404.         break;
  3405.  
  3406. //______________________________________________________________________________
  3407.  
  3408.     case DPF_ANALYSIS:
  3409.         /*
  3410.         ** analysis
  3411.         */
  3412.         /* _____________________________________________________________________
  3413.         **
  3414.         ** Perform Cluster analysis on results of docking,
  3415.         ** _____________________________________________________________________
  3416.         */
  3417.         if (!command_mode) {
  3418.             analysis( Nnb, atomstuff, charge, abs_charge, qsp_abs_charge, B_calcIntElec, clus_rms_tol,
  3419.                       crdpdb, ad_energy_tables, map, econf, nruns,
  3420.                       natom, nonbondlist, nconf, ntor, sHist, FN_ligand,
  3421.                       lig_center, B_symmetry_flag, tlist, type, vt, FN_rms_ref_crds,
  3422.                       torsFreeEnergy, B_write_all_clusmem, ligand_is_inhibitor,
  3423.                       outlev,
  3424.                       ignore_inter, B_include_1_4_interactions, scale_1_4,
  3425.                       parameterArray, unbound_internal_FE,
  3426.                       info, B_use_non_bond_cutoff, B_have_flexible_residues,
  3427.                       B_rms_atoms_ligand_only);
  3428.  
  3429.             (void) fflush(logFile);
  3430.         } else {
  3431.             (void)fprintf(logFile, "NOTE: Command mode has been set, so cluster analysis cannot be performed.\n\n");
  3432.         }
  3433.         break;
  3434.  
  3435. //______________________________________________________________________________
  3436.  
  3437.     case DPF_TORSDOF:
  3438.         /*
  3439.         ** torsdof %d %f
  3440.         */
  3441.         retval = sscanf( line, "%*s %d " FDFMT, &ntorsdof, &torsdoffac );
  3442.         if (retval == 2) {
  3443.             pr( logFile, "WARNING:  The torsional DOF coefficient is now read in from the parameter file; the value specified here (%.4lf) will be ignored.\n\n", (double)torsdoffac);
  3444.         }
  3445.         pr( logFile, "Number of torsional degrees of freedom = %d\n", ntorsdof);
  3446.         pr( logFile, "Free energy coefficient for torsional degrees of freedom = %.4f", AD4.coeff_tors);
  3447.         if (parameter_library_found == 1) {
  3448.             pr( logFile, " as specified in parameter library \"%s\".\n\n", FN_parameter_library );
  3449.         } else {
  3450.             pr( logFile, ", the factory default value.\n\n");
  3451.         }
  3452.  
  3453.         torsFreeEnergy = (Real)ntorsdof * AD4.coeff_tors;
  3454.  
  3455.         pr( logFile, "Estimated loss of torsional free energy upon binding = %+.4f kcal/mol\n\n", torsFreeEnergy);
  3456.         (void) fflush(logFile);
  3457.         break;
  3458.  
  3459. //______________________________________________________________________________
  3460.  
  3461.     case DPF_INVESTIGATE:
  3462.         /*
  3463.         ** Bin energies by RMSD from reference structure
  3464.         **
  3465.         ** investigate 100000 1000000 100
  3466.         */
  3467.         (void) sscanf( line, "%*s %d %d %d", &OutputEveryNTests, &maxTests, &NumLocalTests );
  3468.         (void) fprintf( logFile, "OutputEveryNTests= %d\n", OutputEveryNTests);
  3469.         (void) fprintf( logFile, "maxTests= %d\n", maxTests );
  3470.         (void) fprintf( logFile, "NumLocalTests= %d\n\n", NumLocalTests );
  3471.         (void) investigate( Nnb, charge, abs_charge, qsp_abs_charge, B_calcIntElec,
  3472.                             crd, crdpdb, ad_energy_tables,
  3473.                             maxTests,
  3474.                             map, natom, nonbondlist, ntor,
  3475.                             outlev, tlist, type, vt, B_isGaussTorCon, US_torProfile,
  3476.                             B_isTorConstrained, B_ShowTorE, US_TorE,
  3477.                             F_TorConRange, N_con, B_symmetry_flag, FN_rms_ref_crds,
  3478.                             OutputEveryNTests, NumLocalTests, trnStep0, torStep0,
  3479.                             ignore_inter,
  3480.                             B_include_1_4_interactions, scale_1_4,
  3481.                             parameterArray, unbound_internal_FE,
  3482.                             info, B_use_non_bond_cutoff, B_have_flexible_residues );
  3483.  
  3484.         (void) fflush(logFile);
  3485.         break;
  3486.  
  3487. //______________________________________________________________________________
  3488.  
  3489.     case DPF_LIG_NOT_INHIB:
  3490.         /*
  3491.         ** ligand_is_not_inhibitor
  3492.         */
  3493.         ligand_is_inhibitor = 0;
  3494.         pr( logFile, "\nThis ligand is not an inhibitor, so dissociation constants (Kd) will be calculated, not inhibition constants (Ki).\n\n" );
  3495.         (void) fflush(logFile);
  3496.         break;
  3497.  
  3498. /*____________________________________________________________________________*/
  3499.  
  3500.     case DPF_UNBOUND:
  3501.         /*
  3502.          * unbound 0.0
  3503.          */
  3504.         (void) sscanf( line, "%*s " FDFMT, &unbound_internal_FE );
  3505.         pr(logFile, "The internal energy of the unbound state was set to %+.3lf kcal/mol\n\n", unbound_internal_FE);
  3506.         (void) fflush(logFile);
  3507.         break;
  3508.  
  3509. /*____________________________________________________________________________*/
  3510.  
  3511.     case DPF_COMPUTE_UNBOUND_EXTENDED:
  3512.         /*
  3513.          *  compute_unbound_extended
  3514.          */
  3515.         if (ntor > 0) {
  3516.  
  3517.             pr(logFile, "Computing the energy of the unbound state of the ligand,\ngiven the torsion tree defined in the ligand file.\n\n");
  3518.             (void) fflush( logFile );
  3519.  
  3520.             // The initial goal is to obtain an extended conformation of the ligand.
  3521.  
  3522.             // Step 0 // {
  3523.             //
  3524.             // Set termination criteria for unbound calculations
  3525.             // -------------------------------------------------
  3526.             //
  3527.             // Set the maximum number of energy evaluations for finding the unbound conformation
  3528.             // if num_evals is less than this, then a shorter unbound docking will be performed
  3529.             max_evals_unbound = 1000000; // 1 million
  3530.             num_evals_unbound = num_evals > max_evals_unbound ?  max_evals_unbound :  num_evals;
  3531.             // end of Step 0 // }
  3532.  
  3533.             // Step 1 // {
  3534.             //
  3535.             // Run a hybrid global-local search using the unbound energy tables (set to be repulsive-only)
  3536.             // -------------------------------------------------------------------------------------------
  3537.             //
  3538.             //  *  Turn off the use of the non-bond cutoff
  3539.             //  *  Turn off internal electrostatics
  3540.             //  *  Turn off intermolecular energy calculations
  3541.             // TODO Do not translate or rotate the ligand in unbound searches
  3542.             //
  3543.             /*
  3544.              *  Genetic Algorithm-Local search,  a.k.a.
  3545.              *  Lamarckian Genetic Algorithm
  3546.              */
  3547.             if ((GlobalSearchMethod==NULL)||(LocalSearchMethod==NULL)) {
  3548.                 prStr(error_message, "%s:  ERROR:  You must use \"set_ga\" to allocate both Global Optimization object AND Local Optimization object.\n", programname);
  3549.                 stop(error_message);
  3550.                 exit(-1);
  3551.             } else if (!B_found_elecmap) {
  3552.                 prStr(error_message, "%s:  ERROR:  no \"elecmap\" command has been specified!\n", programname);
  3553.                 stop(error_message);
  3554.                 exit(-1);
  3555.             } else if (!B_found_desolvmap) {
  3556.                 prStr(error_message, "%s:  ERROR:  no \"desolvmap\" command has been specified!\n", programname);
  3557.                 stop(error_message);
  3558.                 exit(-1);
  3559.             }
  3560.             //
  3561.             // Do not use a non-bond cutoff, this helps to produce the "most" extended conformation
  3562.             // especially with long inhibitors
  3563.             B_use_non_bond_cutoff = FALSE;
  3564.             //
  3565.             // Save the current value of B_calcIntElec, so we can restore it later.
  3566.             B_calcIntElec_saved = B_calcIntElec;
  3567.             //
  3568.             // Set the calculation of internal electrostatics to FALSE:
  3569.             // B_calcIntElec = FALSE;
  3570.             //
  3571.             // Assume the unbound state of the receptor is the same as the input coordinates from the
  3572.             // flexible residues file.  This means we must not change the rotatable bonds in the
  3573.             // flexible residues of the receptor during the unbound extended search.
  3574.             // We can turn off rotation of the flexres by setting ntor to ntor_ligand.
  3575.             // Save the current value of "ntor" in the "sInit" state variable, set it to number of torsions
  3576.             // in the ligand for the unbound extended search, then restore it afterwards.
  3577.             saved_sInit_ntor = sInit.ntor;
  3578.             sInit.ntor = ntor_ligand;
  3579.             //
  3580.             // Use the repulsive unbound energy tables, "unbound_energy_tables",
  3581.             // to drive the molecule into an extended conformation
  3582.             evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  3583.                             elec, emap, nonbondlist, unbound_energy_tables, Nnb,
  3584.                             B_calcIntElec, B_isGaussTorCon, B_isTorConstrained,
  3585.                             B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  3586.                             ignore_inter,
  3587.                             B_include_1_4_interactions, scale_1_4,
  3588.                             parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  3589.             //
  3590.             // Turn off computing the intermolecular energy, we will only consider the intramolecular energy
  3591.             // to determine the unbound state of the flexible molecule:
  3592.             evaluate.compute_intermol_energy(FALSE);
  3593.             //
  3594.             (void) fprintf( logFile, "\n\n\tBEGINNING COMPUTATION OF UNBOUND EXTENDED STATE USING LGA\n");
  3595.             (void) fprintf( logFile,     "\t_________________________________________________________\n\n\n");
  3596.             (void) fflush( logFile );
  3597.             //
  3598.             pr(logFile, "Date:\t");
  3599.             printdate( logFile, 2 );
  3600.             (void) fflush( logFile );
  3601.             gaStart = times( &tms_gaStart );
  3602.             //  Can get rid of the following line
  3603.             ((Genetic_Algorithm *)GlobalSearchMethod)->initialize(pop_size, 7+sInit.ntor);
  3604.             //
  3605.             // Start Lamarckian GA run searching only torsions -- Unbound simulation
  3606.             // sUnbound_ext = call_glss_tors( GlobalSearchMethod, LocalSearchMethod,
  3607.             sUnbound_ext = call_glss( GlobalSearchMethod, LocalSearchMethod,
  3608.                                       sInit,
  3609.                                       num_evals_unbound, pop_size,
  3610.                                       outlev,
  3611.                                       outputEveryNgens, &ligand,
  3612.                                       // B_RandomDihe0, // use this line with call_glss_tors()
  3613.                                       B_RandomTran0, B_RandomQuat0, B_RandomDihe0,
  3614.                                       info, FN_pop_file );
  3615.             // State of best individual at end of GA-LS run, sUnbound_ext, is returned.
  3616.             // Finished Lamarckian GA run
  3617.             gaEnd = times( &tms_gaEnd );
  3618.             pr( logFile, "\nFinished Lamarckian Genetic Algorithm (LGA), time taken:\n");
  3619.             timesyshms( gaEnd - gaStart, &tms_gaStart, &tms_gaEnd );
  3620.             pr( logFile, "\n");
  3621.             printdate( logFile, 1 );
  3622.             (void) fflush( logFile );
  3623.             pr(logFile, "\nTotal number of Energy Evaluations: %lu\n", evaluate.evals() );
  3624.             pr(logFile, "Total number of Generations:        %u\n", ((Genetic_Algorithm *)GlobalSearchMethod)->num_generations());
  3625.             // end of Step 1 // }
  3626.  
  3627.             // Step 2 // {
  3628.             //
  3629.             // Do a short local search using the standard internal energy tables
  3630.             // -----------------------------------------------------------------
  3631.             //
  3632.             // turn on internal electrostatics
  3633.             // but keep intermolecular energy calculations off
  3634.             //
  3635.             // Turn on calculation of internal electrostatics:
  3636.             //// B_calcIntElec = TRUE;
  3637.             //
  3638.             // Use the standard AutoDock energy tables to compute the internal energy
  3639.             // Use this value to set unbound_internal_FE
  3640.             //// evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  3641.                             //// elec, emap, nonbondlist, ad_energy_tables, Nnb,
  3642.                             //// B_calcIntElec, B_isGaussTorCon, B_isTorConstrained,
  3643.                             //// B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  3644.                             //// ignore_inter,
  3645.                             //// B_include_1_4_interactions, scale_1_4,
  3646.                             //// parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  3647.             //
  3648.             // --- Start Local Search ---
  3649.             //// pr( logFile, "\nPerforming local search using standard AutoDock scoring function\n" );
  3650.             //// pr( logFile, "\nUsing UnboundLocalSearchMethod = new Solis_Wets1(7+sInit.ntor, 300, 4, 4, 1., 0.01, 2., 0.5, 1.);\n\n" );
  3651.             // Create a local search object
  3652.             // * Use an initial rho value of 0.1 (default is set in DPF by "sw_rho 1.0")
  3653.             //   to ensure smaller, 'more local' steps.
  3654.             // * Use a search frequency of 1.0 (default is set in DPF by "ls_search_freq 0.06")
  3655.             //// unsigned int ls_pop_size = 150;
  3656.             // max_its = 300
  3657.             // max_succ = 4
  3658.             // max_fail = 4
  3659.             // rho = 1.
  3660.             // lb_rho = 0.01
  3661.             // expansion = 2.
  3662.             // contraction = 0.5
  3663.             // search_freq = 1.
  3664.             //// UnboundLocalSearchMethod = new Solis_Wets1(7+sInit.ntor, 300, 4, 4, 1., 0.01, 2., 0.5, 1.);
  3665.             // Perform a local search, using the standard AutoDock 4 scoring function
  3666.             //// sUnbound_ls = call_ls( UnboundLocalSearchMethod, sUnbound_ext, ls_pop_size, &ligand );
  3667.             //// // sUnbound_ext = sUnbound_ls; // if you want to update sUnbound_ext to be sUnbound_ls...
  3668.             // --- Finished Local Search ---
  3669.             // end of Step 2 // }
  3670.  
  3671.             // Step 3 // {
  3672.             //
  3673.             // Restore the AutoDock 4 force field for docking
  3674.             // ----------------------------------------------
  3675.             //
  3676.             // Remember to turn on the use of the non-bond cutoff
  3677.             B_use_non_bond_cutoff = TRUE;
  3678.             //
  3679.             // Restore the setting for calculation of internal electrostatics to the saved value:
  3680.             B_calcIntElec = B_calcIntElec_saved;
  3681.             //
  3682.             // Restore the number of torsions in the state variables "sInit" and "sUnbound_ext"
  3683.             sInit.ntor = saved_sInit_ntor;
  3684.             sUnbound_ext.ntor = saved_sInit_ntor;
  3685.             //
  3686.             // Use the standard AutoDock energy tables to compute the internal energy
  3687.             // Use this value to set unbound_internal_FE
  3688.             evaluate.setup( crd, charge, abs_charge, qsp_abs_charge, type, natom, map,
  3689.                             elec, emap, nonbondlist, ad_energy_tables, Nnb,
  3690.                             B_calcIntElec, B_isGaussTorCon, B_isTorConstrained,
  3691.                             B_ShowTorE, US_TorE, US_torProfile, vt, tlist, crdpdb, crdreo, sInit, ligand,
  3692.                             ignore_inter,
  3693.                             B_include_1_4_interactions, scale_1_4,
  3694.                             parameterArray, unbound_internal_FE, info, B_use_non_bond_cutoff, B_have_flexible_residues);
  3695.             // end of Step 3 // }
  3696.  
  3697.             // Step 4 // {
  3698.             //
  3699.             // Compute the energy of the unbound extended state
  3700.             // ------------------------------------------------
  3701.             //
  3702.             // Convert from unbound state to unbound coordinates
  3703.             cnv_state_to_coords( sUnbound_ext, vt, tlist, sUnbound_ext.ntor, crdpdb, crd, natom );
  3704.             //
  3705.             // Calculate the unbound internal energy using the standard AutoDock energy function
  3706.             (void) eintcalPrint(nonbondlist, ad_energy_tables, crd, Nnb, B_calcIntElec, B_include_1_4_interactions, scale_1_4, qsp_abs_charge, parameterArray, B_use_non_bond_cutoff, B_have_flexible_residues);
  3707.             //
  3708.             // eintcal() and eintcalPrint() set the values of the hideously-global nb_group_energy[]
  3709.             unbound_ext_internal_FE = nb_group_energy[INTRA_LIGAND] + nb_group_energy[INTRA_RECEPTOR];
  3710.             //
  3711.             pr(logFile, "\n\nThe internal energy of the unbound extended state was computed to be %+.3lf kcal/mol\n\n", unbound_ext_internal_FE);
  3712.             // end of Step 4 // }
  3713.  
  3714.             // Step 5 // {
  3715.             //
  3716.             // Decide whether to use extended or AutoDock state for unbound state
  3717.             // ------------------------------------------------------------------
  3718.             //
  3719.             if (unbound_ext_internal_FE > 0.0) {
  3720.                 // Unbound extended state has an internal energy that is positive
  3721.  
  3722.                 // Step 5.1 // {
  3723.                 //
  3724.                 // Repeat Step 1 with the standard AutoDock internal energy potentials
  3725.                 //
  3726.                 // Run a hybrid global-local search using the autodock energy tables
  3727.                 // -----------------------------------------------------------------
  3728.                 //
  3729.                 //  *  Turn off the use of the non-bond cutoff
  3730.                 //  *  Turn off internal electrostatics
  3731.                 //  *  Turn off intermolecular energy calculations
  3732.                 // TODO Do not translate or rotate the ligand in unbound searches
  3733.                 //
  3734.                 /*
  3735.                  *  Genetic Algorithm-Local search,  a.k.a.
  3736.                  *  Lamarckian Genetic Algorithm
  3737.                  */
  3738.                 (void) fprintf( logFile, "\n\n\tBEGINNING COMPUTATION OF UNBOUND AUTODOCK STATE USING LGA\n");
  3739.                 (void) fprintf( logFile,     "\t_________________________________________________________\n\n\n");
  3740.                 (void) fflush( logFile );
  3741.                 //
  3742.                 pr(logFile, "Date:\t");
  3743.                 printdate( logFile, 2 );
  3744.                 (void) fflush( logFile );
  3745.                 gaStart = times( &tms_gaStart );
  3746.                 //  Can get rid of the following line
  3747.                 ((Genetic_Algorithm *)GlobalSearchMethod)->initialize(pop_size, 7+sInit.ntor);
  3748.                 //
  3749.                 // Start Lamarckian GA run searching only torsions -- Unbound simulation
  3750.                 // sUnbound_ad = call_glss_tors( GlobalSearchMethod, LocalSearchMethod,
  3751.                 sUnbound_ad = call_glss( GlobalSearchMethod, LocalSearchMethod,
  3752.                                          sInit,
  3753.                                          num_evals_unbound, pop_size,
  3754.                                          outlev,
  3755.                                          outputEveryNgens, &ligand,
  3756.                                          B_RandomTran0, B_RandomQuat0, B_RandomDihe0,
  3757.                                          info, FN_pop_file );
  3758.                 // State of best individual at end of GA-LS run, sUnbound_ad, is returned.
  3759.                 // Finished Lamarckian GA run
  3760.                 gaEnd = times( &tms_gaEnd );
  3761.                 pr( logFile, "\nFinished Lamarckian Genetic Algorithm (LGA), time taken:\n");
  3762.                 timesyshms( gaEnd - gaStart, &tms_gaStart, &tms_gaEnd );
  3763.                 pr( logFile, "\n");
  3764.                 printdate( logFile, 1 );
  3765.                 (void) fflush( logFile );
  3766.                 pr(logFile, "\nTotal number of Energy Evaluations: %lu\n", evaluate.evals() );
  3767.                 pr(logFile, "Total number of Generations:        %u\n", ((Genetic_Algorithm *)GlobalSearchMethod)->num_generations());
  3768.                 // Restore the number of torsions in the state variable "sUnbound_ad"
  3769.                 sUnbound_ad.ntor = saved_sInit_ntor;
  3770.                 // end of Step 5.1 // }
  3771.  
  3772.                 // Step 5.2 // {
  3773.                 //
  3774.                 // Compute the energy of the unbound AutoDock state
  3775.                 // ------------------------------------------------
  3776.                 //
  3777.                 // Convert from unbound state to unbound coordinates
  3778.                 cnv_state_to_coords( sUnbound_ad, vt, tlist, sUnbound_ad.ntor, crdpdb, crd, natom );
  3779.                 //
  3780.                 // Calculate the unbound internal energy using the standard AutoDock energy function
  3781.                 (void) eintcalPrint(nonbondlist, ad_energy_tables, crd, Nnb, B_calcIntElec, B_include_1_4_interactions, scale_1_4, qsp_abs_charge, parameterArray, B_use_non_bond_cutoff, B_have_flexible_residues);
  3782.                 //
  3783.                 // eintcal() and eintcalPrint() set the values of the hideously-global nb_group_energy[]
  3784.                 unbound_ad_internal_FE = nb_group_energy[INTRA_LIGAND] + nb_group_energy[INTRA_RECEPTOR];
  3785.                 //
  3786.                 pr(logFile, "\n\nThe internal energy of the unbound AutoDock state was computed to be %+.3lf kcal/mol\n\n", unbound_ad_internal_FE);
  3787.                 // end of Step 5.2 // }
  3788.  
  3789.                 if (unbound_ad_internal_FE < unbound_ext_internal_FE) {
  3790.                     pr(logFile, "NOTE:   The AutoDock internal energy of the \"extended\" state was higher\nNOTE:   than that of the state obtained by searching using the AutoDock internal\nNOTE:   energy potentials.\nNOTE:   The unbound state was set to the AutoDock optimum state, not the \"extended\" state.\n\n");
  3791.                     unbound_internal_FE = unbound_ad_internal_FE;
  3792.                     sUnbound = sUnbound_ad;
  3793.                 } else {
  3794.                     pr(logFile, "NOTE:   Although the AutoDock internal energy of the \"extended\" state was positive, it was lower\nNOTE:   than that of the state obtained by searching using the AutoDock internal\nNOTE:   energy potentials.\nNOTE:   The unbound state was set to the \"extended\" state.\n\n");
  3795.                     unbound_internal_FE = unbound_ext_internal_FE;
  3796.                     sUnbound = sUnbound_ext;
  3797.                 }
  3798.             } else {
  3799.                 // Unbound extended state has an internal energy that is negative
  3800.                 unbound_internal_FE = unbound_ext_internal_FE;
  3801.                 sUnbound = sUnbound_ext;
  3802.                 pr(logFile, "NOTE:   The AutoDock internal energy of the \"extended\" state was negative.\n\nNOTE:   The unbound state was set to the \"extended\" state.\n\n");
  3803.             }
  3804.             //
  3805.             pr(logFile, "\n\nThe internal energy of the unbound state was set to %+.3lf kcal/mol\n\n", unbound_internal_FE);
  3806.             // end of Step 5 // }
  3807.  
  3808.             // Step 6 // {
  3809.             //
  3810.             // Convert from unbound state to unbound coordinates
  3811.             cnv_state_to_coords( sUnbound, vt, tlist, sUnbound.ntor, crdpdb, crd, natom );
  3812.             // end of Step 6 // }
  3813.  
  3814.             // Step 7 // {
  3815.             //
  3816.             // Output the coordinates of the unbound state
  3817.             pr( logFile, "\n\n\tFINAL UNBOUND STATE\n" );
  3818.             pr( logFile,     "\t___________________\n\n\n" );
  3819.             //
  3820.             writePDBQT( -1, seed,  FN_ligand, dock_param_fn, lig_center,
  3821.                         sUnbound, ntor, &eintra, &einter, natom, atomstuff,
  3822.                         crd, emap, elec,
  3823.                         charge, abs_charge, qsp_abs_charge,
  3824.                         ligand_is_inhibitor,
  3825.                         torsFreeEnergy,
  3826.                         vt, tlist, crdpdb, nonbondlist,
  3827.                         ad_energy_tables,
  3828.                         type, Nnb, B_calcIntElec,
  3829.                         map,
  3830.                         outlev,
  3831.                         ignore_inter,
  3832.                         B_include_1_4_interactions, scale_1_4, parameterArray, unbound_internal_FE,
  3833.                         info, UNBOUND, PDBQT_record, B_use_non_bond_cutoff, B_have_flexible_residues);
  3834.             // end of Step 7 // }
  3835.  
  3836.             // Step 8 // {
  3837.             //
  3838.             // Remember to reset the energy evaluator back to computing the intermolecular energy between
  3839.             // the flexible and the rigid molecules.
  3840.             evaluate.compute_intermol_energy(TRUE);
  3841.             // end of Step 8 // }
  3842.  
  3843.         } else {
  3844.             pr(logFile, "NOTE:  AutoDock cannot compute the energy of the unbound state, since the ligand is rigid.\n\n");
  3845.             pr(logFile, "NOTE:  Use the \"unbound\" command to set the energy of the unbound state, if known from a previous calculation where the ligand was treated as flexible.\n\n");
  3846.             unbound_internal_FE = 0.0L;
  3847.             pr(logFile, "\n\nThe internal energy of the unbound state was set to %+.3lf kcal/mol\n\n", unbound_internal_FE);
  3848.         }
  3849.  
  3850.         pr( logFile, UnderLine );
  3851.         (void) fflush(logFile);
  3852.         break;
  3853.  
  3854. /*____________________________________________________________________________*/
  3855.  
  3856.     case DPF_EPDB:
  3857.         /*
  3858.          *  epdb
  3859.          *
  3860.          *  Computes the energy of the ligand specified by the "move lig.pdbqt" command.
  3861.          *  Return the energy of the Small Molecule.
  3862.          *  FN_ligand must be in   PDBQT-format;
  3863.          *  flag can be:-
  3864.          *  0 = NEW, or   PDBQT-71, and
  3865.          *  1 = OLD, or   PDBQT-55 (old PDBq format).
  3866.          */
  3867.         outside = FALSE;
  3868.         atoms_outside = FALSE;
  3869.         eintra = 0.0L;
  3870.         einter = 0.0L;
  3871.         etotal = 0.0L;
  3872.  
  3873.         pr(logFile, "WARNING This command, \"epdb\", currently computes the energy of the ligand specified by the \"move lig.pdbqt\" command.\n");
  3874.         retval = sscanf(line, "%*s %s", dummy_FN_ligand);
  3875.         if (retval >= 1) {
  3876.             pr(logFile, "WARNING  -- it will not read in the PDBQT file specified on the \"epdb\" command line.\n");
  3877.         }
  3878.  
  3879.         /*
  3880.         (void) sscanf(line, "%*s %s", FN_ligand);
  3881.         pr(logFile, "epdb %s\n\n", FN_ligand);
  3882.         natom = 0;
  3883.         print_1_4_message(logFile, B_include_1_4_interactions, scale_1_4);
  3884.         //
  3885.         ligand = readPDBQT( line,
  3886.                             num_atom_types,
  3887.                             &natom,
  3888.                             crdpdb, crdreo, charge, &B_haveCharges,
  3889.                             type, bond_index,
  3890.                             pdbaname, FN_ligand, FN_flexres, B_have_flexible_residues, atomstuff, Htype,
  3891.                             &B_constrain_dist, &atomC1, &atomC2,
  3892.                             &sqlower, &squpper,
  3893.                             &ntor1, &ntor, &ntor_ligand,
  3894.                             tlist, vt,
  3895.                             &Nnb, nonbondlist,
  3896.                             jobStart, tms_jobStart, hostnm, &ntorsdof, outlev,
  3897.                             ignore_inter,
  3898.                             B_include_1_4_interactions,
  3899.                             atoms, PDBQT_record );
  3900.  
  3901.         //
  3902.         // pre-calculate some values we will need later in computing the desolvation energy
  3903.         //
  3904.         for (i=0; i<natom; i++) {
  3905.             abs_charge[i] = fabs(charge[i]);
  3906.             qsp_abs_charge[i] = qsolpar * abs_charge[i];
  3907.         }
  3908.         */
  3909.  
  3910.         // to restore the original coordinates, we must temporarily undo the centering transformation
  3911.         for ( i=0; i<true_ligand_atoms; i++ ) {
  3912.             for (xyz = 0;  xyz < SPACE;  xyz++) {
  3913.                 crdpdb[i][xyz] += lig_center[xyz];
  3914.             }
  3915.         }
  3916.         // determine if any atoms are outside the grid box
  3917.         atoms_outside = FALSE;
  3918.         for (i=0; i<natom; i++) {
  3919.             outside = is_out_grid_info(crdpdb[i][X], crdpdb[i][Y], crdpdb[i][Z]);
  3920.             if (outside) {
  3921.                 atoms_outside = TRUE;
  3922.                 (void) sprintf( message, "%s: WARNING: Atom %d (%.3f, %.3f, %.3f) is outside the grid!\n", programname, i+1, crdpdb[i][X], crdpdb[i][Y], crdpdb[i][Z] );
  3923.                 print_2x( logFile, stderr, message );
  3924.                 outside = FALSE; /* Reset outside */
  3925.             }
  3926.         }
  3927.         pr(logFile, "Number of \"true\" ligand atoms:  %d\n", true_ligand_atoms);
  3928.         //
  3929.         for (i=0;i<natom;i++) {
  3930.             if (ignore_inter[i] == 1) {
  3931.                 pr(logFile, "Special Boundary Conditions:\n");
  3932.                 pr(logFile, "____________________________\n\n");
  3933.                 pr(logFile, "AutoDock will ignore the following atoms in the input PDBQT file \nin intermolecular energy calculations:\n");
  3934.                 pr(logFile, "\n(This is because these residue atoms are at the boundary between \nflexible and rigid, and since they cannot move \nthey will not affect the total energy.)\n\n");
  3935.                 break;
  3936.             }
  3937.         }
  3938.         for (i=0;i<natom;i++) {
  3939.             if (ignore_inter[i] == 1) {
  3940.                 pr(logFile, "Atom number %d:  %s\n", i+1, atomstuff[i] );
  3941.             }
  3942.         }
  3943.         pr(logFile, "\n");
  3944.  
  3945.         sInit.ntor = ligand.S.ntor;
  3946.  
  3947.         // save any currently-computed unbound internal FE
  3948.         unbound_internal_FE_saved = unbound_internal_FE;
  3949.  
  3950.         // Initialise to zero, since we may call "epdb" more than once in a single DPF
  3951.         // Set the unbound free energy -- assume it is zero, since this is a "single-point energy calculation"
  3952.         unbound_internal_FE = 0.0;
  3953.  
  3954.         // Calculate the internal energy
  3955.         if (ntor > 0) {
  3956.             (void) eintcalPrint(nonbondlist, ad_energy_tables, crdpdb, Nnb, B_calcIntElec, B_include_1_4_interactions, scale_1_4, qsp_abs_charge, parameterArray, B_use_non_bond_cutoff, B_have_flexible_residues);
  3957.         }
  3958.  
  3959.         // calculate the energy breakdown for the input coordinates, "crdpdb"
  3960.         eb = calculateEnergies( natom, ntor, unbound_internal_FE, torsFreeEnergy, B_have_flexible_residues,
  3961.                                 crdpdb, charge, abs_charge, type, map, info, outside,
  3962.                                 ignore_inter, elec, emap, &elec_total, &emap_total,
  3963.                                 nonbondlist, ad_energy_tables, Nnb, B_calcIntElec,
  3964.                                 B_include_1_4_interactions, scale_1_4, qsp_abs_charge, parameterArray, B_use_non_bond_cutoff);
  3965.  
  3966.         pr(logFile, "\n\n\t\tIntermolecular Energy Analysis\n");
  3967.         pr(logFile,     "\t\t==============================\n\n");
  3968.         pr(logFile, "Atom  vdW+Hb+Elec  vdW+Hbond  Electrosta  Partial          Coordinates         \n");
  3969.         pr(logFile, "Type    Energy      Energy    tic Energy  Charge      x         y         z    \n");
  3970.         pr(logFile, "____  __________  __________  __________  _______  ________  ________  ________\n");
  3971.         //          "1234  0123456789  0123456789  0123456789  1234567  12345678  12345678  12345678"
  3972.  
  3973.         charge_total = 0.;
  3974.         etot = 0.;
  3975.         for (i = 0;  i < natom;  i++) {
  3976.             etot = emap[i] + elec[i];
  3977.             pr(logFile, "%4d  %10.2f  %10.2f  %10.2f  %7.3f  %8.4f  %8.4f  %8.4f\n", (type[i]+1), etot, emap[i], elec[i], charge[i], crdpdb[i][X], crdpdb[i][Y], crdpdb[i][Z]);
  3978.             charge_total += charge[i];
  3979.         } /*i*/
  3980.         pr(logFile, "      __________  __________  __________  _______\n");
  3981.         pr(logFile, "Total %10.2lf  %10.2lf  %10.2lf  %7.3lf\n",        (double)(emap_total + elec_total), (double)emap_total, (double)elec_total, (double)charge_total);
  3982.         pr(logFile, "      __________  __________  __________  _______\n");
  3983.         pr(logFile, "      vdW+Hb+Elec  vdW+Hbond  Electrosta  Partial\n");
  3984.         pr(logFile, "        Energy      Energy    tic Energy  Charge\n\n");
  3985.  
  3986.         pr(logFile, "Total Intermolecular Interaction Energy   = %+.3lf kcal/mol\n", (double)(eb.e_inter + eb.e_intra) );
  3987.         pr(logFile, "Total Intermolecular vdW + Hbond Energy   = %+.3lf kcal/mol\n", (double)emap_total);
  3988.         pr(logFile, "Total Intermolecular Electrostatic Energy = %+.3lf kcal/mol\n\n\n", (double)elec_total);
  3989.  
  3990.         printEnergies( &eb, "epdb: USER    ", ligand_is_inhibitor, emap_total, elec_total, B_have_flexible_residues );
  3991.         pr(logFile, "\n");
  3992.  
  3993.         // remember to re-center the ligand
  3994.         for ( i=0; i<true_ligand_atoms; i++ ) {
  3995.             for (xyz = 0;  xyz < SPACE;  xyz++) {
  3996.                 crdpdb[i][xyz] -= lig_center[xyz];
  3997.             }
  3998.         }
  3999.  
  4000.         // restore the saved unbound internal FE
  4001.         unbound_internal_FE = unbound_internal_FE_saved;
  4002.  
  4003.         (void) fflush(logFile);
  4004.         break;
  4005.  
  4006. /*____________________________________________________________________________*/
  4007.  
  4008.     case DPF_TERMINATION:
  4009.         /*
  4010.          *  ga_termination energy 0.1
  4011.          *  ga_termination evals 25000  // the best energy did not change in this time
  4012.          *  ga_termination time 120 s
  4013.          */
  4014.         /*
  4015.         (void) sscanf( line, "%*s %d", &i );
  4016.         */
  4017.         (void) fflush(logFile);
  4018.         break;
  4019.  
  4020. /*____________________________________________________________________________*/
  4021.  
  4022.     case GA_CROSSOVER_MODE:
  4023.         /*
  4024.          * ga_crossover_mode OnePt
  4025.          * ga_crossover_mode TwoPt
  4026.          * ga_crossover_mode Uniform
  4027.          * ga_crossover_mode Arithmetic
  4028.          *
  4029.          * Xover_Mode c_mode = OnePt;  //  can be: OnePt, TwoPt, Uniform or Arithmetic
  4030.          */
  4031.         (void) sscanf( line, "%*s %s", c_mode_str );
  4032.         if (strcmp(c_mode_str, "onept") == 0) {
  4033.             c_mode = OnePt;
  4034.             pr(logFile, "One-point crossover will be used in GA and LGA searches.\n");
  4035.         } else if (strcmp(c_mode_str, "twopt") == 0) {
  4036.             c_mode = TwoPt;
  4037.             pr(logFile, "Two-point crossover will be used in GA and LGA searches.\n");
  4038.         } else if (strcmp(c_mode_str, "uniform") == 0) {
  4039.             c_mode = Uniform;
  4040.             pr(logFile, "Uniform crossover will be used in GA and LGA searches.\n");
  4041.         } else if (strcmp(c_mode_str, "arithmetic") == 0) {
  4042.             c_mode = Arithmetic;
  4043.             pr(logFile, "Arithmetic crossover will be used in GA and LGA searches.\n");
  4044.         } else {
  4045.             c_mode = Uniform; // default
  4046.         }
  4047.         (void) fflush(logFile);
  4048.         break;
  4049.  
  4050. /*____________________________________________________________________________*/
  4051.  
  4052.     case DPF_POPFILE:
  4053.         /*
  4054.          *  output_pop_file
  4055.          *
  4056.          *  Used to write out the population to a file at the end of
  4057.          *  every GA.
  4058.          */
  4059.         (void) sscanf( line, "%*s %s", FN_pop_file);
  4060.         (void) fflush(logFile);
  4061.         pr( logFile, "The population will be written to the file \"%s\" at the end of every generation.\n", FN_pop_file);
  4062.         break;
  4063.  
  4064.  /*____________________________________________________________________________*/
  4065.  
  4066.      case DPF_CONFSAMPLER:
  4067.         /*
  4068.          * confsampler
  4069.          *
  4070.          * Scan a region around conformations saved in sHist array.
  4071.          *
  4072.          */
  4073.  
  4074.         (void) sscanf( line, "%*s %s %d", confsampler_type, &confsampler_samples);
  4075.         pr( logFile, "Scanning local regions around each docked conformation.\n");
  4076.  
  4077.         if (strcmp(confsampler_type, "systematic") == 0) {
  4078.             systematic_conformation_sampler(sHist, nconf, vt, crdpdb, tlist, lig_center, natom, type, info);
  4079.         }
  4080.        
  4081.         else {
  4082.             random_conformation_sampler(sHist, nconf, confsampler_samples, vt, crdpdb, tlist, lig_center, natom, type, info);
  4083.         }
  4084.         (void) fflush(logFile);
  4085.  
  4086.         break;
  4087.  
  4088. /*____________________________________________________________________________*/
  4089.  
  4090.     case DPF_COPYRIGHT:
  4091.         /*
  4092.          * 'copyright' to show the Gnu GPL copyright
  4093.          */
  4094.         show_copyright(logFile);
  4095.         (void) fflush(logFile);
  4096.         break;
  4097.  
  4098. /*____________________________________________________________________________*/
  4099.  
  4100.     case DPF_WARRANTY:
  4101.         /*
  4102.          * 'warranty' to show the Gnu GPL warranty
  4103.          */
  4104.         show_warranty(logFile);
  4105.         (void) fflush(logFile);
  4106.         break;
  4107.  
  4108. /*_12yy_______________________________________________________________________*/
  4109.  
  4110.     case DPF_:
  4111.         /*
  4112.          *
  4113.          */
  4114.         /*
  4115.         (void) sscanf( line, "%*s %d", &i );
  4116.         (void) fflush(logFile);
  4117.         break;
  4118.         */
  4119.  
  4120. //______________________________________________________________________________
  4121.  
  4122.     default:
  4123.         /*
  4124.         **  Do nothing...
  4125.         */
  4126.         break;
  4127.  
  4128. //______________________________________________________________________________
  4129.  
  4130.     } /* switch( dpf_keyword ) */
  4131.  
  4132. } /* while PARSING-DPF parFile */
  4133.  
  4134. /* __________________________________________________________________________
  4135. **
  4136. ** Close the docking parameter file...
  4137. ** __________________________________________________________________________
  4138. */
  4139. pr( logFile, ">>> Closing the docking parameter file (DPF)...\n\n" );
  4140. //pr( logFile, UnderLine );
  4141. (void) fclose( parFile );
  4142.  
  4143.  
  4144. /* _________________________________________________________________________
  4145. **
  4146. ** If in command-mode, set the command file-pointers to standard i/o,
  4147. ** _________________________________________________________________________
  4148. */
  4149. if (command_mode) {
  4150.     status = cmdmode( natom,jobStart,tms_jobStart,
  4151.                       map, ad_energy_tables, WallEnergy, vt, tlist, ntor,
  4152.                       Nnb, nonbondlist, atomstuff, crdpdb,
  4153.                       hostnm, type, charge, abs_charge, qsp_abs_charge, B_calcIntElec,
  4154.                       atm_typ_str, torsFreeEnergy,
  4155.                       ligand_is_inhibitor,
  4156.                       ignore_inter,
  4157.                       B_include_1_4_interactions, scale_1_4,
  4158.                       parameterArray, unbound_internal_FE,
  4159.                       info, B_have_flexible_residues, B_use_non_bond_cutoff );
  4160.     exit( status );  /* "command_mode" exits here... */
  4161. }
  4162.  
  4163. //______________________________________________________________________________
  4164. /*
  4165. ** Print the time and date when the docking has finished...
  4166. */
  4167.  
  4168. pr( logFile, "This docking finished at:\t\t\t" );
  4169. printdate( logFile, 1 );
  4170. pr( logFile, "\n\n\n" );
  4171.  
  4172. success( hostnm, jobStart, tms_jobStart );
  4173.  
  4174.  if(write_stateFile){
  4175.    fprintf(stateFile,"</autodock>\n");
  4176.    (void) fclose( stateFile );
  4177.  }
  4178. (void) fclose( logFile );
  4179.  
  4180. // delete arrays
  4181. delete []nonbondlist;
  4182.  
  4183.  
  4184. //________________________________________________________________________________
  4185. /*
  4186. ** End of Boinc
  4187. */
  4188. #ifdef BOINCCOMPOUND
  4189.  boinc_fraction_done(1.);
  4190. #endif
  4191. #ifdef BOINC          
  4192.     boinc_finish(0);       /* should not return */
  4193. #endif
  4194.  
  4195. return 0;
  4196.  
  4197. } /* END OF PROGRAM */
  4198.  
  4199. #ifdef BOINC
  4200. /*  Dummy graphics API entry points.
  4201.  *  This app does not do graphics, but it still must provide these callbacks.
  4202.  */
  4203.  
  4204. void app_graphics_render(int xs, int ys, double time_of_day) {}
  4205. void app_graphics_reread_prefs(){}
  4206. void boinc_app_mouse_move(int x, int y, bool left, bool middle, bool right ){}
  4207. void boinc_app_mouse_button(int x, int y, int which, bool is_down){}
  4208. void boinc_app_key_press(int wParam, int lParam){}
  4209. void boinc_app_key_release(int wParam, int lParam){}
  4210. #endif
  4211.  
  4212. /* EOF */
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