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/* NOTICE: this source code file has been modified for use with FreeMOL */ |
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#define notKEG_DEBUG |
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|
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|
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#define EXTERN extern |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "utility.h" |
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#include "vibrate.h" |
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|
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#include <errno.h> |
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|
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struct t_logp { |
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float logp; |
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} logp_calc; |
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|
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EXTERN struct t_files { |
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int nfiles, append, batch, icurrent, ibatno; |
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} files; |
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|
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EXTERN struct t_minim_values { |
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int iprint, ndc, nconst; |
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float dielc; |
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} minim_values; |
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EXTERN struct t_minim_control { |
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int type, method, field, added_const; |
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char added_path[256],added_name[256]; |
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} minim_control; |
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|
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int rd_sdf(FILE *); |
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int setup_calculation(void); |
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void end_calculation(void); |
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void minimize(int natom,int *use,double *x,double *y,double *z); |
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static int close_contact(int); |
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void initialize(void); |
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void type(void); |
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void read_gmmxinp(char*,FILE*,int); |
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void hdel(int); |
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void hadd(void); |
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int FetchRecord(FILE *, char *); |
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void write_sdf(int); |
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void zero_data(void); |
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void type_mmx(void); |
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void read_datafiles(char *); |
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float xlogp(int natom,int *atomnum,int **iat,int **bo,long int *flags,int *type); |
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void print_energy_totals(void); |
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char *get_structure_title(void); |
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void vibrate(int natom,double *atomwt,double *x,double *y,double *z,double *charge); |
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void charge_dipole(int natom,double *x,double *y,double *z,double *atomwt,double *charge); |
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void set_connectivity(void); |
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// ===================================== |
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void read_gmmxinp(char *paramfile, |
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FILE *infile, |
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int flags) |
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{ |
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int i,ncount,nret; |
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int icount; |
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int ngood, nbparam, nbatom,nbcontact; |
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int batom = FALSE; |
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float logp; |
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//char *std_file; |
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char bad_atom[80],bad_contact[80],bad_param[80]; |
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FILE *logfile; |
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|
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// check filetype |
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ncount = 0; |
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|
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/* |
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std_file = strdup(out_file); |
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strcpy(Savebox.fname, out_file); |
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*/ |
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|
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// build filenames |
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strcpy(bad_atom,"_batom.sdf"); |
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strcpy(bad_contact,"_bcontact.sdf"); |
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strcpy(bad_param,"_bparam.sdf"); |
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|
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// open logfile |
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logfile = pcmlogfile; |
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|
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files.nfiles = 0; |
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// |
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minim_control.field = MMFF94; |
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//strcpy(line,paramfile); |
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zero_data(); |
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read_datafiles(paramfile); |
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minim_control.method = 3; // just do first deriv minimization |
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icount = 0; |
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// |
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ngood = nbparam = nbatom = nbcontact = 0; |
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i = 0; |
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while (1) |
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// for (i=1; i <= files.nfiles; i++) |
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{ |
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++i; |
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initialize(); |
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nret = rd_sdf(infile); |
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if (-1 == nret) return ; |
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if (FALSE == nret) |
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{ |
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fprintf(logfile,"Strnum: %d Cannot handle aromatic bonds. Try Kekule version.\n",i); |
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goto L_10; |
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natom = 0; |
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} |
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|
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if (natom == 1) |
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{ |
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fprintf(logfile,"Strnum: %d has only one atom\n",i); |
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goto L_10; |
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} |
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if (nret == TRUE) |
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{ |
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// TJO |
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if (flags & DO_ADDH) |
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{ |
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hdel(0); |
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hadd(); |
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} |
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set_connectivity(); // count number of connections and total bond order for all atoms |
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type(); |
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|
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#ifdef KEG_DEBUG |
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minim_values.iprint = TRUE; |
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for(i=1; i<= natom; i++) |
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fprintf(pcmlogfile,"Atom: %d %d %ld\n",i,atom.type[i],atom.flags[i]); |
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#endif |
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nret = setup_calculation(); |
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|
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#ifdef KEG_DEBUG |
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print_energy_totals(); |
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for(i=1; i<= natom; i++) |
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fprintf(pcmlogfile,"Atom: %d %d %ld\n",i,atom.type[i],atom.flags[i]); |
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if (minim_values.iprint == TRUE) exit(0); |
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minim_values.iprint = FALSE; |
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#endif |
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if (nret == TRUE) |
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{ |
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minimize(natom,atom.use,atom.x,atom.y,atom.z); |
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// compute xlogp |
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if (flags & DO_XLOGP) { |
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if (VERBOSE) fprintf(pcmlogfile, " Evaluating XlogP\n"); |
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logp = xlogp(natom,atom.atomnum,atom.iat,atom.bo,atom.flags,atom.type); |
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logp_calc.logp = logp; |
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} |
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// compute dipole moment |
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if (flags & DO_DIPOLE) { |
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if (VERBOSE) fprintf(pcmlogfile, " Evaluating dipole moment\n"); |
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charge_dipole(natom,atom.x,atom.y,atom.z,atom.atomwt,atom.charge); |
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} |
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// compute vib |
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if (flags & DO_VIBRATION) { |
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if (VERBOSE) fprintf(pcmlogfile, " Evaluating vibrational parameters\n"); |
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vibrate(natom,atom.atomwt,atom.x,atom.y,atom.z,atom.charge); |
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} |
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write_sdf(flags); |
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++ngood; |
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++files.nfiles; |
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#ifdef KEG_DEBUG |
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print_energy_totals(); |
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#endif |
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} else |
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{ |
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strcpy(Savebox.fname,bad_param); |
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files.append = TRUE; |
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//write_sdf(flags); |
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nbparam++; |
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//strcpy(Savebox.fname,std_file); |
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fprintf(logfile,"Strnum: %d CID: %s fails on missing parameters\n",files.nfiles,get_structure_title()); |
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if (VERBOSE) |
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fprintf(stdout, "Missing parameters - no calc - %s\n",get_structure_title()); |
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} |
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end_calculation(); |
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if (VERBOSE) { |
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fprintf(stdout, |
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"Strnum: %d %s natom %d \n",files.nfiles,get_structure_title(), natom); |
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} |
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} else // read_sdf failed |
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{ |
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fprintf(logfile,"Strnum: %d CID: %s fails on unsupported atom\n",files.nfiles,get_structure_title()); |
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strcpy(Savebox.fname,bad_atom); |
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files.append = TRUE; |
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if (batom == FALSE) |
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{ |
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batom = TRUE; |
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files.append = FALSE; |
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} |
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//write_sdf(flags); |
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nbatom++; |
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//strcpy(Savebox.fname,std_file); |
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} |
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L_10: |
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continue; |
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} |
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// fclose(infile); |
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fprintf(logfile,"Ngood: %d Nbparam: %d Nbatom: %d Nbcontact: %d \n",ngood,nbparam,nbatom,nbcontact); |
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if (VERBOSE) { |
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fprintf(stdout, |
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"Ngood: %d Nbparam: %d Nbatom: %d Nbcontact: %d \n", |
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ngood,nbparam,nbatom,nbcontact); |
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} |
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|
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// fclose(logfile); |
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} |
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// ================================================ |
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int close_contact(int mode) |
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{ |
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int i, j; |
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double dx,dy,dz; |
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|
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for (i=1; i < natom; i++) |
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{ |
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for (j=i+1; j <= natom; j++) |
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{ |
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dx = fabs(atom.x[i] - atom.x[j]); |
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dy = fabs(atom.y[i] - atom.y[j]); |
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dz = fabs(atom.z[i] - atom.z[j]); |
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if ( (dx + dy + dz) < 0.1) |
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{ |
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return FALSE; |
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} |
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} |
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} |
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return TRUE; |
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} |
