| 1 |
gilbertke |
67 |
/* NOTICE: this source code file has been modified for use with FreeMOL */
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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 "atom_k.h"
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#include "energies.h"
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#include "fix.h"
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#include "dipmom.h"
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#include "draw.h"
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#include "vibrate.h"
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gilbertke |
90 |
#include "utility.h"
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gilbertke |
67 |
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#define TABULATOR_INCLUDE_IMPLEMENTATION
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#include "tabulator.h"
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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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EXTERN struct ElementType { char symbol[3];
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int atomnum;
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float weight, covradius, vdwradius;
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int s,p,d,f,type ;
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} Elements[];
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EXTERN struct t_logp {
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float logp;
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} logp_calc;
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// ============================
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void quick_type(void);
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int read_sdf(int,int);
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int rd_sdf(FILE *);
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void write_sdf(int);
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void hdel(int);
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FILE * fopen_path ( char * , char * , char * ) ;
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int FetchRecord(FILE *, char *);
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void avgleg(void);
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void get_tag(char *,char *);
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static void mopaco(int start_atom,int end_atom);
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// ==================================
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/*
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* flags - indicates whether dipole, xlogp or vibrational calculations were done
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* and if so write them to the output file. Look at the definitions in pcmod.h
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*
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*/
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void write_sdf(int flags)
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{
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int i,j,lptest,nbond,junk;
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FILE *wfile = pcmoutfile;
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lptest = 0;
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for( i = 1; i <= natom; i++ )
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{
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if( atom[i].mmx_type == 20 )
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{
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lptest = 1;
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hdel( lptest );
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break;
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}
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}
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nbond = 0;
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/* ** calculate the number of bonds in the molecule ** */
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for( j = 1; j <= natom; j++ )
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{
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for( i = 0; i < MAXIAT; i++ )
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{
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if( atom[j].iat[i] != 0 )
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{
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if( atom[j].iat[i] < j )
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nbond = nbond + 1;
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}
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}
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}
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/* now write the concord file */
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/*
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if (files.append)
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wfile = fopen_path(Savebox.path,Savebox.fname,"a");
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else
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wfile = fopen_path(Savebox.path,Savebox.fname,"w");
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*/
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j = strlen(Struct_Title);
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for (i=0; i < j; i++)
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{
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if (Struct_Title[i] == '\n')
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{
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Struct_Title[i] = '\0';
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break;
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}
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}
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fprintf(wfile,"%s\n",Struct_Title);
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fprintf(wfile," MENGINE v1.0 1.00000 0.00000\n");
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fprintf(wfile,"\n");
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fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond);
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for (i=1; i <= natom; i++)
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{
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junk = 0;
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if (atom[i].mmx_type == 41) junk = 3;
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else if (atom[i].mmx_type == 42) junk = 5;
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else if (atom[i].mmx_type == 66)
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{
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if (atom[i].bo[0] == 1)
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junk = 5;
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}
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fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y,
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atom[i].z,Elements[atom[i].atomnum-1].symbol,junk);
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}
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for (i=1; i <= natom; i++)
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{
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for (j=0; j < MAXIAT; j++)
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{
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if (atom[i].iat[j] != 0 && i < atom[i].iat[j])
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fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]);
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}
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}
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fprintf(wfile,"M END\n");
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fprintf(wfile,"> <title>\n");
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fprintf(wfile,"%s\n",Struct_Title);
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fprintf(wfile,"> <MMFF94 energy>\n");
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fprintf(wfile,"%f\n",energies.total);
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fprintf(wfile,"> <MMFF94_Atomtypes>\n");
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fprintf(wfile,"+ Atom Atomtype\n");
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for (i=1; i <=natom; i++)
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fprintf(wfile,"| %d %d\n",i,atom[i].type);
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fprintf(wfile,"\n");
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| 131 |
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if (flags & DO_DIPOLE) {
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fprintf(wfile,"> <dipole moment>\n");
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fprintf(wfile,"%f\n",dipolemom.total);
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}
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| 136 |
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if (flags & DO_XLOGP) {
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fprintf(wfile,"> <xLogP>\n");
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fprintf(wfile,"%f\n",logp_calc.logp);
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}
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| 141 |
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if (flags & DO_VIBRATION) {
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fprintf(wfile,"> <Point Group>\n");
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fprintf(wfile,"%s\n",vibdata.ptgrp);
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| 145 |
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fprintf(wfile,"> <Moments of Inertia>\n");
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| 146 |
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fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz);
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| 147 |
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| 148 |
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fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n");
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fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot,
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vibdata.stot,vibdata.gtot,vibdata.cptot);
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}
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fprintf(wfile,"\n");
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fprintf(wfile,"$$$$\n");
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// fclose(wfile);
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}
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/* =================================== */
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// fast read - assume file is open and positioned
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| 159 |
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// read structure and down to end $$$$
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// and return
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| 161 |
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int rd_sdf(FILE *rfile)
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{
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int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom;
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int ncount,junk,junk1,got_title,istereo,iz,nvalue;
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int jji, jj1, jj2, jj3, jj4;
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| 166 |
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int n_row;
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| 167 |
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int has_Aromatic, xPlus,yPlus,zPlus, planar;
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int icount,itemp[4];
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int Ret_Val;
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gilbertke |
90 |
int numbonds, *ib1, *ib2;
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| 171 |
gilbertke |
67 |
float xtmp, ytmp, ztmp, dz;
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| 172 |
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float fconst,min,max;
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| 173 |
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char c1[4],c2[4];
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| 174 |
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char atomchar[3];
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| 175 |
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char inputline[150];
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char tag[30];
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char ***tab;
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| 178 |
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Ret_Val = TRUE;
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got_title = FALSE;
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xPlus = yPlus = zPlus = FALSE;
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if ( 0 == FetchRecord(rfile,inputline) )return -1;
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// sscanf(inputline,"SDF %s",Struct_Title);
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strncpy(Struct_Title, inputline, sizeof(Struct_Title));
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got_title = TRUE;
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/* if (strlen(inputline) > 4)
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{
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| 188 |
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iz = strlen(inputline);
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if (iz > 60) iz = 59;
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for (i=4; i < iz; i++)
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Struct_Title[i-4] = inputline[i];
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Struct_Title[i] = '\0';
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| 193 |
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got_title = TRUE;
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| 194 |
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} */
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| 195 |
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FetchRecord(rfile,inputline); // blank line
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| 196 |
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FetchRecord(rfile,inputline); // blank line
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| 197 |
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| 198 |
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FetchRecord(rfile,inputline); // natom and nbond
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| 199 |
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for (i=0; i <4; i++)
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| 200 |
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{
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| 201 |
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c1[i] = inputline[i];
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| 202 |
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c2[i] = inputline[i+3];
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| 203 |
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}
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| 204 |
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c1[3] = '\0';c2[3] = '\0';
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| 205 |
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niatom = atoi(c1);
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| 206 |
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nibond = atoi(c2);
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| 207 |
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if (niatom == 0)
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| 208 |
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return FALSE;
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| 209 |
gilbertke |
90 |
// allocate space for aromatic bonds
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| 210 |
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numbonds = 0;
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| 211 |
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ib1 = ivector(0,nibond);
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| 212 |
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ib2 = ivector(0,nibond);
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| 213 |
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//
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| 214 |
gilbertke |
67 |
for (i=0; i < niatom; i++)
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| 215 |
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{
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| 216 |
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FetchRecord(rfile,inputline);
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| 217 |
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sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1);
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| 218 |
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| 219 |
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itype = 0;
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| 220 |
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if (xtmp != 0.0) xPlus= TRUE;
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| 221 |
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if (ytmp != 0.0) yPlus= TRUE;
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| 222 |
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if (ztmp != 0.0) zPlus= TRUE;
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| 223 |
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| 224 |
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iz = strlen(atomchar);
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| 225 |
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if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix
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| 226 |
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{
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| 227 |
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if (atomchar[0] == 'N') itype = 8;
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| 228 |
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if (atomchar[0] == 'O') itype = 6;
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| 229 |
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| 230 |
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if (junk1 != 0)
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| 231 |
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{
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| 232 |
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if (junk1 == 3 && itype == 8)
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| 233 |
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itype = 41; // N+
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| 234 |
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if (junk1 == 5 && itype == 6)
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| 235 |
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itype = 42; // O-
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| 236 |
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}
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| 237 |
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}
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| 238 |
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newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar);
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| 239 |
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if (itype != 0)
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| 240 |
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atom[newatom].mmx_type = itype;
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| 241 |
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if (newatom == -1)
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| 242 |
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{
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| 243 |
|
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fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar);
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| 244 |
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Ret_Val = FALSE;
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| 245 |
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}
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| 246 |
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}
|
| 247 |
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has_Aromatic = FALSE;
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| 248 |
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| 249 |
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planar = TRUE;
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| 250 |
|
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if (xPlus && yPlus && zPlus) planar = FALSE;
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| 251 |
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| 252 |
|
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for (i=0; i < nibond; i++)
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| 253 |
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{
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| 254 |
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FetchRecord(rfile,inputline);
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| 255 |
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for (j=0; j <4; j++)
|
| 256 |
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{
|
| 257 |
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c1[j] = inputline[j];
|
| 258 |
|
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c2[j] = inputline[j+3];
|
| 259 |
|
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}
|
| 260 |
|
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c1[3] = '\0';c2[3] = '\0';
|
| 261 |
|
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ia1 = atoi(c1);
|
| 262 |
|
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ia2 = atoi(c2);
|
| 263 |
|
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istereo = 0;
|
| 264 |
|
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sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo);
|
| 265 |
|
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if (ibond >= 4)
|
| 266 |
|
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{
|
| 267 |
|
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// use bonds array as temporary storage for aromatic bonds
|
| 268 |
|
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make_bond(ia1,ia2,1);
|
| 269 |
gilbertke |
90 |
ib1[numbonds] = ia1;
|
| 270 |
|
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ib2[numbonds] = ia2;
|
| 271 |
|
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numbonds++;
|
| 272 |
gilbertke |
67 |
has_Aromatic = TRUE;
|
| 273 |
|
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} else
|
| 274 |
|
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make_bond(ia1, ia2, ibond);
|
| 275 |
|
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if (istereo == 1 && planar)
|
| 276 |
|
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{
|
| 277 |
|
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atom[ia2].z += 0.7;
|
| 278 |
|
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if (atom[ia2].atomnum == 1)
|
| 279 |
|
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atom[ia2].type = 60;
|
| 280 |
|
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}
|
| 281 |
|
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if (istereo == 6 && planar)
|
| 282 |
|
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{
|
| 283 |
|
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atom[ia2].z -= 0.7;
|
| 284 |
|
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if (atom[ia2].atomnum == 1)
|
| 285 |
|
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atom[ia2].type = 60;
|
| 286 |
|
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}
|
| 287 |
|
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}
|
| 288 |
|
|
// read to end of structure
|
| 289 |
|
|
// parse any tags here
|
| 290 |
|
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// agreed tags
|
| 291 |
|
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// <FIXED_ATOMS>
|
| 292 |
|
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// <RESTRAINED_ATOMS>
|
| 293 |
|
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// <RESTRAINED_DISTANCES>
|
| 294 |
|
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// <RESTRAINED_ANGLES>
|
| 295 |
|
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// <RESTRAINED_DIHEDRALS>
|
| 296 |
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|
|
| 297 |
|
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while (FetchRecord(rfile,inputline))
|
| 298 |
|
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{
|
| 299 |
|
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if (strncasecmp(inputline,"$$$$",4) == 0)
|
| 300 |
|
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{
|
| 301 |
|
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goto L_DONE;
|
| 302 |
|
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} else if (inputline[0] == '>')
|
| 303 |
|
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{
|
| 304 |
|
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get_tag(inputline,tag);
|
| 305 |
|
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if (strcasecmp(tag,"fixed_atoms") == 0)
|
| 306 |
|
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{
|
| 307 |
|
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tab = tabulator_new_from_file_using_header(rfile,"ATOM",0);
|
| 308 |
|
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if (tab)
|
| 309 |
|
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{
|
| 310 |
|
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fprintf(pcmlogfile,"got table\n");
|
| 311 |
|
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n_row = tabulator_height(tab);
|
| 312 |
|
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for (i=0; i < n_row; i++)
|
| 313 |
|
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{
|
| 314 |
|
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ia1 = atoi(tab[i][0]);
|
| 315 |
|
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if (ia1 > 0 && ia1 <= natom)
|
| 316 |
|
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{
|
| 317 |
|
|
fx_atom.katom_fix[fx_atom.natom_fix] = ia1;
|
| 318 |
|
|
fx_atom.natom_fix++;
|
| 319 |
|
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}
|
| 320 |
|
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}
|
| 321 |
|
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}
|
| 322 |
|
|
} else if (strcasecmp(tag,"restrained_atoms") == 0)
|
| 323 |
|
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{
|
| 324 |
|
|
tab = tabulator_new_from_file_using_header(rfile,"ATOM MAX F_CONST X Y Z",0);
|
| 325 |
|
|
if (tab)
|
| 326 |
|
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{
|
| 327 |
|
|
n_row = tabulator_height(tab);
|
| 328 |
|
|
for (i=0; i < n_row; i++)
|
| 329 |
|
|
{
|
| 330 |
|
|
ia1 = atoi(tab[i][0]);
|
| 331 |
|
|
max = atof(tab[i][1]);
|
| 332 |
|
|
fconst = atof(tab[i][2]);
|
| 333 |
|
|
if (ia1 > 0 && ia1 <= natom)
|
| 334 |
|
|
{
|
| 335 |
|
|
restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1;
|
| 336 |
|
|
restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst;
|
| 337 |
|
|
restrain_atom.restrain_max[restrain_atom.natom_restrain] = max;
|
| 338 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions
|
| 339 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y;
|
| 340 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z;
|
| 341 |
|
|
if (strlen(tab[i][3]) > 0) // x postion
|
| 342 |
|
|
{
|
| 343 |
|
|
xtmp = atof(tab[i][3]);
|
| 344 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = xtmp;
|
| 345 |
|
|
}
|
| 346 |
|
|
if (strlen(tab[i][4]) > 0) // y postion
|
| 347 |
|
|
{
|
| 348 |
|
|
xtmp = atof(tab[i][4]);
|
| 349 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = xtmp;
|
| 350 |
|
|
}
|
| 351 |
|
|
if (strlen(tab[i][5]) > 0) // y postion
|
| 352 |
|
|
{
|
| 353 |
|
|
xtmp = atof(tab[i][5]);
|
| 354 |
|
|
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = xtmp;
|
| 355 |
|
|
}
|
| 356 |
|
|
restrain_atom.natom_restrain++;
|
| 357 |
|
|
}
|
| 358 |
|
|
}
|
| 359 |
|
|
}
|
| 360 |
|
|
} else if (strcasecmp(tag,"restrained_distances") == 0)
|
| 361 |
|
|
{
|
| 362 |
|
|
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 MIN MAX F_CONST",0);
|
| 363 |
|
|
if (tab)
|
| 364 |
|
|
{
|
| 365 |
|
|
n_row = tabulator_height(tab);
|
| 366 |
|
|
for (i=0; i < n_row; i++)
|
| 367 |
|
|
{
|
| 368 |
|
|
ia1 = atoi(tab[i][0]);
|
| 369 |
|
|
ia2 = atoi(tab[i][1]);
|
| 370 |
|
|
min = atof(tab[i][2]);
|
| 371 |
|
|
max = atof(tab[i][3]);
|
| 372 |
|
|
fconst = atof(tab[i][4]);
|
| 373 |
|
|
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom))
|
| 374 |
|
|
{
|
| 375 |
|
|
fx_dist.kdfix[fx_dist.ndfix][0] = ia1;
|
| 376 |
|
|
fx_dist.kdfix[fx_dist.ndfix][1] = ia2;
|
| 377 |
|
|
fx_dist.fdconst[fx_dist.ndfix] = fconst;
|
| 378 |
|
|
fx_dist.min_dist[fx_dist.ndfix] = min;
|
| 379 |
|
|
fx_dist.max_dist[fx_dist.ndfix] = max;
|
| 380 |
|
|
fx_dist.ndfix++;
|
| 381 |
|
|
}
|
| 382 |
|
|
}
|
| 383 |
|
|
}
|
| 384 |
|
|
} else if (strcasecmp(tag,"restrained_angles") == 0)
|
| 385 |
|
|
{
|
| 386 |
|
|
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 MIN MAX F_CONST",0);
|
| 387 |
|
|
if (tab)
|
| 388 |
|
|
{
|
| 389 |
|
|
n_row = tabulator_height(tab);
|
| 390 |
|
|
for (i=0; i < n_row; i++)
|
| 391 |
|
|
{
|
| 392 |
|
|
ia1 = atoi(tab[i][0]);
|
| 393 |
|
|
ia2 = atoi(tab[i][1]);
|
| 394 |
|
|
ia3 = atoi(tab[i][2]);
|
| 395 |
|
|
min = atof(tab[i][3]);
|
| 396 |
|
|
max = atof(tab[i][4]);
|
| 397 |
|
|
fconst = atof(tab[i][5]);
|
| 398 |
|
|
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom))
|
| 399 |
|
|
{
|
| 400 |
|
|
fx_angle.kafix[fx_angle.nafix][0] = ia1;
|
| 401 |
|
|
fx_angle.kafix[fx_angle.nafix][1] = ia2;
|
| 402 |
|
|
fx_angle.kafix[fx_angle.nafix][2] = ia3;
|
| 403 |
|
|
fx_angle.faconst[fx_angle.nafix] = fconst;
|
| 404 |
|
|
fx_angle.min_ang[fx_angle.nafix] = min;
|
| 405 |
|
|
fx_angle.max_ang[fx_angle.nafix] = max;
|
| 406 |
|
|
fx_angle.nafix++;
|
| 407 |
|
|
}
|
| 408 |
|
|
}
|
| 409 |
|
|
}
|
| 410 |
|
|
} else if (strcasecmp(tag,"restrained_dihedrals") == 0)
|
| 411 |
|
|
{
|
| 412 |
|
|
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 ATOM4 MIN MAX F_CONST",0);
|
| 413 |
|
|
if (tab)
|
| 414 |
|
|
{
|
| 415 |
|
|
n_row = tabulator_height(tab);
|
| 416 |
|
|
for (i=0; i < n_row; i++)
|
| 417 |
|
|
{
|
| 418 |
|
|
ia1 = atoi(tab[i][0]);
|
| 419 |
|
|
ia2 = atoi(tab[i][1]);
|
| 420 |
|
|
ia3 = atoi(tab[i][2]);
|
| 421 |
|
|
ia4 = atoi(tab[i][3]);
|
| 422 |
|
|
min = atof(tab[i][4]);
|
| 423 |
|
|
max = atof(tab[i][5]);
|
| 424 |
|
|
fconst = atof(tab[i][6]);
|
| 425 |
|
|
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom) && (ia4 > 0 && ia4 <= natom))
|
| 426 |
|
|
{
|
| 427 |
|
|
fx_torsion.ktfix[fx_torsion.ntfix][0] = ia1;
|
| 428 |
|
|
fx_torsion.ktfix[fx_torsion.ntfix][1] = ia2;
|
| 429 |
|
|
fx_torsion.ktfix[fx_torsion.ntfix][2] = ia3;
|
| 430 |
|
|
fx_torsion.ktfix[fx_torsion.ntfix][3] = ia4;
|
| 431 |
|
|
fx_torsion.ftconst[fx_torsion.ntfix] = fconst;
|
| 432 |
|
|
fx_torsion.min_tor[fx_torsion.ntfix] = min;
|
| 433 |
|
|
fx_torsion.max_tor[fx_torsion.ntfix] = max;
|
| 434 |
|
|
fx_torsion.ntfix++;
|
| 435 |
|
|
}
|
| 436 |
|
|
}
|
| 437 |
|
|
}
|
| 438 |
|
|
}
|
| 439 |
|
|
}
|
| 440 |
|
|
}
|
| 441 |
|
|
// if (has_aromatic)
|
| 442 |
|
|
// need to deal with aromatic bonds
|
| 443 |
|
|
L_DONE:
|
| 444 |
|
|
quick_type();
|
| 445 |
|
|
if (has_Aromatic)
|
| 446 |
|
|
{
|
| 447 |
gilbertke |
90 |
for (i=0; i < numbonds; i++)
|
| 448 |
|
|
mopaco(ib1[i],ib2[i]);
|
| 449 |
gilbertke |
67 |
}
|
| 450 |
gilbertke |
90 |
free_ivector(ib1,0,nibond);
|
| 451 |
|
|
free_ivector(ib2,0,nibond);
|
| 452 |
gilbertke |
67 |
return Ret_Val;
|
| 453 |
|
|
}
|
| 454 |
|
|
// =====================
|
| 455 |
|
|
void get_tag(char *line,char *tag)
|
| 456 |
|
|
{
|
| 457 |
|
|
int i,j,icount;
|
| 458 |
|
|
icount = 0;
|
| 459 |
|
|
strcpy(tag,"");
|
| 460 |
|
|
for (i=0; i < strlen(line); i++)
|
| 461 |
|
|
{
|
| 462 |
|
|
if (line[i] == '<')
|
| 463 |
|
|
{
|
| 464 |
|
|
for (j=i+1; j < strlen(line); j++)
|
| 465 |
|
|
{
|
| 466 |
|
|
if (line[j] == '>')
|
| 467 |
|
|
{
|
| 468 |
|
|
tag[icount] = '\0';
|
| 469 |
|
|
return;
|
| 470 |
|
|
} else
|
| 471 |
|
|
{
|
| 472 |
|
|
tag[icount] = line[j];
|
| 473 |
|
|
icount++;
|
| 474 |
|
|
}
|
| 475 |
|
|
}
|
| 476 |
|
|
}
|
| 477 |
|
|
}
|
| 478 |
|
|
}
|
| 479 |
|
|
/* ------------------------------------*/
|
| 480 |
|
|
// new mopaco version - test valency of each atom and add bond if possible
|
| 481 |
|
|
void mopaco(int ia, int ib)
|
| 482 |
|
|
{
|
| 483 |
|
|
int ibi, ibj, it, jt, kk;
|
| 484 |
|
|
|
| 485 |
|
|
it = atom[ia].atomnum;
|
| 486 |
|
|
jt = atom[ib].atomnum;
|
| 487 |
|
|
|
| 488 |
|
|
if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 )
|
| 489 |
|
|
{
|
| 490 |
|
|
if( jt == 6 || jt == 7 || jt == 8 || jt == 15 || jt == 16 )
|
| 491 |
|
|
{
|
| 492 |
|
|
/* c=n */
|
| 493 |
|
|
if( (it == 7 && jt == 6) || (it == 6 && jt == 7) )
|
| 494 |
|
|
{
|
| 495 |
|
|
ibi = 0;
|
| 496 |
|
|
for( kk = 0; kk < MAXIAT; kk++ )
|
| 497 |
|
|
{
|
| 498 |
|
|
if( atom[ia].bo[kk] != 9 )
|
| 499 |
|
|
ibi = ibi + atom[ia].bo[kk];
|
| 500 |
|
|
}
|
| 501 |
|
|
ibj = 0;
|
| 502 |
|
|
for( kk = 0; kk < MAXIAT; kk++ )
|
| 503 |
|
|
{
|
| 504 |
|
|
if( atom[ib].bo[kk] != 9 )
|
| 505 |
|
|
ibj = ibj + atom[ib].bo[kk];
|
| 506 |
|
|
}
|
| 507 |
|
|
if( it == 7 )
|
| 508 |
|
|
{
|
| 509 |
|
|
if( ibi <= 2 && ibj <= 3 )
|
| 510 |
|
|
{
|
| 511 |
|
|
make_bond( ia, ib, 1 );
|
| 512 |
|
|
}
|
| 513 |
|
|
}else if( jt == 7 )
|
| 514 |
|
|
{
|
| 515 |
|
|
if( ibj <= 2 && ibi <= 3 )
|
| 516 |
|
|
{
|
| 517 |
|
|
make_bond( ia, ib, 1 );
|
| 518 |
|
|
}
|
| 519 |
|
|
}
|
| 520 |
|
|
/* c=c bond */
|
| 521 |
|
|
} else if( (it == 6 && jt == 6) )
|
| 522 |
|
|
{
|
| 523 |
|
|
ibi = 0;
|
| 524 |
|
|
for( kk = 0; kk < MAXIAT; kk++ )
|
| 525 |
|
|
{
|
| 526 |
|
|
if( atom[ia].bo[kk] != 9 )
|
| 527 |
|
|
ibi = ibi + atom[ia].bo[kk];
|
| 528 |
|
|
}
|
| 529 |
|
|
ibj = 0;
|
| 530 |
|
|
for( kk = 0; kk < MAXIAT; kk++ )
|
| 531 |
|
|
{
|
| 532 |
|
|
if( atom[ib].bo[kk] != 9 )
|
| 533 |
|
|
ibj = ibj + atom[ib].bo[kk];
|
| 534 |
|
|
}
|
| 535 |
|
|
if( ibi <= 3 && ibj <= 3 )
|
| 536 |
|
|
{
|
| 537 |
|
|
make_bond( ia, ib, 1 );
|
| 538 |
|
|
}
|
| 539 |
|
|
}
|
| 540 |
|
|
}
|
| 541 |
|
|
}
|
| 542 |
|
|
}
|
| 543 |
|
|
|
