| 1 |
/* NOTICE: this source code file has been modified for use with FreeMOL */
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| 2 |
#define EXTERN extern
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| 3 |
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| 4 |
#include "pcwin.h"
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| 5 |
#include "pcmod.h"
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| 6 |
#include "atom_k.h"
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| 7 |
#include "energies.h"
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| 8 |
#include "fix.h"
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| 9 |
#include "dipmom.h"
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| 10 |
#include "draw.h"
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| 11 |
#include "vibrate.h"
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| 12 |
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| 13 |
#define TABULATOR_INCLUDE_IMPLEMENTATION
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#include "tabulator.h"
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| 15 |
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| 16 |
EXTERN struct t_files {
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| 17 |
int nfiles, append, batch, icurrent, ibatno;
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| 18 |
} 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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| 22 |
int s,p,d,f,type ;
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| 23 |
} Elements[];
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| 24 |
EXTERN struct t_logp {
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| 25 |
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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| 42 |
* and if so write them to the output file. Look at the definitions in pcmod.h
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| 43 |
*
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| 44 |
*/
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void write_sdf(int flags)
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| 46 |
{
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| 47 |
int i,j,lptest,nbond,junk;
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| 48 |
FILE *wfile = pcmoutfile;
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| 49 |
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| 50 |
lptest = 0;
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| 51 |
for( i = 1; i <= natom; i++ )
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| 52 |
{
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| 53 |
if( atom[i].mmx_type == 20 )
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| 54 |
{
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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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| 60 |
nbond = 0;
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| 61 |
/* ** calculate the number of bonds in the molecule ** */
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| 62 |
for( j = 1; j <= natom; j++ )
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{
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| 64 |
for( i = 0; i < MAXIAT; i++ )
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| 65 |
{
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| 66 |
if( atom[j].iat[i] != 0 )
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| 67 |
{
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| 68 |
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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| 81 |
j = strlen(Struct_Title);
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| 82 |
for (i=0; i < j; i++)
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{
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| 84 |
if (Struct_Title[i] == '\n')
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{
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| 86 |
Struct_Title[i] = '\0';
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break;
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| 88 |
}
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| 89 |
}
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| 90 |
fprintf(wfile,"%s\n",Struct_Title);
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| 91 |
fprintf(wfile," MENGINE v1.0 1.00000 0.00000\n");
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| 92 |
fprintf(wfile,"\n");
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| 93 |
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| 94 |
fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond);
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| 95 |
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| 96 |
for (i=1; i <= natom; i++)
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| 97 |
{
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| 98 |
junk = 0;
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| 99 |
if (atom[i].mmx_type == 41) junk = 3;
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| 100 |
else if (atom[i].mmx_type == 42) junk = 5;
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| 101 |
else if (atom[i].mmx_type == 66)
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{
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| 103 |
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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| 107 |
atom[i].z,Elements[atom[i].atomnum-1].symbol,junk);
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}
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| 109 |
for (i=1; i <= natom; i++)
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| 110 |
{
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| 111 |
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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| 114 |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]);
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| 115 |
}
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}
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fprintf(wfile,"M END\n");
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| 118 |
fprintf(wfile,"> <title>\n");
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| 119 |
fprintf(wfile,"%s\n",Struct_Title);
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| 121 |
fprintf(wfile,"> <MMFF94 energy>\n");
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| 122 |
fprintf(wfile,"%f\n",energies.total);
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| 123 |
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| 124 |
fprintf(wfile,"> <MMFF94_Atomtypes>\n");
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| 125 |
fprintf(wfile,"+ Atom Atomtype\n");
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| 126 |
for (i=1; i <=natom; i++)
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| 127 |
fprintf(wfile,"| %d %d\n",i,atom[i].type);
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| 128 |
fprintf(wfile,"\n");
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| 129 |
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| 130 |
if (flags & DO_DIPOLE) {
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| 131 |
fprintf(wfile,"> <dipole moment>\n");
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| 132 |
fprintf(wfile,"%f\n",dipolemom.total);
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| 133 |
}
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| 134 |
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| 135 |
if (flags & DO_XLOGP) {
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| 136 |
fprintf(wfile,"> <xLogP>\n");
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| 137 |
fprintf(wfile,"%f\n",logp_calc.logp);
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}
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| 139 |
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| 140 |
if (flags & DO_VIBRATION) {
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fprintf(wfile,"> <Point Group>\n");
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| 142 |
fprintf(wfile,"%s\n",vibdata.ptgrp);
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| 143 |
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| 144 |
fprintf(wfile,"> <Moments of Inertia>\n");
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| 145 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz);
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| 146 |
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| 147 |
fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n");
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| 148 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot,
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| 149 |
vibdata.stot,vibdata.gtot,vibdata.cptot);
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| 150 |
}
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| 151 |
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| 152 |
fprintf(wfile,"\n");
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fprintf(wfile,"$$$$\n");
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// fclose(wfile);
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| 155 |
}
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| 156 |
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| 157 |
/* =================================== */
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| 158 |
// fast read - assume file is open and positioned
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| 159 |
// read structure and down to end $$$$
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| 160 |
// and return
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| 161 |
int rd_sdf(FILE *rfile)
|
| 162 |
{
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| 163 |
int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom;
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| 164 |
int ncount,junk,junk1,got_title,istereo,iz,nvalue;
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| 165 |
int jji, jj1, jj2, jj3, jj4;
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| 166 |
int n_row;
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| 167 |
int has_Aromatic, xPlus,yPlus,zPlus, planar;
|
| 168 |
int icount,itemp[4];
|
| 169 |
int Ret_Val;
|
| 170 |
float xtmp, ytmp, ztmp, dz;
|
| 171 |
float fconst,min,max;
|
| 172 |
char c1[4],c2[4];
|
| 173 |
char atomchar[3];
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| 174 |
char inputline[150];
|
| 175 |
char tag[30];
|
| 176 |
char ***tab;
|
| 177 |
|
| 178 |
Ret_Val = TRUE;
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| 179 |
got_title = FALSE;
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| 180 |
xPlus = yPlus = zPlus = FALSE;
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| 181 |
if ( 0 == FetchRecord(rfile,inputline) )return -1;
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| 182 |
// sscanf(inputline,"SDF %s",Struct_Title);
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| 183 |
strncpy(Struct_Title, inputline, sizeof(Struct_Title));
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| 184 |
got_title = TRUE;
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| 185 |
/* if (strlen(inputline) > 4)
|
| 186 |
{
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| 187 |
iz = strlen(inputline);
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| 188 |
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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got_title = TRUE;
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} */
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| 194 |
FetchRecord(rfile,inputline); // blank line
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| 195 |
FetchRecord(rfile,inputline); // blank line
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| 196 |
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| 197 |
FetchRecord(rfile,inputline); // natom and nbond
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| 198 |
for (i=0; i <4; i++)
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| 199 |
{
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| 200 |
c1[i] = inputline[i];
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| 201 |
c2[i] = inputline[i+3];
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| 202 |
}
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| 203 |
c1[3] = '\0';c2[3] = '\0';
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| 204 |
niatom = atoi(c1);
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| 205 |
nibond = atoi(c2);
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| 206 |
if (niatom == 0)
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| 207 |
return FALSE;
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| 208 |
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| 209 |
for (i=0; i < niatom; i++)
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| 210 |
{
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| 211 |
FetchRecord(rfile,inputline);
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| 212 |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1);
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| 213 |
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| 214 |
itype = 0;
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| 215 |
if (xtmp != 0.0) xPlus= TRUE;
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| 216 |
if (ytmp != 0.0) yPlus= TRUE;
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| 217 |
if (ztmp != 0.0) zPlus= TRUE;
|
| 218 |
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| 219 |
iz = strlen(atomchar);
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| 220 |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix
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| 221 |
{
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| 222 |
if (atomchar[0] == 'N') itype = 8;
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| 223 |
if (atomchar[0] == 'O') itype = 6;
|
| 224 |
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| 225 |
if (junk1 != 0)
|
| 226 |
{
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| 227 |
if (junk1 == 3 && itype == 8)
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| 228 |
itype = 41; // N+
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| 229 |
if (junk1 == 5 && itype == 6)
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| 230 |
itype = 42; // O-
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| 231 |
}
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| 232 |
}
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| 233 |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar);
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| 234 |
if (itype != 0)
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| 235 |
atom[newatom].mmx_type = itype;
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| 236 |
if (newatom == -1)
|
| 237 |
{
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| 238 |
fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar);
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| 239 |
Ret_Val = FALSE;
|
| 240 |
}
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| 241 |
}
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| 242 |
has_Aromatic = FALSE;
|
| 243 |
|
| 244 |
planar = TRUE;
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| 245 |
if (xPlus && yPlus && zPlus) planar = FALSE;
|
| 246 |
|
| 247 |
for (i=0; i < nibond; i++)
|
| 248 |
{
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| 249 |
FetchRecord(rfile,inputline);
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| 250 |
for (j=0; j <4; j++)
|
| 251 |
{
|
| 252 |
c1[j] = inputline[j];
|
| 253 |
c2[j] = inputline[j+3];
|
| 254 |
}
|
| 255 |
c1[3] = '\0';c2[3] = '\0';
|
| 256 |
ia1 = atoi(c1);
|
| 257 |
ia2 = atoi(c2);
|
| 258 |
istereo = 0;
|
| 259 |
sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo);
|
| 260 |
if (ibond >= 4)
|
| 261 |
{
|
| 262 |
// use bonds array as temporary storage for aromatic bonds
|
| 263 |
make_bond(ia1,ia2,1);
|
| 264 |
bonds.ia1[bonds.numbonds] = ia1;
|
| 265 |
bonds.ia2[bonds.numbonds] = ia2;
|
| 266 |
bonds.numbonds++;
|
| 267 |
has_Aromatic = TRUE;
|
| 268 |
} else
|
| 269 |
make_bond(ia1, ia2, ibond);
|
| 270 |
if (istereo == 1 && planar)
|
| 271 |
{
|
| 272 |
atom[ia2].z += 0.7;
|
| 273 |
if (atom[ia2].atomnum == 1)
|
| 274 |
atom[ia2].type = 60;
|
| 275 |
}
|
| 276 |
if (istereo == 6 && planar)
|
| 277 |
{
|
| 278 |
atom[ia2].z -= 0.7;
|
| 279 |
if (atom[ia2].atomnum == 1)
|
| 280 |
atom[ia2].type = 60;
|
| 281 |
}
|
| 282 |
}
|
| 283 |
// read to end of structure
|
| 284 |
// parse any tags here
|
| 285 |
// agreed tags
|
| 286 |
// <FIXED_ATOMS>
|
| 287 |
// <RESTRAINED_ATOMS>
|
| 288 |
// <RESTRAINED_DISTANCES>
|
| 289 |
// <RESTRAINED_ANGLES>
|
| 290 |
// <RESTRAINED_DIHEDRALS>
|
| 291 |
|
| 292 |
while (FetchRecord(rfile,inputline))
|
| 293 |
{
|
| 294 |
if (strncasecmp(inputline,"$$$$",4) == 0)
|
| 295 |
{
|
| 296 |
goto L_DONE;
|
| 297 |
} else if (inputline[0] == '>')
|
| 298 |
{
|
| 299 |
get_tag(inputline,tag);
|
| 300 |
if (strcasecmp(tag,"fixed_atoms") == 0)
|
| 301 |
{
|
| 302 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM",0);
|
| 303 |
if (tab)
|
| 304 |
{
|
| 305 |
fprintf(pcmlogfile,"got table\n");
|
| 306 |
n_row = tabulator_height(tab);
|
| 307 |
for (i=0; i < n_row; i++)
|
| 308 |
{
|
| 309 |
ia1 = atoi(tab[i][0]);
|
| 310 |
if (ia1 > 0 && ia1 <= natom)
|
| 311 |
{
|
| 312 |
fx_atom.katom_fix[fx_atom.natom_fix] = ia1;
|
| 313 |
fx_atom.natom_fix++;
|
| 314 |
}
|
| 315 |
}
|
| 316 |
}
|
| 317 |
} else if (strcasecmp(tag,"restrained_atoms") == 0)
|
| 318 |
{
|
| 319 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM MAX F_CONST X Y Z",0);
|
| 320 |
if (tab)
|
| 321 |
{
|
| 322 |
n_row = tabulator_height(tab);
|
| 323 |
for (i=0; i < n_row; i++)
|
| 324 |
{
|
| 325 |
ia1 = atoi(tab[i][0]);
|
| 326 |
max = atof(tab[i][1]);
|
| 327 |
fconst = atof(tab[i][2]);
|
| 328 |
if (ia1 > 0 && ia1 <= natom)
|
| 329 |
{
|
| 330 |
restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1;
|
| 331 |
restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst;
|
| 332 |
restrain_atom.restrain_max[restrain_atom.natom_restrain] = max;
|
| 333 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions
|
| 334 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y;
|
| 335 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z;
|
| 336 |
if (strlen(tab[i][3]) > 0) // x postion
|
| 337 |
{
|
| 338 |
xtmp = atof(tab[i][3]);
|
| 339 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = xtmp;
|
| 340 |
}
|
| 341 |
if (strlen(tab[i][4]) > 0) // y postion
|
| 342 |
{
|
| 343 |
xtmp = atof(tab[i][4]);
|
| 344 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = xtmp;
|
| 345 |
}
|
| 346 |
if (strlen(tab[i][5]) > 0) // y postion
|
| 347 |
{
|
| 348 |
xtmp = atof(tab[i][5]);
|
| 349 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = xtmp;
|
| 350 |
}
|
| 351 |
restrain_atom.natom_restrain++;
|
| 352 |
}
|
| 353 |
}
|
| 354 |
}
|
| 355 |
} else if (strcasecmp(tag,"restrained_distances") == 0)
|
| 356 |
{
|
| 357 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 MIN MAX F_CONST",0);
|
| 358 |
if (tab)
|
| 359 |
{
|
| 360 |
n_row = tabulator_height(tab);
|
| 361 |
for (i=0; i < n_row; i++)
|
| 362 |
{
|
| 363 |
ia1 = atoi(tab[i][0]);
|
| 364 |
ia2 = atoi(tab[i][1]);
|
| 365 |
min = atof(tab[i][2]);
|
| 366 |
max = atof(tab[i][3]);
|
| 367 |
fconst = atof(tab[i][4]);
|
| 368 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom))
|
| 369 |
{
|
| 370 |
fx_dist.kdfix[fx_dist.ndfix][0] = ia1;
|
| 371 |
fx_dist.kdfix[fx_dist.ndfix][1] = ia2;
|
| 372 |
fx_dist.fdconst[fx_dist.ndfix] = fconst;
|
| 373 |
fx_dist.min_dist[fx_dist.ndfix] = min;
|
| 374 |
fx_dist.max_dist[fx_dist.ndfix] = max;
|
| 375 |
fx_dist.ndfix++;
|
| 376 |
}
|
| 377 |
}
|
| 378 |
}
|
| 379 |
} else if (strcasecmp(tag,"restrained_angles") == 0)
|
| 380 |
{
|
| 381 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 MIN MAX F_CONST",0);
|
| 382 |
if (tab)
|
| 383 |
{
|
| 384 |
n_row = tabulator_height(tab);
|
| 385 |
for (i=0; i < n_row; i++)
|
| 386 |
{
|
| 387 |
ia1 = atoi(tab[i][0]);
|
| 388 |
ia2 = atoi(tab[i][1]);
|
| 389 |
ia3 = atoi(tab[i][2]);
|
| 390 |
min = atof(tab[i][3]);
|
| 391 |
max = atof(tab[i][4]);
|
| 392 |
fconst = atof(tab[i][5]);
|
| 393 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom))
|
| 394 |
{
|
| 395 |
fx_angle.kafix[fx_angle.nafix][0] = ia1;
|
| 396 |
fx_angle.kafix[fx_angle.nafix][1] = ia2;
|
| 397 |
fx_angle.kafix[fx_angle.nafix][2] = ia3;
|
| 398 |
fx_angle.faconst[fx_angle.nafix] = fconst;
|
| 399 |
fx_angle.min_ang[fx_angle.nafix] = min;
|
| 400 |
fx_angle.max_ang[fx_angle.nafix] = max;
|
| 401 |
fx_angle.nafix++;
|
| 402 |
}
|
| 403 |
}
|
| 404 |
}
|
| 405 |
} else if (strcasecmp(tag,"restrained_dihedrals") == 0)
|
| 406 |
{
|
| 407 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 ATOM4 MIN MAX F_CONST",0);
|
| 408 |
if (tab)
|
| 409 |
{
|
| 410 |
n_row = tabulator_height(tab);
|
| 411 |
for (i=0; i < n_row; i++)
|
| 412 |
{
|
| 413 |
ia1 = atoi(tab[i][0]);
|
| 414 |
ia2 = atoi(tab[i][1]);
|
| 415 |
ia3 = atoi(tab[i][2]);
|
| 416 |
ia4 = atoi(tab[i][3]);
|
| 417 |
min = atof(tab[i][4]);
|
| 418 |
max = atof(tab[i][5]);
|
| 419 |
fconst = atof(tab[i][6]);
|
| 420 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom) && (ia4 > 0 && ia4 <= natom))
|
| 421 |
{
|
| 422 |
fx_torsion.ktfix[fx_torsion.ntfix][0] = ia1;
|
| 423 |
fx_torsion.ktfix[fx_torsion.ntfix][1] = ia2;
|
| 424 |
fx_torsion.ktfix[fx_torsion.ntfix][2] = ia3;
|
| 425 |
fx_torsion.ktfix[fx_torsion.ntfix][3] = ia4;
|
| 426 |
fx_torsion.ftconst[fx_torsion.ntfix] = fconst;
|
| 427 |
fx_torsion.min_tor[fx_torsion.ntfix] = min;
|
| 428 |
fx_torsion.max_tor[fx_torsion.ntfix] = max;
|
| 429 |
fx_torsion.ntfix++;
|
| 430 |
}
|
| 431 |
}
|
| 432 |
}
|
| 433 |
}
|
| 434 |
}
|
| 435 |
}
|
| 436 |
// if (has_aromatic)
|
| 437 |
// need to deal with aromatic bonds
|
| 438 |
L_DONE:
|
| 439 |
quick_type();
|
| 440 |
if (has_Aromatic)
|
| 441 |
{
|
| 442 |
for (i=0; i < bonds.numbonds; i++)
|
| 443 |
mopaco(bonds.ia1[i],bonds.ia2[i]);
|
| 444 |
}
|
| 445 |
return Ret_Val;
|
| 446 |
}
|
| 447 |
// =====================
|
| 448 |
void get_tag(char *line,char *tag)
|
| 449 |
{
|
| 450 |
int i,j,icount;
|
| 451 |
icount = 0;
|
| 452 |
strcpy(tag,"");
|
| 453 |
for (i=0; i < strlen(line); i++)
|
| 454 |
{
|
| 455 |
if (line[i] == '<')
|
| 456 |
{
|
| 457 |
for (j=i+1; j < strlen(line); j++)
|
| 458 |
{
|
| 459 |
if (line[j] == '>')
|
| 460 |
{
|
| 461 |
tag[icount] = '\0';
|
| 462 |
return;
|
| 463 |
} else
|
| 464 |
{
|
| 465 |
tag[icount] = line[j];
|
| 466 |
icount++;
|
| 467 |
}
|
| 468 |
}
|
| 469 |
}
|
| 470 |
}
|
| 471 |
}
|
| 472 |
/* ------------------------------------*/
|
| 473 |
// new mopaco version - test valency of each atom and add bond if possible
|
| 474 |
void mopaco(int ia, int ib)
|
| 475 |
{
|
| 476 |
int ibi, ibj, it, jt, kk;
|
| 477 |
|
| 478 |
it = atom[ia].atomnum;
|
| 479 |
jt = atom[ib].atomnum;
|
| 480 |
|
| 481 |
if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 )
|
| 482 |
{
|
| 483 |
if( jt == 6 || jt == 7 || jt == 8 || jt == 15 || jt == 16 )
|
| 484 |
{
|
| 485 |
/* c=n */
|
| 486 |
if( (it == 7 && jt == 6) || (it == 6 && jt == 7) )
|
| 487 |
{
|
| 488 |
ibi = 0;
|
| 489 |
for( kk = 0; kk < MAXIAT; kk++ )
|
| 490 |
{
|
| 491 |
if( atom[ia].bo[kk] != 9 )
|
| 492 |
ibi = ibi + atom[ia].bo[kk];
|
| 493 |
}
|
| 494 |
ibj = 0;
|
| 495 |
for( kk = 0; kk < MAXIAT; kk++ )
|
| 496 |
{
|
| 497 |
if( atom[ib].bo[kk] != 9 )
|
| 498 |
ibj = ibj + atom[ib].bo[kk];
|
| 499 |
}
|
| 500 |
if( it == 7 )
|
| 501 |
{
|
| 502 |
if( ibi <= 2 && ibj <= 3 )
|
| 503 |
{
|
| 504 |
// if( ia < ib )
|
| 505 |
// fprintf(stderr,"cn; %d %d\n",ia,ib);
|
| 506 |
make_bond( ia, ib, 1 );
|
| 507 |
}
|
| 508 |
}else if( jt == 7 )
|
| 509 |
{
|
| 510 |
if( ibj <= 2 && ibi <= 3 )
|
| 511 |
{
|
| 512 |
// if( ia < ib )
|
| 513 |
// fprintf(stderr,"cn1; %d %d\n",ia,ib);
|
| 514 |
make_bond( ia, ib, 1 );
|
| 515 |
}
|
| 516 |
}
|
| 517 |
/* c=c bond */
|
| 518 |
} else if( (it == 6 && jt == 6) )
|
| 519 |
{
|
| 520 |
ibi = 0;
|
| 521 |
for( kk = 0; kk < MAXIAT; kk++ )
|
| 522 |
{
|
| 523 |
if( atom[ia].bo[kk] != 9 )
|
| 524 |
ibi = ibi + atom[ia].bo[kk];
|
| 525 |
}
|
| 526 |
ibj = 0;
|
| 527 |
for( kk = 0; kk < MAXIAT; kk++ )
|
| 528 |
{
|
| 529 |
if( atom[ib].bo[kk] != 9 )
|
| 530 |
ibj = ibj + atom[ib].bo[kk];
|
| 531 |
}
|
| 532 |
if( ibi <= 3 && ibj <= 3 )
|
| 533 |
{
|
| 534 |
if( ia < ib )
|
| 535 |
make_bond( ia, ib, 1 );
|
| 536 |
}
|
| 537 |
}
|
| 538 |
}
|
| 539 |
}
|
| 540 |
}
|
| 541 |
|
