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/* NOTICE: this source code file has been modified for use with FreeMOL */ |
| 2 |
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#define EXTERN extern |
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|
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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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|
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#define TABULATOR_INCLUDE_IMPLEMENTATION |
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#include "tabulator.h" |
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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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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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// ============================ |
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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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|
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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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|
| 81 |
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j = strlen(Struct_Title); |
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for (i=0; i < j; i++) |
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{ |
| 84 |
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if (Struct_Title[i] == '\n') |
| 85 |
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{ |
| 86 |
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Struct_Title[i] = '\0'; |
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break; |
| 88 |
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} |
| 89 |
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} |
| 90 |
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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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|
| 94 |
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fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond); |
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|
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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"); |
| 118 |
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fprintf(wfile,"> <title>\n"); |
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fprintf(wfile,"%s\n",Struct_Title); |
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|
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fprintf(wfile,"> <MMFF94 energy>\n"); |
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fprintf(wfile,"%f\n",energies.total); |
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|
| 124 |
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fprintf(wfile,"> <MMFF94_Atomtypes>\n"); |
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fprintf(wfile,"+ Atom Atomtype\n"); |
| 126 |
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for (i=1; i <=natom; i++) |
| 127 |
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fprintf(wfile,"| %d %d\n",i,atom[i].type); |
| 128 |
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fprintf(wfile,"\n"); |
| 129 |
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|
| 130 |
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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); |
| 133 |
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} |
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|
| 135 |
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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); |
| 138 |
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} |
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|
| 140 |
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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); |
| 143 |
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|
| 144 |
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fprintf(wfile,"> <Moments of Inertia>\n"); |
| 145 |
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fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz); |
| 146 |
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|
| 147 |
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fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n"); |
| 148 |
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fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot, |
| 149 |
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vibdata.stot,vibdata.gtot,vibdata.cptot); |
| 150 |
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} |
| 151 |
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|
| 152 |
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fprintf(wfile,"\n"); |
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fprintf(wfile,"$$$$\n"); |
| 154 |
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// fclose(wfile); |
| 155 |
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} |
| 156 |
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|
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/* =================================== */ |
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// fast read - assume file is open and positioned |
| 159 |
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// read structure and down to end $$$$ |
| 160 |
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// and return |
| 161 |
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int rd_sdf(FILE *rfile) |
| 162 |
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{ |
| 163 |
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int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom; |
| 164 |
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int ncount,junk,junk1,got_title,istereo,iz,nvalue; |
| 165 |
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int jji, jj1, jj2, jj3, jj4; |
| 166 |
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int n_row; |
| 167 |
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int has_Aromatic, xPlus,yPlus,zPlus, planar; |
| 168 |
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int icount,itemp[4]; |
| 169 |
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int Ret_Val; |
| 170 |
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float xtmp, ytmp, ztmp, dz; |
| 171 |
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float fconst,min,max; |
| 172 |
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char c1[4],c2[4]; |
| 173 |
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char atomchar[3]; |
| 174 |
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char inputline[150]; |
| 175 |
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char tag[30]; |
| 176 |
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char ***tab; |
| 177 |
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|
| 178 |
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Ret_Val = TRUE; |
| 179 |
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got_title = FALSE; |
| 180 |
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xPlus = yPlus = zPlus = FALSE; |
| 181 |
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if ( 0 == FetchRecord(rfile,inputline) )return -1; |
| 182 |
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// sscanf(inputline,"SDF %s",Struct_Title); |
| 183 |
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strncpy(Struct_Title, inputline, sizeof(Struct_Title)); |
| 184 |
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got_title = TRUE; |
| 185 |
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/* if (strlen(inputline) > 4) |
| 186 |
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{ |
| 187 |
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iz = strlen(inputline); |
| 188 |
< |
if (iz > 60) iz = 59; |
| 189 |
< |
for (i=4; i < iz; i++) |
| 190 |
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Struct_Title[i-4] = inputline[i]; |
| 191 |
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Struct_Title[i] = '\0'; |
| 192 |
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got_title = TRUE; |
| 193 |
< |
} */ |
| 194 |
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FetchRecord(rfile,inputline); // blank line |
| 195 |
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FetchRecord(rfile,inputline); // blank line |
| 196 |
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|
| 197 |
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FetchRecord(rfile,inputline); // natom and nbond |
| 198 |
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for (i=0; i <4; i++) |
| 199 |
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{ |
| 200 |
< |
c1[i] = inputline[i]; |
| 201 |
< |
c2[i] = inputline[i+3]; |
| 202 |
< |
} |
| 203 |
< |
c1[3] = '\0';c2[3] = '\0'; |
| 204 |
< |
niatom = atoi(c1); |
| 205 |
< |
nibond = atoi(c2); |
| 206 |
< |
if (niatom == 0) |
| 207 |
< |
return FALSE; |
| 208 |
< |
|
| 209 |
< |
for (i=0; i < niatom; i++) |
| 210 |
< |
{ |
| 211 |
< |
FetchRecord(rfile,inputline); |
| 212 |
< |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 213 |
< |
|
| 214 |
< |
itype = 0; |
| 215 |
< |
if (xtmp != 0.0) xPlus= TRUE; |
| 216 |
< |
if (ytmp != 0.0) yPlus= TRUE; |
| 217 |
< |
if (ztmp != 0.0) zPlus= TRUE; |
| 218 |
< |
|
| 219 |
< |
iz = strlen(atomchar); |
| 220 |
< |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 221 |
< |
{ |
| 222 |
< |
if (atomchar[0] == 'N') itype = 8; |
| 223 |
< |
if (atomchar[0] == 'O') itype = 6; |
| 224 |
< |
|
| 225 |
< |
if (junk1 != 0) |
| 226 |
< |
{ |
| 227 |
< |
if (junk1 == 3 && itype == 8) |
| 228 |
< |
itype = 41; // N+ |
| 229 |
< |
if (junk1 == 5 && itype == 6) |
| 230 |
< |
itype = 42; // O- |
| 231 |
< |
} |
| 232 |
< |
} |
| 233 |
< |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 234 |
< |
if (itype != 0) |
| 235 |
< |
atom[newatom].mmx_type = itype; |
| 236 |
< |
if (newatom == -1) |
| 237 |
< |
{ |
| 238 |
< |
fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 239 |
< |
Ret_Val = FALSE; |
| 240 |
< |
} |
| 241 |
< |
} |
| 242 |
< |
has_Aromatic = FALSE; |
| 243 |
< |
|
| 244 |
< |
planar = TRUE; |
| 245 |
< |
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 246 |
< |
|
| 247 |
< |
for (i=0; i < nibond; i++) |
| 248 |
< |
{ |
| 249 |
< |
FetchRecord(rfile,inputline); |
| 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 |
< |
ibond = 1; |
| 263 |
< |
has_Aromatic = TRUE; |
| 264 |
< |
// TJO |
| 265 |
< |
Ret_Val = FALSE; |
| 266 |
< |
} |
| 267 |
< |
make_bond(ia1, ia2, ibond); |
| 268 |
< |
if (istereo == 1 && planar) |
| 269 |
< |
{ |
| 270 |
< |
atom[ia2].z += 0.7; |
| 271 |
< |
if (atom[ia2].atomnum == 1) |
| 272 |
< |
atom[ia2].type = 60; |
| 273 |
< |
} |
| 274 |
< |
if (istereo == 6 && planar) |
| 275 |
< |
{ |
| 276 |
< |
atom[ia2].z -= 0.7; |
| 277 |
< |
if (atom[ia2].atomnum == 1) |
| 278 |
< |
atom[ia2].type = 60; |
| 279 |
< |
} |
| 280 |
< |
} |
| 281 |
< |
// read to end of structure |
| 282 |
< |
// parse any tags here |
| 283 |
< |
// agreed tags |
| 284 |
< |
// <FIXED_ATOMS> |
| 285 |
< |
// <RESTRAINED_ATOMS> |
| 286 |
< |
// <RESTRAINED_DISTANCES> |
| 287 |
< |
// <RESTRAINED_ANGLES> |
| 288 |
< |
// <RESTRAINED_DIHEDRALS> |
| 289 |
< |
|
| 290 |
< |
while (FetchRecord(rfile,inputline)) |
| 291 |
< |
{ |
| 292 |
< |
if (strncasecmp(inputline,"$$$$",4) == 0) |
| 293 |
< |
{ |
| 294 |
< |
goto L_DONE; |
| 295 |
< |
} else if (inputline[0] == '>') |
| 296 |
< |
{ |
| 297 |
< |
get_tag(inputline,tag); |
| 298 |
< |
if (strcasecmp(tag,"fixed_atoms") == 0) |
| 299 |
< |
{ |
| 300 |
< |
tab = tabulator_new_from_file_using_header(rfile,"ATOM",0); |
| 301 |
< |
if (tab) |
| 302 |
< |
{ |
| 303 |
< |
fprintf(pcmlogfile,"got table\n"); |
| 304 |
< |
n_row = tabulator_height(tab); |
| 305 |
< |
for (i=0; i < n_row; i++) |
| 306 |
< |
{ |
| 307 |
< |
ia1 = atoi(tab[i][0]); |
| 308 |
< |
if (ia1 > 0 && ia1 <= natom) |
| 309 |
< |
{ |
| 310 |
< |
fx_atom.katom_fix[fx_atom.natom_fix] = ia1; |
| 311 |
< |
fx_atom.natom_fix++; |
| 312 |
< |
} |
| 313 |
< |
} |
| 314 |
< |
} |
| 315 |
< |
} else if (strcasecmp(tag,"restrained_atoms") == 0) |
| 316 |
< |
{ |
| 317 |
< |
tab = tabulator_new_from_file_using_header(rfile,"ATOM MAX F_CONST X Y Z",0); |
| 318 |
< |
if (tab) |
| 319 |
< |
{ |
| 320 |
< |
n_row = tabulator_height(tab); |
| 321 |
< |
for (i=0; i < n_row; i++) |
| 322 |
< |
{ |
| 323 |
< |
ia1 = atoi(tab[i][0]); |
| 324 |
< |
max = atof(tab[i][1]); |
| 325 |
< |
fconst = atof(tab[i][2]); |
| 326 |
< |
if (ia1 > 0 && ia1 <= natom) |
| 327 |
< |
{ |
| 328 |
< |
restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1; |
| 329 |
< |
restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst; |
| 330 |
< |
restrain_atom.restrain_max[restrain_atom.natom_restrain] = max; |
| 331 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions |
| 332 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y; |
| 333 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z; |
| 334 |
< |
if (strlen(tab[i][3]) > 0) // x postion |
| 335 |
< |
{ |
| 336 |
< |
xtmp = atof(tab[i][3]); |
| 337 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = xtmp; |
| 338 |
< |
} |
| 339 |
< |
if (strlen(tab[i][4]) > 0) // y postion |
| 340 |
< |
{ |
| 341 |
< |
xtmp = atof(tab[i][4]); |
| 342 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = xtmp; |
| 343 |
< |
} |
| 344 |
< |
if (strlen(tab[i][5]) > 0) // y postion |
| 345 |
< |
{ |
| 346 |
< |
xtmp = atof(tab[i][5]); |
| 347 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = xtmp; |
| 348 |
< |
} |
| 349 |
< |
restrain_atom.natom_restrain++; |
| 350 |
< |
} |
| 351 |
< |
} |
| 352 |
< |
} |
| 353 |
< |
} else if (strcasecmp(tag,"restrained_distances") == 0) |
| 354 |
< |
{ |
| 355 |
< |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 MIN MAX F_CONST",0); |
| 356 |
< |
if (tab) |
| 357 |
< |
{ |
| 358 |
< |
n_row = tabulator_height(tab); |
| 359 |
< |
for (i=0; i < n_row; i++) |
| 360 |
< |
{ |
| 361 |
< |
ia1 = atoi(tab[i][0]); |
| 362 |
< |
ia2 = atoi(tab[i][1]); |
| 363 |
< |
min = atof(tab[i][2]); |
| 364 |
< |
max = atof(tab[i][3]); |
| 365 |
< |
fconst = atof(tab[i][4]); |
| 366 |
< |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom)) |
| 367 |
< |
{ |
| 368 |
< |
fx_dist.kdfix[fx_dist.ndfix][0] = ia1; |
| 369 |
< |
fx_dist.kdfix[fx_dist.ndfix][1] = ia2; |
| 370 |
< |
fx_dist.fdconst[fx_dist.ndfix] = fconst; |
| 371 |
< |
fx_dist.min_dist[fx_dist.ndfix] = min; |
| 372 |
< |
fx_dist.max_dist[fx_dist.ndfix] = max; |
| 373 |
< |
fx_dist.ndfix++; |
| 374 |
< |
} |
| 375 |
< |
} |
| 376 |
< |
} |
| 377 |
< |
} else if (strcasecmp(tag,"restrained_angles") == 0) |
| 378 |
< |
{ |
| 379 |
< |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 MIN MAX F_CONST",0); |
| 380 |
< |
if (tab) |
| 381 |
< |
{ |
| 382 |
< |
n_row = tabulator_height(tab); |
| 383 |
< |
for (i=0; i < n_row; i++) |
| 384 |
< |
{ |
| 385 |
< |
ia1 = atoi(tab[i][0]); |
| 386 |
< |
ia2 = atoi(tab[i][1]); |
| 387 |
< |
ia3 = atoi(tab[i][2]); |
| 388 |
< |
min = atof(tab[i][3]); |
| 389 |
< |
max = atof(tab[i][4]); |
| 390 |
< |
fconst = atof(tab[i][5]); |
| 391 |
< |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom)) |
| 392 |
< |
{ |
| 393 |
< |
fx_angle.kafix[fx_angle.nafix][0] = ia1; |
| 394 |
< |
fx_angle.kafix[fx_angle.nafix][1] = ia2; |
| 395 |
< |
fx_angle.kafix[fx_angle.nafix][2] = ia3; |
| 396 |
< |
fx_angle.faconst[fx_angle.nafix] = fconst; |
| 397 |
< |
fx_angle.min_ang[fx_angle.nafix] = min; |
| 398 |
< |
fx_angle.max_ang[fx_angle.nafix] = max; |
| 399 |
< |
fx_angle.nafix++; |
| 400 |
< |
} |
| 401 |
< |
} |
| 402 |
< |
} |
| 403 |
< |
} else if (strcasecmp(tag,"restrained_dihedrals") == 0) |
| 404 |
< |
{ |
| 405 |
< |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 ATOM4 MIN MAX F_CONST",0); |
| 406 |
< |
if (tab) |
| 407 |
< |
{ |
| 408 |
< |
n_row = tabulator_height(tab); |
| 409 |
< |
for (i=0; i < n_row; i++) |
| 410 |
< |
{ |
| 411 |
< |
ia1 = atoi(tab[i][0]); |
| 412 |
< |
ia2 = atoi(tab[i][1]); |
| 413 |
< |
ia3 = atoi(tab[i][2]); |
| 414 |
< |
ia4 = atoi(tab[i][3]); |
| 415 |
< |
min = atof(tab[i][4]); |
| 416 |
< |
max = atof(tab[i][5]); |
| 417 |
< |
fconst = atof(tab[i][6]); |
| 418 |
< |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom) && (ia4 > 0 && ia4 <= natom)) |
| 419 |
< |
{ |
| 420 |
< |
fx_torsion.ktfix[fx_torsion.ntfix][0] = ia1; |
| 421 |
< |
fx_torsion.ktfix[fx_torsion.ntfix][1] = ia2; |
| 422 |
< |
fx_torsion.ktfix[fx_torsion.ntfix][2] = ia3; |
| 423 |
< |
fx_torsion.ktfix[fx_torsion.ntfix][3] = ia4; |
| 424 |
< |
fx_torsion.ftconst[fx_torsion.ntfix] = fconst; |
| 425 |
< |
fx_torsion.min_tor[fx_torsion.ntfix] = min; |
| 426 |
< |
fx_torsion.max_tor[fx_torsion.ntfix] = max; |
| 427 |
< |
fx_torsion.ntfix++; |
| 428 |
< |
} |
| 429 |
< |
} |
| 430 |
< |
} |
| 431 |
< |
} |
| 432 |
< |
} |
| 433 |
< |
} |
| 434 |
< |
// if (has_aromatic) |
| 435 |
< |
// need to deal with aromatic bonds |
| 436 |
< |
L_DONE: |
| 437 |
< |
quick_type(); |
| 438 |
< |
if (has_Aromatic) |
| 439 |
< |
{ |
| 440 |
< |
mopaco(1,natom); |
| 441 |
< |
} |
| 442 |
< |
return Ret_Val; |
| 443 |
< |
} |
| 444 |
< |
// ===================== |
| 445 |
< |
void get_tag(char *line,char *tag) |
| 446 |
< |
{ |
| 447 |
< |
int i,j,icount; |
| 448 |
< |
icount = 0; |
| 449 |
< |
strcpy(tag,""); |
| 450 |
< |
for (i=0; i < strlen(line); i++) |
| 451 |
< |
{ |
| 452 |
< |
if (line[i] == '<') |
| 453 |
< |
{ |
| 454 |
< |
for (j=i+1; j < strlen(line); j++) |
| 455 |
< |
{ |
| 456 |
< |
if (line[j] == '>') |
| 457 |
< |
{ |
| 458 |
< |
tag[icount] = '\0'; |
| 459 |
< |
return; |
| 460 |
< |
} else |
| 461 |
< |
{ |
| 462 |
< |
tag[icount] = line[j]; |
| 463 |
< |
icount++; |
| 464 |
< |
} |
| 465 |
< |
} |
| 466 |
< |
} |
| 467 |
< |
} |
| 468 |
< |
} |
| 469 |
< |
/* ------------------------------------*/ |
| 470 |
< |
// currently based on distance tests |
| 471 |
< |
// this should be changed to only look at bonds passed in with bond order >= 4 |
| 472 |
< |
// but we need a mechanism to mark this -- Kevin |
| 473 |
< |
void mopaco(int istart,int ifinish) |
| 474 |
< |
{ |
| 475 |
< |
int i, ibi, ibj, it, j, jt, kk; |
| 476 |
< |
float disij, dx, dy, dz, r, xii, yii, zii,rbdis[4]; |
| 477 |
< |
|
| 478 |
< |
rbdis[0] = 1.42; |
| 479 |
< |
rbdis[1] = 1.25; |
| 480 |
< |
rbdis[2] = 1.37; |
| 481 |
< |
rbdis[3] = 1.25; |
| 482 |
< |
|
| 483 |
< |
/* find all double and triple bonds - search only types for |
| 484 |
< |
* carbon, oxygen, nitrogen, sulfur, phosphorous */ |
| 485 |
< |
for( i = istart; i <= (ifinish - 1); i++ ) |
| 486 |
< |
{ |
| 487 |
< |
it = atom[i].atomnum; |
| 488 |
< |
if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 ) |
| 489 |
< |
{ |
| 490 |
< |
for( j = 0; j < MAXIAT; j++ ) |
| 491 |
< |
{ |
| 492 |
< |
if( atom[i].iat[j] != 0 ) |
| 493 |
< |
{ |
| 494 |
< |
jt = atom[atom[i].iat[j]].atomnum; |
| 495 |
< |
if( jt == 6 || jt == 7 || jt == 8 || jt == 15 || jt == 16 ) |
| 496 |
< |
{ |
| 497 |
< |
xii = atom[i].x - atom[atom[i].iat[j]].x; |
| 498 |
< |
yii = atom[i].y - atom[atom[i].iat[j]].y; |
| 499 |
< |
zii = atom[i].z - atom[atom[i].iat[j]].z; |
| 500 |
< |
if( fabs( xii ) <= 2.3 ) |
| 501 |
< |
{ |
| 502 |
< |
if( fabs( yii ) <= 2.3 ) |
| 503 |
< |
{ |
| 504 |
< |
if( fabs( zii ) <= 2.3 ) |
| 505 |
< |
{ |
| 506 |
< |
disij = sqrt( xii*xii + yii*yii + zii*zii ); |
| 507 |
< |
/* c=o bond */ |
| 508 |
< |
if( ((it == 8 && jt == 6) || (it == 6 && jt == 8)) && disij <= rbdis[3] + 0.05 ) |
| 509 |
< |
{ |
| 510 |
< |
if( i < atom[i].iat[j] ) |
| 511 |
< |
make_bond( i, atom[i].iat[j],1 ); |
| 512 |
< |
/* alkyne */ |
| 513 |
< |
}else if( (it == 6 && jt == 6) && disij <= rbdis[1] ) |
| 514 |
< |
{ |
| 515 |
< |
if( i < atom[i].iat[j] ) |
| 516 |
< |
make_bond( i, atom[i].iat[j],2 ); |
| 517 |
< |
/* c=n */ |
| 518 |
< |
}else if( ((it == 7 && jt == 6) || (it == 6 && jt == 7)) |
| 519 |
< |
&& disij <= rbdis[2] ) |
| 520 |
< |
{ |
| 521 |
< |
ibi = 0; |
| 522 |
< |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 523 |
< |
{ |
| 524 |
< |
if( atom[i].bo[kk] != 9 ) |
| 525 |
< |
ibi = ibi + atom[i].bo[kk]; |
| 526 |
< |
} |
| 527 |
< |
ibj = 0; |
| 528 |
< |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 529 |
< |
{ |
| 530 |
< |
if( atom[atom[i].iat[j]].bo[kk] != 9 ) |
| 531 |
< |
ibj = ibj + atom[atom[i].iat[j]].bo[kk]; |
| 532 |
< |
} |
| 533 |
< |
if( it == 7 ) |
| 534 |
< |
{ |
| 535 |
< |
if( ibi <= 2 && ibj <= 3 ) |
| 536 |
< |
{ |
| 537 |
< |
if( i < atom[i].iat[j] ) |
| 538 |
< |
make_bond( i, atom[i].iat[j], 1 ); |
| 539 |
< |
break; |
| 540 |
< |
} |
| 541 |
< |
}else if( jt == 7 ) |
| 542 |
< |
{ |
| 543 |
< |
if( ibj <= 2 && ibi <= 3 ) |
| 544 |
< |
{ |
| 545 |
< |
if( i < atom[i].iat[j] ) |
| 546 |
< |
make_bond( i, atom[i].iat[j], 1 ); |
| 547 |
< |
break; |
| 548 |
< |
} |
| 549 |
< |
} |
| 550 |
< |
/*nitrile */ }else if( ((it == 7 && jt == 6) || (it == 6 && jt == 7)) && disij <= 1.18 ) |
| 551 |
< |
{ |
| 552 |
< |
if( i < atom[i].iat[j] ) |
| 553 |
< |
make_bond( i, atom[i].iat[j], 2 ); |
| 554 |
< |
/* N=O */ }else if ( ((it == 7 && jt == 8) || (it == 8 && jt == 7)) && disij <= 1.26) |
| 555 |
< |
{ |
| 556 |
< |
ibi = 0; |
| 557 |
< |
if (it == 7) |
| 558 |
< |
{ |
| 559 |
< |
for (kk = 0; kk < MAXIAT; kk++) |
| 560 |
< |
{ |
| 561 |
< |
if (atom[i].bo[kk] != 9) |
| 562 |
< |
ibi += atom[i].bo[kk]; |
| 563 |
< |
} |
| 564 |
< |
} else |
| 565 |
< |
{ |
| 566 |
< |
for (kk = 0; kk < MAXIAT; kk++) |
| 567 |
< |
{ |
| 568 |
< |
if (atom[atom[i].iat[j]].bo[kk] != 9) |
| 569 |
< |
ibi += atom[atom[i].iat[j]].bo[kk]; |
| 570 |
< |
} |
| 571 |
< |
} |
| 572 |
< |
if (ibi <= 3) |
| 573 |
< |
{ |
| 574 |
< |
if ( i < atom[i].iat[j]) |
| 575 |
< |
make_bond(i,atom[i].iat[j],1); |
| 576 |
< |
break; |
| 577 |
< |
} |
| 578 |
< |
/* c=c bond */ }else if( (it == 6 && jt == 6) && disij <= rbdis[0] ) |
| 579 |
< |
{ |
| 580 |
< |
ibi = 0; |
| 581 |
< |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 582 |
< |
{ |
| 583 |
< |
if( atom[i].bo[kk] != 9 ) |
| 584 |
< |
ibi = ibi + atom[i].bo[kk]; |
| 585 |
< |
} |
| 586 |
< |
ibj = 0; |
| 587 |
< |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 588 |
< |
{ |
| 589 |
< |
if( atom[atom[i].iat[j]].bo[kk] != 9 ) |
| 590 |
< |
ibj = ibj + atom[atom[i].iat[j]].bo[kk]; |
| 591 |
< |
} |
| 592 |
< |
if( ibi <= 3 && ibj <= 3 ) |
| 593 |
< |
{ |
| 594 |
< |
if( i < atom[i].iat[j] ) |
| 595 |
< |
make_bond( i, atom[i].iat[j], 1 ); |
| 596 |
< |
} |
| 597 |
< |
} |
| 598 |
< |
} |
| 599 |
< |
} |
| 600 |
< |
} |
| 601 |
< |
} |
| 602 |
< |
} |
| 603 |
< |
} |
| 604 |
< |
} |
| 605 |
< |
} |
| 606 |
< |
// type(); |
| 607 |
< |
return; |
| 608 |
< |
} |
| 1 |
> |
/* NOTICE: this source code file has been modified for use with FreeMOL */ |
| 2 |
> |
#define EXTERN extern |
| 3 |
> |
|
| 4 |
> |
#include "pcwin.h" |
| 5 |
> |
#include "pcmod.h" |
| 6 |
> |
#include "atom_k.h" |
| 7 |
> |
#include "energies.h" |
| 8 |
> |
#include "fix.h" |
| 9 |
> |
#include "dipmom.h" |
| 10 |
> |
#include "draw.h" |
| 11 |
> |
#include "vibrate.h" |
| 12 |
> |
|
| 13 |
> |
#define TABULATOR_INCLUDE_IMPLEMENTATION |
| 14 |
> |
#include "tabulator.h" |
| 15 |
> |
|
| 16 |
> |
EXTERN struct t_files { |
| 17 |
> |
int nfiles, append, batch, icurrent, ibatno; |
| 18 |
> |
} files; |
| 19 |
> |
EXTERN struct ElementType { char symbol[3]; |
| 20 |
> |
int atomnum; |
| 21 |
> |
float weight, covradius, vdwradius; |
| 22 |
> |
int s,p,d,f,type ; |
| 23 |
> |
} Elements[]; |
| 24 |
> |
EXTERN struct t_logp { |
| 25 |
> |
float logp; |
| 26 |
> |
} logp_calc; |
| 27 |
> |
|
| 28 |
> |
// ============================ |
| 29 |
> |
void quick_type(void); |
| 30 |
> |
int read_sdf(int,int); |
| 31 |
> |
int rd_sdf(FILE *); |
| 32 |
> |
void write_sdf(int); |
| 33 |
> |
void hdel(int); |
| 34 |
> |
FILE * fopen_path ( char * , char * , char * ) ; |
| 35 |
> |
int FetchRecord(FILE *, char *); |
| 36 |
> |
void avgleg(void); |
| 37 |
> |
void get_tag(char *,char *); |
| 38 |
> |
static void mopaco(int start_atom,int end_atom); |
| 39 |
> |
// ================================== |
| 40 |
> |
/* |
| 41 |
> |
* flags - indicates whether dipole, xlogp or vibrational calculations were done |
| 42 |
> |
* and if so write them to the output file. Look at the definitions in pcmod.h |
| 43 |
> |
* |
| 44 |
> |
*/ |
| 45 |
> |
void write_sdf(int flags) |
| 46 |
> |
{ |
| 47 |
> |
int i,j,lptest,nbond,junk; |
| 48 |
> |
FILE *wfile = pcmoutfile; |
| 49 |
> |
|
| 50 |
> |
lptest = 0; |
| 51 |
> |
for( i = 1; i <= natom; i++ ) |
| 52 |
> |
{ |
| 53 |
> |
if( atom[i].mmx_type == 20 ) |
| 54 |
> |
{ |
| 55 |
> |
lptest = 1; |
| 56 |
> |
hdel( lptest ); |
| 57 |
> |
break; |
| 58 |
> |
} |
| 59 |
> |
} |
| 60 |
> |
nbond = 0; |
| 61 |
> |
/* ** calculate the number of bonds in the molecule ** */ |
| 62 |
> |
for( j = 1; j <= natom; j++ ) |
| 63 |
> |
{ |
| 64 |
> |
for( i = 0; i < MAXIAT; i++ ) |
| 65 |
> |
{ |
| 66 |
> |
if( atom[j].iat[i] != 0 ) |
| 67 |
> |
{ |
| 68 |
> |
if( atom[j].iat[i] < j ) |
| 69 |
> |
nbond = nbond + 1; |
| 70 |
> |
} |
| 71 |
> |
} |
| 72 |
> |
} |
| 73 |
> |
/* now write the concord file */ |
| 74 |
> |
/* |
| 75 |
> |
if (files.append) |
| 76 |
> |
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
| 77 |
> |
else |
| 78 |
> |
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
| 79 |
> |
*/ |
| 80 |
> |
|
| 81 |
> |
j = strlen(Struct_Title); |
| 82 |
> |
for (i=0; i < j; i++) |
| 83 |
> |
{ |
| 84 |
> |
if (Struct_Title[i] == '\n') |
| 85 |
> |
{ |
| 86 |
> |
Struct_Title[i] = '\0'; |
| 87 |
> |
break; |
| 88 |
> |
} |
| 89 |
> |
} |
| 90 |
> |
fprintf(wfile,"%s\n",Struct_Title); |
| 91 |
> |
fprintf(wfile," MENGINE v1.0 1.00000 0.00000\n"); |
| 92 |
> |
fprintf(wfile,"\n"); |
| 93 |
> |
|
| 94 |
> |
fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond); |
| 95 |
> |
|
| 96 |
> |
for (i=1; i <= natom; i++) |
| 97 |
> |
{ |
| 98 |
> |
junk = 0; |
| 99 |
> |
if (atom[i].mmx_type == 41) junk = 3; |
| 100 |
> |
else if (atom[i].mmx_type == 42) junk = 5; |
| 101 |
> |
else if (atom[i].mmx_type == 66) |
| 102 |
> |
{ |
| 103 |
> |
if (atom[i].bo[0] == 1) |
| 104 |
> |
junk = 5; |
| 105 |
> |
} |
| 106 |
> |
fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y, |
| 107 |
> |
atom[i].z,Elements[atom[i].atomnum-1].symbol,junk); |
| 108 |
> |
} |
| 109 |
> |
for (i=1; i <= natom; i++) |
| 110 |
> |
{ |
| 111 |
> |
for (j=0; j < MAXIAT; j++) |
| 112 |
> |
{ |
| 113 |
> |
if (atom[i].iat[j] != 0 && i < atom[i].iat[j]) |
| 114 |
> |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]); |
| 115 |
> |
} |
| 116 |
> |
} |
| 117 |
> |
fprintf(wfile,"M END\n"); |
| 118 |
> |
fprintf(wfile,"> <title>\n"); |
| 119 |
> |
fprintf(wfile,"%s\n",Struct_Title); |
| 120 |
> |
|
| 121 |
> |
fprintf(wfile,"> <MMFF94 energy>\n"); |
| 122 |
> |
fprintf(wfile,"%f\n",energies.total); |
| 123 |
> |
|
| 124 |
> |
fprintf(wfile,"> <MMFF94_Atomtypes>\n"); |
| 125 |
> |
fprintf(wfile,"+ Atom Atomtype\n"); |
| 126 |
> |
for (i=1; i <=natom; i++) |
| 127 |
> |
fprintf(wfile,"| %d %d\n",i,atom[i].type); |
| 128 |
> |
fprintf(wfile,"\n"); |
| 129 |
> |
|
| 130 |
> |
if (flags & DO_DIPOLE) { |
| 131 |
> |
fprintf(wfile,"> <dipole moment>\n"); |
| 132 |
> |
fprintf(wfile,"%f\n",dipolemom.total); |
| 133 |
> |
} |
| 134 |
> |
|
| 135 |
> |
if (flags & DO_XLOGP) { |
| 136 |
> |
fprintf(wfile,"> <xLogP>\n"); |
| 137 |
> |
fprintf(wfile,"%f\n",logp_calc.logp); |
| 138 |
> |
} |
| 139 |
> |
|
| 140 |
> |
if (flags & DO_VIBRATION) { |
| 141 |
> |
fprintf(wfile,"> <Point Group>\n"); |
| 142 |
> |
fprintf(wfile,"%s\n",vibdata.ptgrp); |
| 143 |
> |
|
| 144 |
> |
fprintf(wfile,"> <Moments of Inertia>\n"); |
| 145 |
> |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz); |
| 146 |
> |
|
| 147 |
> |
fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n"); |
| 148 |
> |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot, |
| 149 |
> |
vibdata.stot,vibdata.gtot,vibdata.cptot); |
| 150 |
> |
} |
| 151 |
> |
|
| 152 |
> |
fprintf(wfile,"\n"); |
| 153 |
> |
fprintf(wfile,"$$$$\n"); |
| 154 |
> |
// fclose(wfile); |
| 155 |
> |
} |
| 156 |
> |
|
| 157 |
> |
/* =================================== */ |
| 158 |
> |
// fast read - assume file is open and positioned |
| 159 |
> |
// read structure and down to end $$$$ |
| 160 |
> |
// and return |
| 161 |
> |
int rd_sdf(FILE *rfile) |
| 162 |
> |
{ |
| 163 |
> |
int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom; |
| 164 |
> |
int ncount,junk,junk1,got_title,istereo,iz,nvalue; |
| 165 |
> |
int jji, jj1, jj2, jj3, jj4; |
| 166 |
> |
int n_row; |
| 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]; |
| 174 |
> |
char inputline[150]; |
| 175 |
> |
char tag[30]; |
| 176 |
> |
char ***tab; |
| 177 |
> |
|
| 178 |
> |
Ret_Val = TRUE; |
| 179 |
> |
got_title = FALSE; |
| 180 |
> |
xPlus = yPlus = zPlus = FALSE; |
| 181 |
> |
if ( 0 == FetchRecord(rfile,inputline) )return -1; |
| 182 |
> |
// sscanf(inputline,"SDF %s",Struct_Title); |
| 183 |
> |
strncpy(Struct_Title, inputline, sizeof(Struct_Title)); |
| 184 |
> |
got_title = TRUE; |
| 185 |
> |
/* if (strlen(inputline) > 4) |
| 186 |
> |
{ |
| 187 |
> |
iz = strlen(inputline); |
| 188 |
> |
if (iz > 60) iz = 59; |
| 189 |
> |
for (i=4; i < iz; i++) |
| 190 |
> |
Struct_Title[i-4] = inputline[i]; |
| 191 |
> |
Struct_Title[i] = '\0'; |
| 192 |
> |
got_title = TRUE; |
| 193 |
> |
} */ |
| 194 |
> |
FetchRecord(rfile,inputline); // blank line |
| 195 |
> |
FetchRecord(rfile,inputline); // blank line |
| 196 |
> |
|
| 197 |
> |
FetchRecord(rfile,inputline); // natom and nbond |
| 198 |
> |
for (i=0; i <4; i++) |
| 199 |
> |
{ |
| 200 |
> |
c1[i] = inputline[i]; |
| 201 |
> |
c2[i] = inputline[i+3]; |
| 202 |
> |
} |
| 203 |
> |
c1[3] = '\0';c2[3] = '\0'; |
| 204 |
> |
niatom = atoi(c1); |
| 205 |
> |
nibond = atoi(c2); |
| 206 |
> |
if (niatom == 0) |
| 207 |
> |
return FALSE; |
| 208 |
> |
|
| 209 |
> |
for (i=0; i < niatom; i++) |
| 210 |
> |
{ |
| 211 |
> |
FetchRecord(rfile,inputline); |
| 212 |
> |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 213 |
> |
|
| 214 |
> |
itype = 0; |
| 215 |
> |
if (xtmp != 0.0) xPlus= TRUE; |
| 216 |
> |
if (ytmp != 0.0) yPlus= TRUE; |
| 217 |
> |
if (ztmp != 0.0) zPlus= TRUE; |
| 218 |
> |
|
| 219 |
> |
iz = strlen(atomchar); |
| 220 |
> |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 221 |
> |
{ |
| 222 |
> |
if (atomchar[0] == 'N') itype = 8; |
| 223 |
> |
if (atomchar[0] == 'O') itype = 6; |
| 224 |
> |
|
| 225 |
> |
if (junk1 != 0) |
| 226 |
> |
{ |
| 227 |
> |
if (junk1 == 3 && itype == 8) |
| 228 |
> |
itype = 41; // N+ |
| 229 |
> |
if (junk1 == 5 && itype == 6) |
| 230 |
> |
itype = 42; // O- |
| 231 |
> |
} |
| 232 |
> |
} |
| 233 |
> |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 234 |
> |
if (itype != 0) |
| 235 |
> |
atom[newatom].mmx_type = itype; |
| 236 |
> |
if (newatom == -1) |
| 237 |
> |
{ |
| 238 |
> |
fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 239 |
> |
Ret_Val = FALSE; |
| 240 |
> |
} |
| 241 |
> |
} |
| 242 |
> |
has_Aromatic = FALSE; |
| 243 |
> |
|
| 244 |
> |
planar = TRUE; |
| 245 |
> |
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 246 |
> |
|
| 247 |
> |
for (i=0; i < nibond; i++) |
| 248 |
> |
{ |
| 249 |
> |
FetchRecord(rfile,inputline); |
| 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 |
> |
make_bond( ia, ib, 1 ); |
| 506 |
> |
} |
| 507 |
> |
}else if( jt == 7 ) |
| 508 |
> |
{ |
| 509 |
> |
if( ibj <= 2 && ibi <= 3 ) |
| 510 |
> |
{ |
| 511 |
> |
if( ia < ib ) |
| 512 |
> |
make_bond( ia, ib, 1 ); |
| 513 |
> |
} |
| 514 |
> |
} |
| 515 |
> |
/* c=c bond */ |
| 516 |
> |
} else if( (it == 6 && jt == 6) ) |
| 517 |
> |
{ |
| 518 |
> |
ibi = 0; |
| 519 |
> |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 520 |
> |
{ |
| 521 |
> |
if( atom[ia].bo[kk] != 9 ) |
| 522 |
> |
ibi = ibi + atom[ia].bo[kk]; |
| 523 |
> |
} |
| 524 |
> |
ibj = 0; |
| 525 |
> |
for( kk = 0; kk < MAXIAT; kk++ ) |
| 526 |
> |
{ |
| 527 |
> |
if( atom[ib].bo[kk] != 9 ) |
| 528 |
> |
ibj = ibj + atom[ib].bo[kk]; |
| 529 |
> |
} |
| 530 |
> |
if( ibi <= 3 && ibj <= 3 ) |
| 531 |
> |
{ |
| 532 |
> |
if( ia < ib ) |
| 533 |
> |
make_bond( ia, ib, 1 ); |
| 534 |
> |
} |
| 535 |
> |
} |
| 536 |
> |
} |
| 537 |
> |
} |
| 538 |
> |
} |
| 539 |
> |
|
