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tjod |
3 |
#define EXTERN extern |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "substr.h" |
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#include "atom_k.h" |
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#include "energies.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_dipolemom { |
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double total, xdipole, ydipole, zdipole; |
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} dipolemom; |
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EXTERN struct t_logp { |
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float logp; |
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} logp_calc; |
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EXTERN struct t_vibdata { |
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char ptgrp[4]; |
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float mom_ix,mom_iy,mom_iz; |
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float etot,htot,stot,gtot,cptot; |
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} vibdata; |
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int make_atom(int, float, float, float,char *); |
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void make_bond(int, int, int); |
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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 message_alert(char *, char *); |
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void hdel(int); |
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FILE * fopen_path ( char * , char * , char * ) ; |
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void read_schakal(int,int); |
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void write_schakal(void); |
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void mopaco(int,int); |
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int FetchRecord(FILE *, char *); |
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void avgleg(void); |
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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; |
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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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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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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," PCMODEL v9.1 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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| 122 |
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fprintf(wfile,"> <MMFF94 energy>\n"); |
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fprintf(wfile,"%f\n",energies.total); |
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| 125 |
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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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| 130 |
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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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| 135 |
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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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| 139 |
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fprintf(wfile,"> <Moments of Inertia>\n"); |
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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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| 142 |
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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); |
| 145 |
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} |
| 146 |
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| 147 |
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fprintf(wfile,"\n"); |
| 148 |
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fprintf(wfile,"$$$$\n"); |
| 149 |
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fclose(wfile); |
| 150 |
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} |
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/* =================================== */ |
| 152 |
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// fast read - assume file is open and positioned |
| 153 |
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// read structure and down to end $$$$ |
| 154 |
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// and return |
| 155 |
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int rd_sdf(FILE *rfile) |
| 156 |
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{ |
| 157 |
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int i, j, niatom, nibond, ia1, ia2, ibond, itype, newatom; |
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int ncount,junk,junk1,got_title,istereo,iz; |
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int jji, jj1, jj2, jj3, jj4; |
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int has_Aromatic, xPlus,yPlus,zPlus, planar; |
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int icount,itemp[4]; |
| 162 |
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int Ret_Val; |
| 163 |
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float xtmp, ytmp, ztmp, dz; |
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char c1[4],c2[4]; |
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char atomchar[3]; |
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char inputline[150]; |
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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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FetchRecord(rfile,inputline); |
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sscanf(inputline,"SDF %s",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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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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got_title = TRUE; |
| 182 |
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} */ |
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FetchRecord(rfile,inputline); // blank line |
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FetchRecord(rfile,inputline); // blank line |
| 185 |
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| 186 |
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FetchRecord(rfile,inputline); // natom and nbond |
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for (i=0; i <4; i++) |
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{ |
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c1[i] = inputline[i]; |
| 190 |
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c2[i] = inputline[i+3]; |
| 191 |
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} |
| 192 |
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c1[3] = '\0';c2[3] = '\0'; |
| 193 |
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niatom = atoi(c1); |
| 194 |
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nibond = atoi(c2); |
| 195 |
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if (niatom == 0) |
| 196 |
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return FALSE; |
| 197 |
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| 198 |
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for (i=0; i < niatom; i++) |
| 199 |
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{ |
| 200 |
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FetchRecord(rfile,inputline); |
| 201 |
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sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 202 |
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| 203 |
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itype = 0; |
| 204 |
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if (xtmp != 0.0) xPlus= TRUE; |
| 205 |
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if (ytmp != 0.0) yPlus= TRUE; |
| 206 |
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if (ztmp != 0.0) zPlus= TRUE; |
| 207 |
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| 208 |
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iz = strlen(atomchar); |
| 209 |
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if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 210 |
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{ |
| 211 |
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if (atomchar[0] == 'N') itype = 8; |
| 212 |
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if (atomchar[0] == 'O') itype = 6; |
| 213 |
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| 214 |
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if (junk1 != 0) |
| 215 |
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{ |
| 216 |
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if (junk1 == 3 && itype == 8) |
| 217 |
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itype = 41; // N+ |
| 218 |
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if (junk1 == 5 && itype == 6) |
| 219 |
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itype = 42; // O- |
| 220 |
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} |
| 221 |
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} |
| 222 |
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| 223 |
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newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 224 |
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if (itype != 0) |
| 225 |
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atom[newatom].mmx_type = itype; |
| 226 |
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if (newatom == -1) |
| 227 |
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{ |
| 228 |
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printf("Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 229 |
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Ret_Val = FALSE; |
| 230 |
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} |
| 231 |
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} |
| 232 |
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has_Aromatic = FALSE; |
| 233 |
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| 234 |
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planar = TRUE; |
| 235 |
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if (xPlus && yPlus && zPlus) planar = FALSE; |
| 236 |
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| 237 |
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for (i=0; i < nibond; i++) |
| 238 |
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{ |
| 239 |
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FetchRecord(rfile,inputline); |
| 240 |
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for (j=0; j <4; j++) |
| 241 |
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{ |
| 242 |
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c1[j] = inputline[j]; |
| 243 |
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c2[j] = inputline[j+3]; |
| 244 |
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} |
| 245 |
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c1[3] = '\0';c2[3] = '\0'; |
| 246 |
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ia1 = atoi(c1); |
| 247 |
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ia2 = atoi(c2); |
| 248 |
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istereo = 0; |
| 249 |
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sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo); |
| 250 |
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if (ibond >= 4) |
| 251 |
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{ |
| 252 |
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ibond = 1; |
| 253 |
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has_Aromatic = TRUE; |
| 254 |
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} |
| 255 |
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make_bond(ia1, ia2, ibond); |
| 256 |
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if (istereo == 1 && planar) |
| 257 |
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{ |
| 258 |
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atom[ia2].z += 0.7; |
| 259 |
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if (atom[ia2].atomnum == 1) |
| 260 |
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atom[ia2].type = 60; |
| 261 |
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} |
| 262 |
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if (istereo == 6 && planar) |
| 263 |
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{ |
| 264 |
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atom[ia2].z -= 0.7; |
| 265 |
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if (atom[ia2].atomnum == 1) |
| 266 |
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atom[ia2].type = 60; |
| 267 |
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} |
| 268 |
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} |
| 269 |
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// read to end of structure |
| 270 |
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while (FetchRecord(rfile,inputline)) |
| 271 |
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{ |
| 272 |
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if (strncasecmp(inputline,"$$$$",4) == 0) |
| 273 |
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{ |
| 274 |
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return Ret_Val; |
| 275 |
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} |
| 276 |
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} |
| 277 |
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return Ret_Val; |
| 278 |
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} |
| 279 |
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/* =================================== */ |
| 280 |
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int read_sdf(int istruct, int isubred) |
| 281 |
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{ |
| 282 |
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int i, j, niatom, nibond, ia1, ia2, ibond, itype, newatom; |
| 283 |
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int ncount, ibotptr,junk,junk1,got_title,istereo,iz; |
| 284 |
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int jji, jj1, jj2, jj3, jj4; |
| 285 |
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int has_Aromatic, xPlus,yPlus,zPlus, planar; |
| 286 |
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int icount,itemp[4]; |
| 287 |
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float xtmp, ytmp, ztmp, dz; |
| 288 |
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char c1[4],c2[4]; |
| 289 |
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char atomchar[3]; |
| 290 |
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char inputline[150]; |
| 291 |
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FILE *infile; |
| 292 |
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| 293 |
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infile = fopen_path(Openbox.path,Openbox.fname,"r"); |
| 294 |
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| 295 |
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if (infile == NULL) |
| 296 |
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{ |
| 297 |
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message_alert("Error opening Concord file","Concord Setup"); |
| 298 |
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return FALSE; |
| 299 |
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} |
| 300 |
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| 301 |
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if (isubred == 0) |
| 302 |
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ibotptr = 0; |
| 303 |
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else |
| 304 |
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{ |
| 305 |
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ibotptr = natom; |
| 306 |
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substr.istract[substr.icurstr] = TRUE; |
| 307 |
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} |
| 308 |
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| 309 |
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if (istruct > 1) |
| 310 |
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{ |
| 311 |
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ncount = 0; |
| 312 |
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while (FetchRecord(infile,inputline)) |
| 313 |
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{ |
| 314 |
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if (strncasecmp(inputline,"$$$$",4) == 0) |
| 315 |
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{ |
| 316 |
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ncount++; |
| 317 |
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if (ncount+1 == istruct) |
| 318 |
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goto L_1; |
| 319 |
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} |
| 320 |
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} |
| 321 |
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} |
| 322 |
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// start file read here |
| 323 |
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L_1: |
| 324 |
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got_title = FALSE; |
| 325 |
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xPlus = yPlus = zPlus = FALSE; |
| 326 |
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FetchRecord(infile,inputline); |
| 327 |
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sscanf(inputline,"SDF %s",Struct_Title); |
| 328 |
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got_title = TRUE; |
| 329 |
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/* if (strlen(inputline) > 4) |
| 330 |
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{ |
| 331 |
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iz = strlen(inputline); |
| 332 |
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if (iz > 60) iz = 59; |
| 333 |
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for (i=4; i < iz; i++) |
| 334 |
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Struct_Title[i-4] = inputline[i]; |
| 335 |
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Struct_Title[i] = '\0'; |
| 336 |
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got_title = TRUE; |
| 337 |
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} */ |
| 338 |
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FetchRecord(infile,inputline); // blank line |
| 339 |
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FetchRecord(infile,inputline); // blank line |
| 340 |
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| 341 |
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FetchRecord(infile,inputline); // natom and nbond |
| 342 |
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for (i=0; i <4; i++) |
| 343 |
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{ |
| 344 |
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c1[i] = inputline[i]; |
| 345 |
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c2[i] = inputline[i+3]; |
| 346 |
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} |
| 347 |
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c1[3] = '\0';c2[3] = '\0'; |
| 348 |
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niatom = atoi(c1); |
| 349 |
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nibond = atoi(c2); |
| 350 |
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if (niatom == 0) |
| 351 |
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return FALSE; |
| 352 |
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| 353 |
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for (i=0; i < niatom; i++) |
| 354 |
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{ |
| 355 |
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FetchRecord(infile,inputline); |
| 356 |
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sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 357 |
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| 358 |
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itype = 0; |
| 359 |
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if (xtmp != 0.0) xPlus= TRUE; |
| 360 |
|
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if (ytmp != 0.0) yPlus= TRUE; |
| 361 |
|
|
if (ztmp != 0.0) zPlus= TRUE; |
| 362 |
|
|
|
| 363 |
|
|
iz = strlen(atomchar); |
| 364 |
|
|
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 365 |
|
|
{ |
| 366 |
|
|
if (atomchar[0] == 'N') itype = 8; |
| 367 |
|
|
if (atomchar[0] == 'O') itype = 6; |
| 368 |
|
|
|
| 369 |
|
|
if (junk1 != 0) |
| 370 |
|
|
{ |
| 371 |
|
|
if (junk1 == 3 && itype == 8) |
| 372 |
|
|
itype = 41; // N+ |
| 373 |
|
|
if (junk1 == 5 && itype == 6) |
| 374 |
|
|
itype = 42; // O- |
| 375 |
|
|
} |
| 376 |
|
|
} |
| 377 |
|
|
|
| 378 |
|
|
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 379 |
|
|
if (newatom == -1) |
| 380 |
|
|
{ |
| 381 |
|
|
printf("Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 382 |
|
|
return FALSE; |
| 383 |
|
|
} |
| 384 |
|
|
if (isubred == 1) |
| 385 |
|
|
{ |
| 386 |
|
|
atom[newatom].substr[0] = 0; |
| 387 |
|
|
atom[newatom].substr[0] |= (1L << substr.icurstr); |
| 388 |
|
|
} |
| 389 |
|
|
} |
| 390 |
|
|
has_Aromatic = FALSE; |
| 391 |
|
|
|
| 392 |
|
|
planar = TRUE; |
| 393 |
|
|
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 394 |
|
|
|
| 395 |
|
|
for (i=0; i < nibond; i++) |
| 396 |
|
|
{ |
| 397 |
|
|
FetchRecord(infile,inputline); |
| 398 |
|
|
for (j=0; j <4; j++) |
| 399 |
|
|
{ |
| 400 |
|
|
c1[j] = inputline[j]; |
| 401 |
|
|
c2[j] = inputline[j+3]; |
| 402 |
|
|
} |
| 403 |
|
|
c1[3] = '\0';c2[3] = '\0'; |
| 404 |
|
|
ia1 = atoi(c1); |
| 405 |
|
|
ia2 = atoi(c2); |
| 406 |
|
|
istereo = 0; |
| 407 |
|
|
sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo); |
| 408 |
|
|
if (ibond >= 4) |
| 409 |
|
|
{ |
| 410 |
|
|
ibond = 1; |
| 411 |
|
|
has_Aromatic = TRUE; |
| 412 |
|
|
} |
| 413 |
|
|
make_bond(ia1+ibotptr, ia2+ibotptr, ibond); |
| 414 |
|
|
if (istereo == 1 && planar) |
| 415 |
|
|
{ |
| 416 |
|
|
atom[ia2+ibotptr].z += 0.7; |
| 417 |
|
|
if (atom[ia2+ibotptr].atomnum == 1) |
| 418 |
|
|
atom[ia2+ibotptr].type = 60; |
| 419 |
|
|
} |
| 420 |
|
|
if (istereo == 6 && planar) |
| 421 |
|
|
{ |
| 422 |
|
|
atom[ia2+ibotptr].z -= 0.7; |
| 423 |
|
|
if (atom[ia2+ibotptr].atomnum == 1) |
| 424 |
|
|
atom[ia2+ibotptr].type = 60; |
| 425 |
|
|
} |
| 426 |
|
|
} |
| 427 |
|
|
FetchRecord(infile,inputline); // M END line |
| 428 |
|
|
FetchRecord(infile,inputline); |
| 429 |
|
|
if (got_title == FALSE) |
| 430 |
|
|
strcpy(Struct_Title,inputline); |
| 431 |
|
|
fclose(infile); |
| 432 |
|
|
ncount = strlen(Struct_Title); |
| 433 |
|
|
for (i=0; i < ncount; i++) |
| 434 |
|
|
{ |
| 435 |
|
|
if (Struct_Title[i] == '\n') |
| 436 |
|
|
{ |
| 437 |
|
|
Struct_Title[i] = '\0'; |
| 438 |
|
|
break; |
| 439 |
|
|
} |
| 440 |
|
|
} |
| 441 |
|
|
// search for quaternary centers - check if flat |
| 442 |
|
|
dz = 0.0; |
| 443 |
|
|
for (i=1; i <= natom; i++) |
| 444 |
|
|
{ |
| 445 |
|
|
dz += atom[i].z; |
| 446 |
|
|
jji = jj1 = jj2 = jj3 = jj4 = 0; |
| 447 |
|
|
if (atom[i].type != 0) |
| 448 |
|
|
{ |
| 449 |
|
|
for (j=0; j < 6; j++) |
| 450 |
|
|
{ |
| 451 |
|
|
if (atom[i].iat[j] != 0) |
| 452 |
|
|
jji++; |
| 453 |
|
|
} |
| 454 |
|
|
} |
| 455 |
|
|
if (jji == 4) |
| 456 |
|
|
{ |
| 457 |
|
|
if (atom[atom[i].iat[0]].z == 0.0 && atom[atom[i].iat[0]].z == 0.0 && |
| 458 |
|
|
atom[atom[i].iat[0]].z == 0.0 && atom[atom[i].iat[0]].z == 0.0) // flat center |
| 459 |
|
|
{ |
| 460 |
|
|
for (j=0; j < 4; j++) |
| 461 |
|
|
{ |
| 462 |
|
|
itemp[j] = 0; |
| 463 |
|
|
if (atom[atom[i].iat[0]].iat[j] != 0) jj1++; |
| 464 |
|
|
if (atom[atom[i].iat[1]].iat[j] != 0) jj2++; |
| 465 |
|
|
if (atom[atom[i].iat[2]].iat[j] != 0) jj3++; |
| 466 |
|
|
if (atom[atom[i].iat[3]].iat[j] != 0) jj4++; |
| 467 |
|
|
} |
| 468 |
|
|
icount = 0; |
| 469 |
|
|
if (jj1 == 1) |
| 470 |
|
|
{ |
| 471 |
|
|
itemp[icount] = atom[i].iat[0]; |
| 472 |
|
|
icount++; |
| 473 |
|
|
} |
| 474 |
|
|
if (jj2 == 1) |
| 475 |
|
|
{ |
| 476 |
|
|
itemp[icount] = atom[i].iat[1]; |
| 477 |
|
|
icount++; |
| 478 |
|
|
} |
| 479 |
|
|
if (jj3 == 1) |
| 480 |
|
|
{ |
| 481 |
|
|
itemp[icount] = atom[i].iat[2]; |
| 482 |
|
|
icount++; |
| 483 |
|
|
} |
| 484 |
|
|
if (jj3 == 1) |
| 485 |
|
|
{ |
| 486 |
|
|
itemp[icount] = atom[i].iat[3]; |
| 487 |
|
|
icount++; |
| 488 |
|
|
} |
| 489 |
|
|
if (icount >= 2) |
| 490 |
|
|
{ |
| 491 |
|
|
atom[itemp[0]].z += 0.5; |
| 492 |
|
|
atom[itemp[1]].z -= 0.5; |
| 493 |
|
|
} |
| 494 |
|
|
} |
| 495 |
|
|
} |
| 496 |
|
|
} |
| 497 |
|
|
for (i=1; i < natom; i++) |
| 498 |
|
|
{ |
| 499 |
|
|
for (j=i+1; j <= natom; j++) |
| 500 |
|
|
{ |
| 501 |
|
|
xtmp = atom[i].x - atom[j].x; |
| 502 |
|
|
ytmp = atom[i].y - atom[j].y; |
| 503 |
|
|
ztmp = atom[i].z - atom[j].z; |
| 504 |
|
|
if ( (xtmp + ytmp + ztmp) < 0.1) |
| 505 |
|
|
{ |
| 506 |
|
|
atom[i].x += 0.1; |
| 507 |
|
|
atom[i].y += 0.1; |
| 508 |
|
|
atom[i].z += 0.1; |
| 509 |
|
|
atom[j].x -= 0.1; |
| 510 |
|
|
atom[j].y -= 0.1; |
| 511 |
|
|
atom[j].z -= 0.1; |
| 512 |
|
|
} |
| 513 |
|
|
} |
| 514 |
|
|
} |
| 515 |
|
|
|
| 516 |
|
|
if (has_Aromatic == TRUE) |
| 517 |
|
|
mopaco(1,natom); |
| 518 |
|
|
return TRUE; |
| 519 |
|
|
} |
| 520 |
|
|
// ================================================== |
| 521 |
|
|
void read_schakal(int isel,int isubred) |
| 522 |
|
|
{ |
| 523 |
|
|
int i, itype, newatom, iz; |
| 524 |
|
|
float xtmp, ytmp, ztmp; |
| 525 |
|
|
char dummy[30]; |
| 526 |
|
|
char atomchar[6]; |
| 527 |
|
|
char inputline[150]; |
| 528 |
|
|
FILE *infile; |
| 529 |
|
|
|
| 530 |
|
|
infile = fopen_path(Openbox.path,Openbox.fname,"r"); |
| 531 |
|
|
|
| 532 |
|
|
if (infile == NULL) |
| 533 |
|
|
{ |
| 534 |
|
|
message_alert("Error opening Schakal file","Schakal Setup"); |
| 535 |
|
|
return; |
| 536 |
|
|
} |
| 537 |
|
|
while ( FetchRecord(infile,inputline)) |
| 538 |
|
|
{ |
| 539 |
|
|
sscanf(inputline,"%s",dummy); |
| 540 |
|
|
if (strcmp(dummy,"TITLE") == 0) |
| 541 |
|
|
{ |
| 542 |
|
|
sscanf(inputline,"%s %s",dummy,Struct_Title); |
| 543 |
|
|
} else if (strcmp(dummy,"ATOM") == 0) |
| 544 |
|
|
{ |
| 545 |
|
|
sscanf(inputline,"%s %s %f %f %f",dummy,atomchar,&xtmp,&ytmp,&ztmp); |
| 546 |
|
|
// strip off numbers |
| 547 |
|
|
iz = strlen(atomchar); |
| 548 |
|
|
for (i=0; i < iz; i++) |
| 549 |
|
|
{ |
| 550 |
|
|
if (isdigit(atomchar[i])) |
| 551 |
|
|
{ |
| 552 |
|
|
atomchar[i] = '\0'; |
| 553 |
|
|
break; |
| 554 |
|
|
} |
| 555 |
|
|
} |
| 556 |
|
|
itype = 0; |
| 557 |
|
|
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 558 |
|
|
} else if (strcmp(dummy,"END") == 0) |
| 559 |
|
|
{ |
| 560 |
|
|
break; |
| 561 |
|
|
} |
| 562 |
|
|
} |
| 563 |
|
|
fclose(infile); |
| 564 |
|
|
mopaco(1,natom); |
| 565 |
|
|
// |
| 566 |
|
|
} |
| 567 |
|
|
// ================================================== |
| 568 |
|
|
void write_schakal() |
| 569 |
|
|
{ |
| 570 |
|
|
int i,j,lptest; |
| 571 |
|
|
char atomchar[6]; |
| 572 |
|
|
FILE *wfile; |
| 573 |
|
|
|
| 574 |
|
|
lptest = 0; |
| 575 |
|
|
for( i = 1; i <= natom; i++ ) |
| 576 |
|
|
{ |
| 577 |
|
|
if( atom[i].mmx_type == 20 ) |
| 578 |
|
|
{ |
| 579 |
|
|
lptest = 1; |
| 580 |
|
|
hdel( lptest ); |
| 581 |
|
|
break; |
| 582 |
|
|
} |
| 583 |
|
|
} |
| 584 |
|
|
|
| 585 |
|
|
/* now write the schakal file */ |
| 586 |
|
|
if (files.append) |
| 587 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
| 588 |
|
|
else |
| 589 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
| 590 |
|
|
|
| 591 |
|
|
j = strlen(Struct_Title); |
| 592 |
|
|
for (i=0; i < j; i++) |
| 593 |
|
|
{ |
| 594 |
|
|
if (Struct_Title[i] == '\n') |
| 595 |
|
|
{ |
| 596 |
|
|
Struct_Title[i] = '\0'; |
| 597 |
|
|
break; |
| 598 |
|
|
} |
| 599 |
|
|
} |
| 600 |
|
|
fprintf(wfile,"TITLE %s\n",Struct_Title); |
| 601 |
|
|
fprintf(wfile,"CELL \n"); |
| 602 |
|
|
for (i=1; i <= natom; i++) |
| 603 |
|
|
{ |
| 604 |
|
|
sprintf(atomchar,"%s%d",Elements[atom[i].atomnum-1].symbol,i); |
| 605 |
|
|
|
| 606 |
|
|
fprintf(wfile,"ATOM %-5s %12.7f%12.7f%12.7f\n",atomchar,atom[i].x, |
| 607 |
|
|
atom[i].y, atom[i].z); |
| 608 |
|
|
} |
| 609 |
|
|
fprintf(wfile,"END \n"); |
| 610 |
|
|
fclose(wfile); |
| 611 |
|
|
} |
