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/* Write a PDB file */
/* Copyright (c) 2007, 2019 MJ Rutter
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3
* of the Licence, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, see http://www.gnu.org/licenses/
*/
/* Changed 4/07 to start atom numbering at one, not zero
* and to put atomic symbols in the correct place */
/* Excerpted from PDB file format (www.pdb.org):
*
* Columns Thing
*
* 1-6 "ATOM "
* 7-11 Atom serial no (int)
* 13-16 Atom name (lable)
* ...
* 31-38 x co-ord, as Fortran's real(8.3), Angstroms
* 39-46 y co-ord, ditto
* 47-54 z co-ord, ditto
* ...
* 77-78 Element symbol, right justified
*
* 1-6 "CRYST1"
* 7-15 a, as Fortran's real(9.3), Angstroms
* 16-24 b, ditto
* 25-33 c, ditto
* 34-40 alpha, as Fortran's real(7.2), degrees
* 41-47 beta, ditto
* 48-54 gamma, ditto
* 56-66 space group, left justified string
* 67-70 number of polmeric chains per cell (z)
*
* Set z to one, and space group to "P 1" if irrelevant / undetermined
*/
#include<stdio.h>
#include<string.h>
#include<stdlib.h>
#include "c2xsf.h"
extern int periodic_max_el;
void pdb_write(FILE* outfile, struct unit_cell *c, struct contents *m){
int i,*n_in_el=NULL;
double abc[6];
if (m->n>99999)
error_exit("Cannot write pdb file with more than 99,999 atoms");
if (flags&PDBN){
n_in_el=calloc(periodic_max_el+1,sizeof(int));
if (!n_in_el) error_exit("Calloc error in pdbn_write");
}
fprintf(outfile,"REMARK written by c2x\n");
cart2abc(c,m,abc,NULL,1);
fprintf(outfile,"CRYST1 %8.3f %8.3f %8.3f %6.2f %6.2f %6.2f P 1"
" 1\n",
abc[0],abc[1],abc[2],abc[3],abc[4],abc[5]);
/* Ditch chain identifier (X)? */
for(i=0;i<m->n;i++)
if (flags&PDBN){
fprintf(outfile,"ATOM %5d ",i+1);
if(++n_in_el[min(m->atoms[i].atno,periodic_max_el)]<=99)
fprintf(outfile,"%2s%02d",atno2sym(m->atoms[i].atno),
n_in_el[min(m->atoms[i].atno,periodic_max_el)]);
else if((n_in_el[min(m->atoms[i].atno,periodic_max_el)]<=999)&&
(strlen(atno2sym(m->atoms[i].atno))==1))
fprintf(outfile,"%1s%d",atno2sym(m->atoms[i].atno),
n_in_el[min(m->atoms[i].atno,periodic_max_el)]);
else fprintf(outfile,"%2s00",atno2sym(m->atoms[i].atno));
fprintf(outfile," X 1 %7.3f %7.3f %7.3f"
" %2s\n",
m->atoms[i].abs[0],
m->atoms[i].abs[1],m->atoms[i].abs[2],atno2sym(m->atoms[i].atno));
}
else fprintf(outfile,"ATOM %5d %2s X 1 %7.3f %7.3f %7.3f"
" %2s\n",
i+1,atno2sym(m->atoms[i].atno),m->atoms[i].abs[0],
m->atoms[i].abs[1],m->atoms[i].abs[2],atno2sym(m->atoms[i].atno));
fprintf(outfile,"END\n");
if (flags&PDBN) free(n_in_el);
}
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