/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
#include "vec.h"
#include "hackblock.h"
-int cmain (int argc,char *argv[])
+int cmain (int argc, char *argv[])
{
- const char *desc[] = {
- "[TT]g_protonate[tt] reads (a) conformation(s) and adds all missing",
- "hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
- "specified, this conformation will be protonated, if also [TT]-f[tt]",
- "is specified, the conformation(s) will be read from this file, ",
- "which can be either a single conformation or a trajectory.",
- "[PAR]",
- "If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
- "to the GROMACS naming conventions, in which case these residues will",
- "probably not be properly protonated.",
- "[PAR]",
- "If an index file is specified, please note that the atom numbers",
- "should correspond to the [BB]protonated[bb] state."
- };
-
- char title[STRLEN+1];
- const char *infile;
- char *grpnm;
- t_topology top;
- int ePBC;
- t_atoms *atoms,*iatoms;
- t_protonate protdata;
- atom_id *index;
- t_trxstatus *status;
- t_trxstatus *out;
- t_trxframe fr,frout;
- rvec *x,*ix;
- int nidx,natoms,natoms_out;
- matrix box;
- int i,frame,resind;
- gmx_bool bReadMultiple;
- output_env_t oenv;
-
- const char *bugs[] = {
- "For the moment, only .pdb files are accepted to the -s flag"
- };
-
- t_filenm fnm[] = {
- { efTPS, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efTRO, "-o", "protonated", ffWRITE }
- };
+ const char *desc[] = {
+ "[TT]g_protonate[tt] reads (a) conformation(s) and adds all missing",
+ "hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
+ "specified, this conformation will be protonated, if also [TT]-f[tt]",
+ "is specified, the conformation(s) will be read from this file, ",
+ "which can be either a single conformation or a trajectory.",
+ "[PAR]",
+ "If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
+ "to the GROMACS naming conventions, in which case these residues will",
+ "probably not be properly protonated.",
+ "[PAR]",
+ "If an index file is specified, please note that the atom numbers",
+ "should correspond to the [BB]protonated[bb] state."
+ };
+
+ char title[STRLEN+1];
+ const char *infile;
+ char *grpnm;
+ t_topology top;
+ int ePBC;
+ t_atoms *atoms, *iatoms;
+ t_protonate protdata;
+ atom_id *index;
+ t_trxstatus *status;
+ t_trxstatus *out;
+ t_trxframe fr, frout;
+ rvec *x, *ix;
+ int nidx, natoms, natoms_out;
+ matrix box;
+ int i, frame, resind;
+ gmx_bool bReadMultiple;
+ output_env_t oenv;
+
+ const char *bugs[] = {
+ "For the moment, only .pdb files are accepted to the -s flag"
+ };
+
+ t_filenm fnm[] = {
+ { efTPS, NULL, NULL, ffREAD },
+ { efTRX, "-f", NULL, ffOPTRD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efTRO, "-o", "protonated", ffWRITE }
+ };
#define NFILE asize(fnm)
-
- CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,
- NFILE,fnm,0,NULL,asize(desc),desc,asize(bugs),bugs,&oenv);
-
- infile=opt2fn("-s",NFILE,fnm);
- read_tps_conf(infile,title,&top,&ePBC,&x,NULL,box,FALSE);
- atoms=&(top.atoms);
- printf("Select group to process:\n");
- get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
- bReadMultiple = opt2bSet("-f",NFILE,fnm);
- if (bReadMultiple) {
- infile = opt2fn("-f",NFILE,fnm);
- if ( !read_first_frame(oenv,&status, infile, &fr, TRX_NEED_X ) ) {
- gmx_fatal(FARGS,"cannot read coordinate file %s",infile);
+
+ CopyRight(stderr, argv[0]);
+ parse_common_args(&argc, argv, PCA_CAN_TIME,
+ NFILE, fnm, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv);
+
+ infile = opt2fn("-s", NFILE, fnm);
+ read_tps_conf(infile, title, &top, &ePBC, &x, NULL, box, FALSE);
+ atoms = &(top.atoms);
+ printf("Select group to process:\n");
+ get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nidx, &index, &grpnm);
+ bReadMultiple = opt2bSet("-f", NFILE, fnm);
+ if (bReadMultiple)
+ {
+ infile = opt2fn("-f", NFILE, fnm);
+ if (!read_first_frame(oenv, &status, infile, &fr, TRX_NEED_X ) )
+ {
+ gmx_fatal(FARGS, "cannot read coordinate file %s", infile);
+ }
+ natoms = fr.natoms;
}
- natoms = fr.natoms;
- } else {
- clear_trxframe(&fr,TRUE);
- fr.natoms = atoms->nr;
- fr.bTitle = TRUE;
- fr.title = title;
- fr.bX = TRUE;
- fr.x = x;
- fr.bBox = TRUE;
- copy_mat(box, fr.box);
- natoms = fr.natoms;
- }
-
- /* check input */
- if ( natoms == 0 ) {
- gmx_fatal(FARGS,"no atoms in coordinate file %s",infile);
- }
-
- if ( natoms > atoms->nr ) {
- gmx_fatal(FARGS,"topology with %d atoms does not match "
- "coordinates with %d atoms",atoms->nr,natoms);
- }
-
- for(i=0; i<nidx; i++) {
- if (index[i] > natoms) {
- gmx_fatal(FARGS,"An atom number in group %s is larger than the number of "
- "atoms (%d) in the coordinate file %s",grpnm,natoms,infile);
+ else
+ {
+ clear_trxframe(&fr, TRUE);
+ fr.natoms = atoms->nr;
+ fr.bTitle = TRUE;
+ fr.title = title;
+ fr.bX = TRUE;
+ fr.x = x;
+ fr.bBox = TRUE;
+ copy_mat(box, fr.box);
+ natoms = fr.natoms;
}
- }
-
- /* get indexed copy of atoms */
- snew(iatoms,1);
- init_t_atoms(iatoms,nidx,FALSE);
- snew(iatoms->atom, iatoms->nr);
- resind = 0;
- for(i=0; i<nidx; i++) {
- iatoms->atom[i] = atoms->atom[index[i]];
- iatoms->atomname[i] = atoms->atomname[index[i]];
- if ( i>0 && (atoms->atom[index[i]].resind!=atoms->atom[index[i-1]].resind) ) {
- resind++;
+
+ /* check input */
+ if (natoms == 0)
+ {
+ gmx_fatal(FARGS, "no atoms in coordinate file %s", infile);
}
- iatoms->atom[i].resind = resind;
- iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
- /* allocate some space for the rtp name and copy from name */
- snew(iatoms->resinfo[resind].rtp,1);
- *iatoms->resinfo[resind].rtp = gmx_strdup(*atoms->resinfo[resind].name);
-
- iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
- }
-
- init_t_protonate(&protdata);
-
- out = open_trx(opt2fn("-o",NFILE,fnm),"w");
- snew(ix, nidx);
- frame=0;
- do {
- if (debug) {
- fprintf(debug,"FRAME %d (%d %g)\n",frame,fr.step,fr.time);
+
+ if (natoms > atoms->nr)
+ {
+ gmx_fatal(FARGS, "topology with %d atoms does not match "
+ "coordinates with %d atoms", atoms->nr, natoms);
}
- /* get indexed copy of x */
- for(i=0; i<nidx; i++) {
- copy_rvec(fr.x[index[i]], ix[i]);
+
+ for (i = 0; i < nidx; i++)
+ {
+ if (index[i] > natoms)
+ {
+ gmx_fatal(FARGS, "An atom number in group %s is larger than the number of "
+ "atoms (%d) in the coordinate file %s", grpnm, natoms, infile);
+ }
}
- /* protonate */
- natoms_out = protonate(&iatoms, &ix, &protdata);
-
- /* setup output frame */
- frout = fr;
- frout.natoms = natoms_out;
- frout.bAtoms = TRUE;
- frout.atoms = iatoms;
- frout.bV = FALSE;
- frout.bF = FALSE;
- frout.x = ix;
-
- /* write output */
- write_trxframe(out,&frout,NULL);
- frame++;
- } while ( bReadMultiple && read_next_frame(oenv,status, &fr) );
-
- sfree(ix);
- sfree(iatoms);
-
- thanx(stderr);
-
- return 0;
-}
+ /* get indexed copy of atoms */
+ snew(iatoms, 1);
+ init_t_atoms(iatoms, nidx, FALSE);
+ snew(iatoms->atom, iatoms->nr);
+ resind = 0;
+ for (i = 0; i < nidx; i++)
+ {
+ iatoms->atom[i] = atoms->atom[index[i]];
+ iatoms->atomname[i] = atoms->atomname[index[i]];
+ if (i > 0 && (atoms->atom[index[i]].resind != atoms->atom[index[i-1]].resind) )
+ {
+ resind++;
+ }
+ iatoms->atom[i].resind = resind;
+ iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
+ /* allocate some space for the rtp name and copy from name */
+ snew(iatoms->resinfo[resind].rtp, 1);
+ *iatoms->resinfo[resind].rtp = gmx_strdup(*atoms->resinfo[resind].name);
+
+ iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
+ }
+
+ init_t_protonate(&protdata);
+
+ out = open_trx(opt2fn("-o", NFILE, fnm), "w");
+ snew(ix, nidx);
+ frame = 0;
+ do
+ {
+ if (debug)
+ {
+ fprintf(debug, "FRAME %d (%d %g)\n", frame, fr.step, fr.time);
+ }
+ /* get indexed copy of x */
+ for (i = 0; i < nidx; i++)
+ {
+ copy_rvec(fr.x[index[i]], ix[i]);
+ }
+ /* protonate */
+ natoms_out = protonate(&iatoms, &ix, &protdata);
+
+ /* setup output frame */
+ frout = fr;
+ frout.natoms = natoms_out;
+ frout.bAtoms = TRUE;
+ frout.atoms = iatoms;
+ frout.bV = FALSE;
+ frout.bF = FALSE;
+ frout.x = ix;
+
+ /* write output */
+ write_trxframe(out, &frout, NULL);
+ frame++;
+ }
+ while (bReadMultiple && read_next_frame(oenv, status, &fr) );
+
+ sfree(ix);
+ sfree(iatoms);
+
+ thanx(stderr);
+
+ return 0;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff