* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "pdb2gmx.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "pdb2gmx.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/utility/smalloc.h"
-#include "copyrite.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "vec.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "physics.h"
-#include "pgutil.h"
-#include "calch.h"
-#include "resall.h"
-#include "pdb2top.h"
-#include "ter_db.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "genhydro.h"
-#include "readinp.h"
-#include "atomprop.h"
-#include "index.h"
-#include "fflibutil.h"
-#include "macros.h"
-
#include "gromacs/fileio/strdb.h"
-
-#include "hizzie.h"
-#include "specbond.h"
-#include "xlate.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/hizzie.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/specbond.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/xlate.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define RTP_MAXCHAR 5
typedef struct {
static int read_pdball(const char *inf, const char *outf, char *title,
t_atoms *atoms, rvec **x,
int *ePBC, matrix box, gmx_bool bRemoveH,
- t_symtab *symtab, gmx_residuetype_t rt, const char *watres,
+ t_symtab *symtab, gmx_residuetype_t *rt, const char *watres,
gmx_atomprop_t aps, gmx_bool bVerbose)
/* Read a pdb file. (containing proteins) */
{
return pdba->nr;
}
-void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, gmx_residuetype_t rt)
+void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end,
+ gmx_residuetype_t *rt)
{
int i;
const char *p_startrestype;
int gmx_pdb2gmx(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a [TT].pdb[tt] (or [TT].gro[tt]) file, reads",
+ "[THISMODULE] reads a [REF].pdb[ref] (or [REF].gro[ref]) file, reads",
"some database files, adds hydrogens to the molecules and generates",
- "coordinates in GROMACS (GROMOS), or optionally [TT].pdb[tt], format",
+ "coordinates in GROMACS (GROMOS), or optionally [REF].pdb[ref], format",
"and a topology in GROMACS format.",
"These files can subsequently be processed to generate a run input file.",
"[PAR]",
"Check Chapter 5 of the manual for more information about file formats.",
"[PAR]",
- "Note that a [TT].pdb[tt] file is nothing more than a file format, and it",
+ "Note that a [REF].pdb[ref] file is nothing more than a file format, and it",
"need not necessarily contain a protein structure. Every kind of",
"molecule for which there is support in the database can be converted.",
"If there is no support in the database, you can add it yourself.[PAR]",
"This can be turned off (no merging), all non-water chains can be merged into a",
"single molecule, or the selection can be done interactively.[PAR]",
- "[THISMODULE] will also check the occupancy field of the [TT].pdb[tt] file.",
+ "[THISMODULE] will also check the occupancy field of the [REF].pdb[ref] file.",
"If any of the occupancies are not one, indicating that the atom is",
"not resolved well in the structure, a warning message is issued.",
- "When a [TT].pdb[tt] file does not originate from an X-ray structure determination",
+ "When a [REF].pdb[ref] file does not originate from an X-ray structure determination",
"all occupancy fields may be zero. Either way, it is up to the user",
"to verify the correctness of the input data (read the article!).[PAR]",
"from the input and before new hydrogens are added. This means that",
"you should not use [TT]-ignh[tt].[PAR]",
- "The [TT].gro[tt] and [TT].g96[tt] file formats do not support chain",
- "identifiers. Therefore it is useful to enter a [TT].pdb[tt] file name at",
- "the [TT]-o[tt] option when you want to convert a multi-chain [TT].pdb[tt] file.",
+ "The [REF].gro[ref] and [TT].g96[tt] file formats do not support chain",
+ "identifiers. Therefore it is useful to enter a [REF].pdb[ref] file name at",
+ "the [TT]-o[tt] option when you want to convert a multi-chain [REF].pdb[ref] file.",
"[PAR]",
"The option [TT]-vsite[tt] removes hydrogen and fast improper dihedral",
t_hackblock *ah;
t_symtab symtab;
gpp_atomtype_t atype;
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
const char *top_fn;
char fn[256], itp_fn[STRLEN], posre_fn[STRLEN], buf_fn[STRLEN];
char molname[STRLEN], title[STRLEN], quote[STRLEN];
{ "-deuterate", FALSE, etBOOL, {&bDeuterate},
"Change the mass of hydrogens to 2 amu" },
{ "-chargegrp", TRUE, etBOOL, {&bChargeGroups},
- "Use charge groups in the [TT].rtp[tt] file" },
+ "Use charge groups in the [REF].rtp[ref] file" },
{ "-cmap", TRUE, etBOOL, {&bCmap},
- "Use cmap torsions (if enabled in the [TT].rtp[tt] file)" },
+ "Use cmap torsions (if enabled in the [REF].rtp[ref] file)" },
{ "-renum", TRUE, etBOOL, {&bRenumRes},
"Renumber the residues consecutively in the output" },
{ "-rtpres", TRUE, etBOOL, {&bRTPresname},
- "Use [TT].rtp[tt] entry names as residue names" }
+ "Use [REF].rtp[ref] entry names as residue names" }
};
#define NPARGS asize(pa)
chains[i].pdba->atom[j] = pdba_all.atom[pdb_ch[si].start+j];
snew(chains[i].pdba->atomname[j], 1);
*chains[i].pdba->atomname[j] =
- strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
+ gmx_strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
chains[i].pdba->pdbinfo[j] = pdba_all.pdbinfo[pdb_ch[si].start+j];
copy_rvec(pdbx[pdb_ch[si].start+j], chains[i].x[j]);
}
{
chains[i].pdba->resinfo[j] = pdba_all.resinfo[k+j];
snew(chains[i].pdba->resinfo[j].name, 1);
- *chains[i].pdba->resinfo[j].name = strdup(*pdba_all.resinfo[k+j].name);
+ *chains[i].pdba->resinfo[j].name = gmx_strdup(*pdba_all.resinfo[k+j].name);
/* make all chain identifiers equal to that of the chain */
chains[i].pdba->resinfo[j].chainid = pdb_ch[si].chainid;
}
nincl++;
srenew(incls, nincl);
- incls[nincl-1] = strdup(itp_fn);
+ incls[nincl-1] = gmx_strdup(itp_fn);
itp_file = gmx_fio_fopen(itp_fn, "w");
}
else
srenew(mols, nmol+1);
if (cc->bAllWat)
{
- mols[nmol].name = strdup("SOL");
+ mols[nmol].name = gmx_strdup("SOL");
mols[nmol].nr = pdba->nres;
}
else
{
- mols[nmol].name = strdup(molname);
+ mols[nmol].name = gmx_strdup(molname);
mols[nmol].nr = 1;
}
nmol++;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff