*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <math.h>
#include <ctype.h>
-#include "vec.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "symtab.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/futil.h"
#include "pdb2top.h"
#include "gpp_nextnb.h"
#include "topdirs.h"
#include "pgutil.h"
#include "resall.h"
#include "topio.h"
-#include "string2.h"
-#include "physics.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/pdbio.h"
#include "gen_ad.h"
#include "gromacs/fileio/filenm.h"
-#include "index.h"
#include "gen_vsite.h"
#include "add_par.h"
#include "toputil.h"
#include "fflibutil.h"
-#include "strdb.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/programinfo.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
/* this must correspond to enum in pdb2top.h */
const char *hh[ehisNR] = { "HISD", "HISE", "HISH", "HIS1" };
ptr = strrchr(ffdirs[i], '/');
if (ptr == NULL)
{
- ffs[i] = strdup(ffdirs[i]);
+ ffs[i] = gmx_strdup(ffdirs[i]);
ffs_dir[i] = low_gmxlibfn(ffdirs[i], FALSE, FALSE);
if (ffs_dir[i] == NULL)
{
}
else
{
- ffs[i] = strdup(ptr+1);
- ffs_dir[i] = strdup(ffdirs[i]);
+ ffs[i] = gmx_strdup(ptr+1);
+ ffs_dir[i] = gmx_strdup(ffdirs[i]);
}
ffs_dir[i][strlen(ffs_dir[i])-strlen(ffs[i])-1] = '\0';
/* Remove the extension from the ffdir name */
if (gmx_fexist(buf))
{
/* We don't use fflib_open, because we don't want printf's */
- fp = ffopen(buf, "r");
+ fp = gmx_ffopen(buf, "r");
snew(desc[i], STRLEN);
get_a_line(fp, desc[i], STRLEN);
- ffclose(fp);
+ gmx_ffclose(fp);
}
else
{
- desc[i] = strdup(ffs[i]);
+ desc[i] = gmx_strdup(ffs[i]);
}
}
/* Order force fields from the same dir alphabetically
}
else if (strcmp(wmsel, "select") != 0)
{
- *watermodel = strdup(wmsel);
+ *watermodel = gmx_strdup(wmsel);
return;
}
sfree(model[nwm]);
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
fprintf(stderr, "%2d: %s\n", nwm+1, "None");
sel = -1;
}
else
{
- *watermodel = strdup(model[sel]);
+ *watermodel = gmx_strdup(model[sel]);
}
for (i = 0; i < nwm; i++)
sfree(model);
}
-static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
- t_restp restp[], gmx_residuetype_t rt)
+static int name2type(t_atoms *at, int **cgnr,
+ t_restp restp[], gmx_residuetype_t *rt)
{
int i, j, prevresind, resind, i0, prevcg, cg, curcg;
char *name;
j = search_jtype(&restp[resind], name, bNterm);
at->atom[i].type = restp[resind].atom[j].type;
at->atom[i].q = restp[resind].atom[j].q;
- at->atom[i].m = get_atomtype_massA(restp[resind].atom[j].type,
- atype);
- cg = restp[resind].cgnr[j];
+ at->atom[i].m = restp[resind].atom[j].m;
+ cg = restp[resind].cgnr[j];
/* A charge group number -1 signals a separate charge group
* for this atom.
*/
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix(";\t");
- gmx::printBinaryInformation(out, gmx::ProgramInfo::getInstance(),
- settings);
+ gmx::printBinaryInformation(out, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
}
-static atom_id search_res_atom(const char *type, int resind,
- t_atoms *atoms,
- const char *bondtype, gmx_bool bAllowMissing)
-{
- int i;
-
- for (i = 0; (i < atoms->nr); i++)
- {
- if (atoms->atom[i].resind == resind)
- {
- return search_atom(type, i, atoms, bondtype, bAllowMissing);
- }
- }
- return NO_ATID;
-}
static void do_ssbonds(t_params *ps, t_atoms *atoms,
int nssbonds, t_ssbond *ssbonds, gmx_bool bAllowMissing)
{
dist2 = distance2(x[ai], x[aj]);
if (dist2 > long_bond_dist2)
+
{
fprintf(stderr, "Warning: Long Bond (%d-%d = %g nm)\n",
ai+1, aj+1, sqrt(dist2));
}
snew( restp->atomname[at_start+1+k], 1);
restp->atom [at_start+1+k] = *hack->atom;
- *restp->atomname[at_start+1+k] = strdup(buf);
+ *restp->atomname[at_start+1+k] = gmx_strdup(buf);
if (hack->cgnr != NOTSET)
{
restp->cgnr [at_start+1+k] = hack->cgnr;
}
snew( (*restp)[i].atomname[l], 1);
(*restp)[i].atom[l] = *(*hb)[i].hack[j].atom;
- *(*restp)[i].atomname[l] = strdup((*hb)[i].hack[j].nname);
+ *(*restp)[i].atomname[l] = gmx_strdup((*hb)[i].hack[j].nname);
if ( (*hb)[i].hack[j].cgnr != NOTSET)
{
(*restp)[i].cgnr [l] = (*hb)[i].hack[j].cgnr;
}
/* Rename the atom in pdba */
snew(pdba->atomname[atind], 1);
- *pdba->atomname[atind] = strdup(newnm);
+ *pdba->atomname[atind] = gmx_strdup(newnm);
}
else if (hbr->hack[j].oname != NULL && hbr->hack[j].nname == NULL &&
gmx_strcasecmp(oldnm, hbr->hack[j].oname) == 0)
}
#define NUM_CMAP_ATOMS 5
-static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuetype_t rt)
+static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms)
{
int residx, i, j, k;
const char *ptr;
+ const char *pname;
t_resinfo *resinfo = atoms->resinfo;
int nres = atoms->nres;
gmx_bool bAddCMAP;
ptr = "check";
}
- fprintf(stderr, "Making cmap torsions...");
+ fprintf(stderr, "Making cmap torsions...\n");
i = 0;
- /* End loop at nres-1, since the very last residue does not have a +N atom, and
- * therefore we get a valgrind invalid 4 byte read error with atom am */
- for (residx = 0; residx < nres-1; residx++)
+ /* Most cmap entries use the N atom from the next residue, so the last
+ * residue should not have its CMAP entry in that case, but for things like
+ * dipeptides we sometimes define a complete CMAP entry inside a residue,
+ * and in this case we need to process everything through the last residue.
+ */
+ for (residx = 0; residx < nres; residx++)
{
/* Add CMAP terms from the list of CMAP interactions */
for (j = 0; j < restp[residx].rb[ebtsCMAP].nb; j++)
* from residues labelled as protein. */
for (k = 0; k < NUM_CMAP_ATOMS && bAddCMAP; k++)
{
- cmap_atomid[k] = search_atom(restp[residx].rb[ebtsCMAP].b[j].a[k],
+ /* Assign the pointer to the name of the next reference atom.
+ * This can use -/+ labels to refer to previous/next residue.
+ */
+ pname = restp[residx].rb[ebtsCMAP].b[j].a[k];
+ /* Skip this CMAP entry if it refers to residues before the
+ * first or after the last residue.
+ */
+ if (((strchr(pname, '-') != NULL) && (residx == 0)) ||
+ ((strchr(pname, '+') != NULL) && (residx == nres-1)))
+ {
+ bAddCMAP = FALSE;
+ break;
+ }
+
+ cmap_atomid[k] = search_atom(pname,
i, atoms, ptr, TRUE);
bAddCMAP = bAddCMAP && (cmap_atomid[k] != NO_ATID);
if (!bAddCMAP)
bAddCMAP = bAddCMAP &&
cmap_chainnum == resinfo[this_residue_index].chainnum;
}
- bAddCMAP = bAddCMAP && gmx_residuetype_is_protein(rt, *(resinfo[this_residue_index].name));
+ /* Here we used to check that the residuetype was protein and
+ * disable bAddCMAP if that was not the case. However, some
+ * special residues (say, alanine dipeptides) might not adhere
+ * to standard naming, and if we start calling them normal
+ * protein residues the user will be bugged to select termini.
+ *
+ * Instead, I believe that the right course of action is to
+ * keep the CMAP interaction if it is present in the RTP file
+ * and we correctly identified all atoms (which is the case
+ * if we got here).
+ */
}
if (bAddCMAP)
}
}
}
-
/* Start the next residue */
}
int *vsite_type;
int i, nmissat;
int bts[ebtsNR];
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
init_plist(plist);
gmx_residuetype_init(&rt);
atoms, nssbonds, ssbonds,
bAllowMissing);
- nmissat = name2type(atoms, &cgnr, atype, restp, rt);
+ nmissat = name2type(atoms, &cgnr, restp, rt);
if (nmissat)
{
if (bAllowMissing)
/* Make CMAP */
if (TRUE == bCmap)
{
- gen_cmap(&(plist[F_CMAP]), restp, atoms, rt);
+ gen_cmap(&(plist[F_CMAP]), restp, atoms);
if (plist[F_CMAP].nr > 0)
{
fprintf(stderr, "There are %4d cmap torsion pairs\n",
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff