#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/atomprop.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
#include "gstat.h"
+
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "../legacyheaders/oenv.h"
#include "../commandline/pargs.h"
#include "../topology/index.h"
+#include "../topology/residuetypes.h"
#ifdef __cplusplus
extern "C" {
#include "gromacs/math/vec.h"
#include "toputil.h"
#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
#include "names.h"
#include "gromacs/utility/futil.h"
#include "gpp_atomtype.h"
#include "fflibutil.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.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/smalloc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/pdbio.h"
#include "gen_ad.h"
#include "gromacs/fileio/filenm.h"
-#include "gromacs/topology/index.h"
#include "gen_vsite.h"
#include "add_par.h"
#include "toputil.h"
#include "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/fatalerror.h"
#include <string.h>
#include "typedefs.h"
-#include "gromacs/topology/index.h"
#include "fflibutil.h"
#include "hackblock.h"
#include "xlate.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#ifndef GMX_GMXPREPROCESS_XLATE_H
#define GMX_GMXPREPROCESS_XLATE_H
-#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
#ifdef __cplusplus
extern "C" {
#include "gromacs/fileio/strdb.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/invblock.h"
+#include "gromacs/topology/residuetypes.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-const char gmx_residuetype_undefined[] = "Other";
-
-struct gmx_residuetype
-{
- int n;
- char ** resname;
- char ** restype;
-
-};
-
-
static gmx_bool gmx_ask_yesno(gmx_bool bASK)
{
char c;
}
-
-
-/* Return 0 if the name was found, otherwise -1.
- * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
- */
-int
-gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype)
-{
- int i, rc;
-
- rc = -1;
- for (i = 0; i < rt->n && rc; i++)
- {
- rc = gmx_strcasecmp(rt->resname[i], resname);
- }
-
- *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
-
- return rc;
-}
-
-int
-gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype)
-{
- int found;
- const char * p_oldtype;
-
- found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
-
- if (found && gmx_strcasecmp(p_oldtype, newrestype))
- {
- fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
- newresname, p_oldtype, newrestype);
- }
-
- if (found == 0)
- {
- srenew(rt->resname, rt->n+1);
- srenew(rt->restype, rt->n+1);
- rt->resname[rt->n] = strdup(newresname);
- rt->restype[rt->n] = strdup(newrestype);
- rt->n++;
- }
-
- return 0;
-}
-
-
-int
-gmx_residuetype_init(gmx_residuetype_t *prt)
-{
- FILE * db;
- char line[STRLEN];
- char resname[STRLEN], restype[STRLEN], dum[STRLEN];
- struct gmx_residuetype *rt;
-
- snew(rt, 1);
- *prt = rt;
-
- rt->n = 0;
- rt->resname = NULL;
- rt->restype = NULL;
-
- db = libopen("residuetypes.dat");
-
- while (get_a_line(db, line, STRLEN))
- {
- strip_comment(line);
- trim(line);
- if (line[0] != '\0')
- {
- if (sscanf(line, "%s %s %s", resname, restype, dum) != 2)
- {
- gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
- }
- gmx_residuetype_add(rt, resname, restype);
- }
- }
-
- fclose(db);
-
- return 0;
-}
-
-
-
-int
-gmx_residuetype_destroy(gmx_residuetype_t rt)
-{
- int i;
-
- for (i = 0; i < rt->n; i++)
- {
- sfree(rt->resname[i]);
- sfree(rt->restype[i]);
- }
- sfree(rt->resname);
- sfree(rt->restype);
- sfree(rt);
-
- return 0;
-}
-
-int
-gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
- const char *** p_typenames,
- int * ntypes)
-{
- int i, n;
- const char ** my_typename;
-
- n = 0;
- my_typename = NULL;
- for (i = 0; i < rt->n; i++)
- {
- const char *const p = rt->restype[i];
- bool bFound = false;
- for (int j = 0; j < n && !bFound; j++)
- {
- assert(my_typename != NULL);
- bFound = !gmx_strcasecmp(p, my_typename[j]);
- }
- if (!bFound)
- {
- srenew(my_typename, n+1);
- my_typename[n] = p;
- n++;
- }
- }
- *ntypes = n;
- *p_typenames = my_typename;
-
- return 0;
-}
-
-
-
-gmx_bool
-gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "Protein") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-gmx_bool
-gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "DNA") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-gmx_bool
-gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "RNA") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-/* Return the size of the arrays */
-int
-gmx_residuetype_get_size(gmx_residuetype_t rt)
-{
- return rt->n;
-}
-
-/* Search for a residuetype with name resnm within the
- * gmx_residuetype database. Return the index if found,
- * otherwise -1.
- */
-int
-gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
-{
- int i, rc;
-
- rc = -1;
- for (i = 0; i < rt->n && rc; i++)
- {
- rc = gmx_strcasecmp(rt->resname[i], resnm);
- }
-
- return (0 == rc) ? i-1 : -1;
-}
-
-/* Return the name of the residuetype with the given index, or
- * NULL if not found. */
-const char *
-gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
-{
- if (index >= 0 && index < rt->n)
- {
- return rt->resname[index];
- }
- else
- {
- return NULL;
- }
-}
-
-
-
void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
gmx_residuetype_t rt = NULL;
t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
-typedef struct gmx_residuetype *gmx_residuetype_t;
-
-int
-gmx_residuetype_init(gmx_residuetype_t *rt);
-
-int
-gmx_residuetype_destroy(gmx_residuetype_t rt);
-
-int
-gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype);
-
-int
-gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
-
-int
-gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
- const char *** p_typenames,
- int * ntypes);
-
-gmx_bool
-gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
-
-gmx_bool
-gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
-
-gmx_bool
-gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
-
-int
-gmx_residuetype_get_size(gmx_residuetype_t rt);
-
-int
-gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
-
-const char *
-gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
-
-
-
-
-
void write_index(const char *outf, struct t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
/* Writes index blocks to outf (writes an indexfile) */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2010,2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 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.
+ */
+#include "gromacs/topology/residuetypes.h"
+
+#include <cassert>
+#include <cstdio>
+
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+const char gmx_residuetype_undefined[] = "Other";
+
+struct gmx_residuetype
+{
+ int n;
+ char ** resname;
+ char ** restype;
+};
+
+int
+gmx_residuetype_init(gmx_residuetype_t *prt)
+{
+ FILE * db;
+ char line[STRLEN];
+ char resname[STRLEN], restype[STRLEN], dum[STRLEN];
+ struct gmx_residuetype *rt;
+
+ snew(rt, 1);
+ *prt = rt;
+
+ rt->n = 0;
+ rt->resname = NULL;
+ rt->restype = NULL;
+
+ db = libopen("residuetypes.dat");
+
+ while (get_a_line(db, line, STRLEN))
+ {
+ strip_comment(line);
+ trim(line);
+ if (line[0] != '\0')
+ {
+ if (sscanf(line, "%1000s %1000s %1000s", resname, restype, dum) != 2)
+ {
+ gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
+ }
+ gmx_residuetype_add(rt, resname, restype);
+ }
+ }
+
+ fclose(db);
+
+ return 0;
+}
+
+int
+gmx_residuetype_destroy(gmx_residuetype_t rt)
+{
+ int i;
+
+ for (i = 0; i < rt->n; i++)
+ {
+ sfree(rt->resname[i]);
+ sfree(rt->restype[i]);
+ }
+ sfree(rt->resname);
+ sfree(rt->restype);
+ sfree(rt);
+
+ return 0;
+}
+
+/* Return 0 if the name was found, otherwise -1.
+ * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
+ */
+int
+gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype)
+{
+ int i, rc;
+
+ rc = -1;
+ for (i = 0; i < rt->n && rc; i++)
+ {
+ rc = gmx_strcasecmp(rt->resname[i], resname);
+ }
+
+ *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
+
+ return rc;
+}
+
+int
+gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype)
+{
+ int found;
+ const char * p_oldtype;
+
+ found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
+
+ if (found && gmx_strcasecmp(p_oldtype, newrestype))
+ {
+ fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
+ newresname, p_oldtype, newrestype);
+ }
+
+ if (found == 0)
+ {
+ srenew(rt->resname, rt->n+1);
+ srenew(rt->restype, rt->n+1);
+ rt->resname[rt->n] = gmx_strdup(newresname);
+ rt->restype[rt->n] = gmx_strdup(newrestype);
+ rt->n++;
+ }
+
+ return 0;
+}
+
+int
+gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
+ const char *** p_typenames,
+ int * ntypes)
+{
+ int i, n;
+ const char ** my_typename;
+
+ n = 0;
+ my_typename = NULL;
+ for (i = 0; i < rt->n; i++)
+ {
+ const char *const p = rt->restype[i];
+ bool bFound = false;
+ for (int j = 0; j < n && !bFound; j++)
+ {
+ assert(my_typename != NULL);
+ bFound = !gmx_strcasecmp(p, my_typename[j]);
+ }
+ if (!bFound)
+ {
+ srenew(my_typename, n+1);
+ my_typename[n] = p;
+ n++;
+ }
+ }
+ *ntypes = n;
+ *p_typenames = my_typename;
+
+ return 0;
+}
+
+gmx_bool
+gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "Protein") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+gmx_bool
+gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "DNA") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+gmx_bool
+gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "RNA") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+/* Return the size of the arrays */
+int
+gmx_residuetype_get_size(gmx_residuetype_t rt)
+{
+ return rt->n;
+}
+
+/* Search for a residuetype with name resnm within the
+ * gmx_residuetype database. Return the index if found,
+ * otherwise -1.
+ */
+int
+gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
+{
+ int i, rc;
+
+ rc = -1;
+ for (i = 0; i < rt->n && rc; i++)
+ {
+ rc = gmx_strcasecmp(rt->resname[i], resnm);
+ }
+
+ return (0 == rc) ? i-1 : -1;
+}
+
+/* Return the name of the residuetype with the given index, or
+ * NULL if not found. */
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
+{
+ if (index >= 0 && index < rt->n)
+ {
+ return rt->resname[index];
+ }
+ else
+ {
+ return NULL;
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2010,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 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.
+ */
+#ifndef GMX_TOPOLOGY_RESIDUETYPES_H
+#define GMX_TOPOLOGY_RESIDUETYPES_H
+
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+typedef struct gmx_residuetype *gmx_residuetype_t;
+
+int
+gmx_residuetype_init(gmx_residuetype_t *rt);
+
+int
+gmx_residuetype_destroy(gmx_residuetype_t rt);
+
+int
+gmx_residuetype_get_type(gmx_residuetype_t rt, const char *resname, const char **p_restype);
+
+int
+gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
+
+int
+gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
+ const char ***p_typenames,
+ int *ntypes);
+
+gmx_bool
+gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
+
+gmx_bool
+gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
+
+gmx_bool
+gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
+
+int
+gmx_residuetype_get_size(gmx_residuetype_t rt);
+
+int
+gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
+
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff