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37 #include "read-conformation.h"
39 #include "gromacs/fileio/confio.h"
40 #include "gromacs/legacyheaders/typedefs.h"
41 #include "gromacs/legacyheaders/types/simple.h"
42 #include "gromacs/topology/atomprop.h"
43 #include "gromacs/topology/atoms.h"
44 #include "gromacs/utility/cstringutil.h"
45 #include "gromacs/utility/smalloc.h"
47 real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
48 real defaultDistance, real scaleFactor)
51 real *exclusionDistances;
53 snew(exclusionDistances, a->nr);
54 /* initialise arrays with distances usually based on van der Waals
56 fprintf(stderr, "Initialising inter-atomic distances...\n");
57 for (i = 0; (i < a->nr); i++)
59 if (!gmx_atomprop_query(aps, epropVDW,
60 *(a->resinfo[a->atom[i].resind].name),
61 *(a->atomname[i]), &(exclusionDistances[i])))
63 exclusionDistances[i] = defaultDistance;
67 exclusionDistances[i] *= scaleFactor;
70 return exclusionDistances;
73 char *readConformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
74 int *ePBC, matrix box)
80 get_stx_coordnum(confin, &natoms);
82 /* allocate memory for atom coordinates of configuration */
88 init_t_atoms(atoms, natoms, FALSE);
90 /* read residue number, residue names, atomnames, coordinates etc. */
91 fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
92 read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
93 fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
94 title, atoms->nr, atoms->nres);