src/gmxlib/selection/sm_same.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  10  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  11  * Copyright (c) 2001-2009, The GROMACS development team,
  12  * check out http://www.gromacs.org for more information.
  13
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  15  * modify it under the terms of the GNU General Public License
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  30  */
  31 /*! \internal \file
  32  * \brief Implementation of the \p same selection method.
  33  */
  34 #ifdef HAVE_CONFIG_H
  35 #include <config.h>
  36 #endif
  37
  38 #include <macros.h>
  39 #include <smalloc.h>
  40
  41 #include <indexutil.h>
  42 #include <selmethod.h>
  43
  44 /*! \internal \brief
  45  * Data structure for the \p same selection method.
  46  *
  47  * All angle values are in the units of radians.
  48  */
  49 typedef struct
  50 {
  51     /*! \brief Input group. */
  52     gmx_ana_index_t       g;
  53 } t_methoddata_same;
  54
  55 /*! \brief Allocates data for the \p same selection method. */
  56 static void *
  57 init_data_same(int npar, gmx_ana_selparam_t *param);
  58 /*! \brief Initializes the \p same selection method. */
  59 static int
  60 init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
  61 /*! \brief Frees the data allocated for the \p same selection method. */
  62 static void
  63 free_data_same(void *data);
  64 /*! \brief Initializes the evaluation of the \p same selection method for a frame. */
  65 static int
  66 init_frame_same(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
  67 /*! \brief Evaluates the \p same selection method. */
  68 static int
  69 evaluate_same(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  70               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
  71
  72 /*! \brief Enum array for the \p same selection method. */
  73 static char *same_enum[] = { NULL, "residue", NULL };
  74
  75 /*! \brief Parameters for the \p same selection method. */
  76 static gmx_ana_selparam_t smparams_same[] = {
  77     {NULL, {STR_VALUE,   1, {same_enum}}, NULL, SPAR_ENUMVAL},
  78     {"as", {GROUP_VALUE, 1, {NULL}},      NULL, SPAR_DYNAMIC},
  79 };
  80
  81 /*! \internal \brief Selection method data for the \p same method. */
  82 gmx_ana_selmethod_t sm_same = {
  83     "same", GROUP_VALUE, SMETH_REQTOP,
  84     asize(smparams_same), smparams_same,
  85     &init_data_same,
  86     NULL,
  87     NULL,
  88     NULL,
  89     &free_data_same,
  90     NULL,
  91     &evaluate_same,
  92     NULL,
  93     {"same residue as ATOM_EXPR", 0, NULL},
  94 };
  95
  96 /*!
  97  * \param[in]     npar  Not used (should be 2).
  98  * \param[in,out] param Method parameters (should point to
  99  *   \ref smparams_same).
 100  * \returns Pointer to the allocated data (\ref t_methoddata_same).
 101  */
 102 static void *
 103 init_data_same(int npar, gmx_ana_selparam_t *param)
 104 {
 105     t_methoddata_same *data;
 106
 107     snew(data, 1);
 108     gmx_ana_index_clear(&data->g);
 109     param[1].val.u.g = &data->g;
 110     return data;
 111 }
 112
 113 /*!
 114  * \param data Data to free (should point to a \ref t_methoddata_same).
 115  */
 116 static void
 117 free_data_same(void *data)
 118 {
 119     t_methoddata_same *d = (t_methoddata_same *)data;
 120
 121     gmx_ana_index_deinit(&d->g);
 122 }
 123
 124 /*!
 125  * See sel_updatefunc() for description of the parameters.
 126  * \p data should point to a \c t_methoddata_same.
 127  *
 128  * Calculates which atoms in \p g are in the same residues as the atoms in
 129  * \c t_methoddata_same::g.
 130  */
 131 static int
 132 evaluate_same(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 133               gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
 134 {
 135     t_methoddata_same *d = (t_methoddata_same *)data;
 136     int                    i, j, resind;
 137
 138     out->u.g->isize = 0;
 139     i = j = 0;
 140     while (i < d->g.isize)
 141     {
 142         resind = top->atoms.atom[d->g.index[i]].resind;
 143         /* Find the first atom in the current residue */
 144         while (top->atoms.atom[g->index[j]].resind < resind) ++j;
 145         /* Copy all the atoms in the residue to the output */
 146         while (j < g->isize && top->atoms.atom[g->index[j]].resind == resind)
 147         {
 148             out->u.g->index[out->u.g->isize++] = g->index[j];
 149             ++j;
 150         }
 151         /* Skip the rest of the atoms in the residue */
 152         ++i;
 153         while (i < d->g.isize && top->atoms.atom[d->g.index[i]].resind == resind) ++i;
 154     }
 155     return 0;
 156 }
 157