/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <cctype>
#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
+#include "selmethod.h"
+
/** Evaluates the \p all selection keyword. */
static void
evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
static void
evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether molecule information is present in the topology. */
+/*! \brief
+ * Checks whether molecule information is present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if molecule info is present in the topology, -1 otherwise.
+ *
+ * If molecule information is not found, also prints an error message.
+ */
static void
check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p molindex selection keyword. */
static void
evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether atom types are present in the topology. */
+/*! \brief
+ * Checks whether atom types are present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if atom types are present in the topology, -1 otherwise.
+ *
+ * If the atom types are not found, also prints an error message.
+ */
static void
check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p atomtype selection keyword. */
static void
evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Checks whether PDB info is present in the topology. */
+/*! \brief
+ * Checks whether PDB info is present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ * \returns 0 if PDB info is present in the topology, -1 otherwise.
+ *
+ * If PDB info is not found, also prints an error message.
+ */
static void
check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p altloc selection keyword. */
"keywords."
};
-/** \internal Selection method data for \p all selection keyword. */
+/** Selection method data for \p all selection keyword. */
gmx_ana_selmethod_t sm_all = {
"all", GROUP_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p none selection keyword. */
+/** Selection method data for \p none selection keyword. */
gmx_ana_selmethod_t sm_none = {
"none", GROUP_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p atomnr selection keyword. */
+/** Selection method data for \p atomnr selection keyword. */
gmx_ana_selmethod_t sm_atomnr = {
"atomnr", INT_VALUE, 0,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resnr selection keyword. */
+/** Selection method data for \p resnr selection keyword. */
gmx_ana_selmethod_t sm_resnr = {
"resnr", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resindex selection keyword. */
+/** Selection method data for \p resindex selection keyword. */
gmx_ana_selmethod_t sm_resindex = {
"resindex", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p molindex selection keyword. */
+/** Selection method data for \p molindex selection keyword. */
gmx_ana_selmethod_t sm_molindex = {
"molindex", INT_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p atomname selection keyword. */
+/** Selection method data for \p atomname selection keyword. */
gmx_ana_selmethod_t sm_atomname = {
"atomname", STR_VALUE, SMETH_REQTOP,
0, NULL,
{NULL, asize(help_atomname), help_atomname}
};
-/** \internal Selection method data for \p pdbatomname selection keyword. */
+/** Selection method data for \p pdbatomname selection keyword. */
gmx_ana_selmethod_t sm_pdbatomname = {
"pdbatomname", STR_VALUE, SMETH_REQTOP,
0, NULL,
{NULL, asize(help_atomname), help_atomname}
};
-/** \internal Selection method data for \p atomtype selection keyword. */
+/** Selection method data for \p atomtype selection keyword. */
gmx_ana_selmethod_t sm_atomtype = {
"atomtype", STR_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p resname selection keyword. */
+/** Selection method data for \p resname selection keyword. */
gmx_ana_selmethod_t sm_resname = {
"resname", STR_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_insertcode = {
"insertcode", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_chain = {
"chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p mass selection keyword. */
+/** Selection method data for \p mass selection keyword. */
gmx_ana_selmethod_t sm_mass = {
"mass", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p charge selection keyword. */
+/** Selection method data for \p charge selection keyword. */
gmx_ana_selmethod_t sm_charge = {
"charge", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p chain selection keyword. */
+/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_altloc = {
"altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p occupancy selection keyword. */
+/** Selection method data for \p occupancy selection keyword. */
gmx_ana_selmethod_t sm_occupancy = {
"occupancy", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p betafactor selection keyword. */
+/** Selection method data for \p betafactor selection keyword. */
gmx_ana_selmethod_t sm_betafactor = {
"betafactor", REAL_VALUE, SMETH_REQTOP,
0, NULL,
NULL,
};
-/** \internal Selection method data for \p x selection keyword. */
+/** Selection method data for \p x selection keyword. */
gmx_ana_selmethod_t sm_x = {
"x", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
&evaluate_x,
};
-/** \internal Selection method data for \p y selection keyword. */
+/** Selection method data for \p y selection keyword. */
gmx_ana_selmethod_t sm_y = {
"y", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
&evaluate_y,
};
-/** \internal Selection method data for \p z selection keyword. */
+/** Selection method data for \p z selection keyword. */
gmx_ana_selmethod_t sm_z = {
"z", REAL_VALUE, SMETH_DYNAMIC,
0, NULL,
* Copies \p g to \p out->u.g.
*/
static void
-evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_all(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
gmx_ana_index_copy(out->u.g, g, false);
}
* Returns an empty \p out->u.g.
*/
static void
-evaluate_none(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_none(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void * /* data */)
{
out->u.g->isize = 0;
}
* Returns the indices for each atom in \p out->u.i.
*/
static void
-evaluate_atomnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomnr(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the residue numbers for each atom in \p out->u.i.
*/
static void
-evaluate_resnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resnr(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
* Returns the residue indices for each atom in \p out->u.i.
*/
static void
-evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if molecule info is present in the topology, -1 otherwise.
- *
- * If molecule information is not found, also prints an error message.
- */
static void
-check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_molecules(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Returns the molecule indices for each atom in \p out->u.i.
*/
static void
-evaluate_molindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_molindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i, j;
* Returns the atom name for each atom in \p out->u.s.
*/
static void
-evaluate_atomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the PDB atom name for each atom in \p out->u.s.
*/
static void
-evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_pdbatomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if atom types are present in the topology, -1 otherwise.
- *
- * If the atom types are not found, also prints an error message.
- */
static void
-check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_atomtype(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Segfaults if atom types are not found in the topology.
*/
static void
-evaluate_atomtype(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_atomtype(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the residue name for each atom in \p out->u.s.
*/
static void
-evaluate_resname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_resname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
* Returns the insertion code for each atom in \p out->u.s.
*/
static void
-evaluate_insertcode(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_insertcode(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
* Returns the chain for each atom in \p out->u.s.
*/
static void
-evaluate_chain(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_chain(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
int resind;
* Returns the mass for each atom in \p out->u.r.
*/
static void
-evaluate_mass(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_mass(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the charge for each atom in \p out->u.r.
*/
static void
-evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_charge(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
}
}
-/*!
- * \param[in] top Topology structure.
- * \param npar Not used.
- * \param param Not used.
- * \param data Not used.
- * \returns 0 if PDB info is present in the topology, -1 otherwise.
- *
- * If PDB info is not found, also prints an error message.
- */
static void
-check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+check_pdbinfo(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
* Returns the alternate location identifier for each atom in \p out->u.s.
*/
static void
-evaluate_altloc(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_altloc(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_occupancy(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_occupancy(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_betafactor(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_betafactor(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
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