sm_simple.cpp File Reference

#include "gmxpre.h"
#include <cctype>
#include <vector>
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vectypes.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_simple.cpp:

Description

Implements simple keyword selection methods.

Author

Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Functions
static void	evaluate_all (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the all selection keyword. More...
static void	evaluate_none (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the none selection keyword. More...
static void	evaluate_atomnr (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the atomnr selection keyword. More...
static void	evaluate_resnr (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the resnr selection keyword. More...
static void	evaluate_resindex (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the resindex selection keyword. More...
static void	check_molecules (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Checks whether molecule information is present in the topology. More...
static void	evaluate_molindex (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the molindex selection keyword. More...
static void	evaluate_atomname (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the atomname selection keyword. More...
static void	evaluate_pdbatomname (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the pdbatomname selection keyword. More...
static void	check_atomtype (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Checks whether atom types are present in the topology. More...
static void	evaluate_atomtype (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the atomtype selection keyword. More...
static void	evaluate_insertcode (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the insertcode selection keyword. More...
static void	evaluate_chain (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the chain selection keyword. More...
static void	evaluate_mass (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the mass selection keyword. More...
static void	check_charge (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Checks whether charges are present in the topology. More...
static void	evaluate_charge (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the charge selection keyword. More...
static void	check_pdbinfo (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Checks whether PDB info is present in the topology. More...
static void	evaluate_altloc (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the altloc selection keyword. More...
static void	evaluate_occupancy (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the occupancy selection keyword. More...
static void	evaluate_betafactor (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the betafactor selection keyword. More...
static void	evaluate_resname (const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
	Evaluates the resname selection keyword. More...
static void	evaluate_x (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
	Evaluates the x selection keyword. More...
static void	evaluate_y (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
	Evaluates the y selection keyword. More...
static void	evaluate_z (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
	Evaluates the z selection keyword. More...
static void	evaluate_coord (real out[], gmx_ana_pos_t *pos, int d)
	Internal utility function for position keyword evaluation. More...

Variables
static const char	helptitle_atomname [] = "Selecting atoms by name"
	Help title for atom name selection keywords.
static const char *const	help_atomname []
	Help text for atom name selection keywords. More...
static const char	helptitle_resindex [] = "Selecting atoms by residue number"
	Help title for residue index selection keywords.
static const char *const	help_resindex []
	Help text for residue index selection keywords. More...
gmx_ana_selmethod_t	sm_all
	Selection method data for all selection keyword. More...
gmx_ana_selmethod_t	sm_none
	Selection method data for none selection keyword. More...
gmx_ana_selmethod_t	sm_atomnr
	Selection method data for atomnr selection keyword. More...
gmx_ana_selmethod_t	sm_resnr
	Selection method data for resnr selection keyword. More...
gmx_ana_selmethod_t	sm_resindex
	Selection method data for resindex selection keyword. More...
gmx_ana_selmethod_t	sm_molindex
	Selection method data for molindex selection keyword. More...
gmx_ana_selmethod_t	sm_atomname
	Selection method data for atomname selection keyword. More...
gmx_ana_selmethod_t	sm_pdbatomname
	Selection method data for pdbatomname selection keyword. More...
gmx_ana_selmethod_t	sm_atomtype
	Selection method data for atomtype selection keyword. More...
gmx_ana_selmethod_t	sm_resname
	Selection method data for resname selection keyword. More...
gmx_ana_selmethod_t	sm_insertcode
	Selection method data for chain selection keyword. More...
gmx_ana_selmethod_t	sm_chain
	Selection method data for chain selection keyword. More...
gmx_ana_selmethod_t	sm_mass
	Selection method data for mass selection keyword. More...
gmx_ana_selmethod_t	sm_charge
	Selection method data for charge selection keyword. More...
gmx_ana_selmethod_t	sm_altloc
	Selection method data for chain selection keyword. More...
gmx_ana_selmethod_t	sm_occupancy
	Selection method data for occupancy selection keyword. More...
gmx_ana_selmethod_t	sm_betafactor
	Selection method data for betafactor selection keyword. More...
gmx_ana_selmethod_t	sm_x
	Selection method data for x selection keyword. More...
gmx_ana_selmethod_t	sm_y
	Selection method data for y selection keyword. More...
gmx_ana_selmethod_t	sm_z
	Selection method data for z selection keyword. More...

Function Documentation

static void check_atomtype ( const gmx_mtop_t *  top, int  npar, gmx_ana_selparam_t *  param, void *  data  )

static

Checks whether atom types are present in the topology.

Parameters

[in]	top	Topology structure.
	npar	Not used.
	param	Not used.
	data	Not used.

static void check_charge ( const gmx_mtop_t *  top, int  npar, gmx_ana_selparam_t *  param, void *  data  )

static

Checks whether charges are present in the topology.

Parameters

[in]	top	Topology structure.
	npar	Not used.
	param	Not used.
	data	Not used.

static void check_molecules ( const gmx_mtop_t *  top, int  npar, gmx_ana_selparam_t *  param, void *  data  )

static

Checks whether molecule information is present in the topology.

Parameters

[in]	top	Topology structure.
	npar	Not used.
	param	Not used.
	data	Not used.

Exceptions

If	molecule information is not found, throw InconsistentInputError.

static void check_pdbinfo ( const gmx_mtop_t *  top, int  npar, gmx_ana_selparam_t *  param, void *  data  )

static

Checks whether PDB info is present in the topology.

Parameters

[in]	top	Topology structure.
	npar	Not used.
	param	Not used.
	data	Not used.

Exceptions

InconsistentInputError

if PDB info is not found

static void evaluate_all ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the all selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Copies g to out->u.g.

static void evaluate_altloc ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the altloc selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the alternate location identifier for each atom in out->u.s.

static void evaluate_atomname ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the atomname selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the atom name for each atom in out->u.s.

static void evaluate_atomnr ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the atomnr selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the indices for each atom in out->u.i.

static void evaluate_atomtype ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the atomtype selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the atom type for each atom in out->u.s. Segfaults if atom types are not found in the topology.

static void evaluate_betafactor ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the betafactor selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the B-factors for each atom in out->u.r. Segfaults if PDB info is not found in the topology.

static void evaluate_chain ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the chain selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the chain for each atom in out->u.s.

static void evaluate_charge ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the charge selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the charge for each atom in out->u.r.

static void evaluate_coord ( real  out[], gmx_ana_pos_t *  pos, int  d  )

static

Internal utility function for position keyword evaluation.

Parameters

[out]	out	Output array.
[in]	pos	Position data to use instead of atomic coordinates.
[in]	d	Coordinate index to evaluate (XX, YY or ZZ).

This function is used internally by evaluate_x(), evaluate_y() and evaluate_z() to do the actual evaluation.

static void evaluate_insertcode ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the insertcode selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the insertion code for each atom in out->u.s.

static void evaluate_mass ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the mass selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the mass for each atom in out->u.r.

static void evaluate_molindex ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the molindex selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the molecule indices for each atom in out->u.i.

static void evaluate_none ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the none selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns an empty out->u.g.

static void evaluate_occupancy ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the occupancy selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the occupancy numbers for each atom in out->u.r. Segfaults if PDB info is not found in the topology.

static void evaluate_pdbatomname ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the pdbatomname selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the PDB atom name for each atom in out->u.s.

static void evaluate_resindex ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the resindex selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the residue indices for each atom in out->u.i.

static void evaluate_resname ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the resname selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the residue name for each atom in out->u.s.

static void evaluate_resnr ( const gmx::SelMethodEvalContext &  context, gmx_ana_index_t *  g, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the resnr selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the residue numbers for each atom in out->u.i.

static void evaluate_x ( const gmx::SelMethodEvalContext &  context, gmx_ana_pos_t *  pos, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the x selection keyword.

See sel_updatefunc_pos() for description of the parameters. data is not used.

Returns the x coordinate for each position in out->u.r.

static void evaluate_y ( const gmx::SelMethodEvalContext &  context, gmx_ana_pos_t *  pos, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the y selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the y coordinate for each position in out->u.r.

static void evaluate_z ( const gmx::SelMethodEvalContext &  context, gmx_ana_pos_t *  pos, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the z selection keyword.

See sel_updatefunc() for description of the parameters. data is not used.

Returns the z coordinate for each position in out->u.r.

Variable Documentation

const char* const help_atomname[]

static

Initial value:

= {
    "::",
    "",
    "  name",
    "  pdbname",
    "  atomname",
    "  pdbatomname",
    "",
    "These keywords select atoms by name. [TT]name[tt] selects atoms using",
    "the GROMACS atom naming convention.",
    "For input formats other than PDB, the atom names are matched exactly",
    "as they appear in the input file. For PDB files, 4 character atom names",
    "that start with a digit are matched after moving the digit to the end",
    "(e.g., to match 3HG2 from a PDB file, use [TT]name HG23[tt]).",
    "[TT]pdbname[tt] can only be used with a PDB input file, and selects",
    "atoms based on the exact name given in the input file, without the",
    "transformation described above.[PAR]",

    "[TT]atomname[tt] and [TT]pdbatomname[tt] are synonyms for the above two",
    "keywords."
}

Help text for atom name selection keywords.

const char* const help_resindex[]

static

Initial value:

= {
    "::",
    "",
    "  resnr",
    "  resid",
    "  resindex",
    "  residue",
    "",
    "[TT]resnr[tt] selects atoms using the residue numbering in the input",
    "file. [TT]resid[tt] is synonym for this keyword for VMD compatibility.",
    "",
    "[TT]resindex N[tt] selects the [TT]N[tt] th residue starting from the",
    "beginning of the input file. This is useful for uniquely identifying",
    "residues if there are duplicate numbers in the input file (e.g., in",
    "multiple chains).",
    "[TT]residue[tt] is a synonym for [TT]resindex[tt]. This allows",
    "[TT]same residue as[tt] to work as expected."
}

Help text for residue index selection keywords.

gmx_ana_selmethod_t sm_all

Initial value:

= {
    "all",   GROUP_VALUE, 0,       0,       nullptr,       nullptr, nullptr,
    nullptr, nullptr,     nullptr, nullptr, &evaluate_all, nullptr,
}

Selection method data for all selection keyword.

gmx_ana_selmethod_t sm_altloc

Initial value:

= {
    "altloc", STR_VALUE,       1  |  64 ,
    0,        nullptr,        nullptr,
    nullptr,  &check_pdbinfo, nullptr,
    nullptr,  nullptr,        &evaluate_altloc,
    nullptr,
}

Selection method data for chain selection keyword.

gmx_ana_selmethod_t sm_atomname

Initial value:

= {
    "atomname",   STR_VALUE,
     1 , 0,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      &evaluate_atomname,
    nullptr,      { nullptr, helptitle_atomname, asize(help_atomname), help_atomname }
}

Selection method data for atomname selection keyword.

gmx_ana_selmethod_t sm_atomnr

Initial value:

= {
    "atomnr", INT_VALUE, 0,       0,       nullptr,          nullptr, nullptr,
    nullptr,  nullptr,   nullptr, nullptr, &evaluate_atomnr, nullptr,
}

Selection method data for atomnr selection keyword.

gmx_ana_selmethod_t sm_atomtype

Initial value:

= {
    "atomtype", STR_VALUE,        1 , 0,       nullptr, nullptr,
    nullptr,    &check_atomtype, nullptr,      nullptr, nullptr, &evaluate_atomtype,
    nullptr,
}

Selection method data for atomtype selection keyword.

gmx_ana_selmethod_t sm_betafactor

Initial value:

= {
    "betafactor", REAL_VALUE,      1 , 0,       nullptr, nullptr,
    nullptr,      &check_pdbinfo, nullptr,      nullptr, nullptr, &evaluate_betafactor,
    nullptr,
}

Selection method data for betafactor selection keyword.

gmx_ana_selmethod_t sm_chain

Initial value:

= {
    "chain", STR_VALUE,  1  |  64 ,
    0,       nullptr,   nullptr,
    nullptr, nullptr,   nullptr,
    nullptr, nullptr,   &evaluate_chain,
    nullptr,
}

Selection method data for chain selection keyword.

gmx_ana_selmethod_t sm_charge

Initial value:

= {
    "charge",      REAL_VALUE,  1 , 0,       nullptr,          nullptr, nullptr,
    &check_charge, nullptr,    nullptr,      nullptr, &evaluate_charge, nullptr,
}

Selection method data for charge selection keyword.

gmx_ana_selmethod_t sm_insertcode

Initial value:

= {
    "insertcode",
    STR_VALUE,
     1  |  64 ,
    0,
    nullptr,
    nullptr,
    nullptr,
    nullptr,
    nullptr,
    nullptr,
    nullptr,
    &evaluate_insertcode,
    nullptr,
}

Selection method data for chain selection keyword.

gmx_ana_selmethod_t sm_mass

Initial value:

= {
    "mass",  REAL_VALUE,  2 , 0,       nullptr,        nullptr, nullptr,
    nullptr, nullptr,    nullptr,       nullptr, &evaluate_mass, nullptr,
}

Selection method data for mass selection keyword.

gmx_ana_selmethod_t sm_molindex

Initial value:

= {
    "molindex", INT_VALUE,         1 , 0,       nullptr, nullptr,
    nullptr,    &check_molecules, nullptr,      nullptr, nullptr, &evaluate_molindex,
    nullptr,
}

Selection method data for molindex selection keyword.

gmx_ana_selmethod_t sm_none

Initial value:

= {
    "none",  GROUP_VALUE, 0,       0,       nullptr,        nullptr, nullptr,
    nullptr, nullptr,     nullptr, nullptr, &evaluate_none, nullptr,
}

Selection method data for none selection keyword.

gmx_ana_selmethod_t sm_occupancy

Initial value:

= {
    "occupancy", REAL_VALUE,      1 , 0,       nullptr, nullptr,
    nullptr,     &check_pdbinfo, nullptr,      nullptr, nullptr, &evaluate_occupancy,
    nullptr,
}

Selection method data for occupancy selection keyword.

gmx_ana_selmethod_t sm_pdbatomname

Initial value:

= {
    "pdbatomname", STR_VALUE,
     1 ,  0,
    nullptr,       nullptr,
    nullptr,       &check_pdbinfo,
    nullptr,       nullptr,
    nullptr,       &evaluate_pdbatomname,
    nullptr,       { nullptr, helptitle_atomname, asize(help_atomname), help_atomname }
}

Selection method data for pdbatomname selection keyword.

gmx_ana_selmethod_t sm_resindex

Initial value:

= {
    "resindex",   INT_VALUE,
     1 , 0,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      &evaluate_resindex,
    nullptr,      { nullptr, helptitle_resindex, asize(help_resindex), help_resindex }
}

Selection method data for resindex selection keyword.

gmx_ana_selmethod_t sm_resname

Initial value:

= {
    "resname", STR_VALUE,  1 , 0,       nullptr,           nullptr, nullptr,
    nullptr,   nullptr,   nullptr,      nullptr, &evaluate_resname, nullptr,
}

Selection method data for resname selection keyword.

gmx_ana_selmethod_t sm_resnr

Initial value:

= {
    "resnr",      INT_VALUE,
     1 , 0,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      nullptr,
    nullptr,      &evaluate_resnr,
    nullptr,      { nullptr, helptitle_resindex, asize(help_resindex), help_resindex }
}

Selection method data for resnr selection keyword.

gmx_ana_selmethod_t sm_x

Initial value:

= {
    "x",     REAL_VALUE,  4 , 0,       nullptr, nullptr,     nullptr,
    nullptr, nullptr,    nullptr,       nullptr, nullptr, &evaluate_x,
}

Selection method data for x selection keyword.

gmx_ana_selmethod_t sm_y

Initial value:

= {
    "y",     REAL_VALUE,  4 , 0,       nullptr, nullptr,     nullptr,
    nullptr, nullptr,    nullptr,       nullptr, nullptr, &evaluate_y,
}

Selection method data for y selection keyword.

gmx_ana_selmethod_t sm_z

Initial value:

= {
    "z",     REAL_VALUE,  4 , 0,       nullptr, nullptr,     nullptr,
    nullptr, nullptr,    nullptr,       nullptr, nullptr, &evaluate_z,
}

Selection method data for z selection keyword.