#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"

Include dependency graph for mtop_lookup.h:

Description

This file contains inline functions to look up atom information using the global atom index.

Author: Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
static void	mtopGetMolblockIndex (const gmx_mtop_t &mtop, int globalAtomIndex, int moleculeBlock, int moleculeIndex, int *atomIndexInMolecule)
	Look up the molecule block and other indices of a global atom index. More...

static int	mtopGetMoleculeIndex (const gmx_mtop_t &mtop, int globalAtomIndex, int *moleculeBlock)
	Returns the global molecule index of a global atom index. More...

static const t_atom &	mtopGetAtomParameters (const gmx_mtop_t &mtop, int globalAtomIndex, int *moleculeBlock)
	Returns the atom data for an atom based on global atom index. More...

static real	mtopGetAtomMass (const gmx_mtop_t &mtop, int globalAtomIndex, int *moleculeBlock)
	Returns the mass of an atom based on global atom index. More...

static void	mtopGetAtomAndResidueName (const gmx_mtop_t &mtop, int globalAtomIndex, int moleculeBlock, const char atomName, int residueNumber, const char *residueName, int globalResidueIndex)
	Look up the atom and residue name and residue number and index of a global atom index. More...

static const t_resinfo &	mtopGetResidueInfo (const gmx_mtop_t &mtop, int globalAtomIndex, int *moleculeBlock)
	Returns residue information for an atom based on global atom index. More...

static const t_pdbinfo &	mtopGetAtomPdbInfo (const gmx_mtop_t &mtop, int globalAtomIndex, int *moleculeBlock)
	Returns PDB information for an atom based on global atom index. More...

Function Documentation

static void mtopGetAtomAndResidueName	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock,
		const char **	atomName,
		int *	residueNumber,
		const char **	residueName,
		int *	globalResidueIndex
	)

inlinestatic

Look up the atom and residue name and residue number and index of a global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time. Note that this function does a (somewhat expensive) lookup. If you want to look up data sequentially for all atoms in a molecule or the system, use one of the mtop loop functionalities.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`
[out]	atomName	The atom name, input can be NULL
[out]	residueNumber	The residue number, input can be NULL
[out]	residueName	The residue name, input can be NULL
[out]	globalResidueIndex	The gobal residue index, input can be NULL

static real mtopGetAtomMass	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock
	)

inlinestatic

Returns the mass of an atom based on global atom index.

Returns that A-state mass of the atom with global index globalAtomIndex. The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`

static const t_atom& mtopGetAtomParameters	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock
	)

inlinestatic

Returns the atom data for an atom based on global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`

static const t_pdbinfo& mtopGetAtomPdbInfo	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock
	)

inlinestatic

Returns PDB information for an atom based on global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`

static void mtopGetMolblockIndex	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock,
		int *	moleculeIndex,
		int *	atomIndexInMolecule
	)

inlinestatic

Look up the molecule block and other indices of a global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`
[out]	moleculeIndex	The index of the molecule in the block, can be NULL
[out]	atomIndexInMolecule	The atom index in the molecule, can be NULL

static int mtopGetMoleculeIndex	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock
	)

inlinestatic

Returns the global molecule index of a global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`

static const t_resinfo& mtopGetResidueInfo	(	const gmx_mtop_t &	mtop,
		int	globalAtomIndex,
		int *	moleculeBlock
	)

inlinestatic

Returns residue information for an atom based on global atom index.

The atom index has to be in range: 0 <= globalAtomIndex < mtop->natoms. The input value of moleculeBlock should be in range. Use 0 as starting value. For subsequent calls to this function, e.g. in a loop, pass in the previously returned value for best performance. Atoms in a group tend to be in the same molecule(block), so this minimizes the search time.

Parameters

[in]	mtop	The molecule topology
[in]	globalAtomIndex	The global atom index to look up
[in,out]	moleculeBlock	The molecule block index in `mtop`

Description

Functions

Function Documentation