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
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| 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...
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| static int | mtopGetMoleculeIndex (const gmx_mtop_t *mtop, int globalAtomIndex, int *moleculeBlock) |
| | Returns the global molecule index of a global atom index. More...
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| 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...
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| static real | mtopGetAtomMass (const gmx_mtop_t *mtop, int globalAtomIndex, int *moleculeBlock) |
| | Returns the mass of an atom based on global atom index. More...
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| 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...
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| 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...
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| 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...
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| 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...
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| static void mtopGetAtomAndResidueName |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock, |
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const char ** |
atomName, |
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int * |
residueNumber, |
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const char ** |
residueName, |
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int * |
globalResidueIndex |
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) |
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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
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| [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 void mtopGetAtomAndResidueName |
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const gmx_mtop_t & |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock, |
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const char ** |
atomName, |
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int * |
residueNumber, |
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const char ** |
residueName, |
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int * |
globalResidueIndex |
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) |
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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
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| [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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock |
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) |
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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
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| [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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock |
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) |
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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
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| [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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock |
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) |
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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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock, |
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int * |
moleculeIndex, |
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int * |
atomIndexInMolecule |
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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
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| [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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock |
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) |
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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 |
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const gmx_mtop_t * |
mtop, |
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int |
globalAtomIndex, |
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int * |
moleculeBlock |
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) |
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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
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| [in] | mtop | The molecule topology |
| [in] | globalAtomIndex | The global atom index to look up |
| [in,out] | moleculeBlock | The molecule block index in mtop |
Include dependency graph for mtop_lookup.h:
1.8.5