gmx::anonymous_namespace{h5md_topologyutils.cpp} Namespace Reference

Functions
BondPairs	deduceBondsFromMolecule (const gmx_moltype_t &moltype)
BondPairs	deduceDisulfideBondsFromMolecule (const gmx_moltype_t &molType)
void	cacheBondForNBlocks (const BondPairs &bonds, std::vector< int64_t > *bondsBuffer, const int32_t numMols, const int32_t atomsPerMol, const std::optional< IndexMap > &selectedAtomsIndexMap, const int64_t globalOffset)
	Cache bonds for numMols of molecule blocks into bondsBuffer. More...

Variables
constexpr int	c_sulfurAtomicNumber = 16
	Atomic number for sulfur element.

Function Documentation

void gmx::anonymous_namespace{h5md_topologyutils.cpp}::cacheBondForNBlocks	(	const BondPairs &	bonds,
		std::vector< int64_t > *	bondsBuffer,
		const int32_t	numMols,
		const int32_t	atomsPerMol,
		const std::optional< IndexMap > &	selectedAtomsIndexMap,
		const int64_t	globalOffset
	)

Cache bonds for numMols of molecule blocks into bondsBuffer.

This is an internal utility function when iterating over molecule types

Parameters

[in]	bonds	The bond pairs to cache.
[out]	bondsBuffer	The buffer to store the cached bonds.
[in]	numMols	The number of molecule blocks.
[in]	atomsPerMol	The number of atoms per molecule.
[in]	selectedAtomsIndexMap	The index map of the selected atoms, not provided means considering all atoms. Providing an empty map throws an internal error.
[in]	globalOffset	The global index offset for the current molecule type.