Namespaces
namespace	bond
	Functions for bond-related analyses.

Functions
std::vector< std::vector< int > >	bond::populateHbonds (std::string filename, molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &nList, int targetFrame, int Htype, double distCutoff=2.42, double angleCutoff=30.0)
std::vector< std::vector< int > >	bond::populateHbondsWithInputClouds (molSys::PointCloud< molSys::Point< double >, double > &yCloud, molSys::PointCloud< molSys::Point< double >, double > &hCloud, const std::vector< std::vector< int > > &nList, double distCutoff=2.42, double angleCutoff=30.0)
bool	bond::donatedHydrogenBond (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const molSys::PointCloud< molSys::Point< double >, double > &hCloud, int acceptorIndex, int donorIndex, const std::vector< int > &donorHs, double distCutoff=2.42, double angleCutoff=30.0)
std::vector< std::vector< int > >	bond::populateHbondsFromDonors (molSys::PointCloud< molSys::Point< double >, double > &yCloud, molSys::PointCloud< molSys::Point< double >, double > &hCloud, const std::vector< std::vector< int > > &nList, const std::vector< int > &donorHs, double distCutoff=2.42, double angleCutoff=30.0)
double	bond::getHbondDistanceOH (const molSys::PointCloud< molSys::Point< double >, double > &oCloud, const molSys::PointCloud< molSys::Point< double >, double > &hCloud, int oAtomIndex, int hAtomIndex)
std::vector< std::vector< int > >	bond::populateBonds (const std::vector< std::vector< int > > &nList, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
std::vector< std::vector< int > >	bond::populateBonds (const std::vector< std::vector< int > > &nList, const molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< cage::iceType > &atomTypes)
std::vector< std::vector< int > >	bond::createBondsFromCages (const std::vector< std::vector< int > > &rings, std::vector< cage::Cage > &cageList, cage::cageType type, int &nRings)
std::vector< std::vector< int > >	bond::trimBonds (std::vector< std::vector< int > > bonds)
	Remove duplicate bonds.

Detailed Description

Function Documentation

◆ createBondsFromCages()

std::vector< std::vector< int > > bond::createBondsFromCages	(	const std::vector< std::vector< int > > &	rings,
		std::vector< cage::Cage > &	cageList,
		cage::cageType	type,
		int &	nRings )

Creates a vector of vectors containing bond connectivity information from the rings vector of vectors and cage information

◆ donatedHydrogenBond()

bool bond::donatedHydrogenBond	(	const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const molSys::PointCloud< molSys::Point< double >, double > &	hCloud,
		int	acceptorIndex,
		int	donorIndex,
		const std::vector< int > &	donorHs,
		double	distCutoff = 2.42,
		double	angleCutoff = 30.0 )

Geometric test for one donor-acceptor assignment. donorHs are hCloud indices on the donor. O-O is gen::relDist(yCloud, acceptor, donor). O-H uses gen::relDistFromPoint (dump MIC).

◆ getHbondDistanceOH()

double bond::getHbondDistanceOH	(	const molSys::PointCloud< molSys::Point< double >, double > &	oCloud,
		const molSys::PointCloud< molSys::Point< double >, double > &	hCloud,
		int	oAtomIndex,
		int	hAtomIndex )

Calculates the distance of the hydrogen bond between O and H (of different atoms), given the respective pointClouds and the indices to each atom

◆ populateBonds() [1/2]

std::vector< std::vector< int > > bond::populateBonds	(	const std::vector< std::vector< int > > &	nList,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud )

Create a vector of vectors containing bond connectivity information. May contain duplicates! Gets the bond information from the vector of vectors containing the neighbour list by index

◆ populateBonds() [2/2]

std::vector< std::vector< int > > bond::populateBonds	(	const std::vector< std::vector< int > > &	nList,
		const molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< cage::iceType > &	atomTypes )

Create a vector of vectors containing bond connectivity information Gets the bond information from the vector of vectors containing the neighbour list by index. Bonds between dummy atoms are not filled.

◆ populateHbonds()

std::vector< std::vector< int > > bond::populateHbonds	(	std::string	filename,
		molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	nList,
		int	targetFrame,
		int	Htype,
		double	distCutoff = 2.42,
		double	angleCutoff = 30.0 )

Create a vector of vectors (similar to the neighbour list conventions) containing the hydrogen bond connectivity information. Decides the existence of the hydrogen bond depending on the O–O and O–H vectors from the neighbour list already constructed. The geometric criterion defaults to the water values (acceptor–H distance below 2.42 Angstrom, O-O-H angle below 30 degrees); other hydrogen-bonded systems pass their own thresholds

◆ populateHbondsFromDonors()

std::vector< std::vector< int > > bond::populateHbondsFromDonors	(	molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		molSys::PointCloud< molSys::Point< double >, double > &	hCloud,
		const std::vector< std::vector< int > > &	nList,
		const std::vector< int > &	donorHs,
		double	distCutoff = 2.42,
		double	angleCutoff = 30.0 )

Hydrogen-bond network from an explicit donor-H set. donorHs are hCloud indices; each is paired with the heavy atom that shares its molID. Water callers build donorHs from hAtomMolList (two H per molecule).

◆ populateHbondsWithInputClouds()

std::vector< std::vector< int > > bond::populateHbondsWithInputClouds	(	molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		molSys::PointCloud< molSys::Point< double >, double > &	hCloud,
		const std::vector< std::vector< int > > &	nList,
		double	distCutoff = 2.42,
		double	angleCutoff = 30.0 )

Create a vector of vectors (similar to the neighbour list conventions) containing the hydrogen bond connectivity information. Decides the existence of the hydrogen bond depending on the O–O and O–H vectors from the neighbour list already constructed, taking a PointCloud for the H atoms as input

◆ trimBonds()

std::vector< std::vector< int > > bond::trimBonds ( std::vector< std::vector< int > > bonds )

Remove duplicate bonds.

Namespaces

Functions