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| std::vector< std::vector< int > > | populateHbonds (std::string filename, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, int targetFrame, int Htype) |
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| double | getHbondDistanceOH (molSys::PointCloud< molSys::Point< double >, double > *oCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, int oAtomIndex, int hAtomIndex) |
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| std::vector< std::vector< int > > | populateBonds (std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
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| std::vector< std::vector< int > > | populateBonds (std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< cage::iceType > atomTypes) |
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| std::vector< std::vector< int > > | createBondsFromCages (std::vector< std::vector< int >> rings, std::vector< cage::Cage > *cageList, cage::cageType type, int *nRings) |
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| std::vector< std::vector< int > > | trimBonds (std::vector< std::vector< int >> bonds) |
| | Remove duplicate bonds. More...
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Functions for bond-related analyses.
This namespace contains functions that are used for determining the hydrogen bonds, or lists of bonded atoms for write-outs to data files and visualization.
These functions are distinct from the neighbour-list building functions. Bonds can be built from cages, ring lists etc.
Hydrogen bonds are determined using a strict geometric criterion.
A hydrogen bond between two water molecules exists when:
- The distance between the donor oxygen atom and the acceptor hydrogen atom is less than 2.42 Angstrom
- The angle between the O–O vector and the O-H vector should be less than 30 degrees
Changelog