Functions for bond-related analyses. More...
Functions | |
| 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) |
| std::vector< std::vector< int > > | populateHbondsWithInputClouds (molSys::PointCloud< molSys::Point< double >, double > *yCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, std::vector< std::vector< int > > nList) |
| double | getHbondDistanceOH (molSys::PointCloud< molSys::Point< double >, double > *oCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, int oAtomIndex, int hAtomIndex) |
| std::vector< std::vector< int > > | populateBonds (std::vector< std::vector< int > > nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
| std::vector< std::vector< int > > | populateBonds (std::vector< std::vector< int > > nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< cage::iceType > atomTypes) |
| std::vector< std::vector< int > > | createBondsFromCages (std::vector< std::vector< int > > rings, std::vector< cage::Cage > *cageList, cage::cageType type, int *nRings) |
| std::vector< std::vector< int > > | trimBonds (std::vector< std::vector< int > > bonds) |
| Remove duplicate bonds. | |
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:
