bond Namespace Reference

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)
 
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. More...
 

Detailed Description

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:

  1. The distance between the donor oxygen atom and the acceptor hydrogen atom is less than 2.42 Angstrom
  2. The angle between the O–O vector and the O-H vector should be less than 30 degrees

Changelog