bond.hpp File Reference

File for bond-related analyses (hydrogen bonds, bonded atoms for data file write-outs etc.). More...

#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <math.h>
#include <memory>
#include <sstream>
#include <string>
#include <sys/stat.h>
#include <vector>
#include <cage.hpp>
#include <mol_sys.hpp>
#include <seams_input.hpp>

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Namespaces
	bond
	Functions for bond-related analyses.

Functions
std::vector< std::vector< int > >	bond::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 > >	bond::populateHbondsWithInputClouds (molSys::PointCloud< molSys::Point< double >, double > *yCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, std::vector< std::vector< int >> nList)
double	bond::getHbondDistanceOH (molSys::PointCloud< molSys::Point< double >, double > *oCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, int oAtomIndex, int hAtomIndex)
std::vector< std::vector< int > >	bond::populateBonds (std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
std::vector< std::vector< int > >	bond::populateBonds (std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< cage::iceType > atomTypes)
std::vector< std::vector< int > >	bond::createBondsFromCages (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. More...

Detailed Description

File for bond-related analyses (hydrogen bonds, bonded atoms for data file write-outs etc.).

Definition in file bond.hpp.