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 <cmath>
#include <fstream>
#include <iostream>
#include <iterator>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
#include <cage.hpp>
#include <mol_sys.hpp>
#include <seams_input.hpp>

Go to the source code of this file.

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

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

Definition in file bond.hpp.