topo_bulk.hpp File Reference

File containing functions used specific to bulk topological network critera. 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 <order_parameter.hpp>
#include <ring.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
#include <shapeMatch.hpp>

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Namespaces
namespace	ring
	Topological network criteria functions.
namespace	prism3

Functions
int	ring::bulkPolygonRingAnalysis (std::string path, std::vector< std::vector< int > > rings, std::vector< std::vector< int > > nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int maxDepth, int firstFrame)
int	ring::topoBulkAnalysis (std::string path, std::vector< std::vector< int > > rings, std::vector< std::vector< int > > nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int firstFrame, bool onlyTetrahedral=true)
std::vector< int >	ring::findDDC (std::vector< std::vector< int > > rings, std::vector< strucType > *ringType, std::vector< int > listHC, std::vector< cage::Cage > *cageList)
std::vector< int >	ring::findMixedRings (std::vector< std::vector< int > > rings, std::vector< strucType > *ringType, std::vector< int > *listDDC, std::vector< int > *listHC)
std::vector< int >	ring::findHC (std::vector< std::vector< int > > rings, std::vector< strucType > *ringType, std::vector< std::vector< int > > nList, std::vector< cage::Cage > *cageList)
bool	ring::conditionOneDDC (std::vector< std::vector< int > > rings, std::vector< int > *peripheralRings, int iring)
bool	ring::conditionTwoDDC (std::vector< std::vector< int > > rings, std::vector< int > *peripheralRings, int iring)
bool	ring::conditionThreeDDC (std::vector< std::vector< int > > rings, std::vector< int > *peripheralRings)
bool	ring::basalConditions (std::vector< std::vector< int > > nList, std::vector< int > *basal1, std::vector< int > *basal2)
	Tests whether two rings are basal rings (true) or not (false)
bool	ring::basalNeighbours (std::vector< std::vector< int > > nList, std::vector< int > *triplet, int atomOne, int atomTwo)
bool	ring::notNeighboursOfRing (std::vector< std::vector< int > > nList, std::vector< int > *triplet, std::vector< int > *ring)
int	ring::findPrismatic (std::vector< std::vector< int > > rings, std::vector< int > *listHC, std::vector< strucType > *ringType, int iring, int jring, std::vector< int > *prismaticRings)
	Finds the prismatic rings from basal rings iring and jring.
int	ring::getAtomTypesTopoBulk (std::vector< std::vector< int > > rings, std::vector< ring::strucType > ringType, std::vector< cage::iceType > *atomTypes)
int	ring::getStrucNumbers (std::vector< ring::strucType > ringType, std::vector< cage::Cage > cageList, int *numHC, int *numDDC, int *mixedRings, int *prismaticRings, int *basalRings)
	Determines the number of HCs, DDCs, Mixed rings, prismatic and basal rings.
int	prism3::findBulkPrisms (std::vector< std::vector< int > > rings, std::vector< ring::strucType > *ringType, std::vector< std::vector< int > > nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > *rmsdPerAtom, double heightCutoff=8)
	Find out which rings are prisms.
bool	prism3::basalPrismConditions (std::vector< std::vector< int > > nList, std::vector< int > *basal1, std::vector< int > *basal2)
bool	prism3::relaxedPrismConditions (std::vector< std::vector< int > > nList, std::vector< int > *basal1, std::vector< int > *basal2)
bool	prism3::basalRingsSeparation (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< int > basal1, std::vector< int > basal2, double heightCutoff=8)
	Check to see that candidate basal prisms are not really far from each other.

Detailed Description

File containing functions used specific to bulk topological network critera.

Definition in file topo_bulk.hpp.