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
	ring
	Topological network criteria functions.
	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) More...
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. More...
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. More...
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. More...
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. More...

Detailed Description

File containing functions used specific to bulk topological network critera.

Definition in file topo_bulk.hpp.