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| int | topoUnitMatchingBulk (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 printClusters, bool onlyTetrahedral) |
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| Eigen::MatrixXd | buildRefHC (std::string fileName) |
| | Build a reference Hexagonal cage, reading in from a template XYZ file. More...
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| Eigen::MatrixXd | buildRefDDC (std::string fileName) |
| | Build a reference Double-Diamond cage, reading in from a template XYZ file. More...
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| int | shapeMatchHC (molSys::PointCloud< molSys::Point< double >, double > *yCloud, const Eigen::MatrixXd &refPoints, cage::Cage cageUnit, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, std::vector< double > *quat, double *rmsd) |
| | Shape-matching for a target HC. More...
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| int | shapeMatchDDC (molSys::PointCloud< molSys::Point< double >, double > *yCloud, const Eigen::MatrixXd &refPoints, std::vector< cage::Cage > cageList, int cageIndex, std::vector< std::vector< int >> rings, std::vector< double > *quat, double *rmsd) |
| | Shape-matching for a target DDC. More...
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| int | updateRMSDatom (std::vector< std::vector< int >> rings, cage::Cage cageUnit, double rmsd, std::vector< double > *rmsdPerAtom, std::vector< int > *noOfCommonAtoms, std::vector< cage::iceType > atomTypes) |
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| int | averageRMSDatom (std::vector< double > *rmsdPerAtom, std::vector< int > *noOfCommonAtoms) |
| | Average the RMSD per atom. More...
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| std::vector< cage::Cage > | topoBulkCriteria (std::string path, std::vector< std::vector< int >> rings, std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud, int firstFrame, int *numHC, int *numDDC, std::vector< ring::strucType > *ringType) |
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| int | clusterCages (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::string path, std::vector< std::vector< int >> rings, std::vector< cage::Cage > cageList, int numHC, int numDDC) |
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| std::vector< int > | atomsFromCages (std::vector< std::vector< int >> rings, std::vector< cage::Cage > cageList, std::vector< int > clusterCages) |
| | Gets the atoms in the cages of a given cluster. More...
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