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BALL::PoseClustering Member List

This is the complete list of members for BALL::PoseClustering, including all inherited members.

althausCompute_() | BALL::PoseClustering | protected
applyTransformation2System(Index i, System &target_system) | BALL::PoseClustering |
atom_bijection_ | BALL::PoseClustering | protected
BALL_CREATE(PoseClustering) | BALL::PoseClustering |
base_conformation_ | BALL::PoseClustering | protected
base_system_ | BALL::PoseClustering | protected
clear_() | BALL::PoseClustering | protected
clinkInner_(int current_level) | BALL::PoseClustering | protected
cluster_representatives_ | BALL::PoseClustering | protected
cluster_scores_ | BALL::PoseClustering | protected
cluster_tree_ | BALL::PoseClustering | protected
clusters_ | BALL::PoseClustering | protected
ClusterTree typedef | BALL::PoseClustering |
ClusterTreeNode typedef | BALL::PoseClustering |
collectClusterBelow_(ClusterTreeNode const &v) | BALL::PoseClustering | protected
com_ | BALL::PoseClustering | protected
compute() | BALL::PoseClustering |
computeCenterOfMasses_() | BALL::PoseClustering | protected
computeCompleteLinkageRMSD(Index i, Options options, bool initialize=true) | BALL::PoseClustering |
computeCovarianceMatrix(System const &system, Index rmsd_level_of_detail=C_ALPHA) | BALL::PoseClustering | static
computeWardDistance_(ClusterTreeNode i, ClusterTreeNode j, Index rmsd_type) | BALL::PoseClustering | protected
convertSnaphots2Transformations() | BALL::PoseClustering |
convertTransformations2Snaphots() | BALL::PoseClustering |
covariance_matrix_ | BALL::PoseClustering | protected
current_set_ | BALL::PoseClustering | protected
delete_conformation_set_ | BALL::PoseClustering | protected
deserializeWardClusterTree(std::istream &in, bool binary=false) | BALL::PoseClustering |
exportClusterTreeToJSON(std::ostream &out) | BALL::PoseClustering |
exportToJSONDFS_(ClusterTreeNode const &current, String &result) | BALL::PoseClustering | protected
exportWardClusterTreeToGraphViz(std::ostream &out) | BALL::PoseClustering |
extractClustersForThreshold(float threshold, Size min_size=0) | BALL::PoseClustering |
extractNBestClusters(Size n) | BALL::PoseClustering |
filterClusters(Size min_size=1) | BALL::PoseClustering |
findClusterRepresentative(Index i) | BALL::PoseClustering |
getAtomBijection() | BALL::PoseClustering | inline
getAtomBijection() const | BALL::PoseClustering | inline
getCentersOfMass() | BALL::PoseClustering | inline
getCentersOfMass() const | BALL::PoseClustering | inline
getCluster(Index i) const | BALL::PoseClustering |
getCluster(Index i) | BALL::PoseClustering |
getClusterConformationSet(Index i) | BALL::PoseClustering |
getClusterRepresentative(Index i) | BALL::PoseClustering |
getClusterRMSD_(Index i, Index j, Index rmsd_type) | BALL::PoseClustering | protected
getClusterScore(Index i) const | BALL::PoseClustering |
getClusterSize(Index i) const | BALL::PoseClustering |
getConformationSet() const | BALL::PoseClustering | inline
getConformationSet() | BALL::PoseClustering | inline
getNumberOfClusters() const | BALL::PoseClustering | inline
getNumberOfPoses() const | BALL::PoseClustering | inline
getPose(Index i) const | BALL::PoseClustering |
getPoses() const | BALL::PoseClustering | inline
getReducedConformationSet() | BALL::PoseClustering |
getRigidRMSD(Eigen::Vector3f const &t_ab, Eigen::Matrix3f const &M_ab, Eigen::Matrix3f const &covariance_matrix) | BALL::PoseClustering | static
getRigidTransformations() const | BALL::PoseClustering | inline
getRMSD_(Index i, Index j, Index rmsd_type) | BALL::PoseClustering | protected
getScore(const System sys_a, const System sys_b, Options options) const | BALL::PoseClustering |
getSquaredRigidRMSD(Eigen::Vector3f const &t_ab, Eigen::Matrix3f const &M_ab, Eigen::Matrix3f const &covariance_matrix) | BALL::PoseClustering | static
getSystem() const | BALL::PoseClustering |
getSystem() | BALL::PoseClustering |
has_rigid_transformations_ | BALL::PoseClustering | protected
initWardDistance_(Index rmsd_type) | BALL::PoseClustering | protected
isExcludedByLevelOfDetail_(Atom const *atom, Index rmsd_level_of_detail) | BALL::PoseClustering | protected static
lambda_ | BALL::PoseClustering | protected
linearSpaceCompute_() | BALL::PoseClustering | protected
mu_ | BALL::PoseClustering | protected
nearestNeighborChainCompute_() | BALL::PoseClustering | protected
number_of_selected_atoms_ | BALL::PoseClustering | protected
options | BALL::PoseClustering |
pairwise_scores_ | BALL::PoseClustering | protected
pi_ | BALL::PoseClustering | protected
PoseClustering() | BALL::PoseClustering |
PoseClustering(ConformationSet *poses, float rmsd) | BALL::PoseClustering |
PoseClustering(System const &base_system, String transformation_file_name) | BALL::PoseClustering |
poses_ | BALL::PoseClustering | protected
precomputeAtomBijection_() | BALL::PoseClustering | protected
printCluster_(Size i, std::ostream &out=std::cout) const | BALL::PoseClustering | protected
printClusters(std::ostream &out=std::cout) const | BALL::PoseClustering |
printClusterScores(std::ostream &out=std::cout) | BALL::PoseClustering |
printVariables_(int a, int b, double c, int d, double e, int current_level) | BALL::PoseClustering | protected
readTransformationsFromFile_(String filename) | BALL::PoseClustering | protected
refineClustering(Options const &refined_options) | BALL::PoseClustering |
rmsd_level_of_detail_ | BALL::PoseClustering | protected
serializeWardClusterTree(std::ostream &out, bool binary=false) | BALL::PoseClustering |
setBaseSystemAndPoses(System const &base_system, std::vector< PosePointer > const &poses) | BALL::PoseClustering |
setBaseSystemAndTransformations(System const &base_system, String transformation_file_name) | BALL::PoseClustering |
setConformationSet(ConformationSet *new_set, bool precompute_atombijection=false) | BALL::PoseClustering |
setDefaultOptions() | BALL::PoseClustering |
slinkInner_(int current_level) | BALL::PoseClustering | protected
storeSnapShotReferences_() | BALL::PoseClustering | protected
system_i_ | BALL::PoseClustering | protected
system_j_ | BALL::PoseClustering | protected
transformations_ | BALL::PoseClustering | protected
trivialCompute_() | BALL::PoseClustering | protected
updateWardDistance_(ClusterTreeNode parent, ClusterTreeNode i, ClusterTreeNode j, Index rmsd_type) | BALL::PoseClustering | protected
~PoseClustering() | BALL::PoseClustering | virtual