| adjacent_lists_ | protocols::cluster::calibur::Clustering | |
| allocateSpaceForRMSD(int len) | protocols::cluster::calibur::Clustering | |
| autoAdjustPercentile | protocols::cluster::calibur::Clustering | |
| auxClustering() | protocols::cluster::calibur::Clustering | |
| auxiliary_clusters_ | protocols::cluster::calibur::Clustering | |
| bestClusMargin | protocols::cluster::calibur::Clustering | |
| bestClusSize | protocols::cluster::calibur::Clustering | |
| buildAdjacentLists() | protocols::cluster::calibur::Clustering | |
| CLU_RADIUS | protocols::cluster::calibur::Clustering | |
| cluster() | protocols::cluster::calibur::Clustering | |
| Clustering() | protocols::cluster::calibur::Clustering | |
| coord1 | protocols::cluster::calibur::Clustering | |
| coord2 | protocols::cluster::calibur::Clustering | |
| destroyRandomDecoys(StringVec const &, std::vector< StruOP > const &) | protocols::cluster::calibur::Clustering | |
| EST_THRESHOLD | protocols::cluster::calibur::Clustering | |
| estD(int i, int j) | protocols::cluster::calibur::Clustering | |
| estD(Stru const &a, Stru const &b) | protocols::cluster::calibur::Clustering | |
| estimateDist(StringVec const &, int, int, core::Real, core::Real &, core::Real &, core::Real &, core::Real &) | protocols::cluster::calibur::Clustering | |
| estimateDist(std::vector< StruOP > const &, core::Real, core::Real &, core::Real &, core::Real &, core::Real &) | protocols::cluster::calibur::Clustering | |
| eucD(int i, int j) | protocols::cluster::calibur::Clustering | |
| FILTER_MODE | protocols::cluster::calibur::Clustering | |
| findDecoyWithMostNeighbors() | protocols::cluster::calibur::Clustering | |
| findLargestClusters() | protocols::cluster::calibur::Clustering | |
| get_neighbor_list(std::vector< StruOP > const &, StringVec const &, int, std::vector< std::vector< core::Real > > &nbors) | protocols::cluster::calibur::Clustering | |
| get_neighbor_list(std::vector< StruOP > const &, int, core::Real &, core::Real &, std::vector< std::vector< core::Real > > &nbors) | protocols::cluster::calibur::Clustering | |
| get_threshold(std::vector< std::vector< core::Real > > const &nbors, int, int, int, int, core::Real, core::Real) | protocols::cluster::calibur::Clustering | |
| getPDBs(StringVec &, std::vector< StruOP > &, std::vector< int > const &, int) | protocols::cluster::calibur::Clustering | |
| getRandomDecoyNames(StringVec const &, int) | protocols::cluster::calibur::Clustering | |
| getThresholdAndDecoys() | protocols::cluster::calibur::Clustering | |
| initialize(std::string const &filename, core::Real threshold) | protocols::cluster::calibur::Clustering | |
| initRef(int *index) | protocols::cluster::calibur::Clustering | |
| listAdjacentLists() | protocols::cluster::calibur::Clustering | |
| mCen | protocols::cluster::calibur::Clustering | |
| mCluCen | protocols::cluster::calibur::Clustering | |
| mD2C | protocols::cluster::calibur::Clustering | |
| mFinalClusters | protocols::cluster::calibur::Clustering | |
| mFinalDecoy | protocols::cluster::calibur::Clustering | |
| mInputFileName | protocols::cluster::calibur::Clustering | |
| mLen | protocols::cluster::calibur::Clustering | |
| mRemainingSize | protocols::cluster::calibur::Clustering | |
| n_pdbs_ | protocols::cluster::calibur::Clustering | |
| names_ | protocols::cluster::calibur::Clustering | |
| num_neighbors_ | protocols::cluster::calibur::Clustering | |
| PDBs_ | protocols::cluster::calibur::Clustering | |
| pref_ref_use_first_few_decoys | protocols::cluster::calibur::Clustering | |
| pref_use_scud | protocols::cluster::calibur::Clustering | |
| pref_use_sig | protocols::cluster::calibur::Clustering | |
| readDecoyNames() | protocols::cluster::calibur::Clustering | |
| readDecoys(StringVec const &, std::vector< StruOP > const &) | protocols::cluster::calibur::Clustering | |
| readDecoys(StringVec const &) | protocols::cluster::calibur::Clustering | |
| realignDecoys(int ref) | protocols::cluster::calibur::Clustering | |
| refBound(int i, int j, core::Real &lower, core::Real &upper) | protocols::cluster::calibur::Clustering | |
| references_ | protocols::cluster::calibur::Clustering | |
| reinitialize(StringVec const &, std::vector< StruOP > const &, core::Real const threshold) | protocols::cluster::calibur::Clustering | |
| remaining_list_ | protocols::cluster::calibur::Clustering | |
| remaining_list_index_ | protocols::cluster::calibur::Clustering | |
| removeDecoys(AdjacentList &adj) | protocols::cluster::calibur::Clustering | |
| result_coords | protocols::cluster::calibur::Clustering | |
| showClusters(int) | protocols::cluster::calibur::Clustering | |
| spaceAllocatedForRMSD | protocols::cluster::calibur::Clustering | |
| superimposeAndReplace(std::vector< core::Real > &coor1, std::vector< core::Real > &coor2) | protocols::cluster::calibur::Clustering | |
| THRESHOLD | protocols::cluster::calibur::Clustering | |
| trueD(Stru const &a, Stru const &b) | protocols::cluster::calibur::Clustering | |
| trueD(int i, int j) | protocols::cluster::calibur::Clustering | |
| xFactor | protocols::cluster::calibur::Clustering | |
| xPercentile | protocols::cluster::calibur::Clustering | |
1.8.7