|
| | FilterContacts (contacts, chain_names) |
| |
| | GetContacts (entity, calpha_only, dist_thr=12.0) |
| |
| | _AlignAtomSeqs (seq_1, seq_2) |
| |
| | _FixSelectChainNames (ch_names) |
| |
| | _CleanInputEntity (ent) |
| |
| | _GetCAOnlyEntity (ent) |
| |
| | _GetChemGroups (qs_ent, seqid_thr=95.) |
| |
| | _GetAngles (Rt) |
| |
| | _GetChemGroupsMapping (qs_ent_1, qs_ent_2) |
| |
| | _SelectFew (l, max_elements) |
| |
| | _GetAlignedResidues (qs_ent_1, qs_ent_2, chem_mapping, max_ca_per_chain, clustalw_bin) |
| |
| | _FindSymmetry (qs_ent_1, qs_ent_2, ent_to_cm_1, ent_to_cm_2, chem_mapping) |
| |
| | _GetChainMapping (ent_1, ent_2, symm_1, symm_2, chem_mapping, max_mappings_extensive) |
| |
| | _GetSymmetrySubgroups (qs_ent, ent, chem_groups) |
| |
| | _GetDihedralSubgroups (ent, chem_groups, angles, angle_thr) |
| |
| | _GetCyclicSubgroups (ent, chem_groups, axis, axis_thr) |
| |
| | _ClusterData (data, thr, metric) |
| |
| | _AngleArrayDistance (u, v) |
| |
| | _AxisDistance (u, v) |
| |
| | _GetClosestChain (ent, ref_chain, chains) |
| |
| | _GetClosestChainInterface (ent, ref_chain, chains) |
| |
| | _ValidChainGroup (group, ent) |
| |
| | _LimitChemMapping (chem_mapping, limit_1, limit_2) |
| |
| | _CountSuperpositionsAndMappings (symm_1, symm_2, chem_mapping) |
| |
| | _PermutationOrCombinations (sup1, sup2, chem_mapping) |
| |
| | _ListPossibleMappings (sup1, sup2, chem_mapping) |
| |
| | _CheckClosedSymmetry (ent_1, ent_2, symm_1, symm_2, chem_mapping, sup_thr=4, sup_fract=0.8, find_best=True) |
| |
| | _GetSuperpositionMapping (ent_1, ent_2, chem_mapping, transformation, sup_thr, sup_fract) |
| |
| | _GetMappedRMSD (ent_1, ent_2, chain_mapping, transformation) |
| |
| | _CleanUserSymmetry (symm, ent) |
| |
| | _AreValidSymmetries (symm_1, symm_2) |
| |
| | _GetMappedAlignments (ent_1, ent_2, chain_mapping, res_num_alignment) |
| |
| | _GetMappedResidues (alns) |
| |
| | _GetExtraWeights (contacts, done, mapped_residues) |
| |
| | _GetScores (contacts_1, contacts_2, mapped_residues, chain_mapping) |
| |
| | _weight (dist) |
| |
| | _GetQsSuperposition (alns) |
| |
| | _AddResidue (edi, res, rnum, chain, calpha_only) |
| |
| | _MergeAlignedChains (alns, ent_1, ent_2, calpha_only, penalize_extra_chains) |
| |
