|
| | _CSel (ent, cnames) |
| |
| | _GetAlnPropsTwo (aln) |
| |
| | _GetAlnPropsOne (aln) |
| |
| | _GetRefMdlAlns (ref_chem_groups, ref_chem_group_msas, mdl_chem_groups, mdl_chem_group_alns, pairs=None) |
| |
| | _CheckOneToOneMapping (ref_chains, mdl_chains) |
| |
| | _lDDTNaive (trg, mdl, inclusion_radius, thresholds, chem_groups, chem_mapping, ref_mdl_alns, n_max_naive) |
| |
| | _GetSeeds (ref_chem_groups, mdl_chem_groups, mapped_ref_chains=set(), mapped_mdl_chains=set()) |
| |
| | _lDDTGreedyFull (the_greed) |
| |
| | _lDDTGreedyBlock (the_greed, seed_size, blocks_per_chem_group) |
| |
| | _QSScoreNaive (trg, mdl, chem_groups, chem_mapping, ref_mdl_alns, contact_d, n_max_naive) |
| |
| | _QSScoreGreedyFull (the_greed) |
| |
| | _QSScoreGreedyBlock (the_greed, seed_size, blocks_per_chem_group) |
| |
| | _SingleRigidRMSD (initial_transforms, initial_mappings, chem_groups, chem_mapping, trg_group_pos, mdl_group_pos) |
| |
| | _SingleRigidCentroid (initial_transforms, initial_mappings, chem_groups, chem_mapping, trg_group_pos, mdl_group_pos) |
| |
| | _IterativeRigidRMSD (initial_transforms, initial_mappings, chem_groups, chem_mapping, trg_group_pos, mdl_group_pos) |
| |
| | _NaiveRMSD (chem_groups, chem_mapping, trg_group_pos, mdl_group_pos, n_max_naive) |
| |
| | _GetRefPos (trg, mdl, trg_msas, mdl_alns, max_pos=None) |
| |
| | _GetBBPos (ent) |
| |
| | _GetFullyCoveredIndices (msa) |
| |
| | _RefIndicesToColumnIndices (msa, indices) |
| |
| | _ExtractMSAPos (msa, s_idx, indices, bb) |
| |
| | _NChemGroupMappings (ref_chains, mdl_chains) |
| |
| | _NMappings (ref_chains, mdl_chains) |
| |
| | _NMappingsWithin (ref_chains, mdl_chains, max_mappings) |
| |
| | _RefSmallerGenerator (ref_chains, mdl_chains) |
| |
| | _RefLargerGenerator (ref_chains, mdl_chains) |
| |
| | _RefEqualGenerator (ref_chains, mdl_chains) |
| |
| | _RefEmptyGenerator (ref_chains, mdl_chains) |
| |
| | _ConcatIterators (iterators) |
| |
| | _ChainMappings (ref_chains, mdl_chains, n_max=None) |
| |
| | _GetSuperposition (pos_one, pos_two, iterative) |
| |
