API reference#
Public classes and functions, grouped by module. See Concepts for the data model and Score Terms for score-type definitions.
- Top-level API
- Chemical Types
- Parameter Database
- Input and Output
add_metal_coordination()assemble_input()atom_array_from_file()atom_array_from_mol2()cif_from_atom_array()Atom37MappingErrorCanonicalFormCanonicalOrderingPoseBuildContextPreparedAtom37PoseBuilderatom_records_from_coords()atom_records_from_pose_stack()atomworks_from_pose_stack()biotite_from_canonical_form()biotite_from_pose_stack()build_context_from_biotite()canonical_form_from_atomworks()canonical_form_from_biotite()canonical_form_from_pdb()canonical_form_from_pose_stack()canonical_ordering_for_atomworks()canonical_ordering_for_biotite()create_pose_stack_from_sequences()default_canonical_ordering()default_packed_block_types()extended_pose_stack_from_sequences()fetch_pdb()packed_block_types_for_atomworks()packed_block_types_for_biotite()atom37_slot_map_for_ordering()canonical_form_from_atom37()pose_stack_from_atom37()pose_stack_from_canonical_aa_atom37()pose_stack_from_file()pose_stack_from_canonical_form_and_context()prepare_atom37_pose_builder()remove_metal_coordination()pose_stack_from_atom37_and_topology()pose_stack_from_biotite()pose_stack_from_cif()atom_array_from_cif()component_chemistry_from_cif()pose_stack_from_pdb()pose_stack_to_pdb_string()selection_gallery()switchable_view()to_atom_lines()to_pdb()to_pdb_lines()view()write_pose_stack_pdb()
- Kinematics
BondDOFBondDOFTypesCartesianMoveMapCoordArrayDOFMetadataDOFTypesEdgeTypeFoldForestJumpDOFJumpDOFTypesKinDOFKinForestKinForestScanDataKinematicModuleDataMinimizerMapMoveMapNodeTypePoseStackKinematicsModuleconstruct_kin_module_data_for_pose()inverseKin()set_named_torsions()validate_fold_forest()
- Ligands
FragmentConnectionLigandFragmentDefinitionLigandPreparationLigandPreparationErrorOpenBabelUnavailableErrorapply_fragment_connections()build_split_block_mapping()chem_comp_types_from_cif()detect_nonstandard_residues()expand_fragmented_ligands()fragment_ids_from_atom_array()get_chem_comp_type()is_polymer_linking_component_type()polymer_entity_residues()inject_ligand_preparations()inject_params_file()inject_params_files()ligand_smiles_from_atom_array()load_params_file()nonstandard_residue_info_from_mol2()nonstandard_residue_info_from_mol2_block()nonstandard_residue_info_from_smiles_via_mol2()prepare_ligand_from_cif()prepare_ligand_from_mol2()prepare_ligand_from_smiles()prepare_ligands()prepare_polymer_residue()prepare_ligands_from_smiles()prepare_single_ligand()recombine_fragmented_ligands()unsplit_pose_stack()write_params_file()write_params_from_mol2()
- Public constants
- Numerical Utilities
- Optimization
- Packing
- Pose
ConstraintSetInterBlockBondsepPackedBlockTypesannotate_packed_block_types_w_dslf_conn_inds()annotate_packed_block_types_w_kinematic_conns()PoseStackPoseStackBuilderSeqTokenSplitBlockEntrySplitBlockMappingget_named_torsions()get_torsion_names()resolve_block_type_names()smiles_in_tokens()tokenize_sequences()- Public defaults
- Relax
- Scoring
- Analysis Operations
- Score Terms
- Types
CastingConvertAttrsDimNDArrayShapeSubscriptableTypeTensorTensorGroupValidateAttrscat()constructor_convert()convert_args()get_converter()get_validator()like_kwargs()register_converter()register_validator()torch_dtype()union_convert()validate_args()validate_convert()validate_isinstance()
- Utilities
AttrMappingAttrMutableMappingAutoNumberLoggerMixinbind_to_args()classlogger_for()exclusive_cumsum()exclusive_cumsum1d()exclusive_cumsum2d()exclusive_cumsum2d_w_totals()get_all_residue_positions()get_all_segment_positions()ignore_unused_kwargs()just_one()logger_for_class()nvtx_range()qualified_name()resolve_device()u()unique_val()- Public aliases and units
- Tensor utilities