API reference#
The reference groups TMol’s public classes and functions by modeling task. Start with Pose, Input and Output, and Scoring; the Score Terms page maps every score type to its implementation. For an architectural overview and tensor conventions, see Architecture and Data model and conventions.
- Top-level API
- Chemical Types
- Parameter Database
- Input and Output
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()canonical_ordering_for_openfold()canonical_ordering_for_rosettafold2()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()packed_block_types_for_openfold()packed_block_types_for_rosettafold2()pose_stack_from_atomworks()prepare_pose_stack_from_atom37()pose_stack_from_atom37_and_biotite()pose_stack_from_biotite()pose_stack_from_openfold()pose_stack_from_pdb()pose_stack_from_rosettafold2()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()detect_nonstandard_residues()expand_fragmented_ligands()fragment_ids_from_atom_array()get_chem_comp_type()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_ligands_from_smiles()prepare_single_ligand()read_params_file()recombine_fragmented_ligands()unsplit_pose_stack()write_params_file()write_params_from_mol2()
- Public constants
- Numerical Utilities
- Optimization
- Packing
- Pose
- 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