API Documentation

• The core package
  • The Molecule module
    • Making Molecules
    • Modifying Molecules
    • Connecting Molecules
    • Molecule
    • connect()
    • make_smiles()
    • molecule()
    • phosphorylate()
    • polymerize()
    • query_pubchem()
    • read_cif()
    • read_pdb()
    • read_smiles()
    • write_cif()
    • write_pdb()
  • The Linkage module
    • Linkage definitions
    • Linkage
    • linkage()
    • patch()
    • recipe()
  • The base module
    • BaseEntity
    • Atom
    • Bond
    • Chain
    • Model
    • Residue
    • Structure
    • biobuild Molecule
    • biobuild Linkage
    • biobuild base
    • biobuild base_classes
• The resources package
  • PDBe Compounds
  • PubChem
  • CHARMM
  • CHARMMTopology
    • CHARMMTopology.id
    • CHARMMTopology.patches
    • CHARMMTopology.add_patch()
    • CHARMMTopology.from_json()
    • CHARMMTopology.get_patch()
    • CHARMMTopology.has_patch()
    • CHARMMTopology.linkages
    • CHARMMTopology.patches
    • CHARMMTopology.to_json()
  • add_linkage()
  • add_patch()
  • available_linkages()
  • available_patches()
  • export_topology()
  • get_default_topology()
  • get_linkage()
  • get_patch()
  • has_linkage()
  • has_patch()
  • read_topology()
  • restore_default_topology()
  • save_topology()
  • set_default_topology()
  • PDBECompounds
    • PDBECompounds.add()
    • PDBECompounds.formulas
    • PDBECompounds.from_file()
    • PDBECompounds.from_json()
    • PDBECompounds.get()
    • PDBECompounds.has_residue()
    • PDBECompounds.ids
    • PDBECompounds.load()
    • PDBECompounds.merge()
    • PDBECompounds.relabel_atoms()
    • PDBECompounds.remove()
    • PDBECompounds.save()
    • PDBECompounds.to_json()
    • PDBECompounds.translate_ids_1_to_3()
    • PDBECompounds.translate_ids_3_to_1()
  • add_compound()
  • export_compounds()
  • get_compound()
  • get_default_compounds()
  • has_compound()
  • load_all_compounds()
  • load_amino_acids()
  • load_lipids()
  • load_nucleotides()
  • load_small_molecules()
  • load_sugars()
  • read_compounds()
  • restore_default_compounds()
  • save_as_default_compounds()
  • save_compounds()
  • set_default_compounds()
  • subset_compounds_by_types()
  • unload_all_compounds()
  • unload_amino_acids()
  • unload_by_types()
  • unload_lipids()
  • unload_nucleotides()
  • unload_small_molecules()
  • unload_sugars()
  • pubchem_to_cif()
  • query()
• The optimizers package
  • The Rotatron Environments
    • DistanceRotatron
    • concatenation_function_linear()
    • concatenation_function_no_pushback()
    • concatenation_function_no_unfold()
    • concatenation_function_with_penalty()
    • simple_concatenation_function()
    • MVN()
    • OverlapRotatron
    • jensen_shannon_overlap()
    • ForceFieldRotatron
    • Rotatron
  • Optimization algorithms
    • swarm_optimize()
    • genetic_optimize()
    • anneal_optimize()
    • scipy_optimize()
  • Optimization utilities
    • apply_solution()
    • auto_algorithm()
    • optimize()
• The visual module
  • Visualizing from the Molecule class
  • Visualizing with Plotly
    • PlotlyViewer3D
    • MoleculeViewer3D
    • AtomGraphViewer3D
    • ResidueGraphViewer3D
  • Visualizing with NglView
    • NglViewer
  • Visualizing with 3DMol.js
    • Py3DmolViewer
  • Visualizing 2D molecules
    • Chem2DViewer
• The graphs package
  • The BaseGraph module
    • BaseGraph
  • The AtomGraph module
    • AtomGraph
  • The ResidueGraph module
    • ResidueGraph
• The structural package
  • Basic structural operations
    • angle_between()
    • atom_make_full_id()
    • bond_angle()
    • bond_vector()
    • center_of_gravity()
    • chain_make_full_id()
    • compute_angle()
    • compute_dihedral()
    • compute_distance()
    • compute_torsional()
    • distance_between()
    • make_empty_structure()
    • model_make_full_id()
    • norm_vector()
    • plane_vector()
    • rename_residue()
    • residue_make_full_id()
    • set_full_id()
    • vector_between()
  • Inferring structural properties
    • AutoLabel
    • apply_reference_bonds()
    • atoms_in_area()
    • autolabel()
    • compute_atom1_from_others()
    • compute_atom4_from_others()
    • compute_internal_coordinates()
    • compute_outlier_atoms()
    • compute_residue_radius()
    • find_clashes()
    • infer_bonds()
    • infer_residue_connections()
    • infer_surface_residues()
    • relabel_hydrogens()
    • sample_atoms_around_reference()
    • vet_structure()
    • make_smiles()
    • read_smiles()
  • Assembling molecules
    • PatchError
    • Patcher
    • patch()
    • Stitcher
    • stitch()
    • Connector
  • Graph neighborhood in molecular structures
    • AtomNeighborhood
    • Neighborhood
    • Quartet
    • ResidueNeighborhood
    • compute_quartets()
    • compute_triplets()
    • generate_quartets()
    • generate_triplets()
• The utils package
  • Default settings and constants
    • BASE
    • RESOURCES
    • DEFAULT_BOND_LENGTH
    • DEFAULT_CHARMM_TOPOLOGY_FILE
    • DEFAULT_PDBE_COMPONENT_FILES
    • DEFAULT_SASA_N
    • DEFAULT_SASA_PROBE_RADIUS
    • get_default_instance()
    • set_default_instance()
  • File-format related utilities
    • OpenMMBioPythonConverter
    • PDBIO
    • PybelBioPythonConverter
    • RDKITBiopythonConverter
    • is_biopython()
    • is_pybel()
    • is_rdkit()
    • left_adjust()
    • make_atoms_table()
    • make_connect_table()
    • parse_connect_lines()
    • right_adjust()
    • write_connect_lines()
    • write_pdb()
    • make_bond_lines()
    • make_bond_table()
    • make_header()
    • parse_bond_table()
    • write_bond_table()
  • Structure-related utilities
    • InternalCoordinates
    • AbstractAtom
    • AbstractBond
    • AbstractEntity
    • AbstractEntity_with_IC
  • Other auxiliary utilities
    • DummyBar
    • DummyStructure
    • chain_id_maker()
    • change_suffix()
    • filename_to_id()
    • load_pickle()
    • make_formula()
    • remove_nonprintable()
    • save_pickle()