Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | X A AbstractAtom (class in biobuild.utils.abstract) AbstractBond (class in biobuild.utils.abstract) AbstractEntity (class in biobuild.utils.abstract) AbstractEntity_with_IC (class in biobuild.utils.abstract) add() (biobuild.core.base_classes.Chain method), [1] (biobuild.core.base_classes.Model method), [1] (biobuild.core.base_classes.Residue method), [1] (biobuild.resources.pdbe_compounds.PDBECompounds method) (biobuild.utils.visual.PlotlyViewer3D method) add_atom() (biobuild.utils.abstract.AbstractEntity method) add_atomic_bonds() (biobuild.graphs.ResidueGraph method) add_atoms() (biobuild.core.entity.BaseEntity method), [1] add_bond() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.abstract.AbstractEntity method) add_bonds() (biobuild.core.entity.BaseEntity method), [1] add_chains() (biobuild.core.entity.BaseEntity method), [1] add_compound() (in module biobuild.resources.pdbe_compounds) add_delete() (biobuild.core.Linkage.Linkage method), [1] add_ic() (biobuild.utils.abstract.AbstractEntity_with_IC method) add_id_to_delete() (biobuild.core.Linkage.Linkage method), [1] add_internal_coordinates() (biobuild.core.Linkage.Linkage method), [1] (biobuild.utils.abstract.AbstractEntity_with_IC method) add_linkage() (in module biobuild.resources.charmm) add_patch() (biobuild.resources.charmm.CHARMMTopology method) (in module biobuild.resources.charmm) add_residues() (biobuild.core.entity.BaseEntity method), [1] adjust_indexing() (biobuild.core.entity.BaseEntity method), [1] altloc (biobuild.core.base_classes.Atom attribute), [1] angle_123 (biobuild.structural.neighbors.Quartet property) angle_234 (biobuild.structural.neighbors.Quartet property) angle_between() (in module biobuild.structural.base) angles (biobuild.utils.ic.InternalCoordinates property) anisou_array (biobuild.core.base_classes.Atom attribute), [1] anneal_optimize() (in module biobuild.optimizers.algorithms) apply() (biobuild.structural.patch.Patcher method) (biobuild.structural.stitch.Stitcher method) apply_reference_bonds() (in module biobuild.structural.infer) apply_solution() (in module biobuild.optimizers.utils) apply_standard_bonds() (biobuild.core.entity.BaseEntity method), [1] Atom (class in biobuild.core.base_classes), [1] atom1 (biobuild.core.base_classes.Bond attribute), [1], [2], [3] (biobuild.core.Linkage.Linkage property), [1] (biobuild.structural.neighbors.Quartet property) atom2 (biobuild.core.base_classes.Bond attribute), [1], [2], [3] (biobuild.core.Linkage.Linkage property), [1] (biobuild.structural.neighbors.Quartet property) atom3 (biobuild.structural.neighbors.Quartet property) atom4 (biobuild.structural.neighbors.Quartet property) atom_make_full_id() (in module biobuild.structural.base) AtomGraph (class in biobuild.graphs) AtomGraphViewer3D (class in biobuild.utils.visual) atomic_bonds (biobuild.graphs.ResidueGraph property) AtomNeighborhood (class in biobuild.structural.neighbors) atoms (biobuild.core.entity.BaseEntity property), [1] (biobuild.core.Linkage.Linkage attribute), [1] (biobuild.graphs.BaseGraph.BaseGraph property) (biobuild.structural.neighbors.AtomNeighborhood property) (biobuild.structural.neighbors.Quartet property) (biobuild.utils.abstract.AbstractBond property) (biobuild.utils.abstract.AbstractEntity property) (biobuild.utils.ic.InternalCoordinates property) atoms_in_area() (in module biobuild.structural.infer) attach() (biobuild.core.Molecule.Molecule method), [1] attach_residue (biobuild.core.entity.BaseEntity property), [1] auto_algorithm() (in module biobuild.optimizers.utils) AutoLabel (class in biobuild.structural.infer) autolabel() (biobuild.core.entity.BaseEntity method), [1] (biobuild.structural.infer.AutoLabel method) (in module biobuild.structural.infer) available_linkages() (in module biobuild.resources.charmm) available_patches() (in module biobuild.resources.charmm) B BASE (in module biobuild.utils.constants) BaseEntity (class in biobuild.core.entity), [1] BaseGraph (class in biobuild.graphs.BaseGraph) best (biobuild.optimizers.Rotatron.Rotatron property) bfactor (biobuild.core.base_classes.Atom attribute), [1] biobuild.core module biobuild.core.base_classes module, [1] biobuild.core.entity module biobuild.core.Linkage module, [1] biobuild.core.Molecule module, [1] biobuild.optimizers.DistanceRotatron module biobuild.optimizers.ForceFieldRotatron module biobuild.optimizers.OverlapRotatron module biobuild.optimizers.Rotatron module biobuild.optimizers.utils module biobuild.resources module biobuild.resources.charmm module biobuild.resources.pdbe_compounds module biobuild.resources.pubchem module biobuild.structural.base module biobuild.structural.connector module biobuild.structural.infer module biobuild.structural.neighbors module biobuild.structural.patch module biobuild.structural.smiles module biobuild.structural.stitch module biobuild.utils.abstract module biobuild.utils.auxiliary module biobuild.utils.cif module biobuild.utils.constants module biobuild.utils.convert module biobuild.utils.defaults module biobuild.utils.ic module biobuild.utils.pdb module biobuild_to_openmm() (biobuild.utils.convert.OpenMMBioPythonConverter method) biobuild_to_pybel() (biobuild.utils.convert.PybelBioPythonConverter method) biopython_to_openmm() (biobuild.utils.convert.OpenMMBioPythonConverter method) biopython_to_pdbio() (biobuild.utils.convert.PDBIO method) biopython_to_rdkit() (biobuild.utils.convert.RDKITBiopythonConverter method) blank() (biobuild.optimizers.Rotatron.Rotatron method) bond (biobuild.core.Linkage.Linkage attribute), [1] (biobuild.core.Linkage.Linkage property), [1] Bond (class in biobuild.core.base_classes), [1] bond_angle() (in module biobuild.structural.base) bond_vector() (in module biobuild.structural.base) bonds (biobuild.core.entity.BaseEntity property), [1] (biobuild.graphs.BaseGraph.BaseGraph property) (biobuild.structural.neighbors.AtomNeighborhood property) (biobuild.structural.neighbors.ResidueNeighborhood property) C carbons (biobuild.structural.infer.AutoLabel property) center_atom (biobuild.structural.neighbors.Quartet property) center_of_gravity() (in module biobuild.structural.base) centers_of_mass() (biobuild.graphs.ResidueGraph method) central_node (biobuild.graphs.BaseGraph.BaseGraph property) Chain (class in biobuild.core.base_classes), [1] chain_id_maker() (in module biobuild.utils.auxiliary) chain_make_full_id() (in module biobuild.structural.base) chains (biobuild.core.entity.BaseEntity property), [1] (biobuild.graphs.BaseGraph.BaseGraph property) change_suffix() (in module biobuild.utils.auxiliary) CHARMMTopology (class in biobuild.resources.charmm) chem2dview() (biobuild.core.entity.BaseEntity method), [1] Chem2DViewer (class in biobuild.utils.visual) child_dict (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Model attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] (biobuild.core.base_classes.Structure attribute), [1] child_list (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Model attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] (biobuild.core.base_classes.Structure attribute), [1] cleanup() (biobuild.utils.convert.PDBIO method) compute_angle() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.base) compute_angles() (biobuild.core.entity.BaseEntity method), [1] compute_atom1_from_others() (in module biobuild.structural.infer) compute_atom4_from_others() (in module biobuild.structural.infer) compute_dihedral() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.base) compute_dihedrals() (biobuild.core.entity.BaseEntity method), [1] compute_distance() (in module biobuild.structural.base) compute_internal_coordinates() (in module biobuild.structural.infer) compute_length() (biobuild.core.base_classes.Bond method), [1] compute_outlier_atoms() (in module biobuild.structural.infer) compute_quartets() (in module biobuild.structural.neighbors) compute_residue_radius() (in module biobuild.structural.infer) compute_torsional() (in module biobuild.structural.base) compute_triplets() (in module biobuild.structural.neighbors) concatenation_function_linear() (in module biobuild.optimizers.DistanceRotatron) concatenation_function_no_pushback() (in module biobuild.optimizers.DistanceRotatron) concatenation_function_no_unfold() (in module biobuild.optimizers.DistanceRotatron) concatenation_function_with_penalty() (in module biobuild.optimizers.DistanceRotatron) connect() (in module biobuild.core.Molecule), [1] Connector (class in biobuild.structural.connector) convert() (biobuild.utils.convert.PybelBioPythonConverter method) coord (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Residue property), [1] copy() (biobuild.core.entity.BaseEntity method), [1] count_atoms() (biobuild.core.entity.BaseEntity method), [1] count_bonds() (biobuild.core.entity.BaseEntity method), [1] count_chains() (biobuild.core.entity.BaseEntity method), [1] count_clashes() (biobuild.core.entity.BaseEntity method), [1] (biobuild.optimizers.DistanceRotatron.DistanceRotatron method) count_residues() (biobuild.core.entity.BaseEntity method), [1] D DEFAULT_BOND_LENGTH (in module biobuild.utils.defaults) DEFAULT_CHARMM_TOPOLOGY_FILE (in module biobuild.utils.defaults) DEFAULT_PDBE_COMPONENT_FILES (in module biobuild.utils.defaults) DEFAULT_SASA_N (in module biobuild.utils.defaults) DEFAULT_SASA_PROBE_RADIUS (in module biobuild.utils.defaults) deletes (biobuild.core.Linkage.Linkage attribute), [1] (biobuild.core.Linkage.Linkage property), [1] dihedral (biobuild.structural.neighbors.Quartet property) direct_edges() (biobuild.graphs.BaseGraph.BaseGraph method) disordered (biobuild.core.base_classes.Residue attribute), [1] disordered_flag (biobuild.core.base_classes.Atom attribute), [1] dist_12 (biobuild.structural.neighbors.Quartet property) dist_13 (biobuild.structural.neighbors.Quartet property) dist_23 (biobuild.structural.neighbors.Quartet property) dist_34 (biobuild.structural.neighbors.Quartet property) distance_between() (in module biobuild.structural.base) DistanceRotatron (class in biobuild.optimizers.DistanceRotatron) double() (biobuild.core.base_classes.Bond method), [1] draw() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.AtomGraph method) (biobuild.graphs.BaseGraph.BaseGraph method) (biobuild.graphs.ResidueGraph method) (biobuild.utils.visual.Chem2DViewer method) draw_atom() (biobuild.utils.visual.PlotlyViewer3D method) draw_atoms() (biobuild.utils.visual.PlotlyViewer3D method) draw_bond() (biobuild.utils.visual.PlotlyViewer3D method) draw_edges() (biobuild.utils.visual.PlotlyViewer3D method) draw_point() (biobuild.utils.visual.PlotlyViewer3D method) draw_points() (biobuild.utils.visual.PlotlyViewer3D method) draw_residues() (biobuild.utils.visual.PlotlyViewer3D method) draw_vector() (biobuild.utils.visual.PlotlyViewer3D method) DummyBar (class in biobuild.utils.auxiliary) DummyStructure (class in biobuild.utils.auxiliary) E element (biobuild.core.base_classes.Atom attribute), [1] (biobuild.utils.abstract.AbstractAtom property) empty() (biobuild.core.Molecule.Molecule class method), [1] energy() (biobuild.optimizers.ForceFieldRotatron.ForceFieldRotatron method) eval() (biobuild.optimizers.DistanceRotatron.DistanceRotatron method) (biobuild.optimizers.ForceFieldRotatron.ForceFieldRotatron method) (biobuild.optimizers.OverlapRotatron.OverlapRotatron method) (biobuild.optimizers.Rotatron.Rotatron method) export_compounds() (in module biobuild.resources.pdbe_compounds) export_topology() (in module biobuild.resources.charmm) F filename_to_id() (in module biobuild.utils.auxiliary) find_atoms() (biobuild.utils.abstract.AbstractBond method) find_clashes() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.infer) find_rotatable_edges() (biobuild.graphs.BaseGraph.BaseGraph method) (biobuild.graphs.ResidueGraph method) ForceFieldRotatron (class in biobuild.optimizers.ForceFieldRotatron) formulas (biobuild.resources.pdbe_compounds.PDBECompounds property) from_AtomGraph() (biobuild.graphs.ResidueGraph class method) from_biopython() (biobuild.core.base_classes.Atom class method), [1] (biobuild.core.base_classes.Chain class method), [1] (biobuild.core.base_classes.Model class method), [1] (biobuild.core.base_classes.Residue class method), [1] (biobuild.core.base_classes.Structure class method), [1] (biobuild.graphs.AtomGraph class method) from_cif() (biobuild.core.entity.BaseEntity class method), [1] from_compound() (biobuild.core.Molecule.Molecule class method), [1] from_file() (biobuild.resources.pdbe_compounds.PDBECompounds class method) from_json() (biobuild.core.entity.BaseEntity class method), [1] (biobuild.core.Linkage.Linkage class method), [1] (biobuild.resources.charmm.CHARMMTopology class method) (biobuild.resources.pdbe_compounds.PDBECompounds class method) from_molecule() (biobuild.graphs.AtomGraph class method) (biobuild.graphs.ResidueGraph class method) from_molfile() (biobuild.core.entity.BaseEntity class method), [1] from_openmm() (biobuild.core.entity.BaseEntity class method), [1] from_pdb() (biobuild.core.entity.BaseEntity class method), [1] (biobuild.core.Molecule.Molecule class method), [1] from_pubchem() (biobuild.core.Molecule.Molecule class method), [1] from_pybel() (biobuild.core.entity.BaseEntity class method), [1] from_quartet() (biobuild.utils.ic.InternalCoordinates class method) from_rdkit() (biobuild.core.entity.BaseEntity class method), [1] from_smiles() (biobuild.core.Molecule.Molecule class method), [1] full_id (biobuild.core.base_classes.Atom property), [1] (biobuild.core.base_classes.Chain property), [1] (biobuild.core.base_classes.Model property), [1] (biobuild.core.base_classes.Residue property), [1] (biobuild.core.base_classes.Structure property), [1] fullname (biobuild.core.base_classes.Atom attribute), [1] G generate_quartets() (in module biobuild.structural.neighbors) generate_triplets() (in module biobuild.structural.neighbors) genetic_optimize() (in module biobuild.optimizers.algorithms) get() (biobuild.resources.pdbe_compounds.PDBECompounds method) get_ancestors() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) get_anchors() (biobuild.structural.connector.Connector method) (biobuild.structural.patch.Patcher method) get_atom() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.abstract.AbstractEntity method) get_atom_graph() (biobuild.core.entity.BaseEntity method), [1] get_atom_quartets() (biobuild.core.entity.BaseEntity method), [1] get_atom_triplets() (biobuild.core.entity.BaseEntity method), [1] get_atomic_bond() (biobuild.graphs.ResidueGraph method) get_atoms() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.auxiliary.DummyStructure method) get_atoms_by_type() (biobuild.utils.abstract.AbstractEntity method) get_attach_residue() (biobuild.core.entity.BaseEntity method), [1] get_bond() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.abstract.AbstractEntity method) get_bonds() (biobuild.core.entity.BaseEntity method), [1] get_chain() (biobuild.core.entity.BaseEntity method), [1] get_chains() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.auxiliary.DummyStructure method) get_compound() (in module biobuild.resources.pdbe_compounds) get_default_compounds() (in module biobuild.resources.pdbe_compounds) get_default_instance() (in module biobuild.utils.defaults) get_default_topology() (in module biobuild.resources.charmm) get_descendants() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) get_edge_idx() (biobuild.optimizers.Rotatron.Rotatron method) get_edge_vector() (biobuild.optimizers.Rotatron.Rotatron method) get_internal_coordinates() (biobuild.utils.abstract.AbstractEntity_with_IC method) get_linkage() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.resources.charmm) get_locked_edges() (biobuild.graphs.BaseGraph.BaseGraph method) get_models() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.auxiliary.DummyStructure method) get_neighbors() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.AtomGraph method) (biobuild.graphs.BaseGraph.BaseGraph method) (biobuild.graphs.ResidueGraph method) (biobuild.structural.neighbors.AtomNeighborhood method) (biobuild.structural.neighbors.Neighborhood method) (biobuild.structural.neighbors.ResidueNeighborhood method) get_node_coords() (biobuild.optimizers.Rotatron.Rotatron method) get_node_idx() (biobuild.optimizers.Rotatron.Rotatron method) get_parent() (biobuild.utils.abstract.AbstractAtom method) (biobuild.utils.abstract.AbstractBond method) get_patch() (biobuild.resources.charmm.CHARMMTopology method) (in module biobuild.resources.charmm) get_quartets() (biobuild.core.entity.BaseEntity method), [1] get_reference_atoms() (biobuild.utils.ic.InternalCoordinates method) get_residue() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.ResidueGraph method) get_residue_connections() (biobuild.core.entity.BaseEntity method), [1] (biobuild.core.Molecule.Molecule method), [1] get_residue_graph() (biobuild.core.entity.BaseEntity method), [1] get_residues() (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.auxiliary.DummyStructure method) get_root() (biobuild.core.entity.BaseEntity method), [1] get_unlocked_edges() (biobuild.graphs.BaseGraph.BaseGraph method) H has_atom() (biobuild.utils.abstract.AbstractEntity method) has_compound() (in module biobuild.resources.pdbe_compounds) has_IC (biobuild.utils.abstract.AbstractEntity_with_IC property) has_linkage() (in module biobuild.resources.charmm) has_patch() (biobuild.resources.charmm.CHARMMTopology method) (in module biobuild.resources.charmm) has_residue() (biobuild.resources.pdbe_compounds.PDBECompounds method) highlight_atoms() (biobuild.utils.visual.Chem2DViewer method) (biobuild.utils.visual.PlotlyViewer3D method) highlight_bonds() (biobuild.utils.visual.Chem2DViewer method) highlight_residues() (biobuild.utils.visual.PlotlyViewer3D method) I IC_atom_ids (biobuild.utils.abstract.AbstractEntity_with_IC property) id (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Residue property), [1] (biobuild.core.entity.BaseEntity property), [1] (biobuild.core.Linkage.Linkage attribute), [1] (biobuild.resources.charmm.CHARMMTopology attribute) ids (biobuild.resources.pdbe_compounds.PDBECompounds property) (biobuild.utils.ic.InternalCoordinates property) improper (biobuild.structural.neighbors.Quartet property) in_same_cycle() (biobuild.graphs.BaseGraph.BaseGraph method) infer_bonds() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.infer) infer_residue_connections() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.infer) infer_surface_residues() (in module biobuild.structural.infer) internal_coord (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] internal_coordinates (biobuild.core.Linkage.Linkage attribute), [1] InternalCoordinates (class in biobuild.utils.ic) invert() (biobuild.core.base_classes.Bond method), [1] is_biopython() (in module biobuild.utils.convert) is_done() (biobuild.optimizers.DistanceRotatron.DistanceRotatron method) (biobuild.optimizers.Rotatron.Rotatron method) is_double() (biobuild.core.base_classes.Bond method), [1] is_improper (biobuild.utils.ic.InternalCoordinates property) is_locked() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) is_proper (biobuild.utils.ic.InternalCoordinates property) is_pybel() (in module biobuild.utils.convert) is_rdkit() (in module biobuild.utils.convert) is_single() (biobuild.core.base_classes.Bond method), [1] is_triple() (biobuild.core.base_classes.Bond method), [1] J jensen_shannon_overlap() (in module biobuild.optimizers.OverlapRotatron) L left_adjust() (in module biobuild.utils.pdb) lengths (biobuild.utils.ic.InternalCoordinates property) level (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Model attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] (biobuild.core.base_classes.Structure attribute), [1] link() (biobuild.utils.visual.AtomGraphViewer3D method) (biobuild.utils.visual.MoleculeViewer3D method) (biobuild.utils.visual.ResidueGraphViewer3D method) linkage (biobuild.core.entity.BaseEntity property), [1] Linkage (class in biobuild.core.Linkage), [1] linkage() (in module biobuild.core.Linkage), [1] linkages (biobuild.resources.charmm.CHARMMTopology property) load() (biobuild.core.entity.BaseEntity class method), [1] (biobuild.resources.pdbe_compounds.PDBECompounds class method) load_all_compounds() (in module biobuild.resources.pdbe_compounds) load_amino_acids() (in module biobuild.resources.pdbe_compounds) load_lipids() (in module biobuild.resources.pdbe_compounds) load_nucleotides() (in module biobuild.resources.pdbe_compounds) load_pickle() (in module biobuild.utils.auxiliary) load_small_molecules() (in module biobuild.resources.pdbe_compounds) load_sugars() (in module biobuild.resources.pdbe_compounds) lock_all() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) lock_bond() (biobuild.core.entity.BaseEntity method), [1] lock_centers() (biobuild.graphs.ResidueGraph method) lock_edge() (biobuild.graphs.BaseGraph.BaseGraph method) locked_bonds (biobuild.core.entity.BaseEntity property), [1] M make_atom_graph() (biobuild.core.entity.BaseEntity method), [1] make_atoms_table() (in module biobuild.utils.pdb) make_bond_lines() (in module biobuild.utils.cif) make_bond_table() (in module biobuild.utils.cif) make_connect_table() (in module biobuild.utils.pdb) make_detailed() (biobuild.graphs.ResidueGraph method) make_df() (biobuild.utils.visual.AtomGraphViewer3D method) (biobuild.utils.visual.MoleculeViewer3D method) (biobuild.utils.visual.ResidueGraphViewer3D method) make_empty_structure() (in module biobuild.structural.base) make_formula() (in module biobuild.utils.auxiliary) make_header() (in module biobuild.utils.cif) make_residue_graph() (biobuild.core.entity.BaseEntity method), [1] make_smiles() (in module biobuild.core.Molecule), [1] (in module biobuild.structural.smiles) mass (biobuild.core.base_classes.Atom attribute), [1] merge() (biobuild.resources.pdbe_compounds.PDBECompounds method) (biobuild.structural.patch.Patcher method) (biobuild.structural.stitch.Stitcher method) migrate_atoms() (biobuild.utils.abstract.AbstractBond method) migrate_bonds() (biobuild.graphs.AtomGraph method) model (biobuild.core.entity.BaseEntity property), [1] Model (class in biobuild.core.base_classes), [1] model_make_full_id() (in module biobuild.structural.base) module biobuild.core biobuild.core.base_classes, [1] biobuild.core.entity biobuild.core.Linkage, [1] biobuild.core.Molecule, [1] biobuild.optimizers.DistanceRotatron biobuild.optimizers.ForceFieldRotatron biobuild.optimizers.OverlapRotatron biobuild.optimizers.Rotatron biobuild.optimizers.utils biobuild.resources biobuild.resources.charmm biobuild.resources.pdbe_compounds biobuild.resources.pubchem biobuild.structural.base biobuild.structural.connector biobuild.structural.infer biobuild.structural.neighbors biobuild.structural.patch biobuild.structural.smiles biobuild.structural.stitch biobuild.utils.abstract biobuild.utils.auxiliary biobuild.utils.cif biobuild.utils.constants biobuild.utils.convert biobuild.utils.defaults biobuild.utils.ic biobuild.utils.pdb Molecule (class in biobuild.core.Molecule), [1] molecule() (in module biobuild.core.Molecule), [1] molecule_to_pdbio() (biobuild.utils.convert.PDBIO method) MoleculeViewer3D (class in biobuild.utils.visual) MVN() (in module biobuild.optimizers.OverlapRotatron) N name (biobuild.core.base_classes.Atom attribute), [1] Neighborhood (class in biobuild.structural.neighbors) nglview() (biobuild.core.entity.BaseEntity method), [1] NglViewer (class in biobuild.utils.visual) nodes_in_cycles (biobuild.graphs.BaseGraph.BaseGraph property) norm_vector() (in module biobuild.structural.base) O occupancy (biobuild.core.base_classes.Atom attribute), [1] openmm_to_biopython() (biobuild.utils.convert.OpenMMBioPythonConverter method) OpenMMBioPythonConverter (class in biobuild.utils.convert) optimize() (biobuild.core.Molecule.Molecule method), [1] (in module biobuild.optimizers.utils) order (biobuild.core.base_classes.Bond attribute), [1] OverlapRotatron (class in biobuild.optimizers.OverlapRotatron) P parent (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Model attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] (biobuild.core.base_classes.Structure attribute), [1] parse_bond_table() (in module biobuild.utils.cif) parse_connect_lines() (in module biobuild.utils.pdb) patch (biobuild.core.entity.BaseEntity property), [1] patch() (in module biobuild.core.Linkage), [1] (in module biobuild.structural.patch) patch_attach() (biobuild.core.Molecule.Molecule method), [1] Patcher (class in biobuild.structural.patch) PatchError patches (biobuild.resources.charmm.CHARMMTopology attribute) (biobuild.resources.charmm.CHARMMTopology property) PDBECompounds (class in biobuild.resources.pdbe_compounds) PDBIO (class in biobuild.utils.convert) pdbio_to_biopython() (biobuild.utils.convert.PDBIO method) phosphorylate() (in module biobuild.core.Molecule), [1] plane_vector() (in module biobuild.structural.base) PlotlyViewer3D (class in biobuild.utils.visual) polymerize() (in module biobuild.core.Molecule), [1] pqr_charge (biobuild.core.base_classes.Atom attribute), [1] prune_triplets() (biobuild.graphs.ResidueGraph method) pubchem_to_cif() (in module biobuild.resources.pubchem) purge_bonds() (biobuild.core.entity.BaseEntity method), [1] py3dmol() (biobuild.core.entity.BaseEntity method), [1] Py3DmolViewer (class in biobuild.utils.visual) pybel_atom_to_biopython() (biobuild.utils.convert.PybelBioPythonConverter method) pybel_molecule_to_biopython() (biobuild.utils.convert.PybelBioPythonConverter method) pybel_residue_to_biopython() (biobuild.utils.convert.PybelBioPythonConverter method) PybelBioPythonConverter (class in biobuild.utils.convert) Q Quartet (class in biobuild.structural.neighbors) quartet() (biobuild.core.entity.BaseEntity method), [1] query() (in module biobuild.resources.pubchem) query_pubchem() (in module biobuild.core.Molecule), [1] R radius (biobuild.core.base_classes.Atom attribute), [1] rainbow() (biobuild.utils.visual.MoleculeViewer3D method) (biobuild.utils.visual.ResidueGraphViewer3D method) rdkit_to_biopython() (biobuild.utils.convert.RDKITBiopythonConverter method) RDKITBiopythonConverter (class in biobuild.utils.convert) read_cif() (in module biobuild.core.Molecule), [1] read_compounds() (in module biobuild.resources.pdbe_compounds) read_pdb() (in module biobuild.core.Molecule), [1] read_smiles() (in module biobuild.core.Molecule), [1] (in module biobuild.structural.smiles) read_topology() (in module biobuild.resources.charmm) recipe (biobuild.core.entity.BaseEntity property), [1] recipe() (in module biobuild.core.Linkage), [1] reindex() (biobuild.core.entity.BaseEntity method), [1] relabel_atoms() (biobuild.resources.pdbe_compounds.PDBECompounds method) relabel_hydrogens() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.infer) remove() (biobuild.resources.pdbe_compounds.PDBECompounds method) remove_atoms() (biobuild.core.entity.BaseEntity method), [1] remove_bond() (biobuild.core.entity.BaseEntity method), [1] remove_nonprintable() (in module biobuild.utils.auxiliary) remove_residues() (biobuild.core.entity.BaseEntity method), [1] rename_atom() (biobuild.core.entity.BaseEntity method), [1] rename_chain() (biobuild.core.entity.BaseEntity method), [1] rename_residue() (biobuild.core.entity.BaseEntity method), [1] (in module biobuild.structural.base) repeat() (biobuild.core.Molecule.Molecule method), [1] reset() (biobuild.optimizers.Rotatron.Rotatron method) (biobuild.utils.visual.MoleculeViewer3D method) (biobuild.utils.visual.PlotlyViewer3D method) Residue (class in biobuild.core.base_classes), [1] residue_make_full_id() (in module biobuild.structural.base) ResidueGraph (class in biobuild.graphs) ResidueGraphViewer3D (class in biobuild.utils.visual) ResidueNeighborhood (class in biobuild.structural.neighbors) residues (biobuild.core.entity.BaseEntity property), [1] (biobuild.graphs.BaseGraph.BaseGraph property) (biobuild.graphs.ResidueGraph property) (biobuild.structural.neighbors.ResidueNeighborhood property) resname (biobuild.core.base_classes.Residue attribute), [1] RESOURCES (in module biobuild.utils.constants) restore_default_compounds() (in module biobuild.resources.pdbe_compounds) restore_default_topology() (in module biobuild.resources.charmm) right_adjust() (in module biobuild.utils.pdb) root_atom (biobuild.core.entity.BaseEntity property), [1] root_residue (biobuild.core.entity.BaseEntity property), [1] rotate() (biobuild.optimizers.Rotatron.Rotatron method) rotate_ancestors() (biobuild.core.entity.BaseEntity method), [1] rotate_around_bond() (biobuild.core.entity.BaseEntity method), [1] rotate_around_edge() (biobuild.graphs.BaseGraph.BaseGraph method) rotate_descendants() (biobuild.core.entity.BaseEntity method), [1] Rotatron (class in biobuild.optimizers.Rotatron) S sample_atoms_around_reference() (in module biobuild.structural.infer) save() (biobuild.core.entity.BaseEntity method), [1] (biobuild.resources.pdbe_compounds.PDBECompounds method) save_as_default_compounds() (in module biobuild.resources.pdbe_compounds) save_compounds() (in module biobuild.resources.pdbe_compounds) save_pickle() (in module biobuild.utils.auxiliary) save_topology() (in module biobuild.resources.charmm) scipy_optimize() (in module biobuild.optimizers.algorithms) segid (biobuild.core.base_classes.Residue attribute), [1] serial_num (biobuild.core.base_classes.Model property), [1] serial_number (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Model property), [1] set_attach_residue() (biobuild.core.entity.BaseEntity method), [1] set_default_compounds() (in module biobuild.resources.pdbe_compounds) set_default_instance() (in module biobuild.utils.defaults) set_default_topology() (in module biobuild.resources.charmm) set_full_id() (in module biobuild.structural.base) set_linkage() (biobuild.core.entity.BaseEntity method), [1] set_parent() (biobuild.utils.abstract.AbstractAtom method) set_patch() (biobuild.structural.patch.Patcher method) set_root() (biobuild.core.entity.BaseEntity method), [1] set_source() (biobuild.structural.connector.Connector method) set_target() (biobuild.structural.connector.Connector method) should_invert() (in module biobuild.core.entity) show() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) (biobuild.utils.visual.Chem2DViewer method) (biobuild.utils.visual.NglViewer method) (biobuild.utils.visual.PlotlyViewer3D method) (biobuild.utils.visual.Py3DmolViewer method) sigatm_array (biobuild.core.base_classes.Atom attribute), [1] siguij_array (biobuild.core.base_classes.Atom attribute), [1] simple_concatenation_function() (in module biobuild.optimizers.DistanceRotatron) single() (biobuild.core.base_classes.Bond method), [1] step() (biobuild.optimizers.DistanceRotatron.DistanceRotatron method) (biobuild.optimizers.Rotatron.Rotatron method) stitch() (in module biobuild.structural.stitch) stitch_attach() (biobuild.core.Molecule.Molecule method), [1] Stitcher (class in biobuild.structural.stitch) structure (biobuild.core.entity.BaseEntity property), [1] (biobuild.graphs.BaseGraph.BaseGraph property) Structure (class in biobuild.core.base_classes), [1] subset_compounds_by_types() (in module biobuild.resources.pdbe_compounds) swarm_optimize() (in module biobuild.optimizers.algorithms) T to_AtomGraph() (biobuild.graphs.ResidueGraph method) to_biopython() (biobuild.core.base_classes.Atom method), [1] (biobuild.core.base_classes.Chain method), [1] (biobuild.core.base_classes.Model method), [1] (biobuild.core.base_classes.Residue method), [1] (biobuild.core.base_classes.Structure method), [1] (biobuild.core.entity.BaseEntity method), [1] (biobuild.utils.abstract.AbstractAtom method) to_cif() (biobuild.core.entity.BaseEntity method), [1] to_json() (biobuild.core.entity.BaseEntity method), [1] (biobuild.core.Linkage.Linkage method), [1] (biobuild.resources.charmm.CHARMMTopology method) (biobuild.resources.pdbe_compounds.PDBECompounds method) to_molfile() (biobuild.core.entity.BaseEntity method), [1] to_openmm() (biobuild.core.entity.BaseEntity method), [1] to_pdb() (biobuild.core.entity.BaseEntity method), [1] to_pybel() (biobuild.core.entity.BaseEntity method), [1] to_rdkit() (biobuild.core.entity.BaseEntity method), [1] to_smiles() (biobuild.core.Molecule.Molecule method), [1] to_tuple() (biobuild.core.base_classes.Bond method), [1] translate_ids_1_to_3() (biobuild.resources.pdbe_compounds.PDBECompounds method) translate_ids_3_to_1() (biobuild.resources.pdbe_compounds.PDBECompounds method) triple() (biobuild.core.base_classes.Bond method), [1] U unload_all_compounds() (in module biobuild.resources.pdbe_compounds) unload_amino_acids() (in module biobuild.resources.pdbe_compounds) unload_by_types() (in module biobuild.resources.pdbe_compounds) unload_lipids() (in module biobuild.resources.pdbe_compounds) unload_nucleotides() (in module biobuild.resources.pdbe_compounds) unload_small_molecules() (in module biobuild.resources.pdbe_compounds) unload_sugars() (in module biobuild.resources.pdbe_compounds) unlock_all() (biobuild.core.entity.BaseEntity method), [1] (biobuild.graphs.BaseGraph.BaseGraph method) unlock_bond() (biobuild.core.entity.BaseEntity method), [1] unlock_edge() (biobuild.graphs.BaseGraph.BaseGraph method) update_atom_graph() (biobuild.core.entity.BaseEntity method), [1] V vector_between() (in module biobuild.structural.base) vet() (biobuild.core.entity.BaseEntity method), [1] vet_structure() (in module biobuild.structural.infer) view (biobuild.utils.visual.Py3DmolViewer attribute) W write_bond_table() (in module biobuild.utils.cif) write_cif() (in module biobuild.core.Molecule), [1] write_connect_lines() (in module biobuild.utils.pdb) write_html() (biobuild.utils.visual.PlotlyViewer3D method) write_pdb() (in module biobuild.core.Molecule), [1] (in module biobuild.utils.pdb) X xtra (biobuild.core.base_classes.Atom attribute), [1] (biobuild.core.base_classes.Chain attribute), [1] (biobuild.core.base_classes.Model attribute), [1] (biobuild.core.base_classes.Residue attribute), [1] (biobuild.core.base_classes.Structure attribute), [1]