Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A AbstractAtom (class in buildamol.utils.abstract) AbstractBond (class in buildamol.utils.abstract) AbstractEntity (class in buildamol.utils.abstract) AbstractEntity_with_IC (class in buildamol.utils.abstract) acceptable_surplus_charge (in module buildamol.structural.infer) acetylate() (in module buildamol.core.Molecule), [1] add() (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.resources.pdbe_compounds.PDBECompounds method) (buildamol.utils.visual.PlotlyViewer3D method) (buildamol.utils.visual.Py3DmolViewer method) add_atom() (buildamol.utils.abstract.AbstractEntity method) add_atomic_bonds() (buildamol.graphs.ResidueGraph method) add_atoms() (buildamol.core.entity.BaseEntity method), [1] add_bond() (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.abstract.AbstractEntity method) add_bonds() (buildamol.core.entity.BaseEntity method), [1] add_chains() (buildamol.core.entity.BaseEntity method), [1] add_compound() (in module buildamol.resources.pdbe_compounds) add_delete() (buildamol.core.Linkage.Linkage method), [1] add_group() (in module buildamol.structural.groups) add_hydrogens() (buildamol.core.entity.BaseEntity method), [1] (buildamol.structural.infer.Hydrogenator method) add_ic() (buildamol.utils.abstract.AbstractEntity_with_IC method) add_id_to_delete() (buildamol.core.Linkage.Linkage method), [1] add_internal_coordinates() (buildamol.core.Linkage.Linkage method), [1] (buildamol.utils.abstract.AbstractEntity_with_IC method) add_ligand() (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) add_ligands() (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) add_linkage() (in module buildamol.resources.charmm) add_model() (buildamol.core.entity.BaseEntity method), [1] add_patch() (buildamol.resources.charmm.CHARMMTopology method) (in module buildamol.resources.charmm) add_residues() (buildamol.core.entity.BaseEntity method), [1] adjust_bond_length() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.base) adjust_distance() (in module buildamol.structural.base) adjust_indexing() (buildamol.core.entity.BaseEntity method), [1] adjust_protonation() (in module buildamol.structural.infer) adjust_to_ph() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) Aldehyde (class in buildamol.structural.reactivity) align_to() (buildamol.core.entity.BaseEntity method), [1] AlkylHalide (class in buildamol.structural.reactivity) all() (buildamol.extensions.molecular_factories.derivator.Derivator method) all_functional_groups (in module buildamol.structural.groups) alone() (buildamol.structural.neighbors.constraints method) altloc (buildamol.base_classes.Atom attribute), [1] amidate() (in module buildamol.core.Molecule), [1] Amide (class in buildamol.structural.reactivity) aminate() (in module buildamol.core.Molecule), [1] Amine (class in buildamol.structural.reactivity) amino_acid_names_1letter (in module buildamol.extensions.bio.proteins.peptides) amino_acid_names_3letter (in module buildamol.extensions.bio.proteins.peptides) amino_acids (in module buildamol.extensions.bio.proteins.peptides) and_() (buildamol.structural.neighbors.constraints_v2 method) angle (buildamol.structural.geometry.Geometry attribute) (buildamol.structural.geometry.Linear attribute) (buildamol.structural.geometry.Octahedral attribute) (buildamol.structural.geometry.SquarePlanar attribute) (buildamol.structural.geometry.Tetrahedral attribute) (buildamol.structural.geometry.TrigonalBipyramidal attribute) (buildamol.structural.geometry.TrigonalPlanar attribute) angle_123 (buildamol.structural.neighbors.Quartet property) angle_234 (buildamol.structural.neighbors.Quartet property) angle_between() (in module buildamol.structural.base) angles (buildamol.utils.ic.InternalCoordinates property) anisou_array (buildamol.base_classes.Atom attribute), [1] anneal_optimize() (in module buildamol.optimizers.algorithms) apply() (buildamol.core.Linkage.Linkage method), [1] (buildamol.core.Reaction method), [1] (buildamol.structural.geometry.Geometry method) (buildamol.structural.patch.Patcher method) (buildamol.structural.stitch.Stitcher method) apply_bond() (buildamol.core.Linkage.Linkage method), [1] apply_connectivity() (buildamol.structural.groups.BaseFunctionalGroup method) apply_deletes() (buildamol.core.Linkage.Linkage method), [1] apply_reference_bonds() (in module buildamol.structural.infer) apply_rotatron_solution() (in module buildamol.optimizers.utils) apply_standard_bonds() (buildamol.core.entity.BaseEntity method), [1] apply_standard_bonds_for() (buildamol.core.entity.BaseEntity method), [1] apply_translatron_solution() (in module buildamol.optimizers.utils) AromaticGroup (class in buildamol.structural.groups) as_electrophile() (buildamol.structural.reactivity.Reactivity method) as_nucleophile() (buildamol.structural.reactivity.Reactivity method) Assembler (class in buildamol.extensions.molecular_factories.assembler) assign_attribute() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) assign_charges() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) assign_types() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) Atom (class in buildamol.base_classes), [1] atom1 (buildamol.base_classes.Bond attribute), [1], [2], [3] (buildamol.core.Linkage.Linkage property), [1] (buildamol.structural.neighbors.Quartet property) atom2 (buildamol.base_classes.Bond attribute), [1], [2], [3] (buildamol.core.Linkage.Linkage property), [1] (buildamol.structural.neighbors.Quartet property) atom3 (buildamol.structural.neighbors.Quartet property) atom4 (buildamol.structural.neighbors.Quartet property) atom_key() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) (buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer.CHARMMTyper method) atom_make_full_id() (in module buildamol.structural.base) AtomGraph (class in buildamol.graphs) AtomGraphViewer3D (class in buildamol.utils.visual) atomic_bonds (buildamol.graphs.ResidueGraph property) atomic_number (buildamol.base_classes.Atom property), [1] atomic_number() (in module buildamol.structural.infer) AtomIterator (class in buildamol.utils.auxiliary) AtomNeighborhood (class in buildamol.structural.neighbors) atoms (buildamol.base_classes.Chain property), [1] (buildamol.base_classes.Residue property), [1] (buildamol.core.entity.BaseEntity property), [1] (buildamol.core.Linkage.Linkage attribute), [1] (buildamol.graphs.base_graph.BaseGraph property) (buildamol.structural.neighbors.AtomNeighborhood property) (buildamol.structural.neighbors.Quartet property) (buildamol.utils.abstract.AbstractBond property) (buildamol.utils.abstract.AbstractEntity property) (buildamol.utils.ic.InternalCoordinates property) atoms_in_area() (in module buildamol.structural.infer) AtomTyper (class in buildamol.extensions.molecular_dynamics.atom_typing.atom_typer) attach() (buildamol.core.Molecule.Molecule method), [1] attach_residue (buildamol.core.entity.BaseEntity property), [1] auto_algorithm() (in module buildamol.optimizers.utils) AutoLabel (class in buildamol.structural.infer) autolabel() (buildamol.core.entity.BaseEntity method), [1] (buildamol.structural.infer.AutoLabel method) (in module buildamol.structural.infer) autolabel_atoms() (in module buildamol.structural.infer) available_linkages() (in module buildamol.resources.charmm) available_patches() (in module buildamol.resources.charmm) B BASE (in module buildamol.utils.constants) BaseEntity (class in buildamol.core.entity), [1] BaseFunctionalGroup (class in buildamol.structural.groups) BaseGraph (class in buildamol.graphs.base_graph) bend_at_bond() (buildamol.core.entity.BaseEntity method), [1] benzylate() (in module buildamol.core.Molecule), [1] bfactor (buildamol.base_classes.Atom attribute), [1] biopython_to_openmm() (buildamol.utils.convert.OpenMMBioPythonConverter method) biopython_to_pdbio() (buildamol.utils.convert.PDBIO method) biopython_to_rdkit() (buildamol.utils.convert.RDKITBiopythonConverter method) blank() (buildamol.optimizers.base_rotatron.Rotatron method) (buildamol.optimizers.translatron.Translatron method) bond (buildamol.core.Linkage.Linkage attribute), [1] (buildamol.core.Linkage.Linkage property), [1] Bond (class in buildamol.base_classes), [1] bond_angle() (in module buildamol.structural.base) bond_order_changable() (buildamol.extensions.molecular_factories.derivator.Derivator method) bond_vector() (in module buildamol.structural.base) bonds (buildamol.core.entity.BaseEntity property), [1] (buildamol.graphs.base_graph.BaseGraph property) (buildamol.structural.neighbors.AtomNeighborhood property) (buildamol.structural.neighbors.ResidueNeighborhood property) buildamol.base_classes module, [1] buildamol.core module buildamol.core.entity module buildamol.core.Linkage module, [1] buildamol.core.Molecule module, [1] buildamol.extensions.bio.glycans.glycan module buildamol.extensions.bio.glycans.iupac module buildamol.extensions.bio.lipids.simple_lipids module buildamol.extensions.bio.nucleic_acids.simple_sequences module buildamol.extensions.bio.proteins.peptides module buildamol.extensions.complexes.metal_complexer module buildamol.extensions.complexes.rotaxane_builder module buildamol.extensions.molecular_dynamics.atom_typing.atom_typer module buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer module buildamol.extensions.molecular_dynamics.psf module buildamol.extensions.molecular_factories.assembler module buildamol.extensions.molecular_factories.derivator module buildamol.extensions.polymers.nanotubes module buildamol.extensions.polymers.polycarbons module buildamol.optimizers.base_rotatron module buildamol.optimizers.circulatron module buildamol.optimizers.constraint_rotatron module buildamol.optimizers.distance_rotatron module buildamol.optimizers.forcefield_rotatron module buildamol.optimizers.overlap_rotatron module buildamol.optimizers.translatron module buildamol.optimizers.utils module buildamol.resources.__init__ module buildamol.resources.charmm module buildamol.resources.pdbe_compounds module buildamol.resources.pubchem module buildamol.structural.base module buildamol.structural.connector module buildamol.structural.geometry module buildamol.structural.groups module buildamol.structural.infer module buildamol.structural.neighbors module buildamol.structural.patch module buildamol.structural.reactivity module buildamol.structural.smiles module buildamol.structural.stitch module buildamol.utils.abstract module buildamol.utils.auxiliary module buildamol.utils.cif module buildamol.utils.constants module buildamol.utils.convert module buildamol.utils.defaults module buildamol.utils.ic module buildamol.utils.pdb module buildamol_to_openmm() (buildamol.utils.convert.OpenMMBioPythonConverter method) buildamol_to_pybel() (buildamol.utils.convert.PybelBioPythonConverter method) buildamol_to_stk() (buildamol.utils.convert.STKBuildAMolConverter method) C can_apply() (buildamol.core.Linkage.Linkage method), [1] (buildamol.core.Reaction method), [1] can_be_source() (buildamol.core.Linkage.Linkage method), [1] can_be_target() (buildamol.core.Linkage.Linkage method), [1] carbons (buildamol.structural.infer.AutoLabel property) Carboxyl (class in buildamol.structural.reactivity) carboxylate() (in module buildamol.core.Molecule), [1] center_atom (buildamol.structural.neighbors.Quartet property) center_of_geometry (buildamol.core.entity.BaseEntity property), [1] center_of_geometry() (in module buildamol.structural.base) center_of_gravity() (in module buildamol.structural.base) center_of_mass (buildamol.core.entity.BaseEntity property), [1] center_of_mass() (in module buildamol.structural.base) centers_of_mass() (buildamol.graphs.ResidueGraph method) central_node (buildamol.graphs.base_graph.BaseGraph property) Chain (class in buildamol.base_classes), [1] chain_id_maker() (in module buildamol.utils.auxiliary) chain_make_full_id() (in module buildamol.structural.base) chains (buildamol.base_classes.Model property), [1] (buildamol.core.entity.BaseEntity property), [1] (buildamol.graphs.base_graph.BaseGraph property) change_bond_order() (in module buildamol.structural.infer) change_element() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) change_suffix() (in module buildamol.utils.auxiliary) charge (buildamol.base_classes.Atom property), [1] (buildamol.core.entity.BaseEntity property), [1] CHARMMTopology (class in buildamol.resources.charmm) CHARMMTyper (class in buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer) chem2dview() (buildamol.core.entity.BaseEntity method), [1] Chem2DViewer (class in buildamol.utils.visual) child_dict (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Model attribute), [1] (buildamol.base_classes.Residue attribute), [1] (buildamol.base_classes.Structure attribute), [1] child_list (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Model attribute), [1] (buildamol.base_classes.Residue attribute), [1] (buildamol.base_classes.Structure attribute), [1] Circulatron (class in buildamol.optimizers.circulatron) cis() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] cleanup() (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.convert.PDBIO method) clear() (buildamol.core.entity.BaseEntity method), [1] clear_cache() (buildamol.graphs.base_graph.BaseGraph method) (buildamol.structural.groups.AromaticGroup method) (buildamol.structural.groups.BaseFunctionalGroup method) collapse_chains() (buildamol.core.entity.BaseEntity method), [1] compute_angle() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.base) compute_angles() (buildamol.core.entity.BaseEntity method), [1] compute_atom1_from_others() (in module buildamol.structural.infer) compute_atom4_from_others() (in module buildamol.structural.infer) compute_dihedral() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.base) compute_dihedrals() (buildamol.core.entity.BaseEntity method), [1] compute_distance() (in module buildamol.structural.base) compute_internal_coordinates() (in module buildamol.structural.infer) compute_length() (buildamol.base_classes.Bond method), [1] compute_length_along_axis() (buildamol.core.entity.BaseEntity method), [1] compute_normal_axis() (buildamol.core.entity.BaseEntity method), [1] compute_outlier_atoms() (in module buildamol.structural.infer) compute_principal_axis() (buildamol.core.entity.BaseEntity method), [1] compute_quartets() (in module buildamol.structural.neighbors) compute_residue_radius() (in module buildamol.structural.infer) compute_torsional() (in module buildamol.structural.base) compute_triplets() (in module buildamol.structural.neighbors) concatenation_function() (buildamol.optimizers.distance_rotatron.DistanceRotatron method) concatenation_function_linear() (in module buildamol.optimizers.distance_rotatron) concatenation_function_no_pushback() (in module buildamol.optimizers.distance_rotatron) concatenation_function_no_unfold() (in module buildamol.optimizers.distance_rotatron) concatenation_function_with_penalty() (in module buildamol.optimizers.distance_rotatron) connect() (in module buildamol.core.Molecule), [1] Connector (class in buildamol.structural.connector) ConstraintRotatron (class in buildamol.optimizers.constraint_rotatron) constraints (class in buildamol.structural.neighbors) constraints_v2 (class in buildamol.structural.neighbors) convert() (buildamol.utils.convert.PybelBioPythonConverter method) coord (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Residue property), [1] coord_array() (in module buildamol.utils.auxiliary) copy() (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.core.Linkage.Linkage method), [1] (buildamol.optimizers.base_rotatron.Rotatron method) count_atoms() (buildamol.base_classes.Residue method), [1] (buildamol.core.entity.BaseEntity method), [1] count_bonds() (buildamol.core.entity.BaseEntity method), [1] count_chains() (buildamol.base_classes.Model method), [1] (buildamol.core.entity.BaseEntity method), [1] count_clashes() (buildamol.core.entity.BaseEntity method), [1] count_models() (buildamol.core.entity.BaseEntity method), [1] count_residues() (buildamol.base_classes.Chain method), [1] (buildamol.core.entity.BaseEntity method), [1] create_linkage() (buildamol.core.Reaction method), [1] cyclic_alkane() (in module buildamol.extensions.polymers.polycarbons) D decode_pdb() (in module buildamol.utils.pdb) DEFAULT_BOND_LENGTH (in module buildamol.utils.defaults) DEFAULT_CHARMM_TOPOLOGY_FILE (in module buildamol.utils.defaults) DEFAULT_PDBE_COMPONENT_FILES (in module buildamol.utils.defaults) DEFAULT_SASA_N (in module buildamol.utils.defaults) DEFAULT_SASA_PROBE_RADIUS (in module buildamol.utils.defaults) default_style (buildamol.utils.visual.Py3DmolViewer attribute) deletes (buildamol.core.Linkage.Linkage attribute), [1] (buildamol.core.Linkage.Linkage property), [1] deprecation_warning() (in module buildamol.utils.auxiliary) Derivator (class in buildamol.extensions.molecular_factories.derivator) dihedral (buildamol.structural.geometry.Tetrahedral attribute) (buildamol.structural.neighbors.Quartet property) dihedral_between() (in module buildamol.structural.base) direct_edges() (buildamol.graphs.base_graph.BaseGraph method) disordered (buildamol.base_classes.Residue attribute), [1] disordered_flag (buildamol.base_classes.Atom attribute), [1] dist_12 (buildamol.structural.neighbors.Quartet property) dist_13 (buildamol.structural.neighbors.Quartet property) dist_23 (buildamol.structural.neighbors.Quartet property) dist_34 (buildamol.structural.neighbors.Quartet property) distance_between() (in module buildamol.structural.base) DistanceRotatron (class in buildamol.optimizers.distance_rotatron) distribute_along_axle() (buildamol.extensions.complexes.rotaxane_builder.RotaxaneBuilder method) dna() (in module buildamol.extensions.bio.nucleic_acids.simple_sequences) done() (buildamol.optimizers.circulatron.Circulatron method) (buildamol.optimizers.constraint_rotatron.ConstraintRotatron method) dont_use_ic() (in module buildamol.utils.auxiliary) dont_use_numba() (in module buildamol.utils.auxiliary) double() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] draw() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.AtomGraph method) (buildamol.graphs.base_graph.BaseGraph method) (buildamol.graphs.ResidueGraph method) (buildamol.utils.visual.Chem2DViewer method) draw2d() (buildamol.core.entity.BaseEntity method), [1] draw3d() (buildamol.core.entity.BaseEntity method), [1] draw_atom() (buildamol.utils.visual.PlotlyViewer3D method) draw_atoms() (buildamol.utils.visual.PlotlyViewer3D method) draw_bond() (buildamol.utils.visual.PlotlyViewer3D method) draw_edges() (buildamol.utils.visual.PlotlyViewer3D method) draw_point() (buildamol.utils.visual.PlotlyViewer3D method) draw_points() (buildamol.utils.visual.PlotlyViewer3D method) draw_residues() (buildamol.utils.visual.PlotlyViewer3D method) draw_vector() (buildamol.utils.visual.PlotlyViewer3D method) drop_atom_names() (buildamol.core.entity.BaseEntity method), [1] drop_atoms() (buildamol.core.entity.BaseEntity method), [1] drop_bond() (buildamol.core.entity.BaseEntity method), [1] drop_chains() (buildamol.core.entity.BaseEntity method), [1] drop_empty_chains() (buildamol.core.entity.BaseEntity method), [1] drop_empty_models() (buildamol.core.entity.BaseEntity method), [1] drop_empty_residues() (buildamol.core.entity.BaseEntity method), [1] drop_hydrogens() (buildamol.core.entity.BaseEntity method), [1] drop_model() (buildamol.core.entity.BaseEntity method), [1] drop_residues() (buildamol.core.entity.BaseEntity method), [1] DummyBar (class in buildamol.utils.auxiliary) DummyStructure (class in buildamol.utils.auxiliary) E electrophile_deleter() (buildamol.structural.reactivity.AlkylHalide method) (buildamol.structural.reactivity.Amide method) (buildamol.structural.reactivity.Amine method) (buildamol.structural.reactivity.Carboxyl method) (buildamol.structural.reactivity.Hydroxyl method) (buildamol.structural.reactivity.Ketone method) (buildamol.structural.reactivity.Phosphate method) (buildamol.structural.reactivity.Thiol method) electrophile_linker() (buildamol.structural.reactivity.Aldehyde method) (buildamol.structural.reactivity.AlkylHalide method) (buildamol.structural.reactivity.Amide method) (buildamol.structural.reactivity.Amine method) (buildamol.structural.reactivity.Carboxyl method) (buildamol.structural.reactivity.Hydroxyl method) (buildamol.structural.reactivity.Ketone method) (buildamol.structural.reactivity.Phosphate method) (buildamol.structural.reactivity.Thiol method) element (buildamol.base_classes.Atom attribute), [1] (buildamol.utils.abstract.AbstractAtom property) element_changable() (buildamol.extensions.molecular_factories.derivator.Derivator method) element_range() (in module buildamol.utils.auxiliary) empty() (buildamol.core.Molecule.Molecule class method), [1] encode_atom() (in module buildamol.utils.pdb) encode_pdb() (in module buildamol.utils.pdb) encode_psf() (buildamol.extensions.molecular_dynamics.psf.PSFMaker method) energy() (buildamol.optimizers.forcefield_rotatron.ForceFieldRotatron method) equals() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] Ester (class in buildamol.structural.reactivity) eval() (buildamol.optimizers.base_rotatron.Rotatron method) (buildamol.optimizers.circulatron.Circulatron method) (buildamol.optimizers.constraint_rotatron.ConstraintRotatron method) (buildamol.optimizers.forcefield_rotatron.ForceFieldRotatron method) (buildamol.optimizers.overlap_rotatron.OverlapRotatron method) (buildamol.optimizers.translatron.Translatron method) export_compounds() (in module buildamol.resources.pdbe_compounds) export_topology() (in module buildamol.resources.charmm) extended_has_at_least_n_neighbors() (buildamol.structural.neighbors.constraints method) extended_has_at_most_n_neighbors() (buildamol.structural.neighbors.constraints method) extended_has_n_neighbors() (buildamol.structural.neighbors.constraints method) extended_has_neighbor_hist() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) extended_has_not_n_neighbors() (buildamol.structural.neighbors.constraints method) extended_neighbors_all() (buildamol.structural.neighbors.constraints method) extended_neighbors_any() (buildamol.structural.neighbors.constraints method) extended_neighbors_exactly() (buildamol.structural.neighbors.constraints method) extended_neighbors_not() (buildamol.structural.neighbors.constraints method) F fatty_acid() (in module buildamol.extensions.bio.lipids.simple_lipids) filename_to_id() (in module buildamol.utils.auxiliary) fill_hydrogens() (buildamol.structural.geometry.Geometry method) find_atoms() (buildamol.structural.reactivity.Reactivity method) (buildamol.utils.abstract.AbstractBond method) find_axial_hydrogens() (in module buildamol.structural.infer) find_axial_substituents() (in module buildamol.structural.infer) find_clashes() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) find_clashes_between() (in module buildamol.structural.infer) find_clashes_with() (buildamol.core.entity.BaseEntity method), [1] find_cycles() (buildamol.graphs.base_graph.BaseGraph method) find_edges() (buildamol.graphs.base_graph.BaseGraph method) find_edges_in_cycles() (buildamol.graphs.base_graph.BaseGraph method) find_electrophilic_atoms() (buildamol.structural.reactivity.Reactivity method) find_equatorial_hydrogens() (in module buildamol.structural.infer) find_equatorial_substituents() (in module buildamol.structural.infer) find_matches() (buildamol.structural.groups.AromaticGroup method) (buildamol.structural.groups.BaseFunctionalGroup method) (buildamol.structural.groups.FunctionalGroup method) find_models() (in module buildamol.utils.pdb) find_nodes_in_cycles() (buildamol.graphs.base_graph.BaseGraph method) find_nucleophilic_atoms() (buildamol.structural.reactivity.Reactivity method) find_rotatable_edges() (buildamol.graphs.base_graph.BaseGraph method) (buildamol.graphs.ResidueGraph method) flip() (buildamol.core.entity.BaseEntity method), [1] flip_coords() (in module buildamol.structural.base) flip_molecule() (in module buildamol.structural.base) ForceFieldRotatron (class in buildamol.optimizers.forcefield_rotatron) formulas (buildamol.resources.pdbe_compounds.PDBECompounds property) from_AtomGraph() (buildamol.graphs.ResidueGraph class method) from_biopython() (buildamol.base_classes.Atom class method), [1] (buildamol.base_classes.Chain class method), [1] (buildamol.base_classes.Model class method), [1] (buildamol.base_classes.Residue class method), [1] (buildamol.base_classes.Structure class method), [1] (buildamol.graphs.AtomGraph class method) from_bond() (buildamol.core.Linkage.Linkage class method), [1] from_cif() (buildamol.core.entity.BaseEntity class method), [1] from_compound() (buildamol.core.Molecule.Molecule class method), [1] from_dict() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper class method) from_element() (buildamol.base_classes.Atom class method), [1] from_file() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper class method) (buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer.CHARMMTyper class method) (buildamol.resources.pdbe_compounds.PDBECompounds class method) from_functional_groups() (buildamol.core.Linkage.Linkage class method), [1] from_geometry() (buildamol.core.Molecule.Molecule class method), [1] from_json() (buildamol.core.entity.BaseEntity class method), [1] (buildamol.core.Linkage.Linkage class method), [1] (buildamol.resources.charmm.CHARMMTopology class method) (buildamol.resources.pdbe_compounds.PDBECompounds class method) from_molecule() (buildamol.graphs.AtomGraph class method) (buildamol.graphs.ResidueGraph class method) from_molfile() (buildamol.core.entity.BaseEntity class method), [1] from_openmm() (buildamol.core.entity.BaseEntity class method), [1] from_pdb() (buildamol.core.entity.BaseEntity class method), [1] from_pdbqt() (buildamol.core.entity.BaseEntity class method), [1] from_pubchem() (buildamol.core.Molecule.Molecule class method), [1] from_pybel() (buildamol.core.entity.BaseEntity class method), [1] from_quartet() (buildamol.utils.ic.InternalCoordinates class method) from_rdkit() (buildamol.core.entity.BaseEntity class method), [1] from_reactivities() (buildamol.core.Reaction class method), [1] from_smiles() (buildamol.core.Molecule.Molecule class method), [1] from_stk() (buildamol.core.entity.BaseEntity class method), [1] from_xml() (buildamol.core.entity.BaseEntity class method), [1] (buildamol.core.Linkage.Linkage class method), [1] (buildamol.resources.charmm.CHARMMTopology class method) (buildamol.resources.pdbe_compounds.PDBECompounds class method) from_xyz() (buildamol.core.entity.BaseEntity class method), [1] full_id (buildamol.base_classes.Atom property), [1] (buildamol.base_classes.Chain property), [1] (buildamol.base_classes.Model property), [1] (buildamol.base_classes.Residue property), [1] (buildamol.base_classes.Structure property), [1] fullname (buildamol.base_classes.Atom attribute), [1] functional_group_addable() (buildamol.extensions.molecular_factories.derivator.Derivator method) FunctionalGroup (class in buildamol.structural.groups) G generate_quartets() (in module buildamol.structural.neighbors) generate_triplets() (in module buildamol.structural.neighbors) genetic_optimize() (in module buildamol.optimizers.algorithms) Geometry (class in buildamol.structural.geometry) get() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) (buildamol.resources.pdbe_compounds.PDBECompounds method) get_3prime() (in module buildamol.extensions.bio.nucleic_acids.simple_sequences) get_5prime() (in module buildamol.extensions.bio.nucleic_acids.simple_sequences) get_ancestors() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) get_anchors() (buildamol.structural.connector.Connector method) (buildamol.structural.patch.Patcher method) get_args() (in module buildamol.utils.auxiliary) get_atom() (buildamol.base_classes.Residue method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.abstract.AbstractEntity method) get_atom_assignment() (buildamol.structural.groups.BaseFunctionalGroup method) get_atom_graph() (buildamol.core.entity.BaseEntity method), [1] get_atom_quartets() (buildamol.core.entity.BaseEntity method), [1] get_atom_triplets() (buildamol.core.entity.BaseEntity method), [1] get_atomic_bond() (buildamol.graphs.ResidueGraph method) get_atoms() (buildamol.base_classes.Residue method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.auxiliary.AtomIterator method) (buildamol.utils.auxiliary.DummyStructure method) get_atoms_by_type() (buildamol.utils.abstract.AbstractEntity method) get_atoms_within() (buildamol.core.entity.BaseEntity method), [1] get_attach_residue() (buildamol.core.entity.BaseEntity method), [1] get_axial_hydrogen() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] get_axial_hydrogen_neighbor() (in module buildamol.structural.infer) get_axial_neighbor() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) get_bond() (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.abstract.AbstractEntity method) get_bond_array() (buildamol.core.entity.BaseEntity method), [1] get_bond_mask() (buildamol.core.entity.BaseEntity method), [1] get_bonds() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.core.entity.BaseEntity method), [1] get_chain() (buildamol.base_classes.Model method), [1] (buildamol.core.entity.BaseEntity method), [1] get_chains() (buildamol.base_classes.Model method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.auxiliary.DummyStructure method) get_complex() (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) get_compound() (in module buildamol.resources.pdbe_compounds) get_coord() (buildamol.base_classes.Residue method), [1] get_coords() (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.core.entity.BaseEntity method), [1] get_cycle() (buildamol.graphs.base_graph.BaseGraph method) get_data() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) get_default_compounds() (in module buildamol.resources.pdbe_compounds) get_default_instance() (in module buildamol.utils.defaults) get_default_topology() (in module buildamol.resources.charmm) get_degree() (buildamol.core.entity.BaseEntity method), [1] get_descendants() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) get_double_bonds() (buildamol.core.entity.BaseEntity method), [1] get_equatorial_hydrogen() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] get_equatorial_hydrogen_neighbor() (in module buildamol.structural.infer) get_equatorial_neighbor() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) get_hydrogen() (buildamol.core.entity.BaseEntity method), [1] get_hydrogens() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] get_internal_coordinates() (buildamol.utils.abstract.AbstractEntity_with_IC method) get_left_hydrogen() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] get_left_hydrogen_neighbor() (in module buildamol.structural.infer) get_linkage() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.resources.charmm) get_locked_edges() (buildamol.graphs.base_graph.BaseGraph method) get_model() (buildamol.core.entity.BaseEntity method), [1] get_models() (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.auxiliary.DummyStructure method) get_neighbors() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.AtomGraph method) (buildamol.graphs.base_graph.BaseGraph method) (buildamol.graphs.ResidueGraph method) (buildamol.structural.neighbors.AtomNeighborhood method) (buildamol.structural.neighbors.Neighborhood method) (buildamol.structural.neighbors.ResidueNeighborhood method) get_other_atom() (buildamol.base_classes.Bond method), [1] get_parent() (buildamol.utils.abstract.AbstractAtom method) (buildamol.utils.abstract.AbstractBond method) get_patch() (buildamol.resources.charmm.CHARMMTopology method) (in module buildamol.resources.charmm) get_quartets() (buildamol.core.entity.BaseEntity method), [1] get_reference_atoms() (buildamol.utils.ic.InternalCoordinates method) get_residue() (buildamol.base_classes.Chain method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.ResidueGraph method) get_residue_connections() (buildamol.core.entity.BaseEntity method), [1] (buildamol.core.Molecule.Molecule method), [1] get_residue_graph() (buildamol.core.entity.BaseEntity method), [1] get_residues() (buildamol.base_classes.Chain method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.auxiliary.DummyStructure method) get_right_hydrogen() (buildamol.base_classes.Atom method), [1] (buildamol.core.entity.BaseEntity method), [1] get_right_hydrogen_neighbor() (in module buildamol.structural.infer) get_root() (buildamol.core.entity.BaseEntity method), [1] get_single_bonds() (buildamol.core.entity.BaseEntity method), [1] get_structure() (buildamol.core.entity.BaseEntity method), [1] get_triple_bonds() (buildamol.core.entity.BaseEntity method), [1] get_type() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) get_types() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) get_unlocked_edges() (buildamol.graphs.base_graph.BaseGraph method) global_modifiers() (buildamol.extensions.molecular_factories.derivator.Derivator method) globally_applied_groups (in module buildamol.structural.groups) glycan() (in module buildamol.extensions.bio.glycans.glycan) H has_any_element() (buildamol.structural.neighbors.constraints method) has_any_element_of() (buildamol.structural.neighbors.constraints_v2 method) has_any_id() (buildamol.structural.neighbors.constraints method) has_at_least_n_neighbors() (buildamol.structural.neighbors.constraints method) has_at_most_n_neighbors() (buildamol.structural.neighbors.constraints method) has_atom() (buildamol.utils.abstract.AbstractEntity method) has_bond_of_order_with() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_bond_order_hist() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_bonds_of_order() (buildamol.structural.neighbors.constraints_v2 method) has_clashes() (buildamol.core.entity.BaseEntity method), [1] has_compound() (in module buildamol.resources.pdbe_compounds) has_double_bond_with() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_double_bonds() (buildamol.structural.neighbors.constraints_v2 method) has_element() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_free_valence() (in module buildamol.structural.infer) has_hydrogens() (buildamol.core.entity.BaseEntity method), [1] has_IC (buildamol.utils.abstract.AbstractEntity_with_IC property) has_id() (buildamol.structural.neighbors.constraints method) has_linkage() (in module buildamol.resources.charmm) has_n_bonds() (buildamol.structural.neighbors.constraints_v2 method) has_n_neighbors() (buildamol.structural.neighbors.constraints method) has_neighbor_hist() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_not_element() (buildamol.structural.neighbors.constraints method) has_not_id() (buildamol.structural.neighbors.constraints method) has_not_n_neighbors() (buildamol.structural.neighbors.constraints method) has_package() (in module buildamol.utils.auxiliary) has_patch() (buildamol.resources.charmm.CHARMMTopology method) (in module buildamol.resources.charmm) has_residue() (buildamol.resources.pdbe_compounds.PDBECompounds method) has_single_bond_with() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_single_bonds() (buildamol.structural.neighbors.constraints_v2 method) has_triple_bond_with() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) has_triple_bonds() (buildamol.structural.neighbors.constraints_v2 method) higher_order_groups (in module buildamol.structural.groups) highlight_atoms() (buildamol.utils.visual.Chem2DViewer method) (buildamol.utils.visual.PlotlyViewer3D method) highlight_bonds() (buildamol.utils.visual.Chem2DViewer method) highlight_residues() (buildamol.utils.visual.Chem2DViewer method) (buildamol.utils.visual.PlotlyViewer3D method) hydrogen_neighbors() (buildamol.structural.infer.AutoLabel static method) Hydrogenator (class in buildamol.structural.infer) Hydroxyl (class in buildamol.structural.reactivity) hydroxylate() (in module buildamol.core.Molecule), [1] I IC_atom_ids (buildamol.utils.abstract.AbstractEntity_with_IC property) id (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Residue property), [1] (buildamol.core.entity.BaseEntity property), [1] (buildamol.core.Linkage.Linkage attribute), [1] (buildamol.resources.charmm.CHARMMTopology attribute) identify_atoms() (buildamol.core.Linkage.Linkage method), [1] ids (buildamol.resources.pdbe_compounds.PDBECompounds property) (buildamol.utils.ic.InternalCoordinates property) improper (buildamol.structural.neighbors.Quartet property) in_cycle() (buildamol.graphs.base_graph.BaseGraph method) in_same_cycle() (buildamol.graphs.base_graph.BaseGraph method) index_by_chain() (buildamol.core.entity.BaseEntity method), [1] infer_bond_orders() (in module buildamol.structural.infer) infer_bonds() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) infer_bonds_for() (buildamol.core.entity.BaseEntity method), [1] infer_bonds_for_atoms() (buildamol.core.entity.BaseEntity method), [1] infer_bonds_for_residues() (buildamol.core.entity.BaseEntity method), [1] infer_electrophile_atoms() (buildamol.structural.groups.BaseFunctionalGroup method) infer_hydrogens() (buildamol.structural.infer.Hydrogenator method) infer_nucleophile_atoms() (buildamol.structural.groups.BaseFunctionalGroup method) infer_residue_connections() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) infer_search_param() (in module buildamol.core.entity) infer_surface_residues() (in module buildamol.structural.infer) internal_coord (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Residue attribute), [1] internal_coordinates (buildamol.core.Linkage.Linkage attribute), [1] InternalCoordinates (class in buildamol.utils.ic) invert() (buildamol.base_classes.Bond method), [1] is_atom() (buildamol.structural.neighbors.constraints method) is_biopython() (in module buildamol.utils.convert) is_cis() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] is_done() (buildamol.optimizers.base_rotatron.Rotatron method) (buildamol.optimizers.distance_rotatron.DistanceRotatron method) is_double() (buildamol.base_classes.Bond method), [1] is_improper (buildamol.utils.ic.InternalCoordinates property) is_locked() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) is_proper (buildamol.utils.ic.InternalCoordinates property) is_pybel() (in module buildamol.utils.convert) is_rdkit() (in module buildamol.utils.convert) is_residue() (buildamol.structural.neighbors.constraints method) is_single() (buildamol.base_classes.Bond method), [1] is_trans() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] is_triple() (buildamol.base_classes.Bond method), [1] iter_molecules() (buildamol.resources.pdbe_compounds.PDBECompounds method) IUPACParser (class in buildamol.extensions.bio.glycans.iupac) J jensen_shannon_overlap() (in module buildamol.optimizers.overlap_rotatron) K Ketone (class in buildamol.structural.reactivity) L label_atoms() (buildamol.utils.visual.Chem2DViewer method) lazy_module() (in module buildamol.utils.auxiliary) left_adjust() (in module buildamol.utils.pdb) length (buildamol.base_classes.Bond property), [1] length_along_axis() (in module buildamol.structural.base) lengths (buildamol.utils.ic.InternalCoordinates property) level (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Model attribute), [1] (buildamol.base_classes.Residue attribute), [1] (buildamol.base_classes.Structure attribute), [1] linear (buildamol.structural.infer.Hydrogenator attribute) Linear (class in buildamol.structural.geometry) linear (in module buildamol.structural.geometry) linear_alkane() (in module buildamol.extensions.polymers.polycarbons) linear_alkene() (in module buildamol.extensions.polymers.polycarbons) link() (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.utils.visual.AtomGraphViewer3D method) (buildamol.utils.visual.MoleculeViewer3D method) (buildamol.utils.visual.ResidueGraphViewer3D method) link_atoms() (buildamol.core.entity.BaseEntity method), [1] link_chains() (buildamol.core.entity.BaseEntity method), [1] link_residues() (buildamol.core.entity.BaseEntity method), [1] linkage (buildamol.core.entity.BaseEntity property), [1] Linkage (class in buildamol.core.Linkage), [1] linkage() (in module buildamol.core.Linkage), [1] linkages (buildamol.resources.charmm.CHARMMTopology property) load() (buildamol.core.entity.BaseEntity class method), [1] (buildamol.resources.pdbe_compounds.PDBECompounds class method) load_all_compounds() (in module buildamol.resources.pdbe_compounds) load_amino_acids() (in module buildamol.resources.pdbe_compounds) load_lipids() (in module buildamol.resources.pdbe_compounds) load_nucleotides() (in module buildamol.resources.pdbe_compounds) load_pickle() (in module buildamol.utils.auxiliary) load_small_molecules() (in module buildamol.resources.pdbe_compounds) load_sugars() (in module buildamol.resources.pdbe_compounds) lock_all() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) lock_bond() (buildamol.core.entity.BaseEntity method), [1] lock_centers() (buildamol.graphs.ResidueGraph method) lock_edge() (buildamol.graphs.base_graph.BaseGraph method) locked_bonds (buildamol.core.entity.BaseEntity property), [1] M make() (buildamol.extensions.molecular_factories.assembler.Assembler method) (buildamol.extensions.molecular_factories.derivator.Derivator method) make_and_apply() (buildamol.structural.geometry.Geometry method) make_atom_graph() (buildamol.core.entity.BaseEntity method), [1] make_atoms_table() (in module buildamol.utils.pdb) make_bond_lines() (in module buildamol.utils.cif) make_bond_table() (in module buildamol.utils.cif) make_connect_table() (in module buildamol.utils.pdb) make_coords() (buildamol.structural.geometry.Geometry method) (buildamol.structural.geometry.Linear method) (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.SquarePlanar method) (buildamol.structural.geometry.Tetrahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) (buildamol.structural.geometry.TrigonalPlanar method) make_coords_from_one() (buildamol.structural.geometry.Linear method) (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.SquarePlanar method) (buildamol.structural.geometry.Tetrahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) (buildamol.structural.geometry.TrigonalPlanar method) make_coords_from_three() (buildamol.structural.geometry.SquarePlanar method) (buildamol.structural.geometry.Tetrahedral method) (buildamol.structural.geometry.TrigonalPlanar method) make_coords_from_three_mixed() (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) make_coords_from_three_planar() (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) make_coords_from_two() (buildamol.structural.geometry.Linear method) (buildamol.structural.geometry.SquarePlanar method) (buildamol.structural.geometry.Tetrahedral method) (buildamol.structural.geometry.TrigonalPlanar method) make_coords_from_two_axial() (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) make_coords_from_two_planar() (buildamol.structural.geometry.Octahedral method) (buildamol.structural.geometry.TrigonalBipyramidal method) make_core() (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) make_detailed() (buildamol.graphs.ResidueGraph method) make_df() (buildamol.utils.visual.AtomGraphViewer3D method) (buildamol.utils.visual.MoleculeViewer3D method) (buildamol.utils.visual.ResidueGraphViewer3D method) make_empty_structure() (in module buildamol.structural.base) make_formula() (in module buildamol.utils.auxiliary) make_header() (in module buildamol.utils.cif) make_residue_graph() (buildamol.core.entity.BaseEntity method), [1] make_smiles() (in module buildamol.core.Molecule), [1] (in module buildamol.structural.smiles) mass (buildamol.base_classes.Atom attribute), [1] (buildamol.core.entity.BaseEntity property), [1] matches() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.structural.groups.AromaticGroup method) (buildamol.structural.groups.BaseFunctionalGroup method) (buildamol.structural.groups.FunctionalGroup method) max_points (buildamol.structural.geometry.Geometry attribute) (buildamol.structural.geometry.Linear attribute) (buildamol.structural.geometry.Octahedral attribute) (buildamol.structural.geometry.SquarePlanar attribute) (buildamol.structural.geometry.Tetrahedral attribute) (buildamol.structural.geometry.TrigonalBipyramidal attribute) (buildamol.structural.geometry.TrigonalPlanar attribute) merge() (buildamol.core.entity.BaseEntity method), [1] (buildamol.extensions.complexes.rotaxane_builder.RotaxaneBuilder method) (buildamol.resources.pdbe_compounds.PDBECompounds method) (buildamol.structural.patch.Patcher method) (buildamol.structural.stitch.Stitcher method) MetalComplexer (class in buildamol.extensions.complexes.metal_complexer) methylate() (in module buildamol.core.Molecule), [1] migrate_atoms() (buildamol.utils.abstract.AbstractBond method) migrate_bonds() (buildamol.graphs.AtomGraph method) model (buildamol.core.entity.BaseEntity property), [1] Model (class in buildamol.base_classes), [1] model_make_full_id() (in module buildamol.structural.base) models (buildamol.core.entity.BaseEntity property), [1] module buildamol.base_classes, [1] buildamol.core buildamol.core.entity buildamol.core.Linkage, [1] buildamol.core.Molecule, [1] buildamol.extensions.bio.glycans.glycan buildamol.extensions.bio.glycans.iupac buildamol.extensions.bio.lipids.simple_lipids buildamol.extensions.bio.nucleic_acids.simple_sequences buildamol.extensions.bio.proteins.peptides buildamol.extensions.complexes.metal_complexer buildamol.extensions.complexes.rotaxane_builder buildamol.extensions.molecular_dynamics.atom_typing.atom_typer buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer buildamol.extensions.molecular_dynamics.psf buildamol.extensions.molecular_factories.assembler buildamol.extensions.molecular_factories.derivator buildamol.extensions.polymers.nanotubes buildamol.extensions.polymers.polycarbons buildamol.optimizers.base_rotatron buildamol.optimizers.circulatron buildamol.optimizers.constraint_rotatron buildamol.optimizers.distance_rotatron buildamol.optimizers.forcefield_rotatron buildamol.optimizers.overlap_rotatron buildamol.optimizers.translatron buildamol.optimizers.utils buildamol.resources.__init__ buildamol.resources.charmm buildamol.resources.pdbe_compounds buildamol.resources.pubchem buildamol.structural.base buildamol.structural.connector buildamol.structural.geometry buildamol.structural.groups buildamol.structural.infer buildamol.structural.neighbors buildamol.structural.patch buildamol.structural.reactivity buildamol.structural.smiles buildamol.structural.stitch buildamol.utils.abstract buildamol.utils.auxiliary buildamol.utils.cif buildamol.utils.constants buildamol.utils.convert buildamol.utils.defaults buildamol.utils.ic buildamol.utils.pdb mol_to_numpy_array() (in module buildamol.utils.convert) molecule (buildamol.base_classes.Atom property), [1] (buildamol.base_classes.Chain property), [1] (buildamol.base_classes.Model property), [1] (buildamol.base_classes.Residue property), [1] (buildamol.base_classes.Structure property), [1] Molecule (class in buildamol.core.Molecule), [1] molecule() (in module buildamol.core.Molecule), [1] molecule_to_pdbio() (buildamol.utils.convert.PDBIO method) molecules (buildamol.resources.pdbe_compounds.PDBECompounds property) MoleculeViewer3D (class in buildamol.utils.visual) move() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.core.entity.BaseEntity method), [1] move_to() (buildamol.core.entity.BaseEntity method), [1] multi_constraint() (buildamol.structural.neighbors.constraints method) MVN() (in module buildamol.optimizers.overlap_rotatron) N N (buildamol.extensions.molecular_factories.derivator.Derivator property) name (buildamol.base_classes.Atom property), [1] (buildamol.base_classes.Chain property), [1] (buildamol.base_classes.Residue property), [1] nand_() (buildamol.structural.neighbors.constraints_v2 method) nanotube() (in module buildamol.extensions.polymers.nanotubes) Neighborhood (class in buildamol.structural.neighbors) neighbors_all() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) neighbors_any() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) neighbors_exactly() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) neighbors_not() (buildamol.structural.neighbors.constraints method) new() (buildamol.base_classes.Atom class method), [1] (buildamol.base_classes.Chain class method), [1] (buildamol.base_classes.Model class method), [1] (buildamol.base_classes.Residue class method), [1] (buildamol.base_classes.Structure class method), [1] (buildamol.core.Molecule.Molecule class method), [1] nglview() (buildamol.core.entity.BaseEntity method), [1] NglViewer (class in buildamol.utils.visual) njit() (in module buildamol.utils.auxiliary) nodes_in_cycles (buildamol.graphs.base_graph.BaseGraph property) none() (buildamol.structural.neighbors.constraints method) (buildamol.structural.neighbors.constraints_v2 method) nor_() (buildamol.structural.neighbors.constraints_v2 method) norm_vector() (in module buildamol.structural.base) not_() (buildamol.structural.neighbors.constraints_v2 method) not_has_any_element_of() (buildamol.structural.neighbors.constraints_v2 method) not_has_element() (buildamol.structural.neighbors.constraints_v2 method) nothing() (buildamol.extensions.molecular_factories.derivator.Derivator method) nucleic_acid() (in module buildamol.extensions.bio.nucleic_acids.simple_sequences) nucleophile_linker() (buildamol.structural.reactivity.Aldehyde method) (buildamol.structural.reactivity.AlkylHalide method) (buildamol.structural.reactivity.Amide method) (buildamol.structural.reactivity.Amine method) (buildamol.structural.reactivity.Carboxyl method) (buildamol.structural.reactivity.Ester method) (buildamol.structural.reactivity.Hydroxyl method) (buildamol.structural.reactivity.Ketone method) (buildamol.structural.reactivity.Phosphate method) (buildamol.structural.reactivity.Thiol method) O occupancy (buildamol.base_classes.Atom attribute), [1] Octahedral (class in buildamol.structural.geometry) octahedral (in module buildamol.structural.geometry) omega() (in module buildamol.extensions.bio.proteins.peptides) openmm_to_biopython() (buildamol.utils.convert.OpenMMBioPythonConverter method) OpenMMBioPythonConverter (class in buildamol.utils.convert) optimize() (buildamol.core.Molecule.Molecule method), [1] (buildamol.extensions.complexes.rotaxane_builder.RotaxaneBuilder method) (in module buildamol.optimizers.utils) or_() (buildamol.structural.neighbors.constraints_v2 method) order (buildamol.base_classes.Bond attribute), [1] origin (in module buildamol.structural.base) OverlapRotatron (class in buildamol.optimizers.overlap_rotatron) P parallel_optimize() (in module buildamol.optimizers.utils) parent (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Model attribute), [1] (buildamol.base_classes.Residue attribute), [1] (buildamol.base_classes.Structure attribute), [1] parse() (buildamol.extensions.bio.glycans.iupac.IUPACParser method) parse_atom_lines() (in module buildamol.utils.pdb) parse_bond_table() (in module buildamol.utils.cif) parse_connect_lines() (in module buildamol.utils.pdb) patch (buildamol.core.entity.BaseEntity property), [1] patch() (in module buildamol.core.Linkage), [1] (in module buildamol.structural.patch) patch_attach() (buildamol.core.Molecule.Molecule method), [1] Patcher (class in buildamol.structural.patch) PatchError patches (buildamol.resources.charmm.CHARMMTopology attribute) (buildamol.resources.charmm.CHARMMTopology property) PDBECompounds (class in buildamol.resources.pdbe_compounds) PDBIO (class in buildamol.utils.convert) pdbio_to_biopython() (buildamol.utils.convert.PDBIO method) peptide() (in module buildamol.extensions.bio.proteins.peptides) phenolate() (in module buildamol.core.Molecule), [1] phi() (in module buildamol.extensions.bio.proteins.peptides) Phosphate (class in buildamol.structural.reactivity) phospholipid() (in module buildamol.extensions.bio.lipids.simple_lipids) phosphorylate() (in module buildamol.core.Molecule), [1] place() (buildamol.core.entity.BaseEntity method), [1] plane_of_points() (in module buildamol.structural.base) plane_vector() (in module buildamol.structural.base) plotly() (buildamol.core.entity.BaseEntity method), [1] PlotlyViewer3D (class in buildamol.utils.visual) polymerize() (in module buildamol.core.Molecule), [1] pqr_charge (buildamol.base_classes.Atom attribute), [1] prepare_dict_for() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) principal_axis() (in module buildamol.structural.base) progress_bar() (in module buildamol.utils.auxiliary) prune_triplets() (buildamol.graphs.ResidueGraph method) PSFMaker (class in buildamol.extensions.molecular_dynamics.psf) psi() (in module buildamol.extensions.bio.proteins.peptides) pubchem_to_cif() (in module buildamol.resources.pubchem) purge_bonds() (buildamol.core.entity.BaseEntity method), [1] py3dmol() (buildamol.core.entity.BaseEntity method), [1] Py3DmolViewer (class in buildamol.utils.visual) pybel_atom_to_biopython() (buildamol.utils.convert.PybelBioPythonConverter method) pybel_molecule_to_biopython() (buildamol.utils.convert.PybelBioPythonConverter method) pybel_residue_to_biopython() (buildamol.utils.convert.PybelBioPythonConverter method) PybelBioPythonConverter (class in buildamol.utils.convert) Q Quartet (class in buildamol.structural.neighbors) quartet() (buildamol.core.entity.BaseEntity method), [1] query() (in module buildamol.resources.pubchem) query_pubchem() (in module buildamol.core.Molecule), [1] R radius (buildamol.base_classes.Atom attribute), [1] rainbow() (buildamol.utils.visual.MoleculeViewer3D method) (buildamol.utils.visual.ResidueGraphViewer3D method) random() (buildamol.extensions.molecular_factories.assembler.Assembler method) rdkit_to_biopython() (buildamol.utils.convert.RDKITBiopythonConverter method) RDKITBiopythonConverter (class in buildamol.utils.convert) react() (in module buildamol.core.Molecule), [1] react_with() (buildamol.core.Molecule.Molecule method), [1] Reaction (class in buildamol.core), [1] ReactionError Reactivity (class in buildamol.structural.reactivity) read_cif() (in module buildamol.core.Molecule), [1] read_compounds() (in module buildamol.resources.pdbe_compounds) read_molfile() (in module buildamol.core.Molecule), [1] read_pdb() (in module buildamol.core.Molecule), [1] read_smiles() (in module buildamol.core.Molecule), [1] (in module buildamol.structural.smiles) read_topology() (in module buildamol.resources.charmm) recipe (buildamol.core.entity.BaseEntity property), [1] recipe() (in module buildamol.core.Linkage), [1] reindex() (buildamol.core.entity.BaseEntity method), [1] relabel_atoms() (buildamol.resources.pdbe_compounds.PDBECompounds method) relabel_hydrogens() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.infer) remove() (buildamol.resources.pdbe_compounds.PDBECompounds method) remove_atoms() (buildamol.core.entity.BaseEntity method), [1] remove_bond() (buildamol.core.entity.BaseEntity method), [1] remove_chains() (buildamol.core.entity.BaseEntity method), [1] remove_empty_chains() (buildamol.core.entity.BaseEntity method), [1] remove_empty_models() (buildamol.core.entity.BaseEntity method), [1] remove_empty_residues() (buildamol.core.entity.BaseEntity method), [1] remove_hydrogens() (buildamol.core.entity.BaseEntity method), [1] remove_internal_coordinates() (buildamol.utils.abstract.AbstractEntity_with_IC method) remove_model() (buildamol.core.entity.BaseEntity method), [1] remove_nonprintable() (in module buildamol.utils.auxiliary) remove_residues() (buildamol.core.entity.BaseEntity method), [1] rename_atom() (buildamol.core.entity.BaseEntity method), [1] rename_atoms() (buildamol.core.entity.BaseEntity method), [1] rename_chain() (buildamol.core.entity.BaseEntity method), [1] rename_residue() (buildamol.core.entity.BaseEntity method), [1] (in module buildamol.structural.base) rename_residues() (buildamol.core.entity.BaseEntity method), [1] repeat() (buildamol.core.Molecule.Molecule method), [1] reset() (buildamol.extensions.bio.glycans.iupac.IUPACParser method) (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) (buildamol.optimizers.base_rotatron.Rotatron method) (buildamol.optimizers.constraint_rotatron.ConstraintRotatron method) (buildamol.optimizers.translatron.Translatron method) (buildamol.utils.visual.MoleculeViewer3D method) (buildamol.utils.visual.PlotlyViewer3D method) Residue (class in buildamol.base_classes), [1] residue_make_full_id() (in module buildamol.structural.base) residue_names (buildamol.extensions.molecular_dynamics.atom_typing.charmm_typer.CHARMMTyper property) ResidueGraph (class in buildamol.graphs) ResidueGraphViewer3D (class in buildamol.utils.visual) ResidueNeighborhood (class in buildamol.structural.neighbors) residues (buildamol.base_classes.Chain property), [1] (buildamol.core.entity.BaseEntity property), [1] (buildamol.graphs.base_graph.BaseGraph property) (buildamol.graphs.ResidueGraph property) (buildamol.structural.neighbors.ResidueNeighborhood property) resname (buildamol.base_classes.Residue attribute), [1] RESOURCES (in module buildamol.utils.constants) restore_default_compounds() (in module buildamol.resources.pdbe_compounds) restore_default_topology() (in module buildamol.resources.charmm) reverse() (buildamol.core.Linkage.Linkage method), [1] right_adjust() (in module buildamol.utils.pdb) rna() (in module buildamol.extensions.bio.nucleic_acids.simple_sequences) root_atom (buildamol.core.entity.BaseEntity property), [1] root_residue (buildamol.core.entity.BaseEntity property), [1] rotate() (buildamol.core.entity.BaseEntity method), [1] rotate_ancestors() (buildamol.core.entity.BaseEntity method), [1] rotate_around_bond() (buildamol.core.entity.BaseEntity method), [1] rotate_around_edge() (buildamol.graphs.base_graph.BaseGraph method) rotate_coords() (in module buildamol.structural.base) rotate_descendants() (buildamol.core.entity.BaseEntity method), [1] rotate_molecule() (in module buildamol.structural.base) Rotatron (class in buildamol.optimizers.base_rotatron) rotaxane() (in module buildamol.extensions.complexes.rotaxane_builder) RotaxaneBuilder (class in buildamol.extensions.complexes.rotaxane_builder) S sample() (buildamol.extensions.molecular_factories.assembler.Assembler method) (buildamol.extensions.molecular_factories.derivator.Derivator method) sample_atoms_around_reference() (in module buildamol.structural.infer) sample_edges() (buildamol.graphs.base_graph.BaseGraph method) save() (buildamol.core.entity.BaseEntity method), [1] (buildamol.resources.pdbe_compounds.PDBECompounds method) save_as_default_compounds() (in module buildamol.resources.pdbe_compounds) save_compounds() (in module buildamol.resources.pdbe_compounds) save_pickle() (in module buildamol.utils.auxiliary) save_topology() (in module buildamol.resources.charmm) scipy_optimize() (in module buildamol.optimizers.algorithms) search_by_constraints() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.AtomGraph method) (buildamol.graphs.base_graph.BaseGraph method) (buildamol.graphs.ResidueGraph method) (buildamol.structural.neighbors.Neighborhood method) segid (buildamol.base_classes.Residue attribute), [1] sequence() (in module buildamol.extensions.bio.proteins.peptides) sequence_to_1letter() (in module buildamol.extensions.bio.proteins.peptides) sequence_to_3letter() (in module buildamol.extensions.bio.proteins.peptides) serial_num (buildamol.base_classes.Model property), [1] serial_number (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Model property), [1] set_attach_residue() (buildamol.core.entity.BaseEntity method), [1] set_bond() (buildamol.core.entity.BaseEntity method), [1] set_bond_order() (buildamol.core.entity.BaseEntity method), [1] set_bonders() (buildamol.structural.groups.BaseFunctionalGroup method) set_bonds() (buildamol.core.entity.BaseEntity method), [1] set_charge() (buildamol.core.entity.BaseEntity method), [1] set_colors() (buildamol.utils.visual.Chem2DViewer method) set_coord() (buildamol.base_classes.Residue method), [1] set_coords() (buildamol.core.entity.BaseEntity method), [1] set_data() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) set_default_compounds() (in module buildamol.resources.pdbe_compounds) set_default_instance() (in module buildamol.utils.defaults) set_default_topology() (in module buildamol.resources.charmm) set_deletes() (buildamol.structural.groups.BaseFunctionalGroup method) set_element() (buildamol.base_classes.Atom method), [1] set_full_id() (in module buildamol.structural.base) set_id() (buildamol.base_classes.Atom method), [1] set_linkage() (buildamol.core.entity.BaseEntity method), [1] set_model() (buildamol.core.entity.BaseEntity method), [1] set_options() (buildamol.utils.visual.Chem2DViewer method) set_parent() (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.abstract.AbstractAtom method) set_patch() (buildamol.structural.patch.Patcher method) set_reactivity() (buildamol.core.Reaction method), [1] (buildamol.structural.groups.BaseFunctionalGroup method) (buildamol.structural.reactivity.Reactivity method) set_root() (buildamol.core.entity.BaseEntity method), [1] set_source() (buildamol.structural.connector.Connector method) set_steric_constraints() (buildamol.structural.reactivity.Reactivity method) set_style() (buildamol.utils.visual.Py3DmolViewer method) set_target() (buildamol.structural.connector.Connector method) set_type() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) setup() (buildamol.utils.visual.MoleculeViewer3D method) should_invert() (in module buildamol.core.entity) show() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) (buildamol.utils.visual.Chem2DViewer method) (buildamol.utils.visual.NglViewer method) (buildamol.utils.visual.PlotlyViewer3D method) (buildamol.utils.visual.Py3DmolViewer method) show2d() (buildamol.core.entity.BaseEntity method), [1] show3d() (buildamol.core.entity.BaseEntity method), [1] sigatm_array (buildamol.base_classes.Atom attribute), [1] siguij_array (buildamol.base_classes.Atom attribute), [1] simple_concatenation_function() (in module buildamol.optimizers.distance_rotatron) single() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] size (buildamol.structural.geometry.Geometry attribute) (buildamol.structural.geometry.Linear attribute) (buildamol.structural.geometry.Octahedral attribute) (buildamol.structural.geometry.SquarePlanar attribute) (buildamol.structural.geometry.Tetrahedral attribute) (buildamol.structural.geometry.TrigonalBipyramidal attribute) (buildamol.structural.geometry.TrigonalPlanar attribute) specify_attachment_points() (buildamol.extensions.molecular_factories.assembler.Assembler method) sphingolipid() (in module buildamol.extensions.bio.lipids.simple_lipids) split_contiguous() (buildamol.core.entity.BaseEntity method), [1] split_environment() (in module buildamol.optimizers.utils) split_into_contiguous_residues() (in module buildamol.structural.infer) split_models() (buildamol.core.entity.BaseEntity method), [1] split_residues() (buildamol.core.entity.BaseEntity method), [1] square_planar (in module buildamol.structural.geometry) SquarePlanar (class in buildamol.structural.geometry) squash() (buildamol.core.entity.BaseEntity method), [1] squash_chains() (buildamol.core.entity.BaseEntity method), [1] stack() (buildamol.core.entity.BaseEntity method), [1] step() (buildamol.optimizers.base_rotatron.Rotatron method) (buildamol.optimizers.constraint_rotatron.ConstraintRotatron method) (buildamol.optimizers.translatron.Translatron method) stitch() (in module buildamol.structural.stitch) stitch_attach() (buildamol.core.Molecule.Molecule method), [1] Stitcher (class in buildamol.structural.stitch) stk_to_pdbio() (buildamol.utils.convert.STKBuildAMolConverter method) STKBuildAMolConverter (class in buildamol.utils.convert) store() (buildamol.extensions.complexes.metal_complexer.MetalComplexer method) structure (buildamol.core.entity.BaseEntity property), [1] (buildamol.graphs.base_graph.BaseGraph property) Structure (class in buildamol.base_classes), [1] subset_compounds_by_types() (in module buildamol.resources.pdbe_compounds) superimpose_points() (in module buildamol.structural.base) superimpose_to_atom() (buildamol.core.entity.BaseEntity method), [1] superimpose_to_bond() (buildamol.core.entity.BaseEntity method), [1] superimpose_to_pair() (buildamol.core.entity.BaseEntity method), [1] superimpose_to_residue() (buildamol.core.entity.BaseEntity method), [1] superimpose_to_triplet() (buildamol.core.entity.BaseEntity method), [1] swarm_optimize() (in module buildamol.optimizers.algorithms) T tetrahedral (buildamol.structural.infer.Hydrogenator attribute) Tetrahedral (class in buildamol.structural.geometry) tetrahedral (in module buildamol.structural.geometry) Thiol (class in buildamol.structural.reactivity) thiolate() (in module buildamol.core.Molecule), [1] to_AtomGraph() (buildamol.graphs.ResidueGraph method) to_biopython() (buildamol.base_classes.Atom method), [1] (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] (buildamol.core.entity.BaseEntity method), [1] (buildamol.utils.abstract.AbstractAtom method) to_cif() (buildamol.core.entity.BaseEntity method), [1] to_json() (buildamol.core.entity.BaseEntity method), [1] (buildamol.core.Linkage.Linkage method), [1] (buildamol.resources.charmm.CHARMMTopology method) (buildamol.resources.pdbe_compounds.PDBECompounds method) to_list() (buildamol.base_classes.Bond method), [1] to_molfile() (buildamol.core.entity.BaseEntity method), [1] to_numpy() (buildamol.core.entity.BaseEntity method), [1] to_openmm() (buildamol.core.entity.BaseEntity method), [1] to_pdb() (buildamol.core.entity.BaseEntity method), [1] to_pdbqt() (buildamol.core.entity.BaseEntity method), [1] to_pybel() (buildamol.core.entity.BaseEntity method), [1] to_rdkit() (buildamol.core.entity.BaseEntity method), [1] to_smiles() (buildamol.core.Molecule.Molecule method), [1] to_stk() (buildamol.core.entity.BaseEntity method), [1] to_tuple() (buildamol.base_classes.Bond method), [1] to_vector() (buildamol.base_classes.Bond method), [1] to_xml() (buildamol.core.entity.BaseEntity method), [1] (buildamol.core.Linkage.Linkage method), [1] (buildamol.resources.charmm.CHARMMTopology method) (buildamol.resources.pdbe_compounds.PDBECompounds method) to_xyz() (buildamol.core.entity.BaseEntity method), [1] trans() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] translate_ids_1_to_3() (buildamol.resources.pdbe_compounds.PDBECompounds method) translate_ids_3_to_1() (buildamol.resources.pdbe_compounds.PDBECompounds method) Translatron (class in buildamol.optimizers.translatron) transpose() (buildamol.core.entity.BaseEntity method), [1] triacylglycerol() (in module buildamol.extensions.bio.lipids.simple_lipids) trigonal_bipyramidal (in module buildamol.structural.geometry) trigonal_planar (buildamol.structural.infer.Hydrogenator attribute) (in module buildamol.structural.geometry) TrigonalBipyramidal (class in buildamol.structural.geometry) TrigonalPlanar (class in buildamol.structural.geometry) triple() (buildamol.base_classes.Bond method), [1] (buildamol.core.entity.BaseEntity method), [1] U unlink() (buildamol.base_classes.Chain method), [1] (buildamol.base_classes.Model method), [1] (buildamol.base_classes.Residue method), [1] (buildamol.base_classes.Structure method), [1] unlink_atoms() (buildamol.core.entity.BaseEntity method), [1] unlink_chains() (buildamol.core.entity.BaseEntity method), [1] unlink_residues() (buildamol.core.entity.BaseEntity method), [1] unload_all_compounds() (in module buildamol.resources.pdbe_compounds) unload_amino_acids() (in module buildamol.resources.pdbe_compounds) unload_by_types() (in module buildamol.resources.pdbe_compounds) unload_lipids() (in module buildamol.resources.pdbe_compounds) unload_nucleotides() (in module buildamol.resources.pdbe_compounds) unload_small_molecules() (in module buildamol.resources.pdbe_compounds) unload_sugars() (in module buildamol.resources.pdbe_compounds) unlock_all() (buildamol.core.entity.BaseEntity method), [1] (buildamol.graphs.base_graph.BaseGraph method) unlock_bond() (buildamol.core.entity.BaseEntity method), [1] unlock_edge() (buildamol.graphs.base_graph.BaseGraph method) update() (buildamol.extensions.molecular_dynamics.atom_typing.atom_typer.AtomTyper method) (buildamol.utils.auxiliary.DummyBar method) update_atom_graph() (buildamol.core.entity.BaseEntity method), [1] update_layout() (buildamol.utils.visual.PlotlyViewer3D method) use_all_numba() (in module buildamol.utils.auxiliary) use_ic() (in module buildamol.utils.auxiliary) use_numba() (in module buildamol.utils.auxiliary) V vector_between() (in module buildamol.structural.base) vet_structure() (in module buildamol.structural.infer) view (buildamol.utils.visual.Py3DmolViewer attribute) viewbox() (buildamol.utils.visual.PlotlyViewer3D method) W weight (buildamol.base_classes.Atom property), [1] with_reactivity() (buildamol.core.Reaction method), [1] (buildamol.structural.groups.BaseFunctionalGroup method) (buildamol.structural.reactivity.Reactivity method) write_bond_table() (in module buildamol.utils.cif) write_cif() (in module buildamol.core.Molecule), [1] write_connect_lines() (in module buildamol.utils.pdb) write_html() (buildamol.utils.visual.PlotlyViewer3D method) write_molfile() (in module buildamol.core.Molecule), [1] write_pdb() (in module buildamol.core.Molecule), [1] (in module buildamol.utils.pdb) write_psf() (buildamol.extensions.molecular_dynamics.psf.PSFMaker method) (in module buildamol.extensions.molecular_dynamics.psf) X x_axis (in module buildamol.structural.base) xnor_() (buildamol.structural.neighbors.constraints_v2 method) xor_() (buildamol.structural.neighbors.constraints_v2 method) xtra (buildamol.base_classes.Atom attribute), [1] (buildamol.base_classes.Chain attribute), [1] (buildamol.base_classes.Model attribute), [1] (buildamol.base_classes.Residue attribute), [1] (buildamol.base_classes.Structure attribute), [1] xy_plane (in module buildamol.structural.base) xz_plane (in module buildamol.structural.base) Y y_axis (in module buildamol.structural.base) yz_plane (in module buildamol.structural.base) Z z_axis (in module buildamol.structural.base)
