Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | V | W _ __and__() (molr.selection.SelectionExpression method) __getitem__() (molr.BondList method) (molr.Structure method) (molr.StructureEnsemble method) __init__() (molr.bond_detection.DefaultBondDetector method) (molr.BondList method) (molr.mmCIFParser method) (molr.PDBParser method) (molr.selection.AndExpression method) (molr.selection.AtomNameExpression method) (molr.selection.ByResidueExpression method) (molr.selection.ChainExpression method) (molr.selection.ElementExpression method) (molr.selection.IndexExpression method) (molr.selection.NotExpression method) (molr.selection.OrExpression method) (molr.selection.ResidueIdExpression method) (molr.selection.ResidueNameExpression method) (molr.selection.SelectionEngine method) (molr.selection.SelectionParser method) (molr.Structure method) (molr.StructureEnsemble method) __invert__() (molr.selection.SelectionExpression method) __iter__() (molr.StructureEnsemble method) __len__() (molr.BondList method) (molr.Structure method) (molr.StructureEnsemble method) __or__() (molr.selection.SelectionExpression method) __repr__() (molr.BondList method) (molr.selection.SelectionExpression method) (molr.Structure method) (molr.StructureEnsemble method) __str__() (molr.BondList method) (molr.Structure method) (molr.StructureEnsemble method) A add_annotation() (molr.Structure method) add_bond() (molr.BondList method) add_bonds() (molr.BondList method) add_frame() (molr.StructureEnsemble method) add_property() (molr.BondList method) AllExpression (class in molr.selection) AndExpression (class in molr.selection) AROMATIC_CODES (in module molr.constants.pdb_constants) AromaticExpression (class in molr.selection) ATOMIC_MASSES (molr.constants.atomic_data.AtomicData attribute) AtomicData (class in molr.constants.atomic_data) AtomNameExpression (class in molr.selection) B BACKBONE_ATOMS (in module molr.constants.pdb_constants) BACKBONE_SIDECHAIN_CODES (in module molr.constants.pdb_constants) BackboneExpression (class in molr.selection) BondList (class in molr) bonds (molr.Structure property) ByResidueExpression (class in molr.selection) C center_at_origin() (molr.Structure method) center_frames() (molr.StructureEnsemble method) ChainExpression (class in molr.selection) CHARGED_RESIDUES (in module molr.constants.pdb_constants) clear_cache() (molr.selection.SelectionEngine method) coord (molr.Structure property) copy() (molr.Structure method) count() (molr.selection.SelectionEngine method) COVALENT_RADII (molr.constants.atomic_data.AtomicData attribute) D DEFAULT_ATOMIC_MASS (molr.constants.atomic_data.AtomicData attribute) DefaultBondDetector (class in molr.bond_detection) detect_bonds() (in module molr.bond_detection) (molr.bond_detection.DefaultBondDetector method) (molr.Structure method) DNA_RESIDUES (in module molr.constants.pdb_constants) DNA_RNA_BACKBONE_ATOMS (in module molr.constants.pdb_constants) DNA_RNA_BASE_ATOMS (in module molr.constants.pdb_constants) DNAExpression (class in molr.selection) E ELECTRONEGATIVITY (molr.constants.atomic_data.AtomicData attribute) ElementExpression (class in molr.selection) evaluate() (molr.selection.AllExpression method) (molr.selection.AndExpression method) (molr.selection.AromaticExpression method) (molr.selection.AtomNameExpression method) (molr.selection.BackboneExpression method) (molr.selection.ByResidueExpression method) (molr.selection.ChainExpression method) (molr.selection.DNAExpression method) (molr.selection.ElementExpression method) (molr.selection.IndexExpression method) (molr.selection.LigandExpression method) (molr.selection.NoneExpression method) (molr.selection.NotExpression method) (molr.selection.NucleicExpression method) (molr.selection.OrExpression method) (molr.selection.ProteinExpression method) (molr.selection.ResidueIdExpression method) (molr.selection.ResidueNameExpression method) (molr.selection.RNAExpression method) (molr.selection.SelectionExpression method) (molr.selection.SidechainExpression method) (molr.selection.WaterExpression method) F file_bonds (molr.Structure property) filter_by_atoms() (molr.BondList method) from_mmcif() (molr.Structure class method) (molr.StructureEnsemble class method) from_mmcif_string() (molr.Structure class method) (molr.StructureEnsemble class method) from_pdb() (molr.Structure class method) (molr.StructureEnsemble class method) from_pdb_string() (molr.Structure class method) (molr.StructureEnsemble class method) from_structures() (molr.StructureEnsemble class method) G get_annotation_info() (molr.Structure method) get_atoms_between_selections() (molr.Structure method) get_atoms_within_cog_sphere() (molr.Structure method) get_atoms_within_sphere() (molr.Structure method) get_bond_matrix() (molr.BondList method) get_bonds_for_atom() (molr.BondList method) get_bonds_to() (molr.Structure method) get_ccd_data_path() (in module molr.config) get_center() (molr.Structure method) get_closest_atoms() (molr.Structure method) get_element_from_pdb_atom() (in module molr.utilities.atom_utils) get_frame_coords() (molr.StructureEnsemble method) get_indices() (molr.selection.SelectionEngine method) get_masses() (molr.Structure method) get_molr_data_dir() (in module molr.config) get_neighbors() (molr.BondList method) get_neighbors_for_atoms() (molr.Structure method) get_neighbors_within() (molr.Structure method) get_residue_bond_count() (in module molr.constants.residue_bonds) get_residue_bonds() (in module molr.constants.residue_bonds) H HALOGEN_BOND_ACCEPTOR_ELEMENTS (in module molr.constants.pdb_constants) HALOGEN_ELEMENTS (in module molr.constants.pdb_constants) has_aromatic_bonds() (in module molr.constants.residue_bonds) has_bonds() (molr.Structure method) has_file_bonds() (molr.Structure method) has_spatial_index() (molr.Structure method) HYDROGEN_BOND_ACCEPTOR_ELEMENTS (in module molr.constants.pdb_constants) HYDROGEN_BOND_DONOR_ELEMENTS (in module molr.constants.pdb_constants) HYDROGEN_ELEMENTS (in module molr.constants.pdb_constants) HYDROPHOBIC_RESIDUES (in module molr.constants.pdb_constants) I IndexExpression (class in molr.selection) is_aromatic (molr.Structure property) is_backbone (molr.Structure property) is_ligand (molr.Structure property) is_sidechain (molr.Structure property) L LigandExpression (class in molr.selection) M METAL_ELEMENTS (molr.constants.atomic_data.AtomicData attribute) MIN_HYDROGEN_RATIO (molr.constants.atomic_data.AtomicData attribute) mmCIFParser (class in molr) module molr.config molr.constants.atomic_data molr.constants.bond_parameters molr.constants.pdb_constants molr.constants.residue_bonds molr.utilities.atom_utils molr.config module molr.constants.atomic_data module molr.constants.bond_parameters module molr.constants.pdb_constants module molr.constants.residue_bonds module molr.utilities.atom_utils module N NoneExpression (class in molr.selection) NotExpression (class in molr.selection) NucleicExpression (class in molr.selection) O OrExpression (class in molr.selection) P parse() (molr.selection.SelectionParser method) parse_file() (molr.mmCIFParser method) (molr.PDBParser method) parse_selection() (molr.selection.SelectionParser class method) parse_string() (molr.mmCIFParser method) (molr.PDBParser method) PDB_ATOM_TO_ELEMENT (in module molr.constants.pdb_constants) pdb_atom_to_element() (in module molr.utilities.atom_utils) PDBParser (class in molr) PI_INTERACTION_ATOMS (in module molr.constants.pdb_constants) PI_INTERACTION_DONOR (in module molr.constants.pdb_constants) PROTEIN_BACKBONE_ATOMS (in module molr.constants.pdb_constants) PROTEIN_RESIDUES (in module molr.constants.pdb_constants) PROTEIN_SIDECHAIN_ATOMS (in module molr.constants.pdb_constants) PROTEIN_SUBSTITUTIONS (in module molr.constants.pdb_constants) ProteinExpression (class in molr.selection) R remove_bonds() (molr.BondList method) residue_type (molr.Structure property) RESIDUE_TYPE_CODES (in module molr.constants.pdb_constants) RESIDUE_TYPES (in module molr.constants.pdb_constants) ResidueIdExpression (class in molr.selection) ResidueNameExpression (class in molr.selection) RESIDUES (in module molr.constants.pdb_constants) RESIDUES_WITH_AROMATIC_RINGS (in module molr.constants.pdb_constants) RING_ATOMS_FOR_RESIDUES_WITH_AROMATIC_RINGS (in module molr.constants.pdb_constants) rmsd() (molr.StructureEnsemble method) RNA_RESIDUES (in module molr.constants.pdb_constants) RNAExpression (class in molr.selection) S select() (in module molr.selection) (molr.selection.SelectionEngine method) (molr.Structure method) select_atoms() (in module molr.selection) (molr.selection.SelectionEngine method) SelectionEngine (class in molr.selection) SelectionExpression (class in molr.selection) SelectionParser (class in molr.selection) set_frame_coords() (molr.StructureEnsemble method) SIDECHAIN_ATOMS (in module molr.constants.pdb_constants) SidechainExpression (class in molr.selection) Structure (class in molr) StructureEnsemble (class in molr) T translate() (molr.Structure method) V validate_bonds() (molr.BondList method) VDW_RADII (molr.constants.atomic_data.AtomicData attribute) W WATER_MOLECULES (in module molr.constants.pdb_constants) WaterExpression (class in molr.selection)
