Index

A

add_atom() (molli.chem.geometry.CartesianGeometry method) (molli.chem.molecule.Molecule method) add_implicit_hydrogens() (molli.chem.structure.Structure method) aeif() (in module molli.descriptor.gridbased) align_to_ref_coords() (molli.chem.ensemble.ConformerEnsemble method) angle() (molli.chem.geometry.CartesianGeometry method) append() (molli.chem.ensemble.ConformerEnsemble method) append_atom() (molli.chem.atom.Promolecule method) append_bond() (molli.chem.bond.Connectivity method) append_bonds() (molli.chem.bond.Connectivity method) as_dict() (molli.chem.atom.Atom method) (molli.chem.bond.Bond method) as_tuple() (molli.chem.atom.Atom method) (molli.chem.bond.Bond method)

aso() (in module molli.descriptor.gridbased) aso2() (in module molli.descriptor.aso) Atom (class in molli.chem.atom) AtomGeom (class in molli.chem.atom) atomic_charges (molli.chem.ensemble.ConformerEnsemble property) (molli.chem.molecule.Molecule property) atomic_indicator_field() (in module molli.descriptor.gridbased) atomic_weight (molli.chem.atom.Atom property) (molli.chem.atom.Element property) AtomLike (in module molli.chem.atom) atoms (molli.chem.atom.Promolecule property) AtomStereo (class in molli.chem.atom) AtomType (class in molli.chem.atom) attachment_points (molli.chem.atom.Promolecule property)

B

Bond (class in molli.chem.bond) bond_coords() (molli.chem.structure.Structure method) bond_length() (molli.chem.structure.Structure method) bond_vector() (molli.chem.structure.Structure method)

bonded_valence() (molli.chem.bond.Connectivity method) bonds (molli.chem.bond.Connectivity property) bonds_with_atom() (molli.chem.bond.Connectivity method) BondStereo (class in molli.chem.bond) BondType (class in molli.chem.bond)

C

CartesianGeometry (class in molli.chem.geometry) CDXMLSyntaxWarning center_at_atom() (molli.chem.ensemble.ConformerEnsemble method) center_at_core() (molli.chem.ensemble.ConformerEnsemble method) centroid() (molli.chem.geometry.CartesianGeometry method) color_cpk (molli.chem.atom.Atom property) (molli.chem.atom.Element property) concatenate() (molli.chem.structure.Structure class method) Conformer (class in molli.chem.ensemble) ConformerEnsemble (class in molli.chem.ensemble) ConformerLibrary (class in molli.chem.library) connect_like() (molli.chem.bond.Connectivity method) connected_atoms() (molli.chem.bond.Connectivity method)

Connectivity (class in molli.chem.bond) coord_subset() (molli.chem.geometry.CartesianGeometry method) coords (molli.chem.ensemble.ConformerEnsemble property) (molli.chem.geometry.CartesianGeometry property) (molli.chem.structure.Substructure property) coords_as_list (molli.chem.geometry.CartesianGeometry property) cov_radius_1 (molli.chem.atom.Atom property) (molli.chem.atom.Element property) cov_radius_2 (molli.chem.atom.Atom property) (molli.chem.atom.Element property) cov_radius_3 (molli.chem.atom.Atom property) (molli.chem.atom.Element property) cov_radius_grimme (molli.chem.atom.Atom property) (molli.chem.atom.Element property)

D

del_atom() (molli.chem.atom.Promolecule method) (molli.chem.bond.Connectivity method) (molli.chem.geometry.CartesianGeometry method) (molli.chem.molecule.Molecule method) (molli.chem.structure.Structure method) del_bond() (molli.chem.bond.Connectivity method) dftd_coordination_number() (in module molli.descriptor.cov_cn) dihedral() (molli.chem.geometry.CartesianGeometry method) distance() (molli.chem.geometry.CartesianGeometry method) distance_to_point() (molli.chem.geometry.CartesianGeometry method)

DistanceUnit (class in molli.chem.geometry) dump_mol2() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.molecule.Molecule method) (molli.chem.structure.Structure method) dump_xyz() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method) dumps_mol2() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.molecule.Molecule method) (molli.chem.structure.Structure method) dumps_xyz() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method)

E

Element (class in molli.chem.atom) ElementLike (in module molli.chem.atom) elements (molli.chem.atom.Promolecule property) en_pauling (molli.chem.atom.Element property) ensemble_from_molli_old_xml() (in module molli.chem.legacy) evolve() (molli.chem.atom.Atom method) (molli.chem.bond.Bond method)

expected_length (molli.chem.bond.Bond property) extend() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method) (molli.chem.structure.Structure method) extend_bonds() (molli.chem.bond.Connectivity method)

F

find_cycle_containing_atom() (molli.chem.bond.Connectivity method)

formula (molli.chem.atom.Promolecule property)

G

get() (molli.chem.atom.Element class method) get_atom() (molli.chem.atom.Promolecule method) get_atom_coord() (molli.chem.geometry.CartesianGeometry method) get_atom_index() (molli.chem.atom.Promolecule method) get_atom_indices() (molli.chem.atom.Promolecule method) get_atoms() (molli.chem.atom.Promolecule method) get_attachment_points() (molli.chem.atom.Promolecule method)

get_bond() (molli.chem.bond.Connectivity method) get_mol2_type() (molli.chem.atom.Atom method) (molli.chem.bond.Bond method) get_property_value() (molli.chem.atom.Element method) get_substr_indices() (molli.chem.bond.Connectivity method) (molli.chem.ensemble.ConformerEnsemble method) group (molli.chem.atom.Element property)

H

heavy (molli.chem.structure.Structure property)

I

idx (molli.chem.atom.Atom property) IMPLICIT_VALENCE (in module molli.chem.atom) implicit_valence (molli.chem.atom.Atom property) index_atom() (molli.chem.atom.Promolecule method)

index_bond() (molli.chem.bond.Connectivity method) invert() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method) is_attachment_point (molli.chem.atom.Atom property) is_dummy (molli.chem.atom.Atom property)

J

join() (molli.chem.structure.Structure class method)

L

label_atoms() (molli.chem.atom.Promolecule method) load_all_mol2() (molli.chem.structure.Structure class method) load_all_xyz() (molli.chem.geometry.CartesianGeometry class method) load_mol2() (molli.chem.ensemble.ConformerEnsemble class method) (molli.chem.structure.Structure class method) load_xyz() (molli.chem.ensemble.ConformerEnsemble class method) (molli.chem.geometry.CartesianGeometry class method)

loads_all_mol2() (molli.chem.structure.Structure class method) loads_all_xyz() (molli.chem.geometry.CartesianGeometry class method) loads_mol2() (molli.chem.ensemble.ConformerEnsemble class method) (molli.chem.structure.Structure class method) loads_xyz() (molli.chem.ensemble.ConformerEnsemble class method) (molli.chem.geometry.CartesianGeometry class method) lookup_bond() (molli.chem.bond.Connectivity method)

M

match() (molli.chem.bond.Connectivity method) module molli.chem.atom molli.chem.bond molli.chem.ensemble molli.chem.geometry molli.chem.legacy molli.chem.library molli.chem.molecule molli.chem.structure molli.descriptor.aso molli.descriptor.cov_cn molli.descriptor.gridbased molli.ftypes.cdxml molli.math.rotation molecular_weight (molli.chem.atom.Promolecule property) Molecule (class in molli.chem.molecule) MoleculeLibrary (class in molli.chem.library) molli.chem.atom module molli.chem.bond module

molli.chem.ensemble module molli.chem.geometry module molli.chem.legacy module molli.chem.library module molli.chem.molecule module molli.chem.structure module molli.descriptor.aso module molli.descriptor.cov_cn module molli.descriptor.gridbased module molli.ftypes.cdxml module molli.math.rotation module

N

n_atoms (molli.chem.atom.Promolecule property) n_attachment_points (molli.chem.atom.Promolecule property) n_bonds (molli.chem.bond.Connectivity property) n_bonds_with_atom() (molli.chem.bond.Connectivity method)

n_conformers (molli.chem.ensemble.ConformerEnsemble property) name (molli.chem.atom.Promolecule property) (molli.chem.ensemble.Conformer property) nearest_atom_index() (in module molli.descriptor.gridbased) new_atom() (molli.chem.geometry.CartesianGeometry method)

O

optimal_rotation_to_ref_coords() (molli.chem.ensemble.ConformerEnsemble method)

order (molli.chem.bond.Bond property)

P

parent_atom_indices (molli.chem.structure.Substructure property) perceive_atom_properties() (molli.chem.structure.Structure method) perceive_bond_properties() (molli.chem.structure.Structure method)

Promolecule (class in molli.chem.atom) PromoleculeLike (in module molli.chem.atom) prune() (in module molli.descriptor.gridbased)

R

remove_substituent() (molli.chem.structure.Structure method) rmsd() (molli.chem.geometry.CartesianGeometry method) rotate() (molli.chem.ensemble.ConformerEnsemble method)

rotate_dihedral() (molli.chem.structure.Structure method) rotation_matrix_from_axis() (in module molli.math.rotation) rotation_matrix_from_vectors() (in module molli.math.rotation)

S

scale() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method) split() (molli.chem.structure.Structure method) Structure (class in molli.chem.structure)

StructureLike (in module molli.chem.molecule) Substructure (class in molli.chem.structure) substructure() (molli.chem.structure.Structure method) symbol (molli.chem.atom.Element property)

T

to_nxgraph() (molli.chem.bond.Connectivity method) transform() (molli.chem.geometry.CartesianGeometry method)

translate() (molli.chem.ensemble.ConformerEnsemble method) (molli.chem.geometry.CartesianGeometry method)

V

valence_electrons (molli.chem.atom.Atom property) validate_fragment() (in module molli.ftypes.cdxml) validate_label() (in module molli.ftypes.cdxml)

vdw_radius (molli.chem.atom.Atom property) (molli.chem.atom.Element property) vector() (molli.chem.geometry.CartesianGeometry method)

W

weights (molli.chem.ensemble.ConformerEnsemble property)

Y

yield_atoms_by_element() (molli.chem.atom.Promolecule method) yield_atoms_by_label() (molli.chem.atom.Promolecule method) yield_attachment_points() (molli.chem.atom.Promolecule method) yield_bfs() (molli.chem.bond.Connectivity method)

yield_bfsd() (molli.chem.bond.Connectivity method) yield_from_mol2() (molli.chem.structure.Structure class method) yield_from_xyz() (molli.chem.geometry.CartesianGeometry class method) yield_parent_atom_indices() (molli.chem.structure.Substructure method)

Z

Z (molli.chem.atom.Atom property)

z (molli.chem.atom.Element property)