Index

_

__init__() (nuri.core.AtomData method) (nuri.core.BondData method) (nuri.core.Molecule method) (nuri.tools.tm.TMAlign method)

__iter__() (nuri.fmt.MoleculeReader method) __next__() (nuri.fmt.MoleculeReader method)

A

abundance (nuri.core.Isotope property) add() (nuri.core.SubstructureContainer method) add_atom() (nuri.core.Mutator method) add_atoms() (nuri.core.Substructure method) add_bond() (nuri.core.Mutator method) add_bonds() (nuri.core.Substructure method) add_conf() (nuri.core.Molecule method) add_from() (nuri.core.Molecule method) align_points() (in module nuri.core.geometry) align_rmsd() (in module nuri.core.geometry) aligned_pairs() (nuri.tools.tm.TMAlign method) append() (nuri.core.SubstructureContainer method) approx_order() (nuri.core.BondData method) (nuri.core.SubBond method) aromatic (nuri.core.AtomData property) (nuri.core.BondData property)

Aromatic (nuri.core.BondOrder attribute) aromatic (nuri.core.SubAtom property) (nuri.core.SubBond property) as_parent() (nuri.core.SubAtom method) (nuri.core.SubBond method) (nuri.core.SubNeighbor method) Atom (class in nuri.core) atom() (nuri.core.Molecule method) (nuri.core.Substructure method) AtomData (class in nuri.core) atomic_number (nuri.core.AtomData property) (nuri.core.Element property) (nuri.core.SubAtom property) atomic_weight (nuri.core.AtomData property) (nuri.core.Element property) (nuri.core.Isotope property) (nuri.core.SubAtom property)

B

Bond (class in nuri.core) bond (nuri.core.Neighbor property) (nuri.core.SubNeighbor property) bond() (nuri.core.Molecule method) (nuri.core.Substructure method)

BondConfig (class in nuri.core) BondData (class in nuri.core) BondOrder (class in nuri.core) bonds() (nuri.core.Molecule method) (nuri.core.Substructure method)

C

category (nuri.core.Substructure property) CCW (nuri.core.Chirality attribute) Chain (nuri.core.SubstructureCategory attribute) Chirality (class in nuri.core) chirality (nuri.core.AtomData property) (nuri.core.SubAtom property) cif_ddl2_frame_as_dict() (in module nuri.fmt) CifBlock (class in nuri.fmt) CifFrame (class in nuri.fmt) CifParser (class in nuri.fmt) CifTable (class in nuri.fmt) Cis (nuri.core.BondConfig attribute) clear() (nuri.core.Molecule method) (nuri.core.Mutator method) (nuri.core.Substructure method) (nuri.core.SubstructureContainer method) clear_atoms() (nuri.core.Molecule method) (nuri.core.Mutator method) (nuri.core.Substructure method) clear_bonds() (nuri.core.Molecule method) (nuri.core.Mutator method) (nuri.core.Substructure method) clear_confs() (nuri.core.Molecule method)

conceal_hydrogens() (nuri.core.Molecule method) (nuri.core.Substructure method) config (nuri.core.BondData property) (nuri.core.SubBond property) conformers() (nuri.core.Molecule method) (nuri.core.Substructure method) conjugated (nuri.core.AtomData property) (nuri.core.BondData property) (nuri.core.SubAtom property) (nuri.core.SubBond property) copy() (nuri.core.AtomData method) (nuri.core.BondData method) (nuri.core.Molecule method) (nuri.core.ProxySubstructure method) copy_data() (nuri.core.Atom method) (nuri.core.Bond method) (nuri.core.SubAtom method) (nuri.core.SubBond method) count_heavy_neighbors() (nuri.core.Atom method) count_hydrogens() (nuri.core.Atom method) count_neighbors() (nuri.core.Atom method) covalent_radius (nuri.core.Element property) CW (nuri.core.Chirality attribute)

D

data (nuri.fmt.CifBlock property) del_conf() (nuri.core.Molecule method) Double (nuri.core.BondOrder attribute)

dst (nuri.core.Bond property) (nuri.core.Neighbor property) (nuri.core.SubBond property) (nuri.core.SubNeighbor property)

E

Element (class in nuri.core) element (nuri.core.AtomData property) (nuri.core.Isotope property) (nuri.core.SubAtom property) element_name (nuri.core.AtomData property) (nuri.core.SubAtom property)

element_symbol (nuri.core.AtomData property) (nuri.core.SubAtom property) eneg (nuri.core.Element property) erase_atom() (nuri.core.Substructure method) erase_bond() (nuri.core.Substructure method)

F

find_all_rings() (in module nuri.algo) find_relevant_rings() (in module nuri.algo) find_sssr() (in module nuri.algo)

formal_charge (nuri.core.AtomData property) (nuri.core.SubAtom property) from_alignment() (nuri.tools.tm.TMAlign static method)

G

generate_coords() (in module nuri.algo) get() (nuri.core.PeriodicTable static method) get_conf() (nuri.core.Molecule method) (nuri.core.Substructure method) get_isotope() (nuri.core.AtomData method) (nuri.core.Element method) (nuri.core.SubAtom method)

get_pos() (nuri.core.Atom method) (nuri.core.SubAtom method) group (nuri.core.Element property) guess_all_types() (in module nuri.algo) guess_connectivity() (in module nuri.algo) guess_everything() (in module nuri.algo)

H

has_bond() (nuri.core.Molecule method) (nuri.core.Substructure method)

Hyb (class in nuri.core) hyb (nuri.core.AtomData property) (nuri.core.SubAtom property)

I

id (nuri.core.Atom property) (nuri.core.Bond property) (nuri.core.SubAtom property) (nuri.core.SubBond property) (nuri.core.Substructure property)

implicit_hydrogens (nuri.core.AtomData property) (nuri.core.SubAtom property) insert() (nuri.core.SubstructureContainer method) is_global (nuri.fmt.CifBlock property) Isotope (class in nuri.core) isotopes (nuri.core.Element property)

K

keys() (nuri.fmt.CifTable method)

L

length() (nuri.core.Bond method) (nuri.core.SubBond method)

M

major_isotope (nuri.core.Element property) mark_atom_erase() (nuri.core.Mutator method) mark_bond_erase() (nuri.core.Mutator method) mass_number (nuri.core.Isotope property) mmcif_load_frame() (in module nuri.fmt) module nuri nuri.algo nuri.core nuri.core.geometry nuri.fmt nuri.tools nuri.tools.tm

Molecule (class in nuri.core) molecule (nuri.core.Substructure property) MoleculeReader (class in nuri.fmt) Mutator (class in nuri.core) mutator() (nuri.core.Molecule method)

N

name (nuri.core.AtomData property) (nuri.core.BondConfig property) (nuri.core.BondData property) (nuri.core.BondOrder property) (nuri.core.Chirality property) (nuri.core.Element property) (nuri.core.Hyb property) (nuri.core.Molecule property) (nuri.core.SubAtom property) (nuri.core.SubBond property) (nuri.core.Substructure property) (nuri.core.SubstructureCategory property) (nuri.fmt.CifBlock property) (nuri.fmt.CifFrame property) Neighbor (class in nuri.core) neighbor() (nuri.core.Molecule method) (nuri.core.Substructure method) num_atoms() (nuri.core.Molecule method) (nuri.core.Substructure method)

num_bonds() (nuri.core.Molecule method) (nuri.core.Substructure method) num_confs() (nuri.core.Molecule method) (nuri.core.Substructure method) num_fragments() (nuri.core.Molecule method) num_sssr() (nuri.core.Molecule method) nuri module nuri.algo module nuri.core module nuri.core.geometry module nuri.fmt module nuri.tools module nuri.tools.tm module

O

order (nuri.core.BondData property) (nuri.core.SubBond property)

Other (nuri.core.BondOrder attribute) (nuri.core.Hyb attribute)

P

parent_atoms() (nuri.core.Substructure method) parent_bonds() (nuri.core.Substructure method) partial_charge (nuri.core.AtomData property) (nuri.core.SubAtom property) period (nuri.core.Element property) periodic_table (in module nuri) PeriodicTable (class in nuri.core) pop() (nuri.core.SubstructureContainer method)

prefix_search_first() (nuri.fmt.CifFrame method) props (nuri.core.AtomData property) (nuri.core.BondData property) (nuri.core.Molecule property) (nuri.core.SubAtom property) (nuri.core.SubBond property) (nuri.core.Substructure property) ProxySubstructure (class in nuri.core)

Q

Quadruple (nuri.core.BondOrder attribute)

R

read_cif() (in module nuri.fmt) readfile() (in module nuri) readstring() (in module nuri) refresh_bonds() (nuri.core.Substructure method) Residue (nuri.core.SubstructureCategory attribute) reveal_hydrogens() (nuri.core.Molecule method) ring (nuri.core.AtomData property) (nuri.core.BondData property) (nuri.core.SubAtom property) (nuri.core.SubBond property)

rmsd() (nuri.tools.tm.TMAlign method) rotatable() (nuri.core.BondData method) (nuri.core.SubBond method) rotate() (nuri.core.Bond method)

S

sanitize() (nuri.core.Molecule method) save_frames (nuri.fmt.CifBlock property) score() (nuri.tools.tm.TMAlign method) set_conf() (nuri.core.Molecule method) (nuri.core.Substructure method) set_element() (nuri.core.AtomData method) (nuri.core.SubAtom method) set_isotope() (nuri.core.AtomData method) (nuri.core.SubAtom method) set_pos() (nuri.core.Atom method) (nuri.core.SubAtom method) Single (nuri.core.BondOrder attribute) SP (nuri.core.Hyb attribute) SP2 (nuri.core.Hyb attribute) SP3 (nuri.core.Hyb attribute) SP3D (nuri.core.Hyb attribute)

SP3D2 (nuri.core.Hyb attribute) sqlen() (nuri.core.Bond method) (nuri.core.SubBond method) src (nuri.core.Bond property) (nuri.core.Neighbor property) (nuri.core.SubBond property) (nuri.core.SubNeighbor property) sub() (nuri.core.Molecule method) SubAtom (class in nuri.core) SubBond (class in nuri.core) SubNeighbor (class in nuri.core) subs (nuri.core.Molecule property) Substructure (class in nuri.core) SubstructureCategory (class in nuri.core) SubstructureContainer (class in nuri.core) symbol (nuri.core.Element property)

T

Terminal (nuri.core.Hyb attribute) tm_align() (in module nuri.tools.tm) tm_score() (in module nuri.tools.tm) TMAlign (class in nuri.tools.tm) to_mol2() (in module nuri)

to_pdb() (in module nuri.fmt) to_sdf() (in module nuri) to_smiles() (in module nuri) Trans (nuri.core.BondConfig attribute) transform() (in module nuri.core.geometry) Triple (nuri.core.BondOrder attribute)

U

Unbound (nuri.core.Hyb attribute) Unknown (nuri.core.BondConfig attribute) (nuri.core.Chirality attribute) (nuri.core.SubstructureCategory attribute) update() (nuri.core.AtomData method) (nuri.core.BondData method) (nuri.core.SubAtom method) (nuri.core.SubBond method)

update_from() (nuri.core.AtomData method) (nuri.core.BondData method) (nuri.core.SubAtom method) (nuri.core.SubBond method)

V

value (nuri.core.BondConfig property) (nuri.core.BondOrder property) (nuri.core.Chirality property) (nuri.core.Hyb property) (nuri.core.SubstructureCategory property)

vdw_radius (nuri.core.Element property)