Index

_

__init__() (scine_molassembler.AtomEnvironmentComponents method) (scine_molassembler.AtomStereopermutator method) (scine_molassembler.BondIndex method) (scine_molassembler.BondStereopermutator method) (scine_molassembler.BondStereopermutator.Alignment method) (scine_molassembler.BondStereopermutator.FittingMode method) (scine_molassembler.BondType method) (scine_molassembler.ChiralStatePreservation method) (scine_molassembler.Cycles method) (scine_molassembler.dg.Configuration method) (scine_molassembler.dg.Error method) (scine_molassembler.dg.Partiality method) (scine_molassembler.DirectedConformerGenerator method) (scine_molassembler.DirectedConformerGenerator.EnumerationSettings method) (scine_molassembler.DirectedConformerGenerator.IgnoreReason method) (scine_molassembler.DirectedConformerGenerator.Relabeler method) (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo method) (scine_molassembler.editing.Cleaved method) (scine_molassembler.Graph method) (scine_molassembler.interpret.BondDiscretization method) (scine_molassembler.interpret.ComponentMap method) (scine_molassembler.interpret.ComponentMap.ComponentIndexPair method) (scine_molassembler.interpret.GraphsResult method) (scine_molassembler.interpret.MoleculesResult method) (scine_molassembler.io.LineNotation method) (scine_molassembler.JsonSerialization method) (scine_molassembler.JsonSerialization.BinaryFormat method) (scine_molassembler.Molecule method) (scine_molassembler.Options method) (scine_molassembler.Options.Thermalization method) (scine_molassembler.PRNG method) (scine_molassembler.RankingInformation method) (scine_molassembler.RankingInformation.Link method) (scine_molassembler.shapes.Shape method) (scine_molassembler.StereopermutatorList method)

A

A() (scine_molassembler.StereopermutatorList method) add() (scine_molassembler.DirectedConformerGenerator.Relabeler method) add_atom() (scine_molassembler.Graph method) (scine_molassembler.Molecule method) add_bond() (scine_molassembler.Graph method) (scine_molassembler.Molecule method) add_ligand() (in module scine_molassembler.editing) add_permutator() (scine_molassembler.Molecule method) adjacent() (scine_molassembler.Graph method) adjacents() (scine_molassembler.Graph method) All (scine_molassembler.AtomEnvironmentComponents attribute) (scine_molassembler.dg.Partiality attribute) angle() (scine_molassembler.AtomStereopermutator method)

apply() (scine_molassembler.interpret.ComponentMap method) apply_canonicalization_map() (scine_molassembler.Molecule static method) assign_stereopermutator() (scine_molassembler.Molecule method) assign_stereopermutator_randomly() (scine_molassembler.Molecule method) assigned() (scine_molassembler.AtomStereopermutator property) (scine_molassembler.BondStereopermutator property) atom_index() (scine_molassembler.interpret.ComponentMap.ComponentIndexPair property) atom_stereopermutators() (scine_molassembler.StereopermutatorList method) AtomEnvironmentComponents (class in scine_molassembler) atoms() (scine_molassembler.Graph method) atoms_of_element() (scine_molassembler.Graph method) AtomStereopermutator (class in scine_molassembler) AtomStereopermutatorPreconditionsUnmet (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute)

B

B() (scine_molassembler.Graph property) (scine_molassembler.StereopermutatorList method) bad_haptic_ligand_bonds() (in module scine_molassembler.interpret) bartell_mechanism (scine_molassembler.Options.Thermalization attribute) base_64_decode() (scine_molassembler.JsonSerialization static method) base_64_encode() (scine_molassembler.JsonSerialization static method) Bent (scine_molassembler.shapes.Shape attribute) berry_pseudorotation (scine_molassembler.Options.Thermalization attribute) BetweenEclipsedAndStaggered (scine_molassembler.BondStereopermutator.Alignment attribute) BicappedSquareAntiprism (scine_molassembler.shapes.Shape attribute) bin_bounds() (scine_molassembler.DirectedConformerGenerator method) (scine_molassembler.DirectedConformerGenerator.Relabeler method) bin_indices() (scine_molassembler.DirectedConformerGenerator.Relabeler method) bin_midpoint_integers() (scine_molassembler.DirectedConformerGenerator method) (scine_molassembler.DirectedConformerGenerator.Relabeler method)

Binary (scine_molassembler.interpret.BondDiscretization attribute) bins() (scine_molassembler.DirectedConformerGenerator.Relabeler method) bond_list() (scine_molassembler.DirectedConformerGenerator property) bond_orders() (scine_molassembler.Graph method) bond_stereopermutators() (scine_molassembler.StereopermutatorList method) bond_type() (scine_molassembler.Graph method) BondDiscretization (class in scine_molassembler.interpret) BondIndex (class in scine_molassembler) BondOrders (scine_molassembler.AtomEnvironmentComponents attribute) bonds() (scine_molassembler.Graph method) BondStereopermutator (class in scine_molassembler) BondStereopermutator.Alignment (class in scine_molassembler) BondStereopermutator.FittingMode (class in scine_molassembler) BondType (class in scine_molassembler) BSON (scine_molassembler.JsonSerialization.BinaryFormat attribute)

C

can_remove() (scine_molassembler.Graph method) canonical_compare() (scine_molassembler.Molecule method) canonical_components() (scine_molassembler.Molecule property) canonicalize() (scine_molassembler.Molecule method) CappedOctahedron (scine_molassembler.shapes.Shape attribute) CappedSquareAntiprism (scine_molassembler.shapes.Shape attribute) CappedTrigonalPrism (scine_molassembler.shapes.Shape attribute) CBOR (scine_molassembler.JsonSerialization.BinaryFormat attribute) chiral_state_preservation (scine_molassembler.Options attribute) ChiralStatePreservation (class in scine_molassembler) cleave() (in module scine_molassembler.editing) Cleaved (class in scine_molassembler.editing) component() (scine_molassembler.interpret.ComponentMap.ComponentIndexPair property) component_map() (scine_molassembler.editing.Cleaved property) (scine_molassembler.interpret.GraphsResult property) (scine_molassembler.interpret.MoleculesResult property)

ComponentMap (class in scine_molassembler.interpret) ComponentMap.ComponentIndexPair (class in scine_molassembler.interpret) composite() (scine_molassembler.BondStereopermutator property) Configuration (class in scine_molassembler.dg) configuration() (scine_molassembler.DirectedConformerGenerator.EnumerationSettings property) conformation_molecule() (scine_molassembler.DirectedConformerGenerator method) connect() (in module scine_molassembler.editing) Connectivity (scine_molassembler.AtomEnvironmentComponents attribute) consider_bond() (scine_molassembler.DirectedConformerGenerator static method) contains() (scine_molassembler.DirectedConformerGenerator method) coordinates() (in module scine_molassembler.shapes) Cube (scine_molassembler.shapes.Shape attribute) Cuboctahedron (scine_molassembler.shapes.Shape attribute) cycle_sequence() (scine_molassembler.RankingInformation.Link property) Cycles (class in scine_molassembler) cycles() (scine_molassembler.Graph property)

D

decision_list_set_size() (scine_molassembler.DirectedConformerGenerator method) DecisionListMismatch (scine_molassembler.dg.Error attribute) degree() (scine_molassembler.Graph method) density_bins() (scine_molassembler.DirectedConformerGenerator.Relabeler static method) dihedral() (scine_molassembler.BondStereopermutator method) dihedral_retries() (scine_molassembler.DirectedConformerGenerator.EnumerationSettings property) dihedrals() (scine_molassembler.DirectedConformerGenerator.Relabeler property) DirectedConformerGenerator (class in scine_molassembler) DirectedConformerGenerator.EnumerationSettings (class in scine_molassembler)

DirectedConformerGenerator.IgnoreReason (class in scine_molassembler) DirectedConformerGenerator.Relabeler (class in scine_molassembler) DirectedConformerGenerator.Relabeler.DihedralInfo (class in scine_molassembler) disable() (scine_molassembler.Options.Thermalization method) distance() (in module scine_molassembler) (scine_molassembler.DirectedConformerGenerator static method) DoNotPreserve (scine_molassembler.ChiralStatePreservation attribute) Double (scine_molassembler.BondType attribute) dump_graphviz() (scine_molassembler.Molecule method)

E

E() (scine_molassembler.Graph property) Eclipsed (scine_molassembler.BondStereopermutator.Alignment attribute) EclipsedAndStaggered (scine_molassembler.BondStereopermutator.Alignment attribute) EdgeContractedIcosahedron (scine_molassembler.shapes.Shape attribute) EffortlessAndUnique (scine_molassembler.ChiralStatePreservation attribute) element_type() (scine_molassembler.Graph method) elements() (scine_molassembler.Graph method) ElementsAndBonds (scine_molassembler.AtomEnvironmentComponents attribute) ElementsBondsAndShapes (scine_molassembler.AtomEnvironmentComponents attribute) ElementTypes (scine_molassembler.AtomEnvironmentComponents attribute)

emit_smiles() (in module scine_molassembler.io.experimental) empty() (scine_molassembler.StereopermutatorList method) enable() (scine_molassembler.Options.Thermalization method) enabled (scine_molassembler.io.LineNotation attribute) enumerate() (scine_molassembler.DirectedConformerGenerator method) enumerate_random() (scine_molassembler.DirectedConformerGenerator method) equal_decision_lists() (scine_molassembler.JsonSerialization static method) equal_molecules() (scine_molassembler.JsonSerialization static method) EquilateralTriangle (scine_molassembler.shapes.Shape attribute) Error (class in scine_molassembler.dg) Eta (scine_molassembler.BondType attribute)

F

first() (scine_molassembler.BondIndex property) (scine_molassembler.editing.Cleaved property) fitting() (scine_molassembler.DirectedConformerGenerator.EnumerationSettings property) fixed_positions() (scine_molassembler.dg.Configuration property) FourAtom (scine_molassembler.dg.Partiality attribute)

from_canonical_smiles() (scine_molassembler.io.LineNotation static method) from_inchi() (scine_molassembler.io.LineNotation static method) from_isomeric_smiles() (scine_molassembler.io.LineNotation static method) from_smiles() (in module scine_molassembler.io.experimental) from_smiles_multiple() (in module scine_molassembler.io.experimental)

G

generate_conformation() (in module scine_molassembler.dg) (scine_molassembler.DirectedConformerGenerator method) generate_decision_list() (scine_molassembler.DirectedConformerGenerator method) generate_ensemble() (in module scine_molassembler.dg) generate_random_conformation() (in module scine_molassembler.dg) (scine_molassembler.DirectedConformerGenerator method) generate_random_ensemble() (in module scine_molassembler.dg)

get_decision_list() (scine_molassembler.DirectedConformerGenerator method) Graph (class in scine_molassembler) graph() (scine_molassembler.Molecule property) GraphImpossible (scine_molassembler.dg.Error attribute) graphs() (in module scine_molassembler.interpret) (scine_molassembler.interpret.GraphsResult property) GraphsResult (class in scine_molassembler.interpret)

H

has_unassigned_permutators() (scine_molassembler.StereopermutatorList method) has_zero_assignment_permutators() (scine_molassembler.StereopermutatorList method) HasAssignedBondStereopermutator (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute) hash() (scine_molassembler.Molecule method)

HasTerminalConstitutingAtom (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute) HeptagonalBipyramid (scine_molassembler.shapes.Shape attribute) Hexagon (scine_molassembler.shapes.Shape attribute) HexagonalBipyramid (scine_molassembler.shapes.Shape attribute)

I

i_set() (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo property) Icosahedron (scine_molassembler.shapes.Shape attribute) ideal_ensemble_size() (scine_molassembler.DirectedConformerGenerator property) InCycle (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute) index_of_permutation() (scine_molassembler.AtomStereopermutator property) (scine_molassembler.BondStereopermutator property)

insert() (in module scine_molassembler.editing) (scine_molassembler.DirectedConformerGenerator method) integer_bounds() (scine_molassembler.DirectedConformerGenerator.Relabeler static method) invert() (scine_molassembler.interpret.ComponentMap method) IsEtaBond (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute)

J

j() (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo property)

JsonSerialization (class in scine_molassembler) JsonSerialization.BinaryFormat (class in scine_molassembler)

K

k() (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo property)

L

l_set() (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo property) Line (scine_molassembler.shapes.Shape attribute)

LineNotation (class in scine_molassembler.io) links() (scine_molassembler.RankingInformation property)

M

make_bounds() (scine_molassembler.DirectedConformerGenerator.Relabeler static method) modular_isomorphism() (scine_molassembler.Molecule method) module scine_molassembler.dg scine_molassembler.editing scine_molassembler.interpret scine_molassembler.io scine_molassembler.io.experimental scine_molassembler.shapes

Molecule (class in scine_molassembler) molecules() (in module scine_molassembler.interpret) (scine_molassembler.interpret.MoleculesResult property) MoleculesResult (class in scine_molassembler.interpret) MsgPack (scine_molassembler.JsonSerialization.BinaryFormat attribute)

N

N() (scine_molassembler.Graph property) name() (scine_molassembler.AtomEnvironmentComponents property) (scine_molassembler.BondStereopermutator.Alignment property) (scine_molassembler.BondStereopermutator.FittingMode property) (scine_molassembler.BondType property) (scine_molassembler.ChiralStatePreservation property) (scine_molassembler.dg.Error property) (scine_molassembler.dg.Partiality property) (scine_molassembler.DirectedConformerGenerator.IgnoreReason property) (scine_molassembler.interpret.BondDiscretization property) (scine_molassembler.JsonSerialization.BinaryFormat property) (scine_molassembler.shapes.Shape method)

name_from_str() (in module scine_molassembler.shapes) Nearest (scine_molassembler.BondStereopermutator.FittingMode attribute) num_assignments() (scine_molassembler.AtomStereopermutator property) (scine_molassembler.BondStereopermutator property) num_cycle_families() (scine_molassembler.Cycles method) num_relevant_cycles() (scine_molassembler.Cycles method) num_stereopermutations() (scine_molassembler.AtomStereopermutator property) (scine_molassembler.BondStereopermutator property)

O

Octahedron (scine_molassembler.shapes.Shape attribute) option() (scine_molassembler.StereopermutatorList method)

Options (class in scine_molassembler) Options.Thermalization (class in scine_molassembler)

P

Partiality (class in scine_molassembler.dg) partiality() (scine_molassembler.dg.Configuration property) Pentagon (scine_molassembler.shapes.Shape attribute) PentagonalBipyramid (scine_molassembler.shapes.Shape attribute)

PentagonalPyramid (scine_molassembler.shapes.Shape attribute) placement() (scine_molassembler.AtomStereopermutator property) (scine_molassembler.BondStereopermutator property) PRNG (class in scine_molassembler) pyramidal_inversion (scine_molassembler.Options.Thermalization attribute)

Q

Quadruple (scine_molassembler.BondType attribute)

Quintuple (scine_molassembler.BondType attribute)

R

RandomFromMultipleBest (scine_molassembler.ChiralStatePreservation attribute) randomness_engine() (in module scine_molassembler) rank_index_of_site() (scine_molassembler.RankingInformation method) ranked_sites() (scine_molassembler.RankingInformation property) ranked_substituents() (scine_molassembler.RankingInformation property) ranking() (scine_molassembler.AtomStereopermutator property) RankingInformation (class in scine_molassembler) RankingInformation.Link (class in scine_molassembler) read() (in module scine_molassembler.io) RefinedChiralsWrong (scine_molassembler.dg.Error attribute) RefinedStructureInacceptable (scine_molassembler.dg.Error attribute) refinement_gradient_target() (scine_molassembler.dg.Configuration property)

refinement_step_limit() (scine_molassembler.dg.Configuration property) RefinementException (scine_molassembler.dg.Error attribute) RefinementMaxIterationsReached (scine_molassembler.dg.Error attribute) relabeler() (scine_molassembler.DirectedConformerGenerator method) remove_atom() (scine_molassembler.Graph method) (scine_molassembler.Molecule method) remove_bond() (scine_molassembler.Graph method) (scine_molassembler.Molecule method) remove_false_positives() (in module scine_molassembler.interpret) remove_permutator() (scine_molassembler.Molecule method) RotationIsIsotropic (scine_molassembler.DirectedConformerGenerator.IgnoreReason attribute) RoundToNearest (scine_molassembler.interpret.BondDiscretization attribute)

S

scine_molassembler.dg module scine_molassembler.editing module scine_molassembler.interpret module scine_molassembler.io module scine_molassembler.io.experimental module scine_molassembler.shapes module second() (scine_molassembler.BondIndex property) (scine_molassembler.editing.Cleaved property) seed() (scine_molassembler.PRNG method) Seesaw (scine_molassembler.shapes.Shape attribute) sequences() (scine_molassembler.DirectedConformerGenerator.Relabeler property) set_bond_type() (scine_molassembler.Molecule method) set_element_type() (scine_molassembler.Molecule method) set_shape_at_atom() (scine_molassembler.Molecule method) Sextuple (scine_molassembler.BondType attribute) Shape (class in scine_molassembler.shapes)

shape() (scine_molassembler.AtomStereopermutator property) Shapes (scine_molassembler.AtomEnvironmentComponents attribute) Single (scine_molassembler.BondType attribute) site_groups() (scine_molassembler.AtomStereopermutator method) site_index_of_atom() (scine_molassembler.RankingInformation method) sites() (scine_molassembler.RankingInformation property) (scine_molassembler.RankingInformation.Link property) size() (in module scine_molassembler.shapes) spatial_model_loosening() (scine_molassembler.dg.Configuration property) split() (in module scine_molassembler.io) split_along_bridge() (scine_molassembler.Graph method) Square (scine_molassembler.shapes.Shape attribute) SquareAntiprism (scine_molassembler.shapes.Shape attribute) SquarePyramid (scine_molassembler.shapes.Shape attribute) Staggered (scine_molassembler.BondStereopermutator.Alignment attribute) standardize() (scine_molassembler.JsonSerialization method) Stereopermutations (scine_molassembler.AtomEnvironmentComponents attribute) StereopermutatorList (class in scine_molassembler) stereopermutators() (scine_molassembler.Molecule property) substitute() (in module scine_molassembler.editing) superpose() (in module scine_molassembler.editing) symmetry_order() (scine_molassembler.DirectedConformerGenerator.Relabeler.DihedralInfo property)

T

T (scine_molassembler.shapes.Shape attribute) TenPercent (scine_molassembler.dg.Partiality attribute) Tetrahedron (scine_molassembler.shapes.Shape attribute) thermalize_stereopermutator() (scine_molassembler.Molecule method) thermalized() (scine_molassembler.AtomStereopermutator property) Thresholded (scine_molassembler.BondStereopermutator.FittingMode attribute) to_binary() (scine_molassembler.JsonSerialization method)

to_molecule() (scine_molassembler.JsonSerialization method) to_string() (scine_molassembler.JsonSerialization method) TricappedTrigonalPrism (scine_molassembler.shapes.Shape attribute) TrigonalBipyramid (scine_molassembler.shapes.Shape attribute) TrigonalDodecahedron (scine_molassembler.shapes.Shape attribute) TrigonalPrism (scine_molassembler.shapes.Shape attribute) TrigonalPyramid (scine_molassembler.shapes.Shape attribute) Triple (scine_molassembler.BondType attribute)

U

UBJSON (scine_molassembler.JsonSerialization.BinaryFormat attribute) uncertain_bonds() (in module scine_molassembler.interpret)

Unique (scine_molassembler.ChiralStatePreservation attribute) UNKNOWN_DECISION (scine_molassembler.DirectedConformerGenerator attribute) UnknownException (scine_molassembler.dg.Error attribute)

V

V() (scine_molassembler.Graph property) VacantTetrahedron (scine_molassembler.shapes.Shape attribute) value() (scine_molassembler.AtomEnvironmentComponents property) (scine_molassembler.BondStereopermutator.Alignment property) (scine_molassembler.BondStereopermutator.FittingMode property) (scine_molassembler.BondType property) (scine_molassembler.ChiralStatePreservation property) (scine_molassembler.dg.Error property) (scine_molassembler.dg.Partiality property) (scine_molassembler.DirectedConformerGenerator.IgnoreReason property) (scine_molassembler.interpret.BondDiscretization property) (scine_molassembler.JsonSerialization.BinaryFormat property) (scine_molassembler.shapes.Shape property)

vertex_map() (scine_molassembler.AtomStereopermutator property)

W

write() (in module scine_molassembler.io)

Z

ZeroAssignmentStereopermutators (scine_molassembler.dg.Error attribute)