Options

class scine_molassembler.ChiralStatePreservation

Specifies how chiral state is to be propagated on graph modifications. If None is set, no chiral state is preserved. If EffortlessAndUnique is set, only unambiguous zero-effort mappings are used to propagate chiral state. This enables e.g. the propagation of ligand loss in octahedral to square pyramidal and back. If Unique is set, chiral state is propagated if the best mapping is unique, i.e. there are no other mappings with the same quality measures. Enables e.g. the propagation of seesaw to square planar, but not back. Under RandomFromMultipleBest, random mappings are chosen from the set of best mappings, permitting chiral state propagation in all cases.

Members:

DoNotPreserve :

Don’t try to preserve chiral state. Changes at stereopermutators always result in loss of chiral state.

EffortlessAndUnique :

Use only completely unambiguous zero-effort mappings. Note that for instance the ligand gain situation from square planar to square pyramidal is not unique, and therefore chiral state is not propagated there under this option.

Unique :

Propagates if the best shape mapping is unique, i.e. there are no other mappings with the same quality measures.

RandomFromMultipleBest :

Chooses randomly from the set of best mappings, permitting chiral state propagation in all cases. So propagating chiral state from square planar to square pyramidal is now possible – there are two ways of placing the new apical ligand – but you only get one of them.

DoNotPreserve = <ChiralStatePreservation.DoNotPreserve: 0>

EffortlessAndUnique = <ChiralStatePreservation.EffortlessAndUnique: 1>

RandomFromMultipleBest = <ChiralStatePreservation.RandomFromMultipleBest: 3>

Unique = <ChiralStatePreservation.Unique: 2>

__init__(self: scine_molassembler.ChiralStatePreservation, value: int) → None

property name

property value

class scine_molassembler.Options

Contains global library settings

class Thermalization

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

bartell_mechanism = True

berry_pseudorotation = True

disable() → None

Sets a low temperature approximation where all thermalizations are disabled

enable() → None

Sets a high temperature approximation where all thermalizations are enabled

pyramidal_inversion = True

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

chiral_state_preservation = <ChiralStatePreservation.EffortlessAndUnique: 1>

class scine_molassembler.PRNG

Pseudo-random number generator

Central source of pseudo-randomness for the library.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

seed(self: scine_molassembler.PRNG, seed_number: int) → None

Seed the PRNG with state

scine_molassembler.randomness_engine() → scine_molassembler.PRNG