1.1.1.3.1.1.1.4. ExplorationData¶

class molpher.swig_wrappers.core.ExplorationData[source]¶

Note

If an instance of this class is created explicitly, all parameters are set to their default values (see the description of molpher.core.ExplorationData).

Contains data about the state of an exploration tree and provides facilities to read it and change it along with the morphing parameters set.

This class uses getter and setter methods to read and modify the underlying data structure. The naming conventions tightly follow the wrapped C++ implementation and should be consistent with the parameter names published in 1.

1: Hoksza D., Škoda P., Voršilák M., Svozil D. (2014) Molpher: a software framework for systematic chemical space exploration. J Cheminform. 6:7. PubMed, DOI

Warning

Not all methods that can manipulate the tree topology are implemented and exposed in the API, yet. Those few that are exposed, however, should still be considered as experimental.

getSource()[source]¶

Returns the source molecule.

Returns: MolpherMol instance representing the current source molecule
Return type: MolpherMol

getTarget()[source]¶

Returns the target molecule.

Returns: MolpherMol instance representing the current target molecule
Return type: MolpherMol

getChemicalOperators()[source]¶

Returns a tuple of current chemical operators as str identifiers.

Table 1.6 Currently supported chemical operators.¶
Identifier	Description
`OP_ADD_ATOM`	Add a random atom to the molecule.
`OP_REMOVE_ATOM`	Remove an atom from the molecule.
`OP_ADD_BOND`	Add a bond between two random atoms.
`OP_REMOVE_BOND`	Remove a bond between two random atoms.
`OP_MUTATE_ATOM`	Change a randomly selected atom to a different element.
`OP_INTERLAY_ATOM`	Insert an atom between two other atoms.
`OP_BOND_REROUTE`	Move one ending of a bond to another atom.
`OP_BOND_CONTRACTION`	Remove an atom between two atoms and connect them with a new bond.

Returns: current chemical operators
Return type: tuple of str

getFingerprint()[source]¶

Returns an identifier of the currently set molecular fingerprint.

Table 1.7 Currently supported molecular fingerprints.¶
Identifier	Description
`FP_ATOM_PAIRS`	—
`FP_MORGAN`	—
`FP_TOPOLOGICAL`	—
`FP_TOPOLOGICAL_LAYERED_1`	—
`FP_TOPOLOGICAL_LAYERED_2`	—
`FP_VECTORFP`	—
`FP_TOPOLOGICAL_TORSION`	—
`FP_EXT_ATOM_PAIRS`	—
`FP_EXT_MORGAN`	—
`FP_EXT_TOPOLOGICAL`	—
`FP_EXT_TOPOLOGICAL_LAYERED_1`	—
`FP_EXT_TOPOLOGICAL_LAYERED_2`	—
`FP_EXT_TOPOLOGICAL_TORSION`	—

Returns: molecular fingerprint identifier
Return type: str

getSimilarityCoefficient()[source]¶

Returns an identifier of the currently set similarity measure.

Table 1.8 Currently supported similarity measures.¶
Identifier	Description
`SC_ALL_BIT`	—
`SC_ASYMMETRIC`	—
`SC_BRAUN_BLANQUET`	—
`SC_COSINE`	—
`SC_DICE`	—
`SC_KULCZYNSKI`	—
`SC_MC_CONNAUGHEY`	—
`SC_ON_BIT`	—
`SC_RUSSEL`	—
`SC_SOKAL`	—
`SC_TANIMOTO`	—
`SC_TVERSKY_SUBSTRUCTURE`	—
`SC_TVERSKY_SUPERSTRUCTURE`	—

Returns: similarity measure identifier
Return type: str

getMinAcceptableMolecularWeight()[source]¶

Returns: minimum acceptable weight during filtering
Return type: float

getMaxAcceptableMolecularWeight()[source]¶

Returns: maximum acceptable weight during filtering
Return type: float

getCntCandidatesToKeep()[source]¶

Returns: min number of candidates
Return type: int

getCntCandidatesToKeepMax()[source]¶

Returns: max number of candidates
Return type: int

getCntMorphs()[source]¶

Returns
Return type: int

getCntMorphsInDepth()[source]¶

Returns: number of morphs to generate
Return type: int

getDistToTargetDepthSwitch()[source]¶

Returns: distance threshold
Return type: float

getCntMaxMorphs()[source]¶

Returns: maximum number of non-producing morphs per molecule
Return type: int

getItThreshold()[source]¶

Returns: number of generations until non-producing morphs are pruned
Return type: int

setSource(arg2)[source]¶

Set the source molecule.

Parameters: *args (MolpherMol or str) – MolpherMol instance or SMILES representing the current source molecule

setTarget(arg2)[source]¶

Set the target molecule.

Parameters: *args (MolpherMol or str) – MolpherMol instance or SMILES representing the current source molecule

setChemicalOperators(arg2)[source]¶

Set the current chemical operators as str identifiers.

Parameters: *args (tuple of str) – current chemical operators as a tuple of str identifiers

setFingerprint(arg2)[source]¶

Set the molecular fingerprint.

Parameters: *args (str) – molecular fingerprint identifier

setSimilarityCoefficient(arg2)[source]¶

Set the similarity measure.

Parameters: *args (str) – similarity measure identifier

setMinAcceptableMolecularWeight(arg2)[source]¶

Parameters: *args (float) – minimum acceptable weight during filtering

setMaxAcceptableMolecularWeight(arg2)[source]¶

Parameters: *args (float) – maximum acceptable weight during filtering

setCntCandidatesToKeep(arg2)[source]¶

Parameters: *args (int) – min number of candidates

setCntCandidatesToKeepMax(arg2)[source]¶

Parameters: *args (int) – max number of candidates

setCntMorphs(arg2)[source]¶

Parameters: *args (int) –

setCntMorphsInDepth(arg2)[source]¶

Parameters: *args (int) – number of morphs to generate

setDistToTargetDepthSwitch(arg2)[source]¶

Parameters: *args (float) – distance threshold

setCntMaxMorphs(arg2)[source]¶

Parameters: *args (int) – maximum number of non-producing morphs per molecule

setItThreshold(arg2)[source]¶

Parameters: *args (int) – number of generations until non-producing morphs are pruned

static load(filename)¶

Load data and parameters from a tree snapshot or a XML template.

Parameters: filename (str) – path to the file to load from

save(filename)[source]¶

Save data and parameters from a tree snapshot or a XML template.

Parameters: filename (str) – path to the file to save to