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`	—
`OP_BOND_REROUTE`	—
`OP_BOND_CONTRACTION`	—

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.

Table 1.9 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`	—
`OP_BOND_REROUTE`	—
`OP_BOND_CONTRACTION`	—

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

setFingerprint(arg2)[source]¶

Set the molecular fingerprint.

Table 1.10 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`	—

Parameters:	*args (`str`) – `molecular fingerprint` identifier

setSimilarityCoefficient(arg2)[source]¶

Set the similarity measure.

Table 1.11 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`	—

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