1.1.1.3.1.1.1.1. MolpherMol

class molpher.swig_wrappers.core.MolpherMol(*args)

Parameters:other (MolpherMol or str) – another instance of MolpherMol or a SMILES string

Note

If another MolpherMol instance is specified, the tree ownership is not preserved in the new instance. It just acts as a place holder for the data and these are not updated if the original instance changes.

Represents a molecule (usually attached to an exploration tree). It allows the user of the library to read data about the molecule as well as modify it.

copy()

Creates a new MolpherMol instance, which is not bound to any tree. It has the same effect as calling the constructor with another instance as its argument.

Attention

Any modifications to the returned molecule will have no effect on the original instance.

Returns:new instance Return type:MolpherMol

getSMILES()

Returns canonical SMILES of the molecule.

Returns:canonical SMILES representation of the molecule Return type:str

getDistToTarget()

Returns the distance of this molecule to the target molecule.

By default computed as \(1 - similarity\), where \(similarity\) is the similarity computed using the specified molecular fingerprint and similarity measure (see molpher.core.selectors for more information on the available selectors).

Note

Distance to the target can be easily modified, if needed (see setDistToTarget).

See also

molpher.core.ExplorationData

Returns:distance to target molecule Return type:float

getParentSMILES()

Canonical SMILES of the direct parent molecule in the respective exploration tree.

Returns:canonical SMILES of parent Return type:str

getDescendants()

Returns all direct descendants of this molecule in the respective exploration tree as canonical SMILES. Therefore, all molecules returned by this method should be present in the tree at the time of the call.

Returns:an iterable of descendants Return type:tuple of str objects

getHistoricDescendants()

Returns the historic descendants (all morphs created from this molecule) of this molecule in the respective exploration tree as canonical SMILES. Some of the molecules might have been removed from the tree before the call so some of them might be missing from the tree already.

Returns:an iterable of historic descendants Return type:tuple of str objects

getItersWithoutDistImprovement()

Returns the number of morph generations derived from this molecule that did not contain any morphs with an improvement in structural distance from the target molecule.

See also

non_producing_survive, gens_without_improvement

Returns:number of generations without distance improvement Return type:int

getSAScore()

The synthesis feasibility score.

Returns:synthesis feasibility score Return type:float

getMolecularWeight()

Returns the molecular weight of this compound.

Returns:molecular weight Return type:float

setSAScore(score)

Set the synthesis feasibility score as computed using SAScore.dat.

Parameters:score (float) – new synthesis feasibility score

setDistToTarget(dist)

Set the distance to the target molecule.

Parameters:dist (float) – new distance to target

getTree()

Return the exploration tree associated with this molecule.

Parameters:dist (ExplorationTree or None) – new distance to target

setItersWithoutDistImprovement(count)

Sets the number of morph generations derived from this molecule that did not contain any morphs with an improvement in structural distance from the target molecule.

See also

non_producing_survive, gens_without_improvement

lockAtoms(*args)

Locks atoms using SMARTS or a list of atom indices.