ProtoCaller.Ensemble.Perturbation module¶

This Module contains the Perturbation class which needs two parametrised ligands and performs subsequent alignment of the first ligand to a reference ligand (if this is not needed, it can be aligned to itself) and alignment of the second ligand to the first ligand with appropriate atom mapping using routines from rdkitwrapper, RDKit and BioSimSpace.

class ProtoCaller.Ensemble.Perturbation.Perturbation(ligand1, ligand2, name=None)¶

Bases: object

The main class responsible for single-topology perturbations in ProtoCaller.

Parameters

ligand1 (ProtoCaller.Ensemble.Ligand.Ligand) – Initialises ligand1.
ligand2 (ProtoCaller.Ensemble.Ligand.Ligand) – Initialises ligand1.
name (str or None, optional) – Initialises name.

ligand1¶

The first ligand.

Type: ProtoCaller.Ensemble.Ligand.Ligand

ligand2¶

The second ligand.

Type: ProtoCaller.Ensemble.Ligand.Ligand

current_ref¶

The current reference ligand.

Type: ProtoCaller.Ensemble.Ligand.Ligand

alignAndCreateMorph(ref)¶

Default alignment method wrapping the two alignment stages - aligning ligand1 to a reference and aligning and mixing ligand2 to ligand1.

Parameters

ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.

Returns

morph (BioSimSpace.System) – The mixed topology object object.
mcs ([tuple]) – The maximum common substructure of the two molecules.

alignToEachOther(output_filename=None, realign=False, **kwargs)¶

Aligns the second ligand to the first ligand.

Parameters

output_filename (str) – The name of the output file. None uses the default value.
realign (bool) – Whether to realign an already aligned ligand.
kwargs – Keyword arguments to pass to ProtoCaller.Wrappers.rdkitwrapper.alignTwoMolecules.

Returns

morph (BioSimSpace.System) – The mixed topology object.
mcs ([tuple]) – The maximum common substructure of the two molecules.

alignToReference(ref, output_filename=None, realign=False, **kwargs)¶

Aligns the first ligand to a reference ligand.

Parameters

ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.
output_filename (str) – The name of the output file. None uses the default value.
realign (bool) – Whether to realign an already aligned ligand.
kwargs – Keyword arguments to pass to ProtoCaller.Wrappers.rdkitwrapper.alignTwoMolecules.

Returns

mcs – The maximum common substructure of the two molecules.

Return type

[tuple]

get_morph(ref)¶

Returns the mixed topology object corresponding to a reference ligand.

Parameters: ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.
Returns: morph – The mixed topology object aligned to the reference ligand.
Return type: BioSimSpace.System

get_parametrised_files1(ref)¶

Returns parametrised files for the first ligand corresponding to a reference ligand.

Parameters: ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.
Returns: files – The parametrised files for the first ligand aligned to the reference ligand. The first file is a topology file and the second file is a coordinate file.
Return type: [str, str]

get_parametrised_files2(ref)¶

Returns parametrised files for the second ligand corresponding to a reference ligand.

Parameters: ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.
Returns: files – The parametrised files for the first second aligned to the reference ligand. The first file is a topology file and the second file is a coordinate file.
Return type: [str, str]

property isAligned¶: Whether there is a mixed topology file that has been aligned to the current reference ligand.

isAlignedTo(ref)¶

Returns whether there is a mixed topology file that has been aligned to the reference ligand.

Parameters: ref (ProtoCaller.Ensemble.Ligand.Ligand) – The reference ligand.
Returns: exists – Whether the mixed topology file has already been aligned to the reference ligand.
Return type: bool

property morph¶: The mixed topology object corresponding to the current reference ligand.

property name¶: The name of the perturbation.

property parametrised_files1¶: The parametrised files for the first ligand corresponding to the current reference ligand.

property parametrised_files2¶: The parametrised files for the second ligand corresponding to the current reference ligand.