schrodinger.application.combiglide.corehop module

This module contains classes and functions for Core Hopping.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.combiglide.corehop.SubstCoreDatabase(database_fname)

Bases: object

This class can be used to calculate substitution scores, where a core hopping database has been used to generate passed ligands.

frag_handle = None

__init__(database_fname)

The class is initialized with the database used for core hopping, then it is queried with ligands which that core hopping run produced.

get_subst_score(st)

Query the database using the provided Structure to attain a subst score.

class schrodinger.application.combiglide.corehop.AttachmentPoint(from_anum, to_anum, name='', atnum=999, numbonds=999, fcharge=999)

Bases: object

Class to map attachment point parameters to the coresponding rows in the ‘m_attachment’ maestro block. Used to write attachment blocks for core hopping.

__init__(from_anum, to_anum, name='', atnum=999, numbonds=999, fcharge=999)

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

makeRowObject()

Creates a dictionary object for which each key corresponds to a column in the ‘m_attachment’ attachment block used to specify core hopping attachment points.

Returns

dictionary for block_data to easily append a row to ‘m_attachment’ with.

Return type

dict

schrodinger.application.combiglide.corehop.write_attachment_block(st, attachments)

Writes the attachment points specified for a core hopping job to the template core structure for downstream consumption.

Parameters

• st (structure.Structure) – template core structure for core hopping search

• attachments (list(corehop.AttachmentPoint)) – list specifying attachment points