schrodinger.application.desmond.restraint module

Restraint generation for cross-CT terms and all terms supported by desmond backend, including alchemical terms.

Either a single term or a generator can be used. For single term, each selection corresponds to a single atom.

Two kinds of generators are implemented now:

product: The product of all selections is used to generate all

the terms. Use case is to keep alchemical ions way from places they may get stuck.

connected: One selection is evaluated to generate terms for bond, angle

and torsion. Use case is the alchemical restraints on protein conformations.

Reference distance, angle and torsion values are computed for generated terms. For alchemical terms, reference coordinates saved previously will be used for these calculations if avaialble.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.restraint.GeneratorTypes(PRODUCT, CONNECTED)

Bases: tuple

CONNECTED

Alias for field number 1

PRODUCT

Alias for field number 0

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

schrodinger.application.desmond.restraint.is_position_restraint(table_name)

schrodinger.application.desmond.restraint.is_alchemical(table_name)

schrodinger.application.desmond.restraint.get_encoded_restraints(cms_sys)

Get encoded restraints from cms

Return type:str

schrodinger.application.desmond.restraint.set_encoded_restraints(cms_sys, restr)

Store restraints in cms_sys object.

class schrodinger.application.desmond.restraint.RestraintBuilder(res_spec, cms_sys)

Bases: object

__init__(res_spec, cms_sys)

Parameters:

• res_spec (sea.List) – all restraint terms to be added
• cms_sys (cms.Cms) – cms object for molecules

addRestraints()

Add all restraint terms to the cms object passed in the constructor. This should be the only function called to process all the restraints specified

getEncoded()

Return type:str

getJson()

Return type:str