schrodinger.application.desmond.packages.restrain module

This is a module to generate json for restraint terms. Typical usage:

call getNatomsInterm(table) to get number of atoms in the term call getTableSchema(table) to get property names needed. populate atoms tuple and prop dictionary call addTerm on Restraints instance to add terms call toJson on the Restraints instance to convert

all restraints to json

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.packages.restrain.Restraints(existing=None)

Bases: object

__init__(existing=None)

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

static getNatomsInTerm(table_name)

get arity (number of atoms for each term) for table_name :type table_name: str :param table_name: name of the desmond term table :return: number of atoms for each term :rtype: int

static getTableSchema(table_name)

get schema for table_name :type table_name: str :param table_name: name of the desmond term table :return: (param_props, table_props) where both param_props

and table_props are frozensets of property name strings

Return type:tuple(frozenset, frozenset)

addTable(table_name)

add named table if not there :type table_name: str :param table_name: name of the desmond term table :return: named table if it exists;

otherwise an empty table is created.

Return type:dict

addTerm(table_name, atoms, props)

add one restrain term

table_name is the desmond interaction table, stretch_harm, alchemical_improper_harm etc.

An atom is specified by two numbers, ct number and atom number in ct. ct number starts from 0, that means the atom number is gid used by desmond backend. ct number 1 means full system. ct numbers greater than or equal to 2 mean component cts.

props contain the actual force-field parameters, force constants, equilibrium angles and other parameters that specific to the term, e.g. schedule for alchemical terms

Parameters:

• table_name (str) – name of the table, this is one of the term tables supported by desmond
• atoms (tuple) – tuple of atoms specified ct numbers and atom number tuple (ct, atom number)
• props (dict) – dictionary of parameter keyed by name of the parameter (str), including both table properties (e.g. schedule) and force field parameter properties.

Returns:

index of the term added

Return type:

int

toJson()

Returns:json string to be loaded by msys Return type:str

static encode(input_string)

Encodes to a str rather than bytes so that the result can be set as a string property of a CT.

Parameters:input_string (str) – string to be encoded Returns:base64 encoded input Return type:str

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.restrain', '_dummy_msys': <System ''>, '__init__': <function Restraints.__init__>, 'getNatomsInTerm': <staticmethod object>, 'getTableSchema': <staticmethod object>, 'addTable': <function Restraints.addTable>, 'addTerm': <function Restraints.addTerm>, 'toJson': <function Restraints.toJson>, 'encode': <staticmethod object>, 'decode': <staticmethod object>, '__dict__': <attribute '__dict__' of 'Restraints' objects>, '__weakref__': <attribute '__weakref__' of 'Restraints' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.packages.restrain'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

static decode(input_string)

Parameters:input_string (str) – string to be decoded Returns:json string Return type:str