schrodinger.application.phase.packages.mmp3dscreener module

This module contains the MMP3DScreener class, which performs flexible shape-based screens of a 3D matched molecular pairs database with queries supplied as SMILES strings.

class schrodinger.application.phase.packages.mmp3dscreener.MMP3DScreener(mmp3d_db_path, conf_options=None)

Bases: object

Performs flexible shape-based screens of a 3D matched molecular pairs database with queries supplied as SMILES strings.

__init__(mmp3d_db_path, conf_options=None)

Constructor that takes a Maestro file containing a 3D MMP database and conformer generation options. Default conformer generation options are used if conf_options is omitted.

Parameters:

• mmp3d_db_path (str) – Path to 3D MMP database file
• conf_options (phase.PhpConfOptions) – Conformer generation options

screen(smiles, title=None)

Generator that performs a flexible 3D screen against each pair of structures in the MMP database. Each call to this function returns a 3D shape-based alignment of the query to the next MMP, with the shape similarity stored in the property phase.PHASE_DUAL_SHAPE_SIM.

Parameters:

• smiles (str) – SMILES string of the query
• title (str) – Title for all returned structures

Returns:

The best alignment to each MMP in the database

Return type:

structure.Structure

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.mmp3dscreener', '__doc__': '\n Performs flexible shape-based screens of a 3D matched molecular pairs\n database with queries supplied as SMILES strings.\n ', '__init__': <function MMP3DScreener.__init__>, 'screen': <function MMP3DScreener.screen>, '_validateDb': <function MMP3DScreener._validateDb>, '__dict__': <attribute '__dict__' of 'MMP3DScreener' objects>, '__weakref__': <attribute '__weakref__' of 'MMP3DScreener' objects>})

__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.phase.packages.mmp3dscreener'

__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)