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