simple script for maestro to extract QM and MM regions from a single .pdb

maestro_qmmm.py

from schrodinger import maestro
from schrodinger import structure

import PyQt5
from PyQt5.QtWidgets import QFileDialog

__doc__ = """
Extracts QM region around molecule.
"""
#Name: QM/MM:Extract
#Command: pythonrun qmmm.extract

value = None

pt = maestro.project_table_get()

def extract():
    dialog = QFileDialog()
    dialog.setFileMode(QFileDialog.DirectoryOnly)
    directory = None
    if dialog.exec_() == QFileDialog.Accepted:
        directory = dialog.selectedFiles()[0]

    if directory is None:
        maestro.warning("No folder was specified. Aborting.")
        return

    row_data = [(row.entry_id, row.title) for row in pt.selected_rows]

    for k, (entry_id, title) in enumerate(row_data, start=1):
        maestro.command('entrywsincludeonly entry {} '.format(entry_id))
        maestro.command('workspaceselectionreplace mol.num 1')
        maestro.command('workspaceselectionadd fillres within 3.0 atom.selected')
        maestro.command('entrywscreate  removefromsource=false "tmp"  atom.selected')
        maestro.command('entryexport files=single format=pdb "{0:s}/qm_{1:s}_{2:d}.pdb"'.format(directory, title, k))
        maestro.command('entrydelete')
        maestro.command('entrywsincludeonly entry {} '.format(entry_id))
        maestro.command('workspaceselectionreplace mol.num 1')
        maestro.command('workspaceselectionadd fillres within 3.0 atom.selected')
        maestro.command('workspaceselectioninvert all')
        maestro.command('entrywscreate  removefromsource=false "tmp"  atom.selected')
        maestro.command('entryexport files=single format=pdb "{0:s}/mm_{1:s}_{2:d}.pdb"'.format(directory, title, k))
        maestro.command('entrydelete')