annotate utils.py @ 6:b8725fec8c7b draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"

#!/usr/bin/env python
"""
Utility functions for SuCOS and other RDKit modules
"""

from __future__ import print_function

import gzip
import sys

from rdkit import Chem


def log(*args, **kwargs):
    """Log output to STDERR"""
    print(*args, file=sys.stderr, **kwargs)


def open_file_for_reading(filename):
    """Open the file gunzipping it if it ends with .gz."""
    if filename.lower().endswith(".gz"):
        return gzip.open(filename, "rb")
    else:
        return open(filename, "rb")


def open_file_for_writing(filename):
    if filename.lower().endswith(".gz"):
        return gzip.open(filename, "at")
    else:
        return open(filename, "w+")


def read_single_molecule(filename, index=1, format=None):
    """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format.
    If SDF then you can also specify an index of the molecule that is read (default is the first)
    """
    mol = None
    if (
        format == "mol"
        or filename.lower().endswith(".mol")
        or filename.lower().endswith(".mol.gz")
    ):
        file = open_file_for_reading(filename)
        mol = Chem.MolFromMolBlock(file.read())
        file.close()
    elif (
        format == "sdf"
        or filename.lower().endswith(".sdf")
        or filename.lower().endswith(".sdf.gz")
    ):
        file = open_file_for_reading(filename)
        supplier = Chem.ForwardSDMolSupplier(file)
        for i in range(0, index):
            if supplier.atEnd():
                break
            mol = next(supplier)
        file.close()

    if not mol:
        raise ValueError("Unable to read molecule")

    return mol