annotate rdkit_descriptors.py @ 5:67ee76f0e497 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"

#!/usr/bin/env python

import argparse
import inspect
import sys

from rdkit import Chem
from rdkit.Chem import Descriptors


def get_supplier(infile, format="smiles"):
    """
    Returns a generator over a SMILES or InChI file. Every element is of RDKit
    molecule and has its original string as _Name property.
    """
    with open(infile) as handle:
        for line in handle:
            line = line.strip()
            if format == "smiles":
                mol = Chem.MolFromSmiles(line, sanitize=True)
            elif format == "inchi":
                mol = Chem.inchi.MolFromInchi(
                    line,
                    sanitize=True,
                    removeHs=True,
                    logLevel=None,
                    treatWarningAsError=False,
                )
            if mol is None:
                yield False
            else:
                mol.SetProp("_Name", line.split("\t")[0])
                yield mol


def get_rdkit_descriptor_functions():
    """
    Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function)
    """
    ret = [
        (name, f)
        for name, f in inspect.getmembers(Descriptors)
        if inspect.isfunction(f) and not name.startswith("_")
    ]
    # some which are not in the official Descriptors module we need to add manually
    ret.extend([("FormalCharge", Chem.GetFormalCharge), ("SSSR", Chem.GetSSSR)])
    ret.sort()
    return ret


def descriptors(mol, functions):
    """
    Calculates the descriptors of a given molecule.
    """
    for name, function in functions:
        yield (name, function(mol))


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("-i", "--infile", required=True, help="Path to the input file.")
    parser.add_argument("--iformat", help="Specify the input file format.")

    parser.add_argument(
        "-o",
        "--outfile",
        type=argparse.FileType("w+"),
        default=sys.stdout,
        help="path to the result file, default is stdout",
    )

    parser.add_argument(
        "-s",
        "--select",
        default=None,
        help="select a subset of comma-separated descriptors to use",
    )

    parser.add_argument(
        "--header",
        dest="header",
        action="store_true",
        default=False,
        help="Write header line.",
    )

    args = parser.parse_args()

    if args.iformat == "sdf":
        supplier = Chem.SDMolSupplier(args.infile)
    elif args.iformat == "smi":
        supplier = get_supplier(args.infile, format="smiles")
    elif args.iformat == "inchi":
        supplier = get_supplier(args.infile, format="inchi")
    elif args.iformat == "pdb":
        supplier = [Chem.MolFromPDBFile(args.infile)]
    elif args.iformat == "mol2":
        supplier = [Chem.MolFromMol2File(args.infile)]

    functions = get_rdkit_descriptor_functions()
    if args.select and args.select != "None":
        selected = args.select.split(",")
        functions = [(name, f) for name, f in functions if name in selected]

    if args.header:
        args.outfile.write(
            "%s\n" % "\t".join(["MoleculeID"] + [name for name, f in functions])
        )

    for mol in supplier:
        if not mol:
            continue
        descs = descriptors(mol, functions)
        try:
            molecule_id = mol.GetProp("_Name")
        except KeyError:
            molecule_id = Chem.MolToSmiles(mol)
        args.outfile.write(
            "%s\n"
            % "\t".join([molecule_id] + [str(round(res, 6)) for name, res in descs])
        )