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How to use molecule_file method in molecule

Best Python code snippet using molecule_python

molecules_to_cov.py

Source:molecules_to_cov.py

1"""2Given a molecule file (as output by CAMPAREE), generate a coverage file3"""4import argparse5import collections6import re7import numpy8parser = argparse.ArgumentParser(description="Given a molecule file (as output by CAMPAREE), generate a coverage file in the bedGraph format")9parser.add_argument("molecule_file", help="path to the input molecule file")10parser.add_argument("output_file", help="prefix for the output coverage files, two are output as output_file.forward.cov and output_file.reverse.cov")11parser.add_argument("-m", "--max_chromosome_size", help="size of largest chromosome in megabases (250 for humans, 196 for mouse), this can be an overestimate, determines memory use", default=260, type=int)12args = parser.parse_args()13cigar_re = re.compile("[\d]+[MINDSH]")14def make_chrom():15    print(f"Creating the {len(coverages)+1} chromosome")16    return numpy.zeros(args.max_chromosome_size * 1_000_000, dtype="int32")17coverages = collections.defaultdict(make_chrom)18with open(args.molecule_file) as molecule_file:19    for line in molecule_file:20        if line.startswith("#"):21            continue #Skip comment/header line22        transcript_id, chrom, start, cigar, ref_start, ref_cigar, strand, sequence = line.split('\t')23        # Really just need the ref_start, ref_cigar, chromosome and strand for coverage24        ref_start = int(ref_start)25        cigar_parts = cigar_re.findall(ref_cigar)26        reference_idx = ref_start27        for part in cigar_parts:28            match_length = int(part[:-1])29            match_type = part[-1]30            if match_type == "M":31                # Count the match and move along the reference32                coverages[chrom,strand][reference_idx:reference_idx+match_length] += 133                reference_idx += match_length34            elif match_type in "ND":35                # No match but we still move positions on the reference36                reference_idx += match_length37            else:38                # do nothing39                pass40with open(args.output_file + ".forward.cov", "w") as fwd_file, open(args.output_file + ".reverse.cov", "w") as rev_file:41    # Output headers42    fwd_header = f'track type=bedGraph name="Coverage  {args.molecule_file} forward strand" description="Coverage for {args.molecule_file} forward strand" visibility=full color=0,0,255 priority=20\n'43    rev_header = f'track type=bedGraph name="Coverage  {args.molecule_file} reverse strand" description="Coverage for {args.molecule_file} reverse strand" visibility=full color=255,0,0 priority=20\n'44    fwd_file.write(fwd_header)45    rev_file.write(rev_header)46    # Output the coverage of each strand of each chromosome47    # sorted alphabetically48    for chrom,strand in sorted(coverages.keys()):49        print(f"Starting chrom {chrom} strand {strand}")50        coverage = coverages[chrom,strand]51        # We allocated too much space for every chromosome and most didn't use it52        # unused is left as zeros, so we can just drop those on the end53        coverage = numpy.trim_zeros(coverage, 'b')54        print(f"\t{len(coverage)} bases to output")55        if strand == "+":56            cov_file = fwd_file57        else:58            cov_file = rev_file59        block_start = None60        block_height = None61        for i, height in enumerate(coverage):62            if block_height is None:63                # Start our first block64                block_start = i - 1 # Convert to 0-based for UCSC browser65                block_height = height66            elif block_height == height:67                # Still part of the existing block68                continue69            else:70                # Convert to 0-based for UCSC, so this gives the interval (block_start, block_end)71                # which is half-open 0 based and hence goes up to but not including the 1-based position i72                block_end = i - 173                # Don't output anything for 0s, but for everything else output the block74                if block_height != 0:75                    # Write out the block to the bed file76                    cov_file.write('\t'.join([chrom,77                                            str(block_start),78                                            str(block_end),79                                            str(block_height)]) + "\n")80                # Start a new block81                block_start = i - 1# Convert to 0-based for UCSC browser82                block_height = height83        if block_height is not None and block_height != 0:84            # Output the last block85                block_end = i - 1 # Convert to 0-based for UCSC browser86                # Write out the block to the bed file87                cov_file.write('\t'.join([chrom,88                                        str(block_start),89                                        str(block_end),...

load_mol.py

Source:load_mol.py

1from sys import stderr2from io import StringIO3import os4import numpy as np5from rdkit import Chem6from rdkit.Chem import AllChem7class MoleculeLoadException(Exception):8    def __init__(self, *args, **kwargs):9        Exception.__init__(*args, **kwargs)10def get_xyz_from_mol(mol):11    xyz = np.zeros((mol.GetNumAtoms(), 3))12    conf = mol.GetConformer()13    for i in range(conf.GetNumAtoms()):14        position = conf.GetAtomPosition(i)15        xyz[i, 0] = position.x16        xyz[i, 1] = position.y17        xyz[i, 2] = position.z18    return (xyz)19def add_hydrogens_to_mol(mol):20    """21    Add hydrogens to a molecule object22    TODO (LESWING) see if there are more flags to add here for default23    :param mol: Rdkit Mol24    :return: Rdkit Mol25    """26    molecule_file = None27    try:28        pdbblock = Chem.MolToPDBBlock(mol)29        pdb_stringio = StringIO()30        pdb_stringio.write(pdbblock)31        pdb_stringio.seek(0)32        import pdbfixer33        fixer = pdbfixer.PDBFixer(pdbfile=pdb_stringio)34        fixer.findMissingResidues()35        fixer.findMissingAtoms()36        fixer.addMissingAtoms()37        fixer.addMissingHydrogens(7.4)38        hydrogenated_io = StringIO()39        import simtk40        simtk.openmm.app.PDBFile.writeFile(fixer.topology, fixer.positions, hydrogenated_io)41        hydrogenated_io.seek(0)42        return Chem.MolFromPDBBlock(hydrogenated_io.read(), sanitize=False, removeHs=False)43    except ValueError as e:44        print('Unable to add hydrogens %s' % e, file=stderr)45        raise MoleculeLoadException(e)46    finally:47        try:48            os.remove(molecule_file)49        except (OSError, TypeError):50            pass51def compute_charges(mol):52    try:53        AllChem.ComputeGasteigerCharges(mol)54    except Exception as e:55        print('Unable to compute charges for mol', file=stderr)56        raise MoleculeLoadException(e)57    return mol58def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True, sanitize=False):59    if '.mol2' in molecule_file:60        my_mol = Chem.MolFromMol2File(molecule_file, sanitize=False, removeHs=False)61    elif '.sdf' in molecule_file:62        suppl = Chem.SDMolSupplier(str(molecule_file), sanitize=False)63        my_mol = suppl[0]64    elif '.pdb' in molecule_file:65        my_mol = Chem.MolFromPDBFile(str(molecule_file), sanitize=False, removeHs=False)66    else:67        raise ValueError('Unrecognized file type')68    if my_mol is None:69        raise ValueError('Unable to read non None Molecule Object')70    if add_hydrogens or calc_charges:71        my_mol = add_hydrogens_to_mol(my_mol)72    if sanitize:73        Chem.SanitizeMol(my_mol)74    if calc_charges:75        compute_charges(my_mol)76    xyz = get_xyz_from_mol(my_mol)...

test_predictor.py

Source:test_predictor.py

1from pathlib import Path2from click.testing import CliRunner3import bondnet4from bondnet.prediction.predictor import (5    predict_single_molecule,6    predict_multiple_molecules,7    predict_by_reactions,8)9from bondnet.scripts.predict_cli import cli10def test_predict_single_molecule():11    predict_single_molecule(model_name="bdncm", molecule="CC")12    predict_single_molecule(model_name="pubchem", molecule="CC")13def test_predict_multiple_molecules():14    prefix = Path(bondnet.__file__).parent.joinpath("scripts", "examples", "predict")15    molecule_file = prefix.joinpath("molecules.sdf")16    charge_file = prefix.joinpath("charges.txt")17    predict_multiple_molecules(18        model_name="bdncm",19        molecule_file=molecule_file,20        charge_file=charge_file,21        out_file="/tmp/bde.sdf",22        format="sdf",23    )24    predict_multiple_molecules(25        model_name="pubchem",26        molecule_file=molecule_file,27        charge_file=None,28        out_file="/tmp/bde.sdf",29        format="sdf",30    )31def test_predict_by_reaction():32    prefix = Path(bondnet.__file__).parent.joinpath("scripts", "examples", "predict")33    molecule_file = prefix.joinpath("molecules.sdf")34    rxn_file = prefix.joinpath("reactions.csv")35    charge_file = prefix.joinpath("charges.txt")36    predict_by_reactions(37        model_name="bdncm",38        molecule_file=molecule_file,39        reaction_file=rxn_file,40        charge_file=charge_file,41        out_file="/tmp/bde.csv",42        format="sdf",43    )44    predict_by_reactions(45        model_name="bdncm",46        molecule_file=molecule_file,47        reaction_file=rxn_file,48        charge_file=None,49        out_file="/tmp/bde.csv",50        format="sdf",51    )52def test_cli():53    runner = CliRunner()54    result = runner.invoke(cli, ["single", "CC", "0"])55    molecule_file = Path(bondnet.__file__).parent.joinpath(56        "prediction", "examples", "molecules.sdf"57    )...

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