comparison distance_finder.py @ 15:f5d7ffbb2d33 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

14:330514267c57

from openbabel import pybel


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


def execute(ligands_sdf, points_file, outfile):
    """
    :param ligands_sdf: A SDF with the 3D molecules to test

    """

    points = []

    # read the points
    with open(points_file, 'r') as f:
        for line in f.readlines():
            line.strip()
            if line:
                p = line.split()
                if len(p) == 3:
                    points.append((float(p[0]), float(p[1]), float(p[2])))
                    log("Read points", p)
                    continue
            log("Failed to read line:", line)
    log('Found', len(points), 'atom points')

    sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True)

    count = 0
    for mol in pybel.readfile("sdf", ligands_sdf):
        count += 1
        if count % 50000 == 0:
            log('Processed', count)

        try:
            # print("Processing mol", mol.title)
            clone = pybel.Molecule(mol)
            clone.removeh()

            for point in points:
                p += 1
                distances = []
                for i in coords:
                    # calculates distance based on cartesian coordinates
                    distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2)
                    distances.append(distance)
                    # log("distance:", distance)
                min_distance = min(distances)
                # log('Min:', min_distance)
                # log(count, p, min_distance)

                mol.data['distance' + str(p)] = min_distance

            sdf_writer.write(mol)

        except Exception as e:
            log('Failed to handle molecule: ' + str(e))
            continue

    sdf_writer.close()
    log('Wrote', count, 'molecules')


def main():
    global work_dir

    parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points')
    parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)")
    parser.add_argument('-p', '--points', help="PDB format file with atoms")
    parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results")

    args = parser.parse_args()
    log("XChem distances args: ", args)

    execute(args.input, args.points, args.outfile)

15:f5d7ffbb2d33

from openbabel import pybel


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


def execute(ligands_sdf, points_file, outfile):
    """
    :param ligands_sdf: A SDF with the 3D molecules to test

    """

    points = []

    # read the points
    with open(points_file, "r") as f:
        for line in f.readlines():
            line.strip()
            if line:
                p = line.split()
                if len(p) == 3:
                    points.append((float(p[0]), float(p[1]), float(p[2])))
                    log("Read points", p)
                    continue
            log("Failed to read line:", line)
    log("Found", len(points), "atom points")

    sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True)

    count = 0
    for mol in pybel.readfile("sdf", ligands_sdf):
        count += 1
        if count % 50000 == 0:
            log("Processed", count)

        try:
            # print("Processing mol", mol.title)
            clone = pybel.Molecule(mol)
            clone.removeh()

            for point in points:
                p += 1
                distances = []
                for i in coords:
                    # calculates distance based on cartesian coordinates
                    distance = math.sqrt(
                        (point[0] - i[0]) ** 2
                        + (point[1] - i[1]) ** 2
                        + (point[2] - i[2]) ** 2
                    )
                    distances.append(distance)
                    # log("distance:", distance)
                min_distance = min(distances)
                # log('Min:', min_distance)
                # log(count, p, min_distance)

                mol.data["distance" + str(p)] = min_distance

            sdf_writer.write(mol)

        except Exception as e:
            log("Failed to handle molecule: " + str(e))
            continue

    sdf_writer.close()
    log("Wrote", count, "molecules")


def main():
    global work_dir

    parser = argparse.ArgumentParser(
        description="XChem distances - measure distances to particular points"
    )
    parser.add_argument(
        "-i", "--input", help="SDF containing the 3D molecules to score)"
    )
    parser.add_argument("-p", "--points", help="PDB format file with atoms")
    parser.add_argument(
        "-o", "--outfile", default="output.sdf", help="File name for results"
    )

    args = parser.parse_args()
    log("XChem distances args: ", args)

    execute(args.input, args.points, args.outfile)