Source code for mordred.tests.test_mordred_main

import os
import sys
import shutil
import tempfile
from contextlib import contextmanager

from nose.tools import eq_
from rdkit.Chem import AllChem as Chem

from .. import Calculator, __version__, all_descriptors
from ..__main__ import main as mordred

Nd2D = len(Calculator(all_descriptors(), ignore_3D=True).descriptors)
Nd3D = len(Calculator(all_descriptors(), ignore_3D=False).descriptors)


[docs]def in_(a, s):
    assert a in s, '{!r} not in {!r}'.format(a, s)


@contextmanager
[docs]def isolate():
    cwd = os.getcwd()
    try:
        work = tempfile.mkdtemp()
        os.chdir(work)
        yield
    finally:
        os.chdir(cwd)
        shutil.rmtree(work)


[docs]class Result(object):
    def __iter__(self):
        return iter([self.stdout, self.stderr, self.exitcode])

    def __repr__(self):
        return '{!r} {!r} {!r}'.format(self.stdout, self.stderr, self.exitcode)


[docs]def command(cmd, *args):
    r = Result()

    orig = sys.stdout, sys.stderr

    ofd, opath = tempfile.mkstemp()
    efd, epath = tempfile.mkstemp()

    try:
        with os.fdopen(ofd, 'w') as stdout, os.fdopen(efd, 'w') as stderr:
            sys.stdout = stdout
            sys.stderr = stderr

            try:
                cmd(args=args)
                r.exitcode = 0
            except SystemExit as e:
                r.exitcode = e.args[0]

    finally:
        sys.stdout, sys.stderr = orig

        with open(opath) as stdout, open(epath) as stderr:
            r.stdout = stdout.read()
            r.stderr = stderr.read()

        os.remove(opath)
        os.remove(epath)

    return r


[docs]def test_no_args():
    stdout, stderr, exitcode = command(mordred)
    eq_(exitcode, 2)
    eq_(stdout, '')
    in_('usage:', stderr)
    # python3 or python2
    assert 'the following arguments are required: INPUT' in stderr or 'too few arguments' in stderr


[docs]def test_help():
    stdout, stderr, exitcode = command(mordred, '-h')
    eq_(exitcode, 0)
    eq_(stderr, '')
    in_('usage:', stdout)
    in_('descriptors:', stdout)


[docs]def test_version():
    stdout, stderr, exitcode = command(mordred, '--version')
    eq_(exitcode, 0)

    vstr = 'mordred-{}\n'.format(__version__)

    if stderr == '':  # python 3
        eq_(stdout, vstr)
    else:  # python2
        eq_(stderr, vstr)


[docs]def test_missing_file():
    with isolate():
        stdout, stderr, exitcode = command(mordred, 'missing.smi')
        eq_(exitcode, 2)
        eq_(stdout, '')
        in_('usage:', stderr)
        in_('invalid PathType value', stderr)


[docs]def number_of_field(output):
    return len(list(filter(lambda c: c == ',', output.split('\n')[0])))


[docs]def test_smi():
    with isolate():
        with open('input.smi', 'w') as f:
            f.write('c1ccccc1 Benzene\n')

        stdout, stderr, exitcode = command(mordred, 'input.smi', '-q', '-o', '-')

        eq_(exitcode, 0)
        eq_(number_of_field(stdout), Nd2D)
        eq_(stdout.split('\n')[1].split(',')[0], 'Benzene')
        eq_(stderr, '')


[docs]def test_smi_without_name():
    with isolate():
        with open('input.smi', 'w') as f:
            f.write('c1ccccc1\n')

        stdout, stderr, exitcode = command(mordred, 'input.smi', '-q', '-o', '-')

        eq_(exitcode, 0)
        eq_(number_of_field(stdout), Nd2D)
        eq_(stdout.split('\n')[1].split(',')[0], 'c1ccccc1')
        eq_(stderr, '')


[docs]def test_sdf():
    with isolate():
        mol = Chem.MolFromSmiles('c1ccccc1')
        mol.SetProp('_Name', 'Benzene')
        Chem.MolToMolFile(mol, 'input.sdf')

        stdout, stderr, exitcode = command(mordred, 'input.sdf', '-q', '-o', 'output.csv')

        eq_(exitcode, 0)
        eq_(stdout, '')
        eq_(stderr, '')
        output = open('output.csv').read()
        eq_(number_of_field(output), Nd2D)
        eq_(output.split('\n')[1].split(',')[0], 'Benzene')


[docs]def test_sdf_3D():
    with isolate():
        mol = Chem.MolFromSmiles('c1ccccc1')
        Chem.EmbedMolecule(mol)
        mol.SetProp('_Name', 'Benzene')
        Chem.MolToMolFile(mol, 'input.sdf')

        stdout, stderr, exitcode = command(mordred, 'input.sdf', '-q', '-o', 'output.csv', '-3')

        eq_(exitcode, 0)
        eq_(stdout, '')
        eq_(stderr, '')
        output = open('output.csv').read()
        eq_(number_of_field(output), Nd3D)
        eq_(output.split('\n')[1].split(',')[0], 'Benzene')


[docs]def test_verbose():
    with isolate():
        with open('input.smi', 'w') as f:
            f.write('c1ccccc1 Benzene\n')

        r = command(mordred, 'input.smi', '-o', '-', '-q', '-vv')

        eq_(r.exitcode, 0)
        eq_(number_of_field(r.stdout), Nd2D)
        eq_(r.stdout.split('\n')[1].split(',')[0], 'Benzene')
        in_('[Missing]', r.stderr)