def main(out):
out.write(prelude)
i = 0
for mdl in all_descriptors():
mdl_name = '.'.join(mdl.__name__.split('.'))
mdl_ppr = ':py:mod:`~{}`'.format(mdl_name)
first = True
for Desc in get_descriptors_from_module(mdl):
for desc in Desc.preset():
i += 1
if not first:
mdl_ppr = ''
cnst = desc.__class__.__name__
args = ', '.join(Descriptor._pretty(p) for p in desc.parameters())
cnst = ':py:class:`~{}.{}` ({})'.format(mdl_name, cnst, args)
dim = '3D' if desc.require_3D else '2D'
out.write(' {}, {}, {}, "{}", {}\n'.format(i, mdl_ppr, desc, cnst, dim))
first = False
def test_by_references():
calc = Calculator(
d
for d in all_descriptors()
if d.__class__ not in [Polarizability.APol, Polarizability.BPol]
)
calc.register([
Polarizability.APol(True),
Polarizability.BPol(True),
])
actuals = dict()
for mol in Chem.SDMolSupplier(os.path.join(data_dir, 'structures.sdf'), removeHs=False):
actuals[mol.GetProp('_Name')] = {str(d): v for d, v in zip(calc.descriptors, calc(mol))}
for path in glob(os.path.join(data_dir, '*.yaml')) + glob(os.path.join(data_dir, '**/*.yaml')):
for test in yaml.load(open(path), Loader=Loader):
dnames = test['names']
if not isinstance(dnames, list):
dnames = [dnames]
desireds = (
(mname, zip(dnames, values if isinstance(values, list) else [values]))
for mname, values in test['results'].items()
)
digit = test.get('digit')
if digit is None:
assert_f = eq_
else:
def assert_f(a, d, m):
if np.isnan(d):
assert isinstance(a, MissingValueBase)
return
assert_almost_equal(a, d, digit, m)
for mname, descs in desireds:
for dname, desired in descs:
if not desired == 'skip':
yield (
assert_f,
actuals[mname][dname],
desired,
'{} of {}'.format(dname, mname)
)
def test_parallel():
calc = Calculator(all_descriptors())
mols = list(map(Chem.AddHs, [
Chem.MolFromSmiles('c1ccccc1'),
Chem.MolFromSmiles('C1=CC(=C(C=C1C2=C(C=C3C(=CC(=CC3=[O+]2)O)O)O)O)O'),
Chem.MolFromSmiles('CCCCCC'),
]))
for mol in mols:
Chem.EmbedMolecule(mol)
for serial, parallel in zip(calc.map(mols, nproc=1, quiet=True),
calc.map(mols, quiet=True)):
for d, s, p in zip(calc.descriptors, serial, parallel):
if isinstance(s, MissingValueBase):
yield eq_, pickle.dumps(s), pickle.dumps(p), str(d)
else:
yield assert_almost_equal, s, p, 7, str(d)
def test_pickle_calculator():
orig = Calculator(all_descriptors())
d0 = orig.descriptors[0]
d1 = orig.descriptors[1]
orig.register([
d0 + d1, d0 - d1, d0 * d1, d0 // d1, d0 % d1, d0 ** d1,
-d0, +d1, abs(d0), math.trunc(d0),
])
if six.PY3:
orig.register([math.ceil(d0), math.floor(d1)])
pickled = pickle.loads(pickle.dumps(orig))
mol = Chem.MolFromSmiles('c1ccccc1C(O)O')
for a, b in zip(orig.descriptors, pickled.descriptors):
yield eq_, a, b
for a, b in zip(orig(mol), pickled(mol)):
if isinstance(a, MissingValueBase):
yield eq_, a.__class__, b.__class__
else:
yield assert_almost_equal, a, b
def member(self, member):
if is_descriptor_class(member):
for line in self.descriptor(member):
yield line
else:
raise ValueError('unknown member {} in {}'.format(member, self.mdl.__name__))
def members(self):
for m in self.mdl.__all__:
for line in self.member(getattr(self.mdl, m)):
yield line
def module(self):
yield '.. automodule:: {}'.format(self.mdl.__name__)
def print(self, file=sys.stdout):
for line in chain(self.header(), self.module(), self.members()):
print(line, file=file)
if __name__ == '__main__':
print('Submodules')
print('----------')
print('')
print('.. toctree::')
for mdl in all_descriptors():
print(' ' + mdl.__name__)
with open('api/{}.rst'.format(mdl.__name__), 'w') as f:
Generator(mdl).print(file=f)