def test_exception_smarts():
# syntax error: SMARTS Parse Error
with pytest.raises(ValueError):
m = Molecule('fake', 'smarts')
# syntax error: SMARTS Parse Error
with pytest.raises(ValueError):
m = Molecule('[#6](=[#6]', 'smarts')
def mols():
m1 = Molecule('c1ccc1', 'smiles')
m2 = Molecule('CNC', 'smiles')
molecules = [m1, m2]
return molecules
def test_exception_inchi():
# syntax error: SMARTS Parse Error
with pytest.raises(ValueError):
m = Molecule('fake', 'inchi')
# inchi key: syntax error: SMARTS Parse Error
with pytest.raises(ValueError):
m = Molecule('RYYVLZVUVIJVGH-UHFFFAOYSA-N', 'inchi')
def test_mol2xyz_MMFF(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
m.hydrogens('add')
m.to_xyz('MMFF', maxIters=210)
assert m.xyz.geometry.shape[0] == m.rdkit_molecule.GetNumAtoms()
m.to_xyz('MMFF', maxIters=110, mmffVariant='MMFF94s')
assert m.xyz.atomic_symbols.shape[0] == m.rdkit_molecule.GetNumAtoms()
assert m.MMFF_args['mmffVariant'] == 'MMFF94s'
# check default args
m.to_xyz('MMFF', **m._default_MMFF_args)
def test_mol2xyz_UFF(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
m.hydrogens('add')
m.to_xyz('UFF', ignoreInterfragInteractions=False)
assert m.xyz.geometry.shape[0] == m.rdkit_molecule.GetNumAtoms()
m.to_xyz('UFF', maxIters=110)
assert m.xyz.atomic_symbols.shape[0] == m.rdkit_molecule.GetNumAtoms()
assert m.UFF_args['maxIters'] == 110
# check default args
m.to_xyz('UFF', **m._default_UFF_args)
def test_exception_smiles():
# syntax error: SMILES Parse Error
with pytest.raises(ValueError):
m = Molecule('fake', 'smiles')
# wrong SMILES
with pytest.raises(ValueError):
m = Molecule('CO(C)C', 'smiles')
# can't kekulize
with pytest.raises(ValueError):
m = Molecule('c1cc1', 'smiles')
def mols2():
m1 = Molecule('c1ccc1', 'smiles')
m2 = Molecule('CNC', 'smiles')
m3 = Molecule('CC', 'smiles')
m4 = Molecule('CCC', 'smiles')
molecules = [m1, m2, m3, m4]
for mol in molecules:
mol.to_xyz(optimizer='UFF')
return molecules
def mols():
# Oxygen, Hydrogen, Hydrogen
num = np.array([8, 1, 1])
num = num.reshape((3, 1))
sym = np.array(['O', 'H', 'H'])
sym = sym.reshape((3, 1))
c = np.array([[1.464, 0.707, 1.056], [0.878, 1.218, 0.498], [2.319, 1.126, 0.952]])
xyz = XYZ(c,num,sym)
m = Molecule('O', 'smiles')
# forcefully overwrite xyz
m._xyz = xyz
return m
def test_mol2smiles(caffeine_smiles, caffeine_canonical, caffeine_kekulize):
m = Molecule(caffeine_smiles, 'smiles')
m.to_smiles()
assert isinstance(m.rdkit_molecule, Chem.Mol)
assert m.smiles == caffeine_canonical
m.to_smiles(kekuleSmiles=True)
assert m.smiles == caffeine_kekulize
# kekulize takes priority over canonical
m.to_smiles(kekuleSmiles=True)
assert m.smiles == caffeine_kekulize
# if kekule is False, everything is OK
m.to_smiles(canonical=True)
assert m.smiles == caffeine_canonical
def test_mol2xyz_exception(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
m.hydrogens('add')
with pytest.raises(ValueError):
m.to_xyz()
with pytest.raises(ValueError):
m.to_xyz('uff')
def test_mol2inchi_defaultargs(caffeine_inchi):
m = Molecule(caffeine_inchi, 'inchi')
m.to_inchi()
m.to_inchi(**m._default_rdkit_inchi_args)
# all the args & treatWarningAsError=True
args = m._default_rdkit_inchi_args
args['treatWarningAsError'] = True
m.to_inchi(**args)
assert m.inchi_args['treatWarningAsError'] is True
def test_mol2smarts_defaultargs(caffeine_smarts):
m = Molecule(caffeine_smarts, 'smarts')
m.to_smarts()
m.to_smarts(**m._default_rdkit_smarts_args)
# all the args & isomericSmiles=False
args = m._default_rdkit_smarts_args
args['isomericSmiles'] = False
m.to_smarts(**args)
assert m.smarts_args['isomericSmiles'] is False
def test_mol2smiles_defaultargs(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
m.to_smiles()
m.to_smiles(**m._default_rdkit_smiles_args)
# all the args & canonical=False
args = m._default_rdkit_smiles_args
args['canonical'] = False
m.to_smiles(**args)
assert m.smiles_args['canonical'] is False
def load_xyz_polarizability():
"""Load and return xyz files and polarizability (Bohr^3).
The xyz coordinates of small organic molecules are optimized with BP86/def2svp level of theory.
Polarizability of the molecules are also calcualted in the same level of thoery.
================= ======================
rows 50
Columns 1
header polarizability
molecules rep. xyz
Features 0
Returns 1 dataframe and 1 dict
================= ======================
Returns
-------
molecules : list
The list of molecule objects with xyz coordinates.
pol : pandas dataframe
The polarizability of each molecule as a column of dataframe.
Examples
--------
>>> from chemml.datasets import load_xyz_polarizability
>>> molecules, polarizabilities = load_xyz_polarizability()
>>> print(len(molecules))
50
>>> print(polarizabilities.shape)
(50, 1)
"""
DATA_PATH = pkg_resources.resource_filename('chemml', os.path.join('datasets','data','organic_xyz'))
# from chemml.initialization import XYZreader
# reader = XYZreader(path_pattern=['[1-9]_opt.xyz', '[1-9][0-9]_opt.xyz'],
# path_root=DATA_PATH,
# reader='manual',
# skip_lines=[2, 0])
# molecules = reader.read()
molecules = []
for i in range(1,51):
molecule = Molecule(os.path.join(DATA_PATH,"%i_opt.xyz"%i), "xyz")
molecule.to_smiles()
molecule.pybel_molecule = None
molecules.append(molecule)
df = pd.read_csv(os.path.join(DATA_PATH,'pol.csv'))
return molecules, df
def test_load_xyz_scenarios(xyz_path):
path = os.path.join(xyz_path, '1_opt.xyz')
m = Molecule(path, 'xyz')
# 1 : xyz exist and optimizer is none
assert m.to_xyz()
# 2 xyz doesn't exist and pybel exist and optimizer is none
m._xyz = None
m.to_xyz()
assert m.xyz.geometry.shape == (28, 3)
# 3 xyz doesn't exist and pybel exist and optimizer is UFF
m._xyz = None
m.to_xyz(optimizer='UFF', maxIters=10210)
assert m.xyz.geometry.shape == (28, 3)
def test_load_xyzfile(xyz_path):
path = os.path.join(xyz_path, '1_opt.xyz')
m = Molecule(path, 'xyz')
assert m.creator == ('XYZ', path)
assert isinstance(m.pybel_molecule, pybel.Molecule)
assert m.xyz.geometry.shape == (28, 3)
m.to_smiles()
assert m.smiles == 'c1ccc(CC2CCCC2)cc1'
m.to_smarts()
assert m.smarts == '[#6]1-[#6]-[#6]-[#6](-[#6]-1)-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'
m.to_inchi()
assert m.inchi == 'InChI=1S/C12H16/c1-2-6-11(7-3-1)10-12-8-4-5-9-12/h1-3,6-7,12H,4-5,8-10H2'
def test_mol2smarts(caffeine_smarts):
m = Molecule(caffeine_smarts, 'smarts')
m.to_smarts()
assert isinstance(m.rdkit_molecule, Chem.Mol)
assert m.smarts == caffeine_smarts
m.to_smarts(isomericSmiles=False)
assert m.smarts == caffeine_smarts
def bagofbounds(mol2, maxentry):
from chemml.chem import Molecule
#caffeine_smiles = 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C'
#caffeine_smarts = '[#6]-[#7]1:[#6]:[#7]:[#6]2:[#6]:1:[#6](=[#8]):[#7](:[#6](=[#8]):[#7]:2-[#6])-[#6]'
#caffeine_inchi = 'InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3'
mol = Molecule(Chem.MolToSmiles(mol2), 'smiles')
mol.hydrogens('add')
mol.to_xyz(optimizer='MMFF', mmffVariant='MMFF94s', maxIters=300) # 'UFF'
print(mol)
mol.visualize()
#mol.visualize()
from chemml.datasets import load_xyz_polarizability
from chemml.chem import BagofBonds
#coordinates, y = load_xyz_polarizability(mol)
bob = BagofBonds(const=1.0)
features = bob.represent(mol)
print(features)
print("number of entry")
print(features.shape[1])
if features.shape[1] > maxentry:
maxentry = features.shape[1]
return features, maxentry
def mols():
m = Molecule('c1ccc1', 'smiles')
return m
def mol_list():
smi1 = Molecule('c1cc2cnc3c(cnc4cc(-c5ncncn5)c5nsnc5c34)c2c2nsnc12', 'smiles')
smi2 = Molecule('[nH]1ccc2[nH]c3c4CC(=Cc4c4c[nH]cc4c3c12)c1scc2cc[nH]c12', 'smiles')
return [smi1, smi2]
def mols():
m = Molecule('CCO', 'smiles')
return m
def test_load_inchi(caffeine_inchi):
m = Molecule(caffeine_inchi, 'inchi')
assert m.creator == ('InChi', caffeine_inchi)
assert isinstance(m.rdkit_molecule, Chem.Mol)
def test_load_smarts(caffeine_smarts):
m = Molecule(caffeine_smarts, 'smarts')
assert m.creator == ('SMARTS', caffeine_smarts)
assert isinstance(m.rdkit_molecule, Chem.Mol)
def test_load_smiles(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
assert m.creator == ('SMILES', caffeine_smiles)
assert isinstance(m.rdkit_molecule, Chem.Mol)
def chemml_molecule_list():
molecules = ['C', 'CC', 'CCC', 'CC(C)C']
mol_list = [Molecule(i, 'smiles') for i in molecules]
yield mol_list
from chemml.chem import Molecule
caffeine_smiles = 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C'
caffeine_smarts = '[#6]-[#7]1:[#6]:[#7]:[#6]2:[#6]:1:[#6](=[#8]):[#7](:[#6](=[#8]):[#7]:2-[#6])-[#6]'
caffeine_inchi = 'InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3'
mol = Molecule(caffeine_smiles, input_type='smiles')
mol.hydrogens('add')
mol.to_xyz(optimizer='MMFF', mmffVariant='MMFF94s', maxIters=300) # 'UFF'
print(mol)
mol.visualize()
#mol.visualize()
from chemml.datasets import load_xyz_polarizability
from chemml.chem import BagofBonds
#coordinates, y = load_xyz_polarizability(mol)
bob = BagofBonds(const= 1.0)
features = bob.represent(mol)
print(features)
def test_mol2inchi(caffeine_inchi):
m = Molecule(caffeine_inchi, 'inchi')
m.to_inchi()
assert isinstance(m.rdkit_molecule, Chem.Mol)
assert m.inchi == caffeine_inchi
def test_hydrogens(caffeine_smiles, caffeine_canonical, caffeine_inchi):
m = Molecule(caffeine_smiles, 'smiles')
m.to_smiles()
assert isinstance(m.rdkit_molecule, Chem.Mol)
assert m.smiles == caffeine_canonical
# add hydrogens
m.hydrogens('add', explicitOnly=False)
# canonical smiles with hydrogens
m.to_smiles()
assert m.smiles == "[H]c1nc2c(c(=O)n(C([H])([H])[H])c(=O)n2C([H])([H])[H])n1C([H])([H])[H]"
# test inchi
m = Molecule(caffeine_inchi, 'inchi')
m.to_inchi()
assert m.inchi == caffeine_inchi
# add hydrogens
m.hydrogens('add')
m.to_inchi()
assert m.inchi == caffeine_inchi
def test_hydrogens_exception(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
with pytest.raises(ValueError):
m.hydrogens('addHs')
def mol_single():
smi1 = Molecule('c1cc2cnc3c(cnc4cc(-c5ncncn5)c5nsnc5c34)c2c2nsnc12', 'smiles')
return smi1