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_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_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_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 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 test_hydrogens_exception(caffeine_smiles):
m = Molecule(caffeine_smiles, 'smiles')
with pytest.raises(ValueError):
m.hydrogens('addHs')
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)