def test_prop_tofile():
test_mol = 'to_file_pyb_test'
test_mol = aemol(test_mol)
ref_xyz = 'tests/test_mols/qm9_1.nmredata.sdf'
assert os.path.isfile(ref_xyz)
test_mol.from_file_pyb(ref_xyz, 'sdf')
test_mol.from_pybel(test_mol.pybmol)
test_mol.get_bonds()
test_mol.get_path_lengths()
get_coupling_types(test_mol)
atoms = len(test_mol.structure['types'])
test_mol.pair_properties['coupling'] = np.random.randn(atoms, atoms)
test_mol.atom_properties['shift'] = np.random.randn(atoms)
check1 = test_mol.pair_properties['coupling']
check2 = test_mol.atom_properties['shift']
test_mol.prop_tofile('test.nmredata.sdf', 'nmr', 'nmredata')
checkmol = aemol('test')
checkmol.from_file_pyb('test.nmredata.sdf', 'sdf')
checkmol.prop_fromfile('test.nmredata.sdf', 'nmr', 'nmredata')
os.remove('test.nmredata.sdf')
def test_run_all_checks():
test_molid = 'test'
test_file = 'tests/test_dataset/test_xyz.xyz'
test_mol = aemol(test_molid)
test_mol.from_file_pyb(test_file)
test_mol.from_pybel(test_mol.pybmol)
test_bad_molid = 'bad_test'
test_bad_file = 'tests/test_dataset/test_bad_mol.xyz'
test_bad_mol = aemol(test_bad_molid)
test_bad_mol.from_file_pyb(test_bad_file)
test_bad_mol.from_pybel(test_bad_mol.pybmol)
assert run_all_checks(test_mol) == True
assert run_all_checks(test_bad_mol) == False
def test_check_mol_aemol():
test_molid = 'test'
test_file = 'tests/test_dataset/test_xyz.xyz'
test_mol = aemol(test_molid)
test_mol.from_file_pyb(test_file)
pybmol = test_mol.pybmol
test_mol.from_pybel(pybmol)
test_bad_molid = 'bad_test'
test_bad_file = 'tests/test_dataset/test_bad_mol.xyz'
test_bad_mol = aemol(test_bad_molid)
test_bad_mol.from_file_pyb(test_bad_file)
test_bad_mol.from_pybel(test_bad_mol.pybmol)
assert aemol.check_mol_aemol(test_mol) == True
assert aemol.check_mol_aemol(test_bad_mol) == False
def test_from_file():
test_mol = 'to_rd_test'
test_xyz = 'tests/test_dataset/test_xyz.xyz'
mol = aemol(test_mol)
mol.from_file_pyb(test_xyz)
assert mol.structure['types'] is not []
assert mol.structure['xyz'] is not []
assert mol.structure['conn'] is not []
def test_to_pybel():
test_mol = 'to_pyb_test'
mol_test = aemol(test_mol)
ref_mol = 'ref'
mol_ref = aemol(ref_mol)
test_xyz = 'tests/test_dataset/test_xyz.xyz'
pybmol_ref = next(pyb.readfile('xyz', test_xyz))
mol_ref.from_pybel(pybmol_ref)
mol_ref.to_pybel()
test_pybmol = mol_ref.pybmol
mol_test.from_pybel(test_pybmol)
assert (mol_test.structure['xyz'] == mol_ref.structure['xyz']).all() == True
assert (mol_test.structure['types'] == mol_ref.structure['types']).all() == True
assert (mol_test.structure['conn'] == mol_ref.structure['conn']).all() == True
def test_pyb_neutralise():
test_file = ['tests/test_mols/charged_mol1.sdf',
'tests/test_mols/charged_mol2.sdf']
for idx, file in enumerate(test_file):
test_mol = aemol(idx)
test_mol.from_file_pyb(file, ftype = 'sdf')
test_mol.pyb_neutralise(test_mol.pybmol)
test_mol.from_pybel(test_mol.pybmol)
assert test_mol.check_mol_aemol() == True
def test_rd_neutralise():
test_file = ['tests/test_mols/charged_mol1.sdf',
'tests/test_mols/charged_mol2.sdf']
for idx, file in enumerate(test_file):
test_mol = aemol(idx)
test_mol.from_file_rdkit(file)
test_mol.rd_neutralise(test_mol.rdmol)
test_mol.from_rdkit(test_mol.rdmol)
assert test_mol.check_mol_aemol() == True
def test_to_file_ae():
test_mol = 'to_file_ae_test'
test_mol = aemol(test_mol)
ref_xyz = 'tests/test_dataset/test_xyz.xyz'
test_mol.from_file_pyb(ref_xyz)
tmp_file = Path("./tmp_test.xyz")
test_mol.to_file_ae('xyz', 'tmp_test.xyz')
assert tmp_file.is_file() == True
os.remove(tmp_file)
def test_from_rdkit():
test_mol = 'from_rd_test'
mol = aemol(test_mol)
smiles = ' CCCC'
rdmol = Chem.MolFromSmiles(smiles)
rdmol = Chem.AddHs(rdmol)
AllChem.EmbedMolecule(rdmol)
mol.from_rdkit(rdmol)
assert mol.structure['types'] is not []
assert mol.structure['xyz'] is not []
def test_from_pybel():
test_mol = 'from_pyb_test'
test_xyz = 'tests/test_dataset/test_xyz.xyz'
mol = aemol(test_mol)
pybmol = next(pyb.readfile('xyz', test_xyz))
mol.from_pybel(pybmol)
types, xyz, conn = pybmol_to_aemol(pybmol)
assert (mol.structure['types'] == types).all() == True
assert (mol.structure['xyz'] == xyz).all() == True
assert (mol.structure['conn'] == conn).all() == True
def test_to_file_pyb():
test_mol = 'to_file_pyb_test'
test_mol = aemol(test_mol)
ref_xyz = 'tests/test_dataset/test_xyz.xyz'
test_mol.from_file_pyb(ref_xyz)
pybmol = test_mol.pybmol
test_mol.from_pybel(pybmol)
tmp_file = Path("./tmp_pyb.smi")
test_mol.to_file_pyb('smi', 'tmp_pyb.smi')
assert tmp_file.is_file() == True
os.remove(tmp_file)
def test_to_rdkit():
test_mol = 'to_rd_test'
test_xyz = 'tests/test_dataset/test_xyz.xyz'
mol = aemol(test_mol)
mol.from_file_pyb(test_xyz)
assert mol.structure['types'] is not []
assert mol.structure['xyz'] is not []
assert mol.structure['conn'] is not []
mol.to_rdkit()
test_rd = mol.rdmol
assert test_rd is not None
def test_init():
test_mol = 'CCCC'
mol = aemol(test_mol)
assert mol.info['molid'] == test_mol
assert mol.info['filepath'] == ""
assert mol.structure['xyz'] == []
assert mol.structure['types'] == []
assert mol.structure['conn'] == []
assert mol.atom_properties == {}
assert mol.pair_properties == {}
assert mol.mol_properties['energy'] == -404.404
import glob
import sys
sys.path.append('INSERT_PATH_TO_MOL_TRANSLATOR_HERE')
from mol_translator.aemol import aemol
from mol_translator.properties.energy.energy_input import make_g09_optin
from mol_translator.properties.nmr.nmr_input import make_g09_nmrin
files = glob.glob('INPUT/*')
for file in files:
id = file.split('/')[-1].split('.')[0]
ft = file.split('.')[-1]
amol = aemol(id)
amol.from_file_pyb(file, ftype=ft)
prefs = {}
prefs['mol'] = {}
prefs['mol']['charge'] = 0
prefs['mol']['multiplicity'] = 1
prefs['optimisation'] = {}
prefs['optimisation']['software'] = 'g09'
prefs['optimisation']['memory'] = 26
prefs['optimisation']['processors'] = 8
prefs['optimisation']['opt'] = 'tight'
prefs['optimisation']['freq'] = True
prefs['optimisation']['functional'] = 'mPW1PW'
prefs['optimisation']['basisset'] = '6-311g(d,p)'
prefs['optimisation']['solvent'] = None
def test_from_string():
test_mol = 'CCCC'
mol = aemol(test_mol)
pybmol_test = pyb.readstring('smi', test_mol)
return mol.from_string(test_mol)
assert pybmol == pybmol_test
def read_df(atom_df, pair_df):
if 'bond_dist' in pair_df.keys():
pair_df['path_len'] = pair_df['bond_dist']
molnames = atom_df.molecule_name.unique()
mols = []
for molname in tqdm(molnames):
amol = aemol(molname)
mol_atom_df = atom_df.loc[(atom_df.molecule_name == molname)]
mol_pair_df = pair_df.loc[(pair_df.molecule_name == molname)]
atoms = len(mol_atom_df)
xyz = np.zeros((atoms, 3), dtype=np.float64)
types = np.zeros((atoms), dtype=np.int32)
conn = []
path_len = []
for idx in mol_atom_df['atom_index']:
idx_atom_df = mol_atom_df.loc[(mol_atom_df.atom_index == idx)]
xyz[idx][0] = idx_atom_df['x'].to_numpy().squeeze()
xyz[idx][1] = idx_atom_df['y'].to_numpy().squeeze()
xyz[idx][2] = idx_atom_df['z'].to_numpy().squeeze()
types[idx] = idx_atom_df['typeint'].to_numpy().squeeze()
conn.append(*idx_atom_df['conn'].to_list())
path = []
for jdx in mol_atom_df['atom_index']:
plen = mol_pair_df.loc[
(mol_pair_df.atom_index_0 == idx)
& (mol_pair_df.atom_index_1 == jdx)]['path_len'].to_list()
if len(plen) == 1:
path.append(plen[0])
else:
path.append(0)
path_len.append([*path])
amol.structure['xyz'] = xyz
amol.structure['types'] = types
amol.structure['conn'] = conn
amol.structure['path_len'] = np.asarray(path_len)
propnames = []
for prop in mol_atom_df.keys():
if not prop in [
'molecule_name', 'atom_index', 'typestr', 'typeint', 'x',
'y', 'z', 'conn'
]:
propnames.append(prop)
for prop in propnames:
amol.atom_properties[prop] = mol_atom_df[prop].to_numpy()
propnames = []
for prop in mol_pair_df.keys():
if not prop in [
'molecule_name', 'atom_index_0', 'atom_index_1', 'dist',
'path_len', 'bond_dist'
]:
propnames.append(prop)
amol.pair_properties[prop] = []
for prop in propnames:
for idx in mol_atom_df['atom_index']:
prop_list = []
for jdx in mol_atom_df['atom_index']:
df_prop = mol_pair_df.loc[
(mol_pair_df.atom_index_0 == idx)
& (mol_pair_df.atom_index_1 == jdx)][prop].to_list()[0]
prop_list.append(df_prop)
amol.pair_properties[prop].append(prop_list)
mols.append(amol)
return mols
