def prep_mol_ecfp4(aemol):
aemol.get_bonds()
aemol.get_path_lengths()
get_coupling_types(aemol)
aemol.atom_properties['ecfp4'] = aemol.mol_properties['ecfp4']
return aemol
def prep_mol(aemol):
aemol.get_bonds()
aemol.get_path_lengths()
get_coupling_types(aemol)
return aemol
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 prep_mol_mulliken(aemol, mc_file="", mc_format=""):
aemol.get_bonds()
aemol.get_path_lengths()
get_coupling_types(aemol)
if os.path.isfile(mc_file):
aemol.prop_from_file(mc_file, mc_format, 'mc')
else:
print('Setting fake mulliken charge values', mc_file)
aemol.atom_properties['mull_chg'] = np.zeros(len(
aemol.structure['types']),
dtype=np.float64)
return aemol
def prep_mol_ic50(aemol, ic50_file="", ic50_type=""):
aemol.get_bonds()
aemol.get_path_lengths()
get_coupling_types(aemol)
if os.path.isfile(ic50_file):
aemol.prop_from_file(ic50_file, ic50_type, 'ic50')
aemol.atom_properties['ic50'] = np.full(len(aemol.structure['types']),
aemol.mol_properties['ic50'],
dtype=np.float64)
else:
print('Setting fake ic50 values', ic50_file)
aemol.atom_properties['ic50'] = np.zeros(len(aemol.structure['types']),
dtype=np.float64)
return aemol
def prep_mol_nmr(aemol, nmr_file="", nmr_type=""):
aemol.get_bonds()
aemol.get_path_lengths()
get_coupling_types(aemol)
if os.path.isfile(nmr_file):
aemol.prop_from_file(nmr_file, 'nmr', nmr_type)
else:
aemol.atom_properties['shift'] = np.zeros(len(
aemol.structure['types']),
dtype=np.float64)
aemol.pair_properties['coupling'] = np.zeros(
(len(aemol.structure['types']), len(aemol.structure['types'])),
dtype=np.float64)
return aemol
amol = aemol(id)
#amol.from_file(file, ftype='g09')
amol.from_file_pyb(file, ftype='log')
opt_file = f'OPT/{str(id)}.log'
amol.prop_from_file(opt_file, 'g09', 'scf')
assert amol.mol_properties['energy'] < 1000000, print(
amol.mol_properties)
amol.prop_from_file(file, 'g09', 'nmr')
#amol.prop_fromfile(file, 'nmredata', 'nmr')
amol.get_bonds()
amol.get_path_lengths()
get_coupling_types(amol)
scale_chemical_shifts(amol)
write_nmredata(outfile, amol)
amols.append(amol)
except:
print('Bad file, ID', id)
file = 'NMR/' + file
with open('NMR_RESUB_ARRAY.txt', 'a') as f:
print(file, file=f)
eops.calc_pops(amols)
with open('energies.txt', 'w') as f:
string = "{0:<10s}\t{1:<10s}\t{2:<10s}".format("Molid", "Energy", "Pop")