def Get3dDescriptor(molObject):
"""
Get all 3D descriptor
Args:
Returns:
List
Raise:
Exceptions
"""
value_list = []
value_list.append(Descriptors3D.Asphericity(molObject))
value_list.append(Descriptors3D.Eccentricity(molObject))
value_list.append(Descriptors3D.InertialShapeFactor(molObject))
value_list.append(Descriptors3D.NPR1(molObject))
value_list.append(Descriptors3D.NPR2(molObject))
value_list.append(Descriptors3D.PMI1(molObject))
value_list.append(Descriptors3D.PMI2(molObject))
value_list.append(Descriptors3D.PMI3(molObject))
value_list.append(
Descriptors3D.RadiusOfGyration(molObject)) # Radius of gyration
value_list.append(
Descriptors3D.SpherocityIndex(molObject)) # Spherocity Index
value_list.append(rdMolDescriptors.CalcPBF(
molObject)) # Returns the PBF (plane of best fit) descriptor
value_list += rdMolDescriptors.CalcAUTOCORR3D(molObject)
value_list += rdMolDescriptors.CalcRDF(molObject)
value_list += rdMolDescriptors.CalcMORSE(molObject)
value_list += rdMolDescriptors.CalcWHIM(molObject)
value_list += rdMolDescriptors.CalcGETAWAY(molObject)
return value_list
def get3D(m,is3d): if not is3d: m = Chem.AddHs(m) AllChem.EmbedMolecule(m) AllChem.MMFFOptimizeMolecule(m) r= rdMD.CalcAUTOCORR3D(m)+rdMD.CalcRDF(m)+rdMD.CalcMORSE(m)+rdMD.CalcWHIM(m)+rdMD.CalcGETAWAY(m) return r
def get_3d_representation(xyz, smiles, method, mol=None):
"""
Args:
xyz (torch.Tensor): atom type and xyz of geometry.
smiles (str): SMILES string
method (str): RDKit method for 3D representation
mol (rdkit.Chem.rdchem.Mol): RDKit mol object
Returns:
result (np.array): fingerprint
"""
representation_fn = {
'autocorrelation_3d': rdMD.CalcAUTOCORR3D,
'rdf': rdMD.CalcRDF,
'morse': rdMD.CalcMORSE,
'whim': rdMD.CalcWHIM,
'getaway': lambda x: rdMD.CalcWHIM(x, precision=0.001)
}
# if a `mol` is not given, generate it from the xyz and smiles
if mol is None:
mol = get_mol(xyz=xyz, smiles=smiles)
fn = representation_fn[method]
result = fn(mol)
return result
def get3D(m,is3d):
if not is3d:
m = Chem.AddHs(m)
# define the new code from RDKit Molecule 3D ETKDG.
ps = AllChem.ETKDG()
ps.randomSeed = 0xf00d
AllChem.EmbedMolecule(m,ps)
r= rdMD.CalcAUTOCORR3D(m)+rdMD.CalcRDF(m)+rdMD.CalcMORSE(m)+rdMD.CalcWHIM(m)+rdMD.CalcGETAWAY(m, precision=0.001)
return r
def get_WHIM(x, from_smiles):
if from_smiles:
mol = Chem.MolFromSmiles(x)
else:
mol = x
if (mol is None) or (len(mol.GetAtoms()) == 0):
return [0] * 114
else:
mol_3D = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol_3D)
AllChem.MMFFOptimizeMolecule(mol_3D)
return rdMolDescriptors.CalcWHIM(mol_3D)
def test6WHIM(self):
with open(os.path.join(self.dataDir, 'whim.new.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10: break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, lambda x: rdMD.CalcWHIM(x, thresh=0.01))
for rv, nv in zip(split, vs):
self.assertAlmostEqual(float(rv), nv, delta=0.01)
def getWHIM(mol3D):
dout = {}
try:
lwhim = rdMolDescriptors.CalcWHIM(mol3D)
except:
lwhim = []
if lwhim != []:
for i in range(1, len(lwhim) + 1):
val = lwhim[i - 1]
if math.isnan(val) == True:
dout["WHIM" + str(i)] = "NA"
else:
dout["WHIM" + str(i)] = round(val, 6)
return dout
else:
for desc in _whim3D.keys():
dout[desc] = "NA"
return dout
A = [
'[H][H]', 'B', 'O=O', 'C', 'CC', 'CCC', 'CCCC', 'CCCCC', 'CCCCCC', 'CO',
'CCO', 'CCCO', 'CCCCO', 'CCCCCO', 'CCCCCCO', 'CCl', 'CCCl', 'CCCCl',
'CCCCCl', 'CCCCCCl', 'CCCCCCCl', 'CBr', 'CCBr', 'CCCBr', 'CCCCBr',
'CCCCCBr', 'CCCCCCBr', 'CI', 'CCI', 'CCCI', 'CCCCI', 'CCCCCI', 'CCCCCCI',
'CF', 'CCF', 'CCCF', 'CCCCF', 'CCCCCF', 'CCCCCCF', 'CS', 'CCS', 'CCCS',
'CCCCS', 'CCCCCS', 'CCCCCCS', 'CN', 'CCN', 'CCCN', 'CCCCN', 'CCCCCN',
'CCCCCCN'
]
for smi in A:
m = Chem.MolFromSmiles(smi)
m = localopt(m, 100)
#r=get3D(m,True)
print smi
print "---------"
r = rdMD.CalcWHIM(m)
print "Ei:" + str(r[0]) + "," + str(r[1]) + "," + str(r[2]) + "\n"
print "Gi:" + str(r[5]) + "," + str(r[6]) + "," + str(r[7]) + "\n"
print "SI:" + str(rdMD.CalcSpherocityIndex(m))
print "AS:" + str(rdMD.CalcAsphericity(m))
print "EX:" + str(rdMD.CalcEccentricity(m))
for item in r:
thefile.write("%.3f," % item)
thefile.write("\n")
#m.SetProp("smi", smi)
#writer.write(m)
thefile = open('testBPA.txt', 'w')
writer = Chem.SDWriter('3DBPAmol.sdf')
B = [
'CN(C)CC(Br)c1ccccc1', 'CN(C)CC(Br)c1ccc(F)cc1', 'CN(C)CC(Br)c1ccc(Cl)cc1',
