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 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)
# 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_AUTOCORR3D(x, from_smiles):
if from_smiles:
mol = Chem.MolFromSmiles(x)
else:
mol = x
if (mol is None) or (len(mol.GetAtoms()) == 0):
return [0] * 80
else:
mol_3D = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol_3D)
AllChem.MMFFOptimizeMolecule(mol_3D)
return rdMolDescriptors.CalcAUTOCORR3D(mol_3D)