def calculate_scalar_descriptors(molecule, symbols):
features = list()
features.append(rdMD.CalcAsphericity(molecule))
features += list(rdMD.CalcCrippenDescriptors(molecule))
features.append(rdMD.CalcExactMolWt(molecule))
features.append(rdMD.CalcEccentricity(molecule))
features.append(rdMD.CalcFractionCSP3(molecule))
features.append(rdMD.CalcLabuteASA(molecule))
features.append(rdMD.CalcNPR1(molecule))
features.append(rdMD.CalcNPR2(molecule))
features.append(rdMD.CalcHallKierAlpha(molecule))
# elemental distribution
symbols = np.array(symbols)
features.append(np.sum(symbols == 'H'))
features.append(np.sum(symbols == 'C'))
features.append(np.sum(symbols == 'N'))
features.append(np.sum(symbols == 'O'))
features.append(np.sum(symbols == 'F'))
# ring features
features.append(rdMD.CalcNumAliphaticCarbocycles(molecule))
features.append(rdMD.CalcNumAliphaticHeterocycles(molecule))
features.append(rdMD.CalcNumAromaticCarbocycles(molecule))
features.append(rdMD.CalcNumAromaticHeterocycles(molecule))
features.append(rdMD.CalcNumSaturatedCarbocycles(molecule))
features.append(rdMD.CalcNumSaturatedHeterocycles(molecule))
features.append(rdMD.CalcNumSpiroAtoms(
molecule)) # atom shared between rings with one bond
features.append(rdMD.CalcNumBridgeheadAtoms(
molecule)) # atom shared between rings with at least two bonds
# other counts
features.append(rdMD.CalcNumAmideBonds(molecule))
features.append(rdMD.CalcNumHBA(molecule)) # number of hydrogen acceptors
features.append(rdMD.CalcNumHBD(molecule)) # number of hydrogen donors
return np.array(features)
def extract(x, from_smiles):
if from_smiles:
mol = Chem.MolFromSmiles(x)
else:
mol = x
if (mol is None) or (len(mol.GetAtoms()) == 0):
if include_3D:
return [0] * 29
else:
return [0] * 24
else:
logP = Crippen.MolLogP(mol)
refractivity = Crippen.MolMR(mol)
weight = Descriptors.MolWt(mol)
exact_weight = Descriptors.ExactMolWt(mol)
heavy_weight = Descriptors.HeavyAtomMolWt(mol)
heavy_count = Lipinski.HeavyAtomCount(mol)
nhoh_count = Lipinski.NHOHCount(mol)
no_count = Lipinski.NOCount(mol)
hacceptor_count = Lipinski.NumHAcceptors(mol)
hdonor_count = Lipinski.NumHDonors(mol)
hetero_count = Lipinski.NumHeteroatoms(mol)
rotatable_bond_count = Lipinski.NumRotatableBonds(mol)
valance_electron_count = Descriptors.NumValenceElectrons(mol)
amide_bond_count = rdMolDescriptors.CalcNumAmideBonds(mol)
aliphatic_ring_count = Lipinski.NumAliphaticRings(mol)
aromatic_ring_count = Lipinski.NumAromaticRings(mol)
saturated_ring_count = Lipinski.NumSaturatedRings(mol)
aliphatic_cycle_count = Lipinski.NumAliphaticCarbocycles(mol)
aliphaticHetero_cycle_count = Lipinski.NumAliphaticHeterocycles(
mol)
aromatic_cycle_count = Lipinski.NumAromaticCarbocycles(mol)
aromaticHetero_cycle_count = Lipinski.NumAromaticHeterocycles(mol)
saturated_cycle_count = Lipinski.NumSaturatedCarbocycles(mol)
saturatedHetero_cycle_count = Lipinski.NumSaturatedHeterocycles(
mol)
tpsa = rdMolDescriptors.CalcTPSA(mol)
if include_3D:
mol_3D = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol_3D)
AllChem.MMFFOptimizeMolecule(mol_3D)
eccentricity = rdMolDescriptors.CalcEccentricity(mol_3D)
asphericity = rdMolDescriptors.CalcAsphericity(mol_3D)
spherocity = rdMolDescriptors.CalcSpherocityIndex(mol_3D)
inertial = rdMolDescriptors.CalcInertialShapeFactor(mol_3D)
gyration = rdMolDescriptors.CalcRadiusOfGyration(mol_3D)
return [
logP, refractivity, weight, exact_weight, heavy_weight,
heavy_count, nhoh_count, no_count, hacceptor_count,
hdonor_count, hetero_count, rotatable_bond_count,
valance_electron_count, amide_bond_count,
aliphatic_ring_count, aromatic_ring_count,
saturated_ring_count, aliphatic_cycle_count,
aliphaticHetero_cycle_count, aromatic_cycle_count,
aromaticHetero_cycle_count, saturated_cycle_count,
saturatedHetero_cycle_count, tpsa, eccentricity,
asphericity, spherocity, inertial, gyration
]
else:
return [
logP, refractivity, weight, exact_weight, heavy_weight,
heavy_count, nhoh_count, no_count, hacceptor_count,
hdonor_count, hetero_count, rotatable_bond_count,
valance_electron_count, amide_bond_count,
aliphatic_ring_count, aromatic_ring_count,
saturated_ring_count, aliphatic_cycle_count,
aliphaticHetero_cycle_count, aromatic_cycle_count,
aromaticHetero_cycle_count, saturated_cycle_count,
saturatedHetero_cycle_count, tpsa
]
https://doi.org/10.1002/9783527618279.ch37
Definition:
sqrt(pm3**2 -pm1**2) / pm3**2
**Arguments**
- inMol: a molecule
- confId: (optional) the conformation ID to use
- useAtomicMasses: (optional) toggles use of atomic masses in the
calculation. Defaults to True
"""
Asphericity = lambda *x, **y: rdMolDescriptors.CalcAsphericity(*x, **y)
Asphericity.version = rdMolDescriptors._CalcAsphericity_version
Asphericity.__doc__ = """ molecular asphericity
from Todeschini and Consoni "Descriptors from Molecular Geometry"
Handbook of Chemoinformatics
https://doi.org/10.1002/9783527618279.ch37
Definition:
0.5 * ((pm3-pm2)**2 + (pm3-pm1)**2 + (pm2-pm1)**2)/(pm1**2+pm2**2+pm3**2)
**Arguments**
- inMol: a molecule
- confId: (optional) the conformation ID to use
'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',
'CN(C)CC(Br)c1ccc(Cl)cc1', 'CN(C)CC(Br)c1ccc(I)cc1',
'CN(C)CC(Br)c1ccc(C)cc1', 'CN(C)CC(Br)c1cccc(F)c1',
'CN(C)CC(Br)c1cccc(Cl)c1', 'CN(C)CC(Br)c1cccc(Br)c1',
'CN(C)CC(Br)c1cccc(I)c1', 'CN(C)CC(Br)c1cccc(C)c1',
