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import os
import time
from rdkit import Chem, RDConfig, rdBase
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolDescriptors as rdMD
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 generateAll():
filename = '/Users/GVALMTGG/Github/rdkit_mine/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf'
suppl = Chem.SDMolSupplier(filename, removeHs=False)
mols = [x for x in suppl]
start = time.time()
for m in mols:
r = get3D(m, True)
print(r)
end = time.time()
print(end - start)
def simple_case():
start = time.time()
smi = 'CCC(C)COCCCC'
m = Chem.MolFromSmiles(smi)
T = get3D(m, False)
print(T)
end = time.time()
print(end - start)
if (__name__ == '__main__'):
# FIX: We need to actually add some tests here, but this doees not need to
# to be done until the C++ code and tests are straightened out.
generateAll()
start = time.time()
smi = 'CCC(C)COCCCC'
m = Chem.MolFromSmiles(smi)
T = get3D(m, False)
print(T)
end = time.time()
print(end - start)
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