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from rdkit import Chem
from rdkit import rdBase
from rdkit import RDConfig
import os
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
import time
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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