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55 lines
1.3 KiB
Python
55 lines
1.3 KiB
Python
import os
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import time
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from rdkit import Chem, RDConfig, rdBase
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from rdkit.Chem import AllChem
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from rdkit.Chem import rdMolDescriptors as rdMD
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def get3D(m, is3d):
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if not is3d:
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m = Chem.AddHs(m)
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# define the new code from RDKit Molecule 3D ETKDG.
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ps = AllChem.ETKDG()
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ps.randomSeed = 0xf00d
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AllChem.EmbedMolecule(m, ps)
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r = rdMD.CalcAUTOCORR3D(m) + rdMD.CalcRDF(m) + rdMD.CalcMORSE(m) + rdMD.CalcWHIM(
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m) + rdMD.CalcGETAWAY(m, precision=0.001)
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return r
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def generateAll():
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filename = '/Users/GVALMTGG/Github/rdkit_mine/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf'
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suppl = Chem.SDMolSupplier(filename, removeHs=False)
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mols = [x for x in suppl]
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start = time.time()
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for m in mols:
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r = get3D(m, True)
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print(r)
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end = time.time()
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print end - start
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def simple_case():
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start = time.time()
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smi = 'CCC(C)COCCCC'
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m = Chem.MolFromSmiles(smi)
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T = get3D(m, False)
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print T
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end = time.time()
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print end - start
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if (__name__ == '__main__'):
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# FIX: We need to actually add some tests here, but this doees not need to
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# to be done until the C++ code and tests are straightened out.
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generateAll()
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start = time.time()
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smi = 'CCC(C)COCCCC'
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m = Chem.MolFromSmiles(smi)
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T = get3D(m, False)
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print T
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end = time.time()
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print end - start
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