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b9e8ab4a53
* fix for calculation of prinicipal moments of inertia * fix a typo update expected values * PMI and NPR tests working * cleanup some of the other descriptors and tests * Test against Moments.py descriptors * add new tests from Brian * remove some warnings
48 lines
1.4 KiB
Python
48 lines
1.4 KiB
Python
#
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# Copyright (C) 2016 Greg Landrum
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#
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# @@ All Rights Reserved @@
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# This file is part of the RDKit.
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# The contents are covered by the terms of the BSD license
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# which is included in the file license.txt, found at the root
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# of the RDKit source tree.
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# generates reference data for the PMI descriptors
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from rdkit import Chem
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from rdkit.Chem import AllChem
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import numpy as np
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def GetMoments(mol, includeWeights):
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conf = mol.GetConformer()
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if includeWeights:
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masses = np.array([x.GetMass() for x in mol.GetAtoms()])
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else:
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masses = [1.0] * mol.GetNumAtoms()
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ps = conf.GetPositions()
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mps = [x*y for x,y in zip(ps,masses)]
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centroid = np.sum(mps,axis=0)/sum(masses)
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cps = ps - centroid
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xx = xy = xz = yy = yz = zz = 0.0
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for m,p in zip(masses,cps):
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xx += m*(p[1]*p[1] + p[2]*p[2])
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yy += m*(p[0]*p[0] + p[2]*p[2])
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zz += m*(p[1]*p[1] + p[0]*p[0])
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xy -= m*p[0]*p[1]
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xz -= m*p[0]*p[2]
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yz -= m*p[1]*p[2]
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covm = np.array([[xx,xy,xz],[xy,yy,yz],[xz,yz,zz]])
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res = np.linalg.eigvals(covm)
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return sorted(res)
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if __name__ == '__main__':
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suppl = Chem.SDMolSupplier('./PBF_egfr.sdf', removeHs=False)
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output = open('./PMI_egfr.out', 'w+')
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for m in suppl:
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i1, i2, i3 = GetMoments(m, True)
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mi1, mi2, mi3 = GetMoments(m, False)
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print("%s %.4f %.4f %.4f %.4f %.4f %.4f" % (m.GetProp("_Name"), i1, i2, i3, mi1, mi2, mi3),
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file=output)
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