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* Issue #1071: add yapf configuration file * yapf formatting of Code directory * yapf formatting of Contrib directory * yapf formatting of Data directory * yapf formatting of Docs directory * yapf formatting of External directory * yapf formatting of Projects directory * yapf formatting of Regress directory * yapf formatting of Scripts directory * yapf formatting of Web directory * yapf formatting of rdkit directory
119 lines
4.2 KiB
Python
119 lines
4.2 KiB
Python
# $Id$
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#
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# Copyright (C) 2006-2008 Greg Landrum
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#
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# @@ All Rights Reserved @@
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#
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from __future__ import print_function
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import os, sys
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import io
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import unittest
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from rdkit.six.moves import cPickle
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from rdkit import RDConfig
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from rdkit import Chem
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from rdkit.Chem import ChemicalFeatures
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from rdkit.Geometry import rdGeometry as geom
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def feq(v1, v2, tol2=1e-4):
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return abs(v1 - v2) <= tol2
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def lstFeq(l1, l2, tol=1.e-4):
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if (len(l1) != len(l2)):
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return 0
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for i in range(len(l1)):
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if not feq(l1[i], l2[i], tol):
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return 0
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return 1
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def ptFeq(pt1, pt2, tol=0.0001):
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dist = pt1.Distance(pt2)
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return feq(dist, 0.0, tol)
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def testBasic(self):
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ffeat = ChemicalFeatures.FreeChemicalFeature()
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ffeat.SetId(123)
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pos = ffeat.GetId()
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self.assertTrue(pos == 123)
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ffeat.SetFamily("HBondDonor")
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self.assertTrue(ffeat.GetFamily() == "HBondDonor")
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ffeat.SetPos(geom.Point3D(1.0, 2.0, 3.0))
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pos = ffeat.GetPos()
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self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
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ffeat.SetType("HBondDonor1")
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self.assertTrue(ffeat.GetType() == "HBondDonor1")
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ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0,
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3.0))
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self.assertTrue(ffeat.GetId() == -1)
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self.assertTrue(ffeat.GetFamily() == "HBondDonor")
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self.assertTrue(ffeat.GetType() == "HBondDonor1")
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ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1",
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geom.Point3D(1.0, 2.0, 3.0), id=123)
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self.assertTrue(ffeat.GetId() == 123)
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self.assertTrue(ffeat.GetFamily() == "HBondDonor")
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self.assertTrue(ffeat.GetType() == "HBondDonor1")
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pos = ffeat.GetPos()
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self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
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ffeat = ChemicalFeatures.FreeChemicalFeature(id=123, type="HBondDonor1", family="HBondDonor",
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loc=geom.Point3D(1.0, 2.0, 3.0))
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self.assertTrue(ffeat.GetId() == 123)
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self.assertTrue(ffeat.GetFamily() == "HBondDonor")
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self.assertTrue(ffeat.GetType() == "HBondDonor1")
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pos = ffeat.GetPos()
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self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
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def testPickle(self):
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ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1",
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geom.Point3D(1.0, 2.0, 3.0), 123)
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pkl = cPickle.dumps(ffeat)
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ffeat2 = cPickle.loads(pkl, encoding='bytes')
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self.assertTrue(ffeat2.GetId() == ffeat.GetId())
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self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
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self.assertTrue(ffeat2.GetType() == ffeat.GetType())
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self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
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# Check that the old pickled versions have not been broken
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inTF = open(
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os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/feat.pkl'), 'r')
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buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
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inTF.close()
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inF = io.BytesIO(buf)
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ffeat2 = cPickle.load(inF, encoding='bytes')
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# this version (1.0) does not have an id in the byte stream
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self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
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self.assertTrue(ffeat2.GetType() == ffeat.GetType())
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self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
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# Test the new version also has the id and works as expected
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# uncomment the following to generate (overrwrite) new version of pickled
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# data file
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#cPickle.dump(ffeat,file(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'wb+'))
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inTF = open(
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os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'), 'r')
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buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
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inTF.close()
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inF = io.BytesIO(buf)
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ffeat2 = cPickle.load(inF, encoding='bytes')
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self.assertTrue(ffeat2.GetId() == ffeat.GetId())
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self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
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self.assertTrue(ffeat2.GetType() == ffeat.GetType())
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self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
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if __name__ == '__main__':
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print("Testing ChemicalFeatures Wrapper code:")
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unittest.main()
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