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# $Id$
#
# Copyright (C) 2006-2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
from rdkit import RDConfig
import os
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
import unittest
import cPickle
from rdkit.Geometry import rdGeometry as geom
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def lstFeq(l1, l2, tol=1.e-4):
if (len(l1) != len(l2)):
return 0
for i in range(len(l1)):
if not feq(l1[i], l2[i], tol):
return 0
return 1
def ptFeq(pt1, pt2, tol=0.0001):
dist = pt1.Distance(pt2)
return feq(dist, 0.0, tol)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testBasic(self):
ffeat = ChemicalFeatures.FreeChemicalFeature()
ffeat.SetId(123)
pos = ffeat.GetId()
self.failUnless(pos == 123)
ffeat.SetFamily("HBondDonor")
self.failUnless(ffeat.GetFamily() == "HBondDonor")
ffeat.SetPos(geom.Point3D(1.0, 2.0, 3.0))
pos = ffeat.GetPos()
self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
ffeat.SetType("HBondDonor1")
self.failUnless(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0))
self.failUnless(ffeat.GetId() == -1)
self.failUnless(ffeat.GetFamily() == "HBondDonor")
self.failUnless(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0),id=123)
self.failUnless(ffeat.GetId() == 123)
self.failUnless(ffeat.GetFamily() == "HBondDonor")
self.failUnless(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
ffeat = ChemicalFeatures.FreeChemicalFeature(id = 123, type="HBondDonor1", family="HBondDonor", loc=geom.Point3D(1.0, 2.0, 3.0))
self.failUnless(ffeat.GetId() == 123)
self.failUnless(ffeat.GetFamily() == "HBondDonor")
self.failUnless(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
def testPickle(self):
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0),123)
pkl = cPickle.dumps(ffeat)
ffeat2 = cPickle.loads(pkl)
self.failUnless(ffeat2.GetId()==ffeat.GetId());
self.failUnless(ffeat2.GetFamily()==ffeat.GetFamily())
self.failUnless(ffeat2.GetType()==ffeat.GetType())
self.failUnless(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
# Check that the old pickled versions have not been broken
inF = file(os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/feat.pkl'),'rb')
ffeat2=cPickle.load(inF)
# this version (1.0) does not have an id in the byte stream
self.failUnless(ffeat2.GetFamily()==ffeat.GetFamily())
self.failUnless(ffeat2.GetType()==ffeat.GetType())
self.failUnless(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
# Test the new version also has the id and works as expected
# uncomment the following to generate (overrwrite) new version of pickled
# data file
#cPickle.dump(ffeat,file(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'wb+'))
inF = file(os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'rb')
ffeat2=cPickle.load(inF)
self.failUnless(ffeat2.GetId()==ffeat.GetId());
self.failUnless(ffeat2.GetFamily()==ffeat.GetFamily())
self.failUnless(ffeat2.GetType()==ffeat.GetType())
self.failUnless(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
if __name__ == '__main__':
print "Testing ChemicalFeatures Wrapper code:"
unittest.main()
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