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# $Id$
#
# Copyright (C) 2006-2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import io
import os
import pickle
import sys
import unittest
from rdkit import Chem, RDConfig
from rdkit.Chem import ChemicalFeatures
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 ll1, ll2 in zip(l1, l2):
if not feq(ll1, ll2, 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.assertTrue(pos == 123)
ffeat.SetFamily("HBondDonor")
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
ffeat.SetPos(geom.Point3D(1.0, 2.0, 3.0))
pos = ffeat.GetPos()
self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
ffeat.SetType("HBondDonor1")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1",
geom.Point3D(1.0, 2.0, 3.0))
self.assertTrue(ffeat.GetId() == -1)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1",
geom.Point3D(1.0, 2.0, 3.0), id=123)
self.assertTrue(ffeat.GetId() == 123)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.assertTrue(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.assertTrue(ffeat.GetId() == 123)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.assertTrue(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 = pickle.dumps(ffeat)
ffeat2 = pickle.loads(pkl, encoding='bytes')
self.assertTrue(ffeat2.GetId() == ffeat.GetId())
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
# Check that the old pickled versions have not been broken
inTF = open(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/feat.pkl'),
'r')
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
inF = io.BytesIO(buf)
ffeat2 = pickle.load(inF, encoding='bytes')
# this version (1.0) does not have an id in the byte stream
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
# Test the new version also has the id and works as expected
# uncomment the following to generate (overwrite) new version of pickled
# data file
#pickle.dump(ffeat,file(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'wb+'))
inTF = open(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),
'r')
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
inF = io.BytesIO(buf)
ffeat2 = pickle.load(inF, encoding='bytes')
self.assertTrue(ffeat2.GetId() == ffeat.GetId())
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
if __name__ == '__main__':
print("Testing ChemicalFeatures Wrapper code:")
unittest.main()
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