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# $Id$
#
# Copyright (C) 2006-2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
from __future__ import print_function
import os, sys
import io
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
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 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.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 = cPickle.dumps(ffeat)
ffeat2 = cPickle.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 = cPickle.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 (overrwrite) new version of pickled
# data file
#cPickle.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 = cPickle.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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