testall.py - cinfony - Project Hosting on Google Code

‹r154

r177

Source path: svn/ trunk/ test/ testall.py

import pdb
import os
import sys
import unittest

ironable = rdkit = cdk = obabel = None
if sys.platform[:4] == "java":
    from cinfony import cdk, obabel
elif sys.platform[:3] == "cli":
    from cinfony import ironable
else:
    try:
        from cinfony import cdk
    except ImportError:
        pass
    try:
        from cinfony import obabel
    except ImportError:
        pass
    try:
        from cinfony import rdkit
    except ImportError:
        pass
    try:
        import pybel as obabel
    except ImportError:
        pass


# For compatability with Python2.3
try:
    from sets import Set as set
except ImportError:
    pass

class myTestCase(unittest.TestCase):
    """Additional methods not present in Jython 2.2"""
    # Taken from unittest.py in Python 2.5 distribution
    def assertFalse(self, expr, msg=None):
        "Fail the test if the expression is true."
        if expr: raise self.failureException, msg
    def assertTrue(self, expr, msg=None):
        """Fail the test unless the expression is true."""
        if not expr: raise self.failureException, msg
    def assertAlmostEqual(self, first, second, places=7, msg=None):
        """Fail if the two objects are unequal as determined by their
           difference rounded to the given number of decimal places
           (default 7) and comparing to zero.

           Note that decimal places (from zero) are usually not the same
           as significant digits (measured from the most signficant digit).
        """
        if round(second-first, places) != 0:
            raise self.failureException, \
                  (msg or '%r != %r within %r places' % (first, second, places))

class TestToolkit(myTestCase):
    
    def setUp(self):
        self.mols = [self.toolkit.readstring("smi", "CCCC"),
                     self.toolkit.readstring("smi", "CCCN")]
        self.head = list(self.toolkit.readfile("sdf", "head.sdf"))
        self.atom = self.head[0].atoms[1]

    def testattributes(self):
        """Test attributes like informats, descs and so on"""
        informats, outformats = self.toolkit.informats, self.toolkit.outformats
        self.assertNotEqual(len(self.toolkit.informats.keys()), 0)
        self.assertNotEqual(len(self.toolkit.outformats.keys()), 0)
        self.assertNotEqual(len(self.toolkit.descs), 0)
        self.assertNotEqual(len(self.toolkit.forcefields), 0)
        self.assertNotEqual(len(self.toolkit.fps), 0)

    def FPaccesstest(self):
        # Should raise AttributeError
        return self.mols[0].calcfp().nosuchname

    def testFPTanimoto(self):
        """Test the calculation of the Tanimoto coefficient"""
        fps = [x.calcfp() for x in self.mols]
        self.assertAlmostEqual(fps[0] | fps[1], self.tanimotoresult, 3)
        
    def testFPstringrepr(self):
        """Test the string representation and corner cases."""
        self.assertRaises(ValueError, self.mols[0].calcfp, "Nosuchname")
        self.assertRaises(AttributeError, self.FPaccesstest)
        r = str(self.mols[0].calcfp())
        t = r.split(", ")
        self.assertEqual(len(t), self.Nfpbits)
        
    def testFPbits(self):
        """Test whether the bits are set correctly."""
        bits = [x.calcfp().bits for x in self.mols]
        self.assertEqual(len(bits[0]), self.Nbits)
        bits = [set(x) for x in bits]
        # Calculate the Tanimoto coefficient the old-fashioned way
        tanimoto = len(bits[0] & bits[1]) / float(len(bits[0] | bits[1]))
        self.assertAlmostEqual(tanimoto, self.tanimotoresult, 3)

    def RSaccesstest(self):
        # Should raise AttributeError
        return self.mols[0].nosuchname

    def testRSformaterror(self):
        """Test that invalid formats raise an error"""
        self.assertRaises(ValueError, self.toolkit.readstring, "noel", "jkjk")
        self.assertRaises(IOError, self.toolkit.readstring, "smi", "&*)(%)($)")

    def testselfconversion(self):
        """Test that the toolkit can eat its own dog-food."""
        newmol = self.toolkit.Molecule(self.head[0])
        self.assertEqual(newmol._exchange,
                         self.head[0]._exchange)
        newmol = self.toolkit.Molecule(self.mols[0])
        self.assertEqual(newmol._exchange,
                         self.mols[0]._exchange)

    def testLocalOpt(self):
        """Test that local optimisation affects the coordinates"""
        oldcoords = self.head[0].atoms[0].coords
        self.head[0].localopt()
        newcoords = self.head[0].atoms[0].coords
        self.assertNotEqual(oldcoords, newcoords)

    def notestMake3D(self):
        """Test that 3D coordinate generation does something"""
        mol = self.mols[0]
        mol.make3D()
        self.assertNotEqual(mol.atoms[3].coords, (0., 0., 0.))

    def testDraw(self):
        """Create a 2D depiction"""
        self.mols[0].draw(show=False,
                          filename="%s.png" % self.toolkit.__name__)
        self.mols[0].draw(show=False) # Just making sure that it doesn't raise an Error
        self.mols[0].draw(show=False, update=True)
        coords = [x.coords for x in self.mols[0].atoms[0:2]]
        self.assertNotEqual(coords, [(0., 0., 0.), (0., 0., 0.)])
        self.mols[0].draw(show=False, usecoords=True,
                          filename="%s_b.png" % self.toolkit.__name__)

    def testRSgetprops(self):
        """Get the values of the properties."""
        # self.assertAlmostEqual(self.mols[0].exactmass, 58.078, 3)
        # Only OpenBabel has a working exactmass
        self.assertAlmostEqual(self.mols[0].molwt, 58.12, 2)
        self.assertEqual(len(self.mols[0].atoms), 4)
        self.assertRaises(AttributeError, self.RSaccesstest)

    def testRoundTripSMILES(self):
        """Convert the SMILES of benzene to itself"""
        benzene = "c1ccccc1"
        mol = self.toolkit.readstring("smi", benzene)
        smi = mol.write("smi")
        self.assertEqual(smi, benzene)

    def testRSconversiontoMOL(self):
        """Convert to mol"""
        as_mol = self.mols[0].write("mol")
        test = """
 OpenBabel04220815032D

  4  3  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
  1  2  1  0  0  0
  2  3  1  0  0  0
  3  4  1  0  0  0
M  END
"""
        data, result = test.split("\n"), as_mol.split("\n")
        self.assertEqual(len(data), len(result))
        self.assertEqual(data[-2], result[-2].rstrip()) # M  END

    def testRSconversiontoMOL2(self):
        """Convert to mol2"""
        as_mol2 = self.mols[0].write("mol2")
        print as_mol2
        test = """@<TRIPOS>MOLECULE
*****
 4 3 0 0 0
SMALL
GASTEIGER
Energy = 0

@<TRIPOS>ATOM
      1 C1          0.0000    0.0000    0.0000 C.3     1  <1>         0.0000
      2 C2          0.0000    0.0000    0.0000 C.3     1  <1>         0.0000
      3 C3          0.0000    0.0000    0.0000 C.3     1  <1>         0.0000
      4 C4          0.0000    0.0000    0.0000 C.3     1  <1>         0.0000
@<TRIPOS>BOND
     1     1     2    1
     2     2     3    1
     3     3     4    1
"""
        self.assertEqual(as_mol2, test)

    def testRSstringrepr(self):
        """Test the string representation of a molecule"""
        self.assertEqual(str(self.mols[0]).strip(), "CCCC")


    def testRFread(self):
        """Is the right number of molecules read from the file?"""
        self.assertEqual(len(self.mols), 2)

    def RFreaderror(self):
        mol = self.toolkit.readfile("sdf", "nosuchfile.sdf").next()

    def testRFmissingfile(self):
        """Test that reading from a non-existent file raises an error."""
        self.assertRaises(IOError, self.RFreaderror)

    def RFformaterror(self):
        mol = self.toolkit.readfile("noel", "head.sdf").next()
    
    def testRFformaterror(self):
        """Test that invalid formats raise an error"""
        self.assertRaises(ValueError, self.RFformaterror)

    def RFunitcellerror(self):
        unitcell = self.mols[0].unitcell
    
    def testRFunitcellerror(self):
        """Test that accessing the unitcell raises an error"""
        self.assertRaises(AttributeError, self.RFunitcellerror)

    def testRFconversion(self):
        """Convert to smiles"""
        as_smi = [mol.write("smi").split("\t")[0] for mol in self.mols]
        ans = []
        for smi in as_smi:
            t = list(smi)
            t.sort()
            ans.append("".join(t))
        test = ['CCCC', 'CCCN']
        self.assertEqual(ans, test)

    def testRFsingletofile(self):
        """Test the molecule.write() method"""
        mol = self.mols[0]
        mol.write("smi", "testoutput.txt")
        test = 'CCCC'
        input = open("testoutput.txt", "r")
        filecontents = input.readlines()[0].split("\t")[0].strip()
        input.close()
        self.assertEqual(filecontents, test)
        self.assertRaises(IOError, mol.write, "smi", "testoutput.txt")
        os.remove("testoutput.txt")
        self.assertRaises(ValueError, mol.write, "noel", "testoutput.txt")
    
    def testRFoutputfile(self):
        """Test the Outputfile class"""
        self.assertRaises(ValueError, self.toolkit.Outputfile, "noel", "testoutput.txt")
        outputfile = self.toolkit.Outputfile("sdf", "testoutput.txt")
        for mol in self.head:
            outputfile.write(mol)
        outputfile.close()
        self.assertRaises(IOError, outputfile.write, mol)
        self.assertRaises(IOError, self.toolkit.Outputfile, "sdf", "testoutput.txt")
        input = open("testoutput.txt", "r")
        numdollar = len([x for x in input.readlines()
                         if x.rstrip() == "$$$$"])
        input.close()
        os.remove("testoutput.txt")
        self.assertEqual(numdollar, 2)

    def RFdesctest(self):
        # Should raise ValueError
        self.mols[0].calcdesc("BadDescName")

    def testRFdesc(self):
        """Test the descriptors"""
        desc = self.mols[1].calcdesc()
        self.assertEqual(len(desc), self.Ndescs)
        self.assertAlmostEqual(desc[self.tpsaname], 26.02, 2)
        self.assertRaises(ValueError, self.RFdesctest)

    def MDaccesstest(self):
        # Should raise KeyError
        return self.head[0].data['noel']

    def testMDaccess(self):
        """Change the value of a field"""
        data = self.head[0].data
        self.assertRaises(KeyError, self.MDaccesstest)
        data['noel'] = 'testvalue'
        self.assertEqual(data['noel'], 'testvalue')
        newvalues = {'hey':'there', 'yo':1}
        data.update(newvalues)
        self.assertEqual(data['yo'], '1')
        self.assertTrue('there' in data.values())

    def testMDglobalaccess(self):
        """Check out the keys"""
        data = self.head[0].data
        self.assertFalse(data.has_key('Noel'))
        self.assertEqual(len(data), len(self.datakeys))
        for key in data:
            self.assertEqual(key in self.datakeys, True)
        r = repr(data)
        self.assertTrue(r[0]=="{" and r[-2:]=="'}", r)

    def testMDdelete(self):
        """Delete some keys"""
        data = self.head[0].data
        self.assertTrue(data.has_key('NSC'))
        del data['NSC']
        self.assertFalse(data.has_key('NSC'))
        data.clear()
        self.assertEqual(len(data), 0)

    def testAiteration(self):
        """Test the ability to iterate over the atoms"""
        atoms = [atom for atom in self.head[0]]
        self.assertEqual(len(atoms), self.Natoms)

    def Atomaccesstest(self):
        # Should raise AttributeError
        return self.atom.nosuchname

    def testAattributes(self):
        """Get the values of some properties"""
        self.assertRaises(AttributeError, self.Atomaccesstest)
        self.assertAlmostEqual(self.atom.coords[0], -0.0691, 4)

    def testAstringrepr(self):
        """Test the string representation of the Atom"""
        test = "Atom: 8 (-0.07 5.24 0.03)"
        self.assertEqual(str(self.atom), test)

    def testSMARTS(self):
        """Searching for ethyl groups in triethylamine"""
        mol = self.toolkit.readstring("smi", "CCN(CC)CC")
        smarts = self.toolkit.Smarts("[#6][#6]")
        ans = smarts.findall(mol)
        self.assertEqual(len(ans), 3)

    def testAddh(self):
        """Adding and removing hydrogens"""
        self.assertEqual(len(self.mols[0].atoms),4)
        self.mols[0].addh()
        self.assertEqual(len(self.mols[0].atoms),14)
        self.mols[0].removeh()
        self.assertEqual(len(self.mols[0].atoms),4)
        
class TestOBabel(TestToolkit):
    toolkit = obabel
    tanimotoresult = 1/3.
    Ndescs = 3
    Natoms = 15
    tpsaname = "TPSA"
    Nbits = 3
    Nfpbits = 32
    datakeys = ['NSC', 'Comment']

    def testFP_FP3(self):
        "Checking the results from FP3"
        fps = [x.calcfp("FP3") for x in self.mols]
        self.assertEqual(fps[0] | fps[1], 0.)

    def testunitcell(self):
        """Testing unit cell access"""
        mol = self.toolkit.readfile("cif", "hashizume.cif").next()
        cell = mol.unitcell
        self.assertAlmostEqual(cell.GetAlpha(), 92.9, 1)

    def testMDcomment(self):
        """Mess about with the comment field"""
        data = self.head[0].data
        self.assertEqual('Comment' in data, True)
        self.assertEqual(data['Comment'], 'CORINA 2.61 0041  25.10.2001')
        data['Comment'] = 'New comment'
        self.assertEqual(data['Comment'], 'New comment')

    def importtest(self):
        self.mols[0].draw(show=True, usecoords=True)

    def testDrawdependencies(self):
        "Testing the draw dependencies"
        t = self.toolkit.tk
        self.toolkit.tk = None
        self.mols[0].draw(show=False, usecoords=True,
                          filename="%s_b.png" % self.toolkit.__name__)
        self.assertRaises(ImportError,
                          self.importtest)
        self.toolkit.tk = t

        t = self.toolkit.oasa
        self.toolkit.oasa = None
        self.assertRaises(ImportError,
                          self.importtest)

    def testRSgetprops(self):
        """Get the values of the properties."""
        self.assertAlmostEqual(self.mols[0].exactmass, 58.078, 3)
        self.assertAlmostEqual(self.mols[0].molwt, 58.122, 3)
        self.assertEqual(len(self.mols[0].atoms), 4)
        self.assertRaises(AttributeError, self.RSaccesstest)

class TestJybel(TestOBabel):
    def testDrawdependencies(self):
        "No testing the draw dependencies"
        pass


    def testDraw(self):
        """No creating a 2D depiction"""
        pass

class TestIronable(TestJybel):
    toolkit = ironable

class TestRDKit(TestToolkit):
    toolkit = rdkit
    tanimotoresult = 1/3.
    Ndescs = 176
    Natoms = 9
    tpsaname = "TPSA"
    Nbits = 12
    Nfpbits = 64
    datakeys = ['NSC']

    def testRSconversiontoMOL2(self):
        """No conversion to MOL2 done"""
        pass

class TestCDK(TestToolkit):
    toolkit = cdk
    tanimotoresult = 0.571
    Ndescs = 269
    Natoms = 15
    tpsaname = "tpsa"
    Nbits = 4
    Nfpbits = 4 # The CDK uses a true java.util.Bitset
    datakeys = ['NSC', 'cdk:Remark', 'cdk:Title']

    def testSMARTS(self):
        """No SMARTS testing done"""
        pass

    def testLocalOpt(self):
        """No local opt testing done"""
        pass

    def testMake3D(self):
        """No 3D coordinate generation done"""
        pass

    def testRSgetprops(self):
        """Get the values of the properties."""
        # self.assertAlmostEqual(self.mols[0].exactmass, 58.078, 3)
        # Only OpenBabel has a working exactmass
        self.assertAlmostEqual(self.mols[0].molwt, 58.12, 2)
        self.assertEqual(len(self.mols[0].atoms), 4)
        self.assertRaises(AttributeError, self.RSaccesstest)

##    def testRFoutputfile(self):
##        pass

if __name__=="__main__":
    if os.path.isfile("testoutput.txt"):
        os.remove("testoutput.txt")

    lookup = {'cdk': TestCDK, 'obabel':TestOBabel, 'rdkit':TestRDKit}
    testcases = [TestCDK, TestOBabel, TestRDKit]
    if sys.platform[:4] == "java":
        lookup['obabel'] = TestJybel
        testcases = [TestCDK, TestJybel]
    elif sys.platform[:3] == "cli":
        lookup['obabel'] = TestIronable
        testcases = [TestIronable]
    if len(sys.argv) > 1:
        testcases = [lookup[x] for x in sys.argv[1:]]

    for testcase in testcases:
        print "\n\n\nTESTING %s\n%s\n\n" % (testcase.__name__, "== "*10)
        myunittest = unittest.defaultTestLoader.loadTestsFromTestCase(testcase)
        unittest.TextTestRunner(verbosity=2).run(myunittest)

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Change log

r177 by baoilleach on Dec 20, 2009 Diff

Fix bug reported by Tom Sheldon. Wasn't
aromatising the SMILES output.

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Older revisions

r154 by baoilleach on Jul 10, 2009 Diff

Update tests

r144 by baoilleach on Dec 19, 2008 Diff

Testing should now work both for Pybel
and Cinfony

r138 by baoilleach on Nov 24, 2008 Diff

Add hydrogens before calculating molwt
for the CDK.

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