cinfony - Google Code

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

‹ r86 r93

import os
import sys
import unittest

pybel = obpybel = rdkit = cdk = jybel = None
if sys.platform[:4] == "java":
    from cinfony import cdk, jybel
else:
    try:
        from cinfony import cdk, pybel, rdkit
    except ImportError:
        pass
    try:
        import pybel as obpybel
    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.assertEqual(fps[0] | fps[1], self.tanimotoresult)
        
    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.assertEqual(tanimoto, self.tanimotoresult)

    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
        # CDK doesn't include implicit Hs when calculating the molwt
        self.assertAlmostEqual(self.mols[0].molwt, 58.12, 2)
        self.assertEqual(len(self.mols[0].atoms), 4)
        self.assertRaises(AttributeError, self.RSaccesstest)

    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")
        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"""
        if self.toolkit.__name__ == "cinfony.cdk":
            # For the CDK, you need to call addh()
            # or some descriptors will be incorrectly calculated
            # (even those that are supposed to be immune like TPSA)
            self.mols[1].addh()
        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 TestPybel(TestToolkit):
    toolkit = pybel
    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 TestOBPybel(TestPybel):
    toolkit = obpybel

class TestJybel(TestPybel):
    toolkit = jybel
    def testDrawdependencies(self):
        "No testing the draw dependencies"
        pass

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

class TestRDKit(TestToolkit):
    toolkit = rdkit
    tanimotoresult = 1/3.
    Ndescs = 177
    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 = 0.375
    Ndescs = 143
    Natoms = 15
    tpsaname = "tpsa"
    Nbits = 4
    Nfpbits = 4 # The CDK uses a true java.util.Bitset
    datakeys = ['NSC', 'Remark', '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
        # CDK doesn't include implicit Hs when calculating the molwt
        self.mols[0].addh()
        self.assertAlmostEqual(self.mols[0].molwt, 58.12, 2)
        self.assertEqual(len(self.mols[0].atoms), 14)
        self.assertRaises(AttributeError, self.RSaccesstest)

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

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

    # 

    # testcases = [TestCDK]
    #testcases = [TestJybel]
    # testcases = [TestRDKit]
    # testcases = [TestOBPybel]
    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

r89 by baoilleach on Yesterday (25 hours ago) Diff

Update to use properties.

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Older revisions

r86 by baoilleach on Yesterday (28 hours ago) Diff

r79 by baoilleach on Jul 21 (3 days ago) Diff

Renamed cpybel back to pybel, and the
convenience module to obabel.

r78 by baoilleach on Jul 16, 2008 Diff

Renaming openbabel.py to pybel.py, and
pybel.py to cpybel.py

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