def test_AddResidue_Standard(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
r1 = c.addResidue('ALA', 1, Nterminal=True)
if r1:
r1.addAllAtoms()
r2 = c.addResidue('VAL', 2)
if r2:
r2.addAllAtoms()
r2 = c.addResidue('PHE', 3)
if r2:
r2.addAllAtoms()
r2 = c.addResidue('ARG', 4)
if r2:
r2.addAllAtoms()
r3 = c.addResidue('GLU', 5, Cterminal=True)
if r3:
r3.addAllAtoms()
mol.updateAll()
nTmessage(mol.format())
def test_AddResidue_Standard(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
r1 = c.addResidue('ALA', 1, Nterminal = True)
if r1:
r1.addAllAtoms()
r2 = c.addResidue('VAL', 2)
if r2:
r2.addAllAtoms()
r2 = c.addResidue('PHE', 3)
if r2:
r2.addAllAtoms()
r2 = c.addResidue('ARG', 4)
if r2:
r2.addAllAtoms()
r3 = c.addResidue('GLU', 5, Cterminal = True)
if r3:
r3.addAllAtoms()
mol.updateAll()
nTmessage( mol.format() )
def _test_HTMLfile(self):
"""
Create two html files (project and molecule) that have relative links to each other.
Exercising the machinery in HTMLfile class.
"""
entryId = "test_HTMLfile"
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule)
# initialize project html page
# per item always set 2 top level attributes:
project.htmlLocation = (project.path('index.html'), None)
project.html = HTMLfile(project.htmlLocation[0],
project,
title='Project')
nTdebug("project.htmlLocation[0]: %s" % project.htmlLocation[0])
#create new folders for Molecule/HTML
htmlPath = project.htmlPath()
if os.path.exists(htmlPath):
removedir(htmlPath)
os.makedirs(htmlPath)
nTdebug("htmlPath: %s" % htmlPath)
# initialize molecule html page
for subdir in htmlDirectories.values():
project.mkdir(project.molecule.name, moleculeDirectories.html,
subdir)
# NB project.htmlPath is different from project.path
molecule.htmlLocation = (project.htmlPath('indexMolecule.html'), None)
nTdebug("molecule.htmlLocation[0]: %s" % molecule.htmlLocation[0])
molecule.html = HTMLfile(molecule.htmlLocation[0],
project,
title='Molecule ' + molecule.name)
# nb: destination is a destination obj (eg molecule object) that is to
# have a html attribute that points to an HTMLfile instance.
# In the validate.py code, the source argument is the 'main' section in
# project.html. JFD doesn't understand why.
project.html.insertHtmlLinkInTag('li',
section=project.html.main,
source=project,
destination=molecule,
text='mol ref',
id=None)
# rerun for testing.
_link = project.html.findHtmlLocation(project, molecule, id=None)
# self.assertEquals('moleculeName/HTML/indexMolecule.html#_top', link)
project.html.main('ul', openTag=False)
for htmlObj in [project.html, molecule.html]:
self.assertFalse(htmlObj.render())
def testROGscore(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
# Add some crud to prevent warnings/errors later.
molecule.addChain('top')
top = molecule.allChains()[0]
# Disable warnings temporarily
v = cing.verbosity
cing.verbosity = verbosityNothing
for i in range(1 * 10):
res = top.addResidue(repr(random()), i)
for j in range(5):
_atom = res.addAtom(repr(random()), j)
cing.verbosity = v
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
a = Atom(resName='ALA', atomName='HN')
a.criticize()
self.assertTrue(a)
self.assertEquals(a.rogScore.colorLabel, COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][0], COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][1],
ROGscore.ROG_COMMENT_NO_COOR)
lotr_remark = 'One ring to rule them all'
preserved_remark = 'Preserved'
nowHasEffect_remark = 'Now has effect'
nowHasEffectToo_remark = 'Now has effect too'
# Next line will have to wipe out the orange comments.
a.rogScore.setMaxColor(COLOR_RED, lotr_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffect_remark)
a.rogScore.setMaxColor(COLOR_RED, preserved_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffectToo_remark)
self.assertEquals(len(a.rogScore.colorCommentList), 5)
self.assertEquals(a.rogScore.colorCommentList[0][1],
ROGscore.ROG_COMMENT_NO_COOR)
self.assertEquals(a.rogScore.colorCommentList[1][1],
nowHasEffect_remark)
myhtml = HTMLfile('testROGscore.html', project, 'A Test')
myhtml.main("a main")
a.rogScore.createHtmlForComments(myhtml.main)
kw = {}
a.rogScore.addHTMLkeywords(kw)
myhtml.main("a", 'or by popup', **kw)
myhtml.render()
def testROGscore(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
# Add some crud to prevent warnings/errors later.
molecule.addChain('top')
top = molecule.allChains()[0]
# Disable warnings temporarily
v = cing.verbosity
cing.verbosity = verbosityNothing
for i in range( 1*10):
res = top.addResidue( repr(random()),i )
for j in range( 5):
_atom = res.addAtom( repr(random()),j )
cing.verbosity = v
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
a = Atom(resName='ALA', atomName='HN')
a.criticize()
self.assertTrue(a)
self.assertEquals(a.rogScore.colorLabel, COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][0], COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][1], ROGscore.ROG_COMMENT_NO_COOR)
lotr_remark = 'One ring to rule them all'
preserved_remark = 'Preserved'
nowHasEffect_remark = 'Now has effect'
nowHasEffectToo_remark = 'Now has effect too'
# Next line will have to wipe out the orange comments.
a.rogScore.setMaxColor(COLOR_RED, lotr_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffect_remark )
a.rogScore.setMaxColor(COLOR_RED, preserved_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffectToo_remark)
self.assertEquals(len(a.rogScore.colorCommentList), 5)
self.assertEquals(a.rogScore.colorCommentList[0][1], ROGscore.ROG_COMMENT_NO_COOR)
self.assertEquals(a.rogScore.colorCommentList[1][1], nowHasEffect_remark)
myhtml = HTMLfile('testROGscore.html', project, 'A Test')
myhtml.main("a main")
a.rogScore.createHtmlForComments(myhtml.main)
kw = {}
a.rogScore.addHTMLkeywords(kw)
myhtml.main("a", 'or by popup', **kw)
myhtml.render()
def test_GetNextAvailableChainId(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule) # Needed for html.
chainId = molecule.getNextAvailableChainId()
self.assertEquals( chainId, Chain.defaultChainId)
n = 26 * 2 + 10 + 1 # alpha numeric including an extra and lower cased.
for _c in range(n):
chainId = molecule.getNextAvailableChainId()
self.assertTrue( molecule.addChain(chainId))
nTdebug("Added %d chains to: %s" % (n, molecule.format()))
self.assertEqual( len(molecule.allChains()), n)
def test_GetNextAvailableChainId(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule) # Needed for html.
chainId = molecule.getNextAvailableChainId()
self.assertEquals(chainId, Chain.defaultChainId)
n = 26 * 2 + 10 + 1 # alpha numeric including an extra and lower cased.
for _c in range(n):
chainId = molecule.getNextAvailableChainId()
self.assertTrue(molecule.addChain(chainId))
nTdebug("Added %d chains to: %s" % (n, format(molecule)))
self.assertEqual(len(molecule.allChains()), n)
def _test_HTMLfile(self):
"""
Create two html files (project and molecule) that have relative links to each other.
Exercising the machinery in HTMLfile class.
"""
entryId = "test_HTMLfile"
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule)
# initialize project html page
# per item always set 2 top level attributes:
project.htmlLocation = (project.path('index.html'), None)
project.html = HTMLfile(project.htmlLocation[0], project, title = 'Project')
nTdebug("project.htmlLocation[0]: %s" % project.htmlLocation[0])
#create new folders for Molecule/HTML
htmlPath = project.htmlPath()
if os.path.exists(htmlPath):
removedir(htmlPath)
os.makedirs(htmlPath)
nTdebug("htmlPath: %s" % htmlPath)
# initialize molecule html page
for subdir in htmlDirectories.values():
project.mkdir(project.molecule.name, moleculeDirectories.html, subdir)
# NB project.htmlPath is different from project.path
molecule.htmlLocation = (project.htmlPath('indexMolecule.html'), None)
nTdebug("molecule.htmlLocation[0]: %s" % molecule.htmlLocation[0])
molecule.html = HTMLfile(molecule.htmlLocation[0], project,
title = 'Molecule ' + molecule.name)
# nb: destination is a destination obj (eg molecule object) that is to
# have a html attribute that points to an HTMLfile instance.
# In the validate.py code, the source argument is the 'main' section in
# project.html. JFD doesn't understand why.
project.html.insertHtmlLinkInTag('li', section=project.html.main,
source=project, destination=molecule, text='mol ref', id=None)
# rerun for testing.
_link = project.html.findHtmlLocation(project, molecule, id=None)
# self.assertEquals('moleculeName/HTML/indexMolecule.html#_top', link)
project.html.main('ul', openTag=False)
for htmlObj in [ project.html, molecule.html ]:
self.assertFalse(htmlObj.render())
def setupSimplestProject(self):
entryId = 'setupSimplestProject'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
c = molecule.addChain('A')
r1 = c.addResidue('ALA', 1, Nterminal=True)
if r1:
r1.addAllAtoms()
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
return project
def setupSimplestProject(self):
entryId = 'setupSimplestProject'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
c = molecule.addChain('A')
r1 = c.addResidue('ALA', 1, Nterminal = True)
if r1:
r1.addAllAtoms()
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
return project
def test_RangeSelection(self):
cing.verbosity = verbosityDebug
entryId = 'testEntry'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('testMol')
project.appendMolecule(mol)
offset1 = -10
# h**o dimer
chainList = ( 'A', 'B' )
sequence = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
seqL = len(sequence)
lastResidueI = seqL - 1
for cId in chainList:
c = mol.addChain(cId)
for i, rName in enumerate(sequence):
rNumber = i+offset1
Nterminal = False # pylint: disable=C0103
Cterminal = False # pylint: disable=C0103
if i == 0:
Nterminal = True # pylint: disable=C0103
if i == lastResidueI:
Cterminal = True # pylint: disable=C0103
r = c.addResidue(rName, rNumber, Nterminal = Nterminal, Cterminal = Cterminal)
if r:
# nTdebug("Adding atoms to residue: %s" % r)
r.addAllAtoms()
for atom in r.allAtoms():
atom.addCoordinate(0.0, 1.0, 2.0, 40.0)
# else:
# nTdebug("Skipping atoms for residue: %s" % r)
# end if
# end for
# end for chain
# another h**o dimer with renumbering.
chainList = ( 'C', 'D' )
offset2 = 100
for cId in chainList:
c = mol.addChain(cId)
for i, rName in enumerate(sequence):
rNumber = i+offset2
Nterminal = False # pylint: disable=C0103
Cterminal = False # pylint: disable=C0103
if i == 0:
Nterminal = True # pylint: disable=C0103
if i == lastResidueI:
Cterminal = True # pylint: disable=C0103
r = c.addResidue(rName, rNumber, Nterminal = Nterminal, Cterminal = Cterminal)
if r:
# nTdebug("Adding atoms to residue: %s" % r)
r.addAllAtoms()
# else:
# nTdebug("Skipping atoms for residue: %s" % r)
# end if
# end for
# end for chain
nTdebug("Done creating simple fake molecule")
self.assertFalse( mol.updateAll() )
nTmessage( mol.format() )
# Nada
selectedResidueList = mol.ranges2list('')
self.assertEquals( len(selectedResidueList), 2*len(chainList)*seqL)
# Single residue
selectedResidueList = mol.ranges2list('A.'+str(offset1))
self.assertEquals( len(selectedResidueList), 1)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Two residues
selectedResidueList = mol.ranges2list(str(offset1))
self.assertEquals( len(selectedResidueList), 2)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Four residues in ranges
selectedResidueList = mol.ranges2list('1-2')
self.assertEquals( len(selectedResidueList), 4)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Eight residues in negative crossing ranges
selectedResidueList = mol.ranges2list('-1-2')
self.assertEquals( len(selectedResidueList), 8)
nTdebug("Selected residues: %s" % str(selectedResidueList))
selectedResidueList = mol.ranges2list('A.-5--2')
self.assertEquals( len(selectedResidueList), 4)
nTdebug("Selected residues: %s" % str(selectedResidueList))
selectedResidueList = mol.ranges2list('-999-999')
nTdebug("Selected residues: %s" % str(selectedResidueList))
self.assertEquals( len(selectedResidueList), 2*len(chainList)*seqL)
residueList2StartStopList = mol.ranges2StartStopList('-999-999')
nTdebug('residueList2StartStopList: %s' % str(residueList2StartStopList))
self.assertEquals( len(residueList2StartStopList), 8 )
# """
# Possible 5 situations:
# a # 1 # positive int
# -a # 2 # single int
# -a-b # 3 #
# -a--b # 4 #
# a-b # 5 # most common
# """
inputList = """
A.1
A.1-3
A.-2--1
A.-2-1
A.-3
""".split()
for i, ranges in enumerate(inputList):
nTdebug("test_RangeSelection: %d %s" % (i, ranges))
residueList = mol.setResiduesFromRanges(ranges)
# nTdebug('residueList: [%s]' % residueList)
rangesRecycled = mol.residueList2Ranges(residueList)
# nTdebug('rangesRecycled: [%s]' % rangesRecycled)
self.assertEquals( ranges, rangesRecycled )
res1, res2 = mol.ranges2list('A.1,A.3')
self.assertEquals( 2, residueNumberDifference(res1, res2))
res3, res4 = mol.ranges2list('A.5,A.8')
self.assertEquals( 3, residueNumberDifference(res3, res4))
res5, res6 = mol.ranges2list('B.9,B.10')
self.assertEquals( 1, residueNumberDifference(res5, res6))
ranges = mol.startStopList2ranges([res1, res2])
self.assertEquals( 'A.1-3', ranges)
ranges = mol.startStopList2ranges([res1, res2, res3, res4])
self.assertEquals( 'A.1-3,A.5-8', ranges)
ranges = mol.startStopList2ranges([res1, res2, res5, res6])
self.assertEquals( 'A.1-3,B.9-10', ranges)
# Check other routine
chain0 = mol.allChains()[0]
chain1 = mol.allChains()[1]
atomList = chain0.getRepresentingAtomListsPerResidue(chain1)
nTdebug("atomList: %s" % str(atomList))
self.assertEquals( len(atomList[0]), 5)
def test_GetMolTypeCountList(self):
cing.verbosity = verbosityDebug
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
c.addResidue('ALA', 1, Nterminal = True)
c.addResidue('VAL', 2)
c.addResidue('PHE', 3)
c.addResidue('ARG', 4)
c.addResidue('GLU', 5, Cterminal = True)
c = mol.addChain('B')
c.addResidue('DG', 1, Nterminal = True)
c.addResidue('DA', 2)
c.addResidue('DT', 3)
c.addResidue('DC', 4, Cterminal = True)
c = mol.addChain('C')
c.addResidue('RGUA', 1, convention=INTERNAL_0, Nterminal = True)
c.addResidue('RADE', 2, convention=INTERNAL_0, )
c.addResidue('URA', 3, convention=INTERNAL_0, ) # not RTHY normally of course.
c.addResidue('RTHY', 4, convention=INTERNAL_0, )
c.addResidue('RCYT', 5, convention=INTERNAL_0, Cterminal = True)
c = mol.addChain('D')
for i in range(1,11):
c.addResidue('HOH', i )
# end for
c = mol.addChain('E') # Unknown residue to CING
c.addResidue('ACE', 1 )
c = mol.addChain('F') # Ions are also other
c.addResidue('CA2P', 1 )
for residue in mol.allResidues():
residue.addAllAtoms()
# end for
mol.updateAll()
nTmessage( mol.format() )
for c in mol.allChains():
nTmessage( c.format() )
nTmessage( "idxMolType: %s" % (c.getIdxMolType()))
# end for
nTmessage("Count the molecule types")
molTypeCountList = mol.getMolTypeCountList()
p_protein_count = molTypeCountList[ mapMoltypeToInt[PROTEIN_STR] ]
p_dna_count = molTypeCountList[ mapMoltypeToInt[DNA_STR] ]
p_rna_count = molTypeCountList[ mapMoltypeToInt[RNA_STR] ]
p_water_count = molTypeCountList[ mapMoltypeToInt[WATER_STR] ]
p_other_count = molTypeCountList[ mapMoltypeToInt[OTHER_STR] ]
self.assertEqual(1, p_protein_count)
self.assertEqual(1, p_dna_count )
self.assertEqual(1, p_rna_count )
self.assertEqual(1, p_water_count)
self.assertEqual(2, p_other_count)
nTmessage("Count the residue types")
molTypeResidueCountList = mol.getMolTypeResidueCountList()
p_res_protein_count = molTypeResidueCountList[ mapMoltypeToInt[PROTEIN_STR] ]
p_res_dna_count = molTypeResidueCountList[ mapMoltypeToInt[DNA_STR] ]
p_res_rna_count = molTypeResidueCountList[ mapMoltypeToInt[RNA_STR] ]
p_res_water_count = molTypeResidueCountList[ mapMoltypeToInt[WATER_STR] ]
p_res_other_count = molTypeResidueCountList[ mapMoltypeToInt[OTHER_STR] ]
self.assertEqual(5, p_res_protein_count)
self.assertEqual(4, p_res_dna_count )
self.assertEqual(5, p_res_rna_count )
self.assertEqual(10, p_res_water_count)
self.assertEqual(2, p_res_other_count)
nTmessage("Select a list of residues.")
inputResList = (('A', 5),('B', 2),('A', 6),('X', 1)) # The last 2 are non-existing residues
# should give two warnings for a non-existing residue
resList = project.decodeResidueList( inputResList )
self.assertEqual(2, len(resList) )
def test_RangeSelection(self):
cing.verbosity = verbosityDebug
entryId = 'testEntry'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('testMol')
project.appendMolecule(mol)
offset1 = -10
# h**o dimer
chainList = ('A', 'B')
sequence = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
seqL = len(sequence)
lastResidueI = seqL - 1
for cId in chainList:
c = mol.addChain(cId)
for i, rName in enumerate(sequence):
rNumber = i + offset1
Nterminal = False # pylint: disable=C0103
Cterminal = False # pylint: disable=C0103
if i == 0:
Nterminal = True # pylint: disable=C0103
if i == lastResidueI:
Cterminal = True # pylint: disable=C0103
r = c.addResidue(rName,
rNumber,
Nterminal=Nterminal,
Cterminal=Cterminal)
if r:
# nTdebug("Adding atoms to residue: %s" % r)
r.addAllAtoms()
for atom in r.allAtoms():
atom.addCoordinate(0.0, 1.0, 2.0, 40.0)
# else:
# nTdebug("Skipping atoms for residue: %s" % r)
# end if
# end for
# end for chain
# another h**o dimer with renumbering.
chainList = ('C', 'D')
offset2 = 100
for cId in chainList:
c = mol.addChain(cId)
for i, rName in enumerate(sequence):
rNumber = i + offset2
Nterminal = False # pylint: disable=C0103
Cterminal = False # pylint: disable=C0103
if i == 0:
Nterminal = True # pylint: disable=C0103
if i == lastResidueI:
Cterminal = True # pylint: disable=C0103
r = c.addResidue(rName,
rNumber,
Nterminal=Nterminal,
Cterminal=Cterminal)
if r:
# nTdebug("Adding atoms to residue: %s" % r)
r.addAllAtoms()
# else:
# nTdebug("Skipping atoms for residue: %s" % r)
# end if
# end for
# end for chain
nTdebug("Done creating simple fake molecule")
self.assertFalse(mol.updateAll())
nTmessage(mol.format())
# Nada
selectedResidueList = mol.ranges2list('')
self.assertEquals(len(selectedResidueList), 2 * len(chainList) * seqL)
# Single residue
selectedResidueList = mol.ranges2list('A.' + str(offset1))
self.assertEquals(len(selectedResidueList), 1)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Two residues
selectedResidueList = mol.ranges2list(str(offset1))
self.assertEquals(len(selectedResidueList), 2)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Four residues in ranges
selectedResidueList = mol.ranges2list('1-2')
self.assertEquals(len(selectedResidueList), 4)
nTdebug("Selected residues: %s" % str(selectedResidueList))
# Eight residues in negative crossing ranges
selectedResidueList = mol.ranges2list('-1-2')
self.assertEquals(len(selectedResidueList), 8)
nTdebug("Selected residues: %s" % str(selectedResidueList))
selectedResidueList = mol.ranges2list('A.-5--2')
self.assertEquals(len(selectedResidueList), 4)
nTdebug("Selected residues: %s" % str(selectedResidueList))
selectedResidueList = mol.ranges2list('-999-999')
nTdebug("Selected residues: %s" % str(selectedResidueList))
self.assertEquals(len(selectedResidueList), 2 * len(chainList) * seqL)
residueList2StartStopList = mol.ranges2StartStopList('-999-999')
nTdebug('residueList2StartStopList: %s' %
str(residueList2StartStopList))
self.assertEquals(len(residueList2StartStopList), 8)
# """
# Possible 5 situations:
# a # 1 # positive int
# -a # 2 # single int
# -a-b # 3 #
# -a--b # 4 #
# a-b # 5 # most common
# """
inputList = """
A.1
A.1-3
A.-2--1
A.-2-1
A.-3
""".split()
for i, ranges in enumerate(inputList):
nTdebug("test_RangeSelection: %d %s" % (i, ranges))
residueList = mol.setResiduesFromRanges(ranges)
# nTdebug('residueList: [%s]' % residueList)
rangesRecycled = mol.residueList2Ranges(residueList)
# nTdebug('rangesRecycled: [%s]' % rangesRecycled)
self.assertEquals(ranges, rangesRecycled)
res1, res2 = mol.ranges2list('A.1,A.3')
self.assertEquals(2, residueNumberDifference(res1, res2))
res3, res4 = mol.ranges2list('A.5,A.8')
self.assertEquals(3, residueNumberDifference(res3, res4))
res5, res6 = mol.ranges2list('B.9,B.10')
self.assertEquals(1, residueNumberDifference(res5, res6))
ranges = mol.startStopList2ranges([res1, res2])
self.assertEquals('A.1-3', ranges)
ranges = mol.startStopList2ranges([res1, res2, res3, res4])
self.assertEquals('A.1-3,A.5-8', ranges)
ranges = mol.startStopList2ranges([res1, res2, res5, res6])
self.assertEquals('A.1-3,B.9-10', ranges)
# Check other routine
chain0 = mol.allChains()[0]
chain1 = mol.allChains()[1]
atomList = chain0.getRepresentingAtomListsPerResidue(chain1)
nTdebug("atomList: %s" % str(atomList))
self.assertEquals(len(atomList[0]), 5)
def test_GetMolTypeCountList(self):
cing.verbosity = verbosityDebug
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
mol = Molecule('test')
project.appendMolecule(mol)
c = mol.addChain('A')
c.addResidue('ALA', 1, Nterminal=True)
c.addResidue('VAL', 2)
c.addResidue('PHE', 3)
c.addResidue('ARG', 4)
c.addResidue('GLU', 5, Cterminal=True)
c = mol.addChain('B')
c.addResidue('DG', 1, Nterminal=True)
c.addResidue('DA', 2)
c.addResidue('DT', 3)
c.addResidue('DC', 4, Cterminal=True)
c = mol.addChain('C')
c.addResidue('RGUA', 1, convention=INTERNAL_0, Nterminal=True)
c.addResidue(
'RADE',
2,
convention=INTERNAL_0,
)
c.addResidue(
'URA',
3,
convention=INTERNAL_0,
) # not RTHY normally of course.
c.addResidue(
'RTHY',
4,
convention=INTERNAL_0,
)
c.addResidue('RCYT', 5, convention=INTERNAL_0, Cterminal=True)
c = mol.addChain('D')
for i in range(1, 11):
c.addResidue('HOH', i)
# end for
c = mol.addChain('E') # Unknown residue to CING
c.addResidue('ACE', 1)
c = mol.addChain('F') # Ions are also other
c.addResidue('CA2P', 1)
for residue in mol.allResidues():
residue.addAllAtoms()
# end for
mol.updateAll()
nTmessage(mol.format())
for c in mol.allChains():
nTmessage(c.format())
nTmessage("idxMolType: %s" % (c.getIdxMolType()))
# end for
nTmessage("Count the molecule types")
molTypeCountList = mol.getMolTypeCountList()
p_protein_count = molTypeCountList[mapMoltypeToInt[PROTEIN_STR]]
p_dna_count = molTypeCountList[mapMoltypeToInt[DNA_STR]]
p_rna_count = molTypeCountList[mapMoltypeToInt[RNA_STR]]
p_water_count = molTypeCountList[mapMoltypeToInt[WATER_STR]]
p_other_count = molTypeCountList[mapMoltypeToInt[OTHER_STR]]
self.assertEqual(1, p_protein_count)
self.assertEqual(1, p_dna_count)
self.assertEqual(1, p_rna_count)
self.assertEqual(1, p_water_count)
self.assertEqual(2, p_other_count)
nTmessage("Count the residue types")
molTypeResidueCountList = mol.getMolTypeResidueCountList()
p_res_protein_count = molTypeResidueCountList[
mapMoltypeToInt[PROTEIN_STR]]
p_res_dna_count = molTypeResidueCountList[mapMoltypeToInt[DNA_STR]]
p_res_rna_count = molTypeResidueCountList[mapMoltypeToInt[RNA_STR]]
p_res_water_count = molTypeResidueCountList[mapMoltypeToInt[WATER_STR]]
p_res_other_count = molTypeResidueCountList[mapMoltypeToInt[OTHER_STR]]
self.assertEqual(5, p_res_protein_count)
self.assertEqual(4, p_res_dna_count)
self.assertEqual(5, p_res_rna_count)
self.assertEqual(10, p_res_water_count)
self.assertEqual(2, p_res_other_count)
nTmessage("Select a list of residues.")
inputResList = (('A', 5), ('B', 2), ('A', 6), ('X', 1)
) # The last 2 are non-existing residues
# should give two warnings for a non-existing residue
resList = project.decodeResidueList(inputResList)
self.assertEqual(2, len(resList))
class AllChecks(TestCase):
'Test case'
cingDirTmpTest = os.path.join( cingDirTmp, 'test_classes2' )
mkdirs( cingDirTmpTest )
os.chdir(cingDirTmpTest)
def __init__(self, *args, **kwds):
TestCase.__init__(self, *args, **kwds)
self.project = None
self.r1 = None
self.r2 = None
self.r3 = None
self.r4 = None
self.r5 = None
self.r6 = None
self.r7 = None
self.r8 = None
def createSimpleFastProject(self):
'create simple fast project'
entryId = 'test'
self.project = Project( entryId )
self.project.removeFromDisk()
self.project = Project.open( entryId, status='new' )
mol = Molecule('test')
self.project.appendMolecule(mol)
c = mol.addChain('A')
self.r1 = c.addResidue('VAL', 1, Nterminal = True)
self.r2 = c.addResidue('VAL', 2)
self.r3 = c.addResidue('GLU', 3)
self.r4 = c.addResidue('TYR', 4)
self.r5 = c.addResidue('PHE', 5)
self.r6 = c.addResidue('GLY', 6)
self.r7 = c.addResidue('ARG', 7)
self.r8 = c.addResidue('LEU', 8, Cterminal = True)
for r in mol.allResidues():
r.addAllAtoms()
mol.updateAll()
# nTmessage( mol.format() )
def test_simplifyForFcFeature(self):
'test simplify Specifically For Fc Feature'
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist()
r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r1.MG1, r2.MG1))
atomPairs.append((r1.MG2, r2.MG1))
atomPairs.append((r1.MG1, r2.MG2))
atomPairs.append((r1.MG2, r2.MG2))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
if distanceRestraint.isValid:
_distanceRestraintList.append(distanceRestraint)
else:
nTerror('Failed to initialize DR with %s' % atomPairs)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
# Takes 4 simplification iterations.
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 2: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 3: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("dr after 4: %s" % formatall(distanceRestraint)) # don't print as it contains error token.
_x = "dr after 4: %s" % formatall(distanceRestraint)
def test_simplifyForFcFeature_2(self):
'test simplify Specifically For Fc Feature 2'
# disfunctional as of yet
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist()
# r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r2.HN, r2.MG1))
atomPairs.append((r2.MG2, r2.HN))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
_distanceRestraintList.append(distanceRestraint)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
def test_CombinationToPseudo(self):
' test combination to Pseudo'
self.createSimpleFastProject()
r1 = self.r1
r2 = self.r2
r3 = self.r3
atomLoL = [[r2.HN],
[r3.HB2, r3.HB3],
[r3.HB2],
[r1.HG11, r1.HG12, r1.HG13],
[r1.HG12, r1.HG11, r1.HG13],
[r1.HG11, r1.HG12, r1.HG13, r1.HG21, r1.HG22, r1.HG23], # unrepresented by below method.
]
pseudoListResultExpected = [ None,
r3.QB,
None,
r1.MG1, # TODO: update these to MD1 when CING has IUPAC internally.
r1.MG1,
None,
]
i = -1
for atomList in atomLoL:
i += 1
firstAtom = atomList[0]
self.assertEqual( firstAtom.getRepresentativePseudoAtom(atomList), pseudoListResultExpected[i])
def test_CombinationToPseudoDouble(self):
' test combination to Pseudo Double'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QG'
self.createSimpleFastProject()
e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((e.HG2, y.HB2),
(e.HG3, y.HB2),
(e.HG2, y.HB3),
(e.HG3, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_CombiToPseudoDouble_2(self):
'test_CombiToPseudoDouble_2'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QB'
self.createSimpleFastProject()
# e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.HE1, y.HB2),
(y.HE2, y.HB2),
(y.HE1, y.HB3),
(y.HE2, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_CombiToPseudoQuadruple(self):
' test combination to Pseudo 4 some.'
# 'Simulate 1a24 1254.00 A 3 TYR QR A 8 GLN QB'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QD, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify(self):
'test Simplify'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QE, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify2(self):
'test Simplify2'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QE, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify3(self):
'test simplify 3'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r8 # LEU
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QD, y.H),
(y.MD1, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.removeDuplicateAtomPairs2(), DistanceRestraint.STATUS_REMOVED_DUPLICATE)
class AllChecks(TestCase):
'Test case'
cingDirTmpTest = os.path.join(cingDirTmp, 'test_classes2')
mkdirs(cingDirTmpTest)
os.chdir(cingDirTmpTest)
def __init__(self, *args, **kwds):
TestCase.__init__(self, *args, **kwds)
self.project = None
self.r1 = None
self.r2 = None
self.r3 = None
self.r4 = None
self.r5 = None
self.r6 = None
self.r7 = None
self.r8 = None
def createSimpleFastProject(self):
'create simple fast project'
entryId = 'test'
self.project = Project(entryId)
self.project.removeFromDisk()
self.project = Project.open(entryId, status='new')
mol = Molecule('test')
self.project.appendMolecule(mol)
c = mol.addChain('A')
self.r1 = c.addResidue('VAL', 1, Nterminal=True)
self.r2 = c.addResidue('VAL', 2)
self.r3 = c.addResidue('GLU', 3)
self.r4 = c.addResidue('TYR', 4)
self.r5 = c.addResidue('PHE', 5)
self.r6 = c.addResidue('GLY', 6)
self.r7 = c.addResidue('ARG', 7)
self.r8 = c.addResidue('LEU', 8, Cterminal=True)
for r in mol.allResidues():
r.addAllAtoms()
mol.updateAll()
# nTmessage( mol.format() )
def test_simplifyForFcFeature(self):
'test simplify Specifically For Fc Feature'
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist()
r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r1.MG1, r2.MG1))
atomPairs.append((r1.MG2, r2.MG1))
atomPairs.append((r1.MG1, r2.MG2))
atomPairs.append((r1.MG2, r2.MG2))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
if distanceRestraint.isValid:
_distanceRestraintList.append(distanceRestraint)
else:
nTerror('Failed to initialize DR with %s' % atomPairs)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
# Takes 4 simplification iterations.
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 2: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 3: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("dr after 4: %s" % formatall(distanceRestraint)) # don't print as it contains error token.
_x = "dr after 4: %s" % formatall(distanceRestraint)
def test_simplifyForFcFeature_2(self):
'test simplify Specifically For Fc Feature 2'
# disfunctional as of yet
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist()
# r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r2.HN, r2.MG1))
atomPairs.append((r2.MG2, r2.HN))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
_distanceRestraintList.append(distanceRestraint)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
def test_CombinationToPseudo(self):
' test combination to Pseudo'
self.createSimpleFastProject()
r1 = self.r1
r2 = self.r2
r3 = self.r3
atomLoL = [
[r2.HN],
[r3.HB2, r3.HB3],
[r3.HB2],
[r1.HG11, r1.HG12, r1.HG13],
[r1.HG12, r1.HG11, r1.HG13],
[r1.HG11, r1.HG12, r1.HG13, r1.HG21, r1.HG22,
r1.HG23], # unrepresented by below method.
]
pseudoListResultExpected = [
None,
r3.QB,
None,
r1.
MG1, # TODO: update these to MD1 when CING has IUPAC internally.
r1.MG1,
None,
]
i = -1
for atomList in atomLoL:
i += 1
firstAtom = atomList[0]
self.assertEqual(firstAtom.getRepresentativePseudoAtom(atomList),
pseudoListResultExpected[i])
def test_CombinationToPseudoDouble(self):
' test combination to Pseudo Double'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QG'
self.createSimpleFastProject()
e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((e.HG2, y.HB2), (e.HG3, y.HB2), (e.HG2, y.HB3),
(e.HG3, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_CombiToPseudoDouble_2(self):
'test_CombiToPseudoDouble_2'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QB'
self.createSimpleFastProject()
# e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.HE1, y.HB2), (y.HE2, y.HB2), (y.HE1, y.HB3),
(y.HE2, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_CombiToPseudoQuadruple(self):
' test combination to Pseudo 4 some.'
# 'Simulate 1a24 1254.00 A 3 TYR QR A 8 GLN QB'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QD, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify(self):
'test Simplify'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QE, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify2(self):
'test Simplify2'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QE, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("after: %r" % distanceRestraint )
def test_Simplify3(self):
'test simplify 3'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r8 # LEU
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QD, y.H), (y.MD1, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.removeDuplicateAtomPairs2(),
DistanceRestraint.STATUS_REMOVED_DUPLICATE)
