def test_cyana2cing(self):
# SETUP FIRST
projectId = "1pdb"
cyanaDirectory = os.path.join( cingDirTestsData, "cyana", projectId )
self.assertTrue( os.path.exists( cyanaDirectory) and os.path.isdir(cyanaDirectory ) )
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
projectRootPath = os.path.join( cingDirTmp, projectId )
projectRoot = Project.rootPath( projectRootPath )[0] # xeasy_project.cing in /tmp
if os.path.exists( projectRoot ):
nTwarning('Output directory "%s" already exists. It will now be removed.' % projectRoot )
self.failIf( shutil.rmtree(projectRoot), "Failed to remove old project directory." )
project = Project.open(projectRootPath, 'new')
project.cyana2cing( #project=project,
cyanaDirectory=cyanaDirectory,
uplFiles = [projectId],
acoFiles = [projectId,"talos"],
pdbFile = projectId,
nmodels = 2,
copy2sources = True
)
if not project:
nTwarning("No project generated. Aborting further execution.")
sys.exit(0)
project.save()
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 testPdbFile(self):
nTwarning("This test case will take about 5 (+3 for 1v0e) minutes and is recommended to be done before major releases.")
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# entryList = "1kr8".split()
# entryList = "1otz".split() # 61 chains of which one is ' '
# entryList = "1v0e".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 1otz 2hgh 2k0e".split()
entryList = "1a4d 1ai0 1brv 1bus 1hue 1iv6 1kr8".split()
for entryId in entryList:
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
cingDirTmpTest = os.path.join( cingDirTmp, 'test2_pdb' )
mkdirs( cingDirTmpTest )
os.chdir(cingDirTmpTest)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
self.assertTrue( project.initPDB( pdbFile=pdbFilePath, convention=IUPAC, allowNonStandardResidue=True ))
self.assertTrue( project.save() )
def printSequenceFromPdbFile(fn):
verbosityOriginal = cing.verbosity
cing.verbosity = cing.verbosityError
entryId = 'getSequenceFromPdbFile'
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=fn, convention=IUPAC)
fastaString = ''
for res in project.molecule.allResidues():
# db doesn't always exist.
fastaString += getDeepByKeysOrDefault(res, defaultPrintChainCode, 'db',
'shortName')
cing.verbosity = verbosityOriginal
nTmessage("Sequence from PDB file:")
nTmessage(fastaString)
for res in project.molecule.allResidues():
nTmessageNoEOL(res.shortName)
nTmessage('')
cing.verbosity = cing.verbosityError
project.removeFromDisk()
del project
cing.verbosity = verbosityOriginal
def _test_Yasara(self):
'Test is incomplete; do NOT use.'
entryId = "testYasara"
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
project = Project( entryId )
# project = Project.open( entryId, status='old' )
project.yasaraShell()
yasara.Exit() # FAILS to ext really.
def _test_Yasara(self):
'Test is incomplete; do NOT use.'
entryId = "testYasara"
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
project = Project(entryId)
# project = Project.open( entryId, status='old' )
project.yasaraShell()
yasara.Exit() # FAILS to ext really.
def test_Procheck(self):
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
runAqua = True
showProcheckResults = False
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
entryId = "1bus"
# entryId = "1brv_1model" # Small much studied PDB NMR entry
ranges = None
if entryId.startswith("1brv"):
ranges = "173-186"
if entryId.startswith("1ai0"):
ranges = "2-20"
if entryId == "2hgh":
# in the case of 2hgh this is not a problem because the residue numbering doesn't
# overlap between the chain A protein and chain B RNA.
ranges = "2-11,13-33,35-54"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
ranges += ",104-105,115-136,145-190"
# 106-114 is a loop
# 137-144 is a loop
# 191-193 are 3 Zn ions.
#This leads to a procheck ranges file like:
# RESIDUES 2 B 11 B
# RESIDUES 13 B 33 B
# RESIDUES 35 B 54 B
# RESIDUES 104 A 105 A
# RESIDUES 115 A 136 A
# RESIDUES 145 A 190 A
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.molecule.setRanges(ranges)
project.save()
self.failIf(
project.runProcheck(createPlots=True, runAqua=runAqua) is None)
if showProcheckResults:
for res in project.molecule.allResidues():
nTdebug(repr(res) + " " + repr(res.procheck.secStruct))
def test_Whatif(self):
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "2hgh" # Small much studied PDB NMR entry; 48 models
# entryId = "1bus" # Small much studied PDB NMR entry: 5 models of 57 AA.: 285 residues.
entryId = "1brv" # DEFAULT is not to do more than 2 models because it takes quite a while.
# entryId = "1brv_cs_pk_2mdl"
# entryId = "1tgq_1model"
# pdbConvention = IUPAC
parseOnly = False # normal is False
showValues = True
ranges='cv'
# ranges='172-177'
# ranges='6-13,29-45'
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
project = Project( entryId )
if not parseOnly:
project.removeFromDisk()
project = Project.open( entryId, status='new' )
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=2))
self.assertFalse(runWhatif(project, ranges=ranges, parseOnly=False))
else:
project = Project.open( entryId, status='old' )
# print project.cingPaths.format()
project.save()
if showValues:
for res in project.molecule.allResidues():
nTdebug(repr(res))
whatifResDict = res.getDeepByKeys(WHATIF_STR)
if not whatifResDict:
continue
# checkIDList = whatifResDict.keys()
checkIDList = 'RAMCHK'.split()
for checkID in checkIDList:
valueList = whatifResDict.getDeepByKeys(checkID,VALUE_LIST_STR)
qualList = whatifResDict.getDeepByKeys(checkID,QUAL_LIST_STR)
nTdebug("%10s valueList: %-80s qualList: %-80s" % ( checkID, valueList, qualList))
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
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_fullRedo(self):
'Full recalculation and refinement by xplor nih. Too big to run by default.'
nTdebug("Now in %s" % getCallerName())
entryList = "1brv_023 1dum ".split()
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest), msg=
"Failed to change to test directory for files: " + cingDirTmpTest)
for i, entryId in enumerate(entryList):
if i != 0: # Selection of the entries.
continue
# end if
inputArchiveDir = os.path.join(cingDirTestsData, "cing")
cingDir = entryId + ".cing"
cingFileLocalTgz = entryId + ".cing.tgz"
cingFile = os.path.join(inputArchiveDir, cingFileLocalTgz)
if not os.path.exists(cingFile):
self.fail("Neither %s or the .tgz exist" % cingFile)
if os.path.exists(cingDir):
rmtree(cingDir)
if os.path.exists(cingFileLocalTgz):
os.unlink( cingFileLocalTgz )
copyfile(cingFile, cingFileLocalTgz )
project = Project.open(entryId, status='old')
self.assertTrue(project)
self.assertFalse(project.fullRedo(modelCountAnneal = 4, bestAnneal = 3, best = 2))
def test_exportXplor(self):
modelCount = 1
entryList = "1brv 2fws ".split()
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for i, entryId in enumerate(entryList):
if i != 0: # Selection of the entries.
continue
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if not os.path.exists(entryId + ".tgz"):
copyfile(ccpnFile, os.path.join('.', entryId + ".tgz"))
project = Project.open(entryId, status='new')
self.assertTrue(
project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount))
molecule = project.molecule
chain0 = molecule.allChains()[0]
chain = molecule.removeChain(chain0)
self.assertTrue(chain)
if molecule.allChains():
pdbFileName = entryId + "%03d.pdb"
molecule.export2xplor(pdbFileName)
def _test_fullRedo(self):
'Full recalculation and refinement by xplor nih. Too big to run by default.'
nTdebug("Now in %s" % getCallerName())
entryList = "1brv_023 1dum ".split()
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for i, entryId in enumerate(entryList):
if i != 0: # Selection of the entries.
continue
# end if
inputArchiveDir = os.path.join(cingDirTestsData, "cing")
cingDir = entryId + ".cing"
cingFileLocalTgz = entryId + ".cing.tgz"
cingFile = os.path.join(inputArchiveDir, cingFileLocalTgz)
if not os.path.exists(cingFile):
self.fail("Neither %s or the .tgz exist" % cingFile)
if os.path.exists(cingDir):
rmtree(cingDir)
if os.path.exists(cingFileLocalTgz):
os.unlink(cingFileLocalTgz)
copyfile(cingFile, cingFileLocalTgz)
project = Project.open(entryId, status='old')
self.assertTrue(project)
self.assertFalse(
project.fullRedo(modelCountAnneal=4, bestAnneal=3, best=2))
def test_makeDihedralHistogramPlot(self):
'''
See test_NTplot2 for simpler test
'''
cing.verbosity = verbosityDebug
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
# entryId = "1brv_cs_pk_2mdl"
entryId = "2kq3"
project = Project.open(entryId, status='new')
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertFalse(project.validateDihedrals())
# residue = project.molecule.A.PRO172
residue = project.molecule.A.ASP19
# Dihedral plots
for dihed in residue.db.dihedrals.zap('name'):
if dihed in residue and residue[dihed]:
# d = residue[dihed] # List of values with outliers etc attached.
# nTdebug("Residue %s: generating dihedral %s plot", residue, dihed )
ps = makeDihedralHistogramPlot(project, residue, dihed)
tmpPath = os.path.join(dihed + '.png')
if ps and isinstance(ps, NTplotSet):
ps.hardcopy(fileName=tmpPath)
def _testNmrStar(self):
"Testing conversion from CCPN to NMR-STAR using Wim Vranken's FC. Disabled test because only JFD uses it."
# failing entries: 1ai0, 1kr8 (same for 2hgh)
entryList = "1a4d".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
#1iv6 needs better ccpn file from FC
# if you have a local copy you can use it; make sure to adjust the path setting below.
useNrgArchive = False # Default is False
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile))
self.assertTrue(project.save())
fileName = os.path.join( cingDirTmp, entryId + ".str")
nmrStar = NmrStar(project)
self.assertTrue( nmrStar )
self.assertTrue( nmrStar.toNmrStarFile( fileName ))
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def test_makeDihedralHistogramPlot(self):
'''
See test_NTplot2 for simpler test
'''
cing.verbosity = verbosityDebug
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
# entryId = "1brv_cs_pk_2mdl"
entryId = "2kq3"
project = Project.open(entryId, status = 'new')
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile ))
self.assertFalse( project.validateDihedrals() )
# residue = project.molecule.A.PRO172
residue = project.molecule.A.ASP19
# Dihedral plots
for dihed in residue.db.dihedrals.zap('name'):
if dihed in residue and residue[dihed]:
# d = residue[dihed] # List of values with outliers etc attached.
# nTdebug("Residue %s: generating dihedral %s plot", residue, dihed )
ps = makeDihedralHistogramPlot( project, residue, dihed )
tmpPath = os.path.join( dihed + '.png')
if ps and isinstance(ps, NTplotSet):
ps.hardcopy( fileName = tmpPath )
def test_exportXplor(self):
modelCount = 1
entryList = "1brv 2fws ".split()
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest), msg=
"Failed to change to test directory for files: " + cingDirTmpTest)
for i, entryId in enumerate(entryList):
if i != 0: # Selection of the entries.
continue
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if not os.path.exists(entryId + ".tgz"):
copyfile(ccpnFile, os.path.join('.', entryId + ".tgz"))
project = Project.open(entryId, status = 'new')
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=modelCount))
molecule = project.molecule
chain0 = molecule.allChains()[0]
chain = molecule.removeChain(chain0)
self.assertTrue( chain )
if molecule.allChains():
pdbFileName = entryId +"%03d.pdb"
molecule.export2xplor( pdbFileName )
def _testDihedralComboPlot(self):
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (image2DdihedralWidth, image2Ddihedralheight)
dihedralName1 = 'PHI'
dihedralName2 = 'PSI'
projectName = 'testDihedralComboPlot'
project = Project(projectName)
plotparams1 = project.plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plot = NTplot(title=projectName,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
ps.hardcopy(projectName, 'png')
def test_BMRBcounts2(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = '1brv'
bmrbId = 4020
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
project = Project.open(entryId, status = 'new')
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile))
assignmentCountMap = project.molecule.getAssignmentCountMap()
# p_cs_count = assignmentCountMap['overall']
p_cs1H_count = assignmentCountMap['1H']
p_cs13C_count = assignmentCountMap['13C']
p_cs15N_count = assignmentCountMap['15N']
bmrbCountMap = getBmrbCsCounts()
nTdebug("bmrbCountMap %r" % bmrbCountMap)
entryMap = getDeepByKeysOrAttributes( bmrbCountMap, bmrbId )
nTdebug("entryMap %r" % entryMap)
d_cs1H_count = getDeepByKeysOrAttributes( entryMap, '1H' )
d_cs13C_count = getDeepByKeysOrAttributes( entryMap, '13C' )
d_cs15N_count = getDeepByKeysOrAttributes( entryMap, '15N' )
nTdebug("db: %s project: %s" % ( d_cs1H_count, p_cs1H_count ) )
nTdebug("db: %s project: %s" % ( d_cs13C_count, p_cs13C_count ) )
nTdebug("db: %s project: %s" % ( d_cs15N_count, p_cs15N_count ) )
def test_pdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "tightTurn_IIb"
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = IUPAC )
m = project.molecule
ranges = 'A.173-178'
nTdebug("m: %s" % m)
self.assertTrue( m.toPDB('m001.pdb', model=0, ranges=ranges, convention='XPLOR'))
# nTdebug("Manual reimport")
# m.initCoordinates()
# m.importFromPDB('m001.pdb',convention='XPLOR')
nTdebug("Reimport 1")
m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', convention=IUPAC)
# nTdebug("Reimport 2")
# m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', useModels = "1", convention=IUPAC)
self.assertFalse(project.mkMacros())
def testMolgrapRunFromPdbFile(self):
# SETUP FIRST
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1a4d" # Small much studied PDB NMR entry
# entryId = "1zwj" # X-ray entry of CESG interest.
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# does it matter to import it just now?
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.save()
gifFileName = entryId + ".gif"
pathGif = os.path.join(self.cingDirTmpTest, gifFileName)
self.assertFalse(project.molecule.export2gif(pathGif, project=project))
self.assertTrue(os.path.exists(pathGif))
pathMolGifPinup = pathGif[:-4] + '_pin.gif'
self.assertTrue(os.path.exists(pathMolGifPinup))
pathGifDefault = os.path.join(cingPythonCingDir, 'PluginCode',
DATA_STR, 'UnknownImage.gif')
self.assertFalse(
os.path.getsize(pathGif) == os.path.getsize(pathGifDefault))
nTmessage("Created new molecular imagery at: %s" % self.cingDirTmpTest)
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 loadProject(self):
modelCount = 1
ccpnFile = self.compressedCcpnProject
project = Project.open(self.idCode, status='new')
# Can read tgz files.
if project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount) == None:
nTerror("Failed to read: %s" % ccpnFile)
return True
# self.ccpnProject = loadCcpnTgzProject(os.path.join(self.loadDir, self.idCode, 'linkNmrStarData'))
self.ccpnProject = project.ccpn
def _test_cingTestData(self): # Disabled all together because JFD can't figure out why it works on all but the master node.
# and even there it works fine when testing manually with right setup and:
# nosetests /Users/jd/.jenkins/jobs/CING/workspace/Slaves/master/python/cing/PluginCode/test/test_cingTestData.py
entryList = "1brv_023 1brv_024 1brv_025".split() # 0.24 version project with CS from NRG-CING.
# entryList = "1brv_024 1brv_025".split() # 0.23 version skipped because unknown error causes it to fail.
# entryList = "1brv_025".split()
# entryList = "H2_2Ca_64_100".split() # 0.24 version project with CS.
# entryList = "1i1s 1ka3 1tgq 1y4o".split()
# if you have a local copy you can use it; make sure to adjust the path setting below.
validateFastest = True
htmlOnly = False # default is False but enable it for faster runs without some actual data.
doWhatif = False # disables whatif actual run
doProcheck = False
doWattos = False
useNrgArchive = False
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in entryList:
nTmessage('Doing %s' % entryId)
if useNrgArchive: # default is False
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
# Mounted from nmr.cmbi.ru.nl
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
inputArchiveDir = os.path.join('/Users/jd/ccpn_tmp/data/recoord', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "cing")
# end if
cingFile = os.path.join(inputArchiveDir, entryId + ".cing.tgz")
self.assertTrue( os.path.exists(cingFile), "Failed to find file: " + cingFile)
cingDirNew = os.path.join(cingDirTestsData, entryId + ".cing")
if os.path.exists(cingDirNew):
nTmessage("Removing old cing project directory: " + cingDirNew )
shutil.rmtree( cingDirNew )
# end if
shutil.copy(cingFile, cingDirTmpTest)
project = Project.open(entryId, status = 'old')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if 1:
self.assertFalse(project.validate(htmlOnly = htmlOnly,
doProcheck = doProcheck,
doWhatif = doWhatif,
doWattos=doWattos,
validateFastest=validateFastest ))
# end if
self.assertTrue(project.save())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def changeCoordinates(proj_path, prl_name):
'''
Load the coordinates from the PDB file into CING project.
NB: also already saves the project.
Return True on error.
'''
prl = Project.open('%s/%s' % (proj_path, prl_name), status='old')
molec = prl.molecule
molec.initCoordinates()
molec.importFromPDB('%s/%s.pdb' % (proj_path, prl_name), convention='IUPAC')
prl.save()
def test_Procheck(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
runAqua = True
showProcheckResults = False
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
entryId = "1bus"
# entryId = "1brv_1model" # Small much studied PDB NMR entry
ranges = None
if entryId.startswith("1brv"):
ranges = "173-186"
if entryId.startswith("1ai0"):
ranges = "2-20"
if entryId == "2hgh":
# in the case of 2hgh this is not a problem because the residue numbering doesn't
# overlap between the chain A protein and chain B RNA.
ranges = "2-11,13-33,35-54"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
ranges += ",104-105,115-136,145-190"
# 106-114 is a loop
# 137-144 is a loop
# 191-193 are 3 Zn ions.
#This leads to a procheck ranges file like:
# RESIDUES 2 B 11 B
# RESIDUES 13 B 33 B
# RESIDUES 35 B 54 B
# RESIDUES 104 A 105 A
# RESIDUES 115 A 136 A
# RESIDUES 145 A 190 A
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
project = Project( entryId )
self.failIf( project.removeFromDisk() )
project = Project.open( entryId, status='new' )
cyanaFile = os.path.join(cingDirTestsData, "cyana", entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder = cyanaFile))
project.molecule.setRanges(ranges)
project.save()
self.failIf(project.runProcheck(createPlots=True, runAqua=runAqua) is None)
if showProcheckResults:
for res in project.molecule.allResidues():
nTdebug(repr(res) +" "+ repr(res.procheck.secStruct))
def open(self, path, status='old'):
"""
Open a project and append
return project or None on error
"""
project = Project.open( path, status=status)
if not project:
nTerror('Projects.open: aborting')
sys.exit(1)
self.append( project )
return project
def upgrade100(project, restore):
"""
Do all things to upgrade project to current configuration
All versions <= 1.00
"""
nTmessage('*** upgrade100: upgrading %s from version %s ***', project, project.version)
verbosity = cing.verbosity
# make sure we get all if we heave debug on
if cing.verbosity < cing.verbosityDebug:
cing.verbosity = cing.verbosityWarning
# Molecules
for molName in project.moleculeNames:
pathName = project.molecules.path(molName)
mol = Molecule.open(pathName)
if mol:
mol.status = 'keep'
project.appendMolecule(mol)
#end if
nTdebug('upgrade100: restored %s', mol)
#end for
# restore the lists
for pl in [project.peaks, project.distances, project.dihedrals, project.rdcs, project.coplanars]:
pl.restore()
#end for
# Now patch talos+
nTmessage('==> upgrade100: talosPlus')
if restoreTalosPlus100(project):
io.error('upgrade100: restoring talosPlus data failed\n')
# Now patch queeny
# nTmessage('==> upgrade100: queeny')
# if restoreQueeny100(project):
# nTerror('upgrade100: restoring queeny data failed')
# project.saveQueeny()
#
# # Now patch shiftx
# if restoreShiftx100(project):
# nTerror('upgrade100: restoring shiftx data failed')
# return None
# project.saveShiftx()
# Plugin registered functions
nTdebug('upgrade100: calling plugins')
project._callPluginRestores()
# save to consolidate
project.save()
cing.verbosity = verbosity
return Project.open(project.name, constants.PROJECT_OLD, restore=restore)
def test_Wattos(self):
"Testing wattos reading and working on a star file that first gets created by Wim's FC."
# failing entries: 1ai0, 1kr8 (same for 2hgh)
# entryList = "1kr8".split()
entryList = "1brv".split()
# entryList = "basp2".split()
# entryList = "1bus".split()
# entryList = "1a4d".split()
# entryList = "2k0e_all".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
# entryList = "1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e".split()
#1iv6 needs better ccpn file from FC
# entryList = ["Parvulustat"]
# entryList = ["SRYBDNA"]
# if you have a local copy you can use it; make sure to adjust the path setting below.
useNrgArchive = False # Default is False
ranges = 'cv'
# ranges='16-29'
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
inputArchiveDir = os.path.join(
'/Library/WebServer/Documents/NRG-CING/recoordSync',
entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
# self.assertTrue(project.save())
self.assertFalse(project.molecule.setRanges(ranges))
self.assertTrue(runWattos(project))
mol = project.molecule
completenessMol = mol.getDeepByKeys(WATTOS_STR, COMPLCHK_STR,
VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys(WATTOS_STR, COMPLCHK_STR,
VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
self.assertTrue(completenessMol)
def changeCoordinates(proj_path, prl_name):
'''
Load the coordinates from the PDB file into CING project.
NB: also already saves the project.
Return True on error.
'''
prl = Project.open('%s/%s' % (proj_path, prl_name), status='old')
molec = prl.molecule
molec.initCoordinates()
molec.importFromPDB('%s/%s.pdb' % (proj_path, prl_name),
convention='IUPAC')
prl.save()
def testPdbFile(self):
nTwarning(
"This test case will take about 5 (+3 for 1v0e) minutes and is recommended to be done before major releases."
)
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# entryList = "1kr8".split()
# entryList = "1otz".split() # 61 chains of which one is ' '
# entryList = "1v0e".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 1otz 2hgh 2k0e".split()
entryList = "1a4d 1ai0 1brv 1bus 1hue 1iv6 1kr8".split()
for entryId in entryList:
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
cingDirTmpTest = os.path.join(cingDirTmp, 'test2_pdb')
mkdirs(cingDirTmpTest)
os.chdir(cingDirTmpTest)
# does it matter to import it just now?
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
self.assertTrue(
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
allowNonStandardResidue=True))
self.assertTrue(project.save())
def test_pdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "tightTurn_IIb"
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb"+entryId+".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = IUPAC )
m = project.molecule
ranges = 'A.173-178'
nTdebug("m: %s" % m)
self.assertTrue( m.toPDB('m001.pdb', model=0, ranges=ranges, convention='XPLOR'))
# nTdebug("Manual reimport")
# m.initCoordinates()
# m.importFromPDB('m001.pdb',convention='XPLOR')
nTdebug("Reimport 1")
m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', convention=IUPAC)
# nTdebug("Reimport 2")
# m.replaceCoordinatesByPdb(pdbFilePath, name = entryId+'_reimport', useModels = "1", convention=IUPAC)
self.assertFalse(project.mkMacros())
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_xplor_nih(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
entryId = "gb1"
pdbDirectory = os.path.join(cingDirTestsData,"xplor", entryId)
pdbFileName = entryId+".pdb"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = XPLOR )
# project.validate(ranges, parseOnly, htmlOnly, doProcheck, doWhatif, doWattos, doTalos)
project.validate(htmlOnly=True, doProcheck=False, doWhatif=False, doWattos=False, doTalos=False)
project.save()
def _testAnalysisRpf(self):
'Skip until project has been improved; looks like peaks without CS are found.'
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True
modelCount = 99
if fastestTest:
modelCount = 2
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in AllChecks.entryList:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
self.assertTrue(
project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount))
analysis = Analysis(project)
if analysis.initAnalysis():
self.fail("%s Failed to analysis.initAnalysis()" % entryId)
continue
# If unit testing without output then Analysis needs to be silenced separately.
if cing.verbosity <= cing.verbosityNothing:
switchOutput(False)
self.assertTrue(
analysis.runRpf(
doAlised=DEFAULT_CONSIDER_ALIASED_POSITIONS,
distThreshold=DEFAULT_DISTANCE_THRESHOLD,
prochiralExclusion=DEFAULT_PROCHIRAL_EXCLUSION_SHIFT,
diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT))
if cing.verbosity <= cing.verbosityNothing:
switchOutput(True)
self.assertTrue(project.save())
del project
del analysis # Calls quit?
def run():
nTdebug("Remove previous project if present")
pdir = n+".cing"
if os.path.exists(pdir):
rmtree(pdir)
nTdebug("Load project from .tgz")
project = Project.open(n, status='old')
if not project:
sys.exit(1)
nTdebug("Set convenience variables")
m = project.molecule
rangesNew = m.rangesByCv()
nTdebug("rangesNew: %s" % rangesNew)
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()
def run():
nTdebug("Remove previous project if present")
pdir = n + ".cing"
if os.path.exists(pdir):
rmtree(pdir)
nTdebug("Load project from .tgz")
project = Project.open(n, status='old')
if not project:
sys.exit(1)
nTdebug("Set convenience variables")
m = project.molecule
rangesNew = m.rangesByCv()
nTdebug("rangesNew: %s" % rangesNew)
def test_TalosPlus(self):
if not cingPaths.talos:
raise ImportWarning('No Talos installed.')
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True
modelCount = 99
if fastestTest:
modelCount = 2
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in AllChecks.entryList:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile, modelCount=modelCount))
# self.assertFalse(project.runTalosPlus())
# self.assertTrue(project.save())
self.assertFalse(project.validate(htmlOnly=True, doProcheck=False, doWhatif=False, doWattos=False, doQueeny=False))
for r, res in enumerate(project.molecule.allResidues()):
nTdebug("Working on %s" % res)
for c, valueToCheck in enumerate(keyList):
if c == 2: # TODO: re-enable this check when debugged.
continue
valueDetermined = getDeepByKeysOrAttributes(res, TALOSPLUS_STR, valueToCheck)
valueReference = valueKnownList[r][c] # r/c is for row/column
if isNaN(valueDetermined) and isNaN(valueReference):
continue
if isNaN(valueDetermined) or isNaN(valueReference):
self.fail("Working on %s %s %s valueDetermined %s is not valueReference %s because only one of them isNaN" % (
res, c, valueToCheck, valueDetermined, valueReference))
self.assertAlmostEquals(valueReference, valueDetermined, 3)
self.assertTrue(project.save())
# project.close()
# del project
#
# project = Project.open(entryId, status = 'old')
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def test_superpose(self):
pdbConvention = IUPAC
entryId = "1brv"
# entryId = "2vb1_simple" # Protein solved by X-ray.
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
pdbDirectory = os.path.join(cingDirTestsData,"pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join( pdbDirectory, pdbFileName)
self.failIf( not os.path.exists(pdbFilePath), msg= "Failed to find file: "+pdbFilePath)
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
project.initPDB( pdbFile=pdbFilePath, convention = pdbConvention )
# Compare with molmol on 1brv's 48 models:
# mean global bb RMSD: 0.98 +/- 0.40 A ( 0.10.. 2.19 A)
# mean global heavy RMSD: 1.75 +/- 0.51 A ( 0.54.. 3.33 A)
# Note that in molmol the backbone protein atoms are defined: N, CA, C
# CING used to include the carbonyl atom
# using default parameters.
ens = project.molecule.superpose(backboneOnly=True, includeProtons = False, iterations=2)
nTdebug( 'ens %s' % ens)
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.7643199324863148, ens.averageModel.rmsd, 3 )
# Confirmed to be the 'averaage RMSD to mean: 0.698' in molmol using command
# Fit 'to_mean'.
ens = project.molecule.superpose(backboneOnly=False, includeProtons = False,
iterations=3) # no improvement to do 3 over the default 2 but left in for speed checking.
nTdebug( 'ens.averageModel %s' % ens.averageModel)
self.assertAlmostEquals( 0.99383582432002637, ens.averageModel.rmsd, 3 )
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()
def test_xplor_nih(self):
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
entryId = "gb1"
pdbDirectory = os.path.join(cingDirTestsData, "xplor", entryId)
pdbFileName = entryId + ".pdb"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=XPLOR)
# project.validate(ranges, parseOnly, htmlOnly, doProcheck, doWhatif, doWattos, doTalos)
project.validate(htmlOnly=True,
doProcheck=False,
doWhatif=False,
doWattos=False,
doTalos=False)
project.save()
def _testAnalysisRpf(self):
'Skip until project has been improved; looks like peaks without CS are found.'
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True
modelCount=99
if fastestTest:
modelCount=2
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in AllChecks.entryList:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=modelCount))
analysis = Analysis(project)
if analysis.initAnalysis():
self.fail("%s Failed to analysis.initAnalysis()" % entryId)
continue
# If unit testing without output then Analysis needs to be silenced separately.
if cing.verbosity <= cing.verbosityNothing:
switchOutput(False)
self.assertTrue(analysis.runRpf(
doAlised=DEFAULT_CONSIDER_ALIASED_POSITIONS,
distThreshold=DEFAULT_DISTANCE_THRESHOLD,
prochiralExclusion=DEFAULT_PROCHIRAL_EXCLUSION_SHIFT,
diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT
))
if cing.verbosity <= cing.verbosityNothing:
switchOutput(True)
self.assertTrue(project.save())
del project
del analysis # Calls quit?
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_x3dna(self):
if osType != OS_TYPE_MAC: # only installed for mac os currently.
return
try:
from cing.PluginCode.x3dna import createHtmlX3dna
except:
nTerror("Failed to import x3dna on a mac osx.")
return
entryList = "1b4y".split(
) # triple helix but it only gets analyzed to a double helix.
# entryList = "1cjg".split()
# entryList = "2hgh".split()
# entryList = "1a4d".split()
# entryList = "1brv".split() # protein only entry
# entryList = ["SRYBDNA"]
useNrgArchive = False
showValues = True
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
inputArchiveDir = os.path.join(
'/Library/WebServer/Documents/NRG-CING/recoordSync',
entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
project.save()
self.assertTrue(project.runX3dna())
project.save()
self.assertFalse(createHtmlX3dna(project))
if showValues:
for coplanar in project.coplanars[0]:
# nTdebug(coplanar.format())
nTdebug('%r' % coplanar[X3DNA_STR])
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
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_Wattos(self):
"Testing wattos reading and working on a star file that first gets created by Wim's FC."
# failing entries: 1ai0, 1kr8 (same for 2hgh)
# entryList = "1kr8".split()
entryList = "1brv".split()
# entryList = "basp2".split()
# entryList = "1bus".split()
# entryList = "1a4d".split()
# entryList = "2k0e_all".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
# entryList = "1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e".split()
#1iv6 needs better ccpn file from FC
# entryList = ["Parvulustat"]
# entryList = ["SRYBDNA"]
# if you have a local copy you can use it; make sure to adjust the path setting below.
useNrgArchive = False # Default is False
ranges='cv'
# ranges='16-29'
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile))
# self.assertTrue(project.save())
self.assertFalse(project.molecule.setRanges(ranges))
self.assertTrue(runWattos(project))
mol = project.molecule
completenessMol = mol.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
self.assertTrue(completenessMol)
def test_cyana2cing(self):
# SETUP FIRST
projectId = "1pdb"
cyanaDirectory = os.path.join(cingDirTestsData, "cyana", projectId)
self.assertTrue(
os.path.exists(cyanaDirectory) and os.path.isdir(cyanaDirectory))
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
projectRootPath = os.path.join(cingDirTmp, projectId)
projectRoot = Project.rootPath(projectRootPath)[
0] # xeasy_project.cing in /tmp
if os.path.exists(projectRoot):
nTwarning(
'Output directory "%s" already exists. It will now be removed.'
% projectRoot)
self.failIf(shutil.rmtree(projectRoot),
"Failed to remove old project directory.")
project = Project.open(projectRootPath, 'new')
project.cyana2cing( #project=project,
cyanaDirectory=cyanaDirectory,
uplFiles=[projectId],
acoFiles=[projectId, "talos"],
pdbFile=projectId,
nmodels=2,
copy2sources=True)
if not project:
nTwarning("No project generated. Aborting further execution.")
sys.exit(0)
project.save()
def _test_2ccpn(self):
# failing entries: 1ai0, 1kr8 (same for 2hgh)
entryList = "1iv6".split()
# entryList = "1brv".split()
# entryList = "1a4d".split()
# entryList = "2k0e_all".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e".split()
# entryList = "1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
#1iv6 needs better ccpn file from FC
# entryList = ["Parvulustat"]
# entryList = ["1a4d"]
fastestTest = True
htmlOnly = True # default is False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
if fastestTest:
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
ccpnFile = os.path.join(cingDirTestsData, "ccpn", entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertTrue(project.save())
self.assertFalse(
project.validate(
htmlOnly=htmlOnly,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
))
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def test_x3dna(self):
if cing.systemDefinitions.osType != OS_TYPE_MAC: # only installed for mac os currently.
return
try:
from cing.PluginCode.x3dna import createHtmlX3dna
except:
nTerror("Failed to import x3dna on a mac osx.")
return
entryList = "1b4y".split() # triple helix but it only gets analyzed to a double helix.
# entryList = "1cjg".split()
# entryList = "2hgh".split()
# entryList = "1a4d".split()
# entryList = "1brv".split() # protein only entry
# entryList = ["SRYBDNA"]
useNrgArchive = False
showValues = True
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in entryList:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile))
project.save()
self.assertTrue(project.runX3dna())
project.save()
self.assertFalse(createHtmlX3dna(project))
if showValues:
for coplanar in project.coplanars[0]:
# nTdebug(coplanar.format())
nTdebug('%r' % coplanar[X3DNA_STR])
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
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 _testCreateCcpn(self):
'Disabled test because...'
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in AllChecks.entryList:
# Allow pdb files to be of different naming systems for this test.
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFolder = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
nTdebug("Reading files from: " + cyanaFolder)
project.initCyana(cyanaFolder)
project.save()
nTmessage("Project: %s" % project)
ccpnFolder = entryId + "New"
self.assertTrue(project.saveCcpn(ccpnFolder))
def _testMolgrapRunFromCcpnFile(self):
# entryId = "1cjg" # Nucleic acid entry.
entryId = "1brv" # Nucleic acid entry.
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
ccpnFile = os.path.join(cingDirTestsData, "ccpn", entryId + ".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertTrue(project.save())
gifFileName = entryId + ".gif"
pathGif = os.path.join(cingDirTmp, gifFileName)
self.assertFalse(project.molecule.export2gif(pathGif, project=None))
self.assertTrue(os.path.exists(pathGif))
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def _testMolgrapRunFromCcpnFile(self):
# entryId = "1cjg" # Nucleic acid entry.
entryId = "1brv" # Nucleic acid entry.
project = Project.open( entryId, status='new' )
self.assertTrue(project, 'Failed opening project: ' + entryId)
ccpnFile = os.path.join(cingDirTestsData,"ccpn", entryId+".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertTrue(project.save())
gifFileName = entryId+".gif"
pathGif = os.path.join( cingDirTmp, gifFileName)
self.assertFalse(project.molecule.export2gif(pathGif, project=None))
self.assertTrue(os.path.exists(pathGif))
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def _test_2ccpn(self):
# failing entries: 1ai0, 1kr8 (same for 2hgh)
entryList = "1iv6".split()
# entryList = "1brv".split()
# entryList = "1a4d".split()
# entryList = "2k0e_all".split()
# entryList = "1a4d 1a24 1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e".split()
# entryList = "1afp 1ai0 1brv 1bus 1cjg 1hue 1ieh 1iv6 1kr8 2hgh 2k0e SRYBDNA Parvulustat".split()
#1iv6 needs better ccpn file from FC
# entryList = ["Parvulustat"]
# entryList = ["1a4d"]
fastestTest = True
htmlOnly = True # default is False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
if fastestTest:
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in entryList:
project = Project.open( entryId, status='new' )
self.assertTrue(project, 'Failed opening project: ' + entryId)
ccpnFile = os.path.join(cingDirTestsData,"ccpn", entryId+".tgz")
self.assertTrue(project.initCcpn(ccpnFolder=ccpnFile))
self.assertTrue(project.save())
self.assertFalse(project.validate(htmlOnly=htmlOnly,
doProcheck = doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
))
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def test_shiftx(self):
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model" RNA-protein complex.
entryId = "1brv"
# entryId = "1tgq_1model" # withdrawn entry
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.runShiftx()
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 updateProjectHtml(pdb_id, extraArgListStr):
# extraArgList = extraArgListStr.split()
htmlOnly = True
project = Project.open(pdb_id, status='old')
nTmessage("Opened existing project")
if not project:
nTerror("Failed to init old project")
return True
# end if
archive_id = getArchiveIdFromDirectoryName(os.getcwd())
# Derives the related entry codes in PDB and BMRB.
project.molecule.setArchiveId(archive_id)
if True: # DEFAULT: True
nTmessage("Updating project html")
# project.runCingChecks(toFile=True, ranges=ranges)
project.setupHtml()
project.generateHtml(htmlOnly=htmlOnly)
project.renderHtml()
# end if
project.save()
nTmessage("Done with updateProjectHtml")
