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_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_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 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 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_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 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 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_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_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, format(molecule)))
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, molecule.format()))
self.assertEqual( len(molecule.allChains()), n)
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_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 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 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_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 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 _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 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 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 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 _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 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 main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
force_redo = True
force_retrieve_input = True
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [
'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention',
'archiveType', 'projectType', 'storeCING2db'
]
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3,
entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if force_redo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if force_retrieve_input:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId,
inputDir,
archiveType=archiveType,
formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.updateProject()
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doTalos=doTalos):
nTerror("Failed to validate project read")
return True
if storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db(entryId, ARCHIVE_CASP_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
def plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# 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)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1,
'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2,
'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
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)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys(
) # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR,
0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR,
VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
else:
fprintf(fpGood,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
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)
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage(
"consider updating code to include all sequential parameters: %s" %
str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int(extraArgList[IDX_VERBOSITY])
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR,
entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[
IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue(
getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList,
IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList,
IDX_SINGLE_CORE_OPERATION)
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
if archiveType == ARCHIVE_TYPE_FLAT:
pass # default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName(outputDir)
nTdebug("Using program arguments:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split(inputDir, ':')[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId,
inputDir,
archiveType=archiveType,
formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
else:
nTdebug(
"Entry not retrieved which might be normal in some situations.")
# end if.
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
# fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
# shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doQueeny=doQueeny,
doTalos=doTalos,
filterVasco=filterVasco):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db(entryId, archive_id, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" %
(status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax=2):
nTerror(
"Failed to send File By Scp status: %s with result %s" %
(status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage("consider updating code to include all sequential parameters: %s" % str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int( extraArgList[IDX_VERBOSITY] )
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue( getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList, IDX_SINGLE_CORE_OPERATION )
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
if archiveType == ARCHIVE_TYPE_FLAT:
pass # default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName( outputDir )
nTdebug("Using program arguments:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split( inputDir, ':' )[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId, inputDir, archiveType=archiveType, formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
else:
nTdebug("Entry not retrieved which might be normal in some situations.")
# end if.
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
# fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
# shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC, nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doQueeny = doQueeny, doTalos=doTalos, filterVasco = filterVasco ):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db( entryId, archive_id, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" % (status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax = 2):
nTerror("Failed to send File By Scp status: %s with result %s" % (status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
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)
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) )
def plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# 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)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
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)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys() # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, 0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
else:
fprintf(fpGood, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
force_redo = True
force_retrieve_input = True
nTmessage(cing.cingDefinitions.getHeaderString())
nTmessage(cing.systemDefinitions.getStartMessage())
expectedArgumentList = [ 'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention', 'archiveType','projectType','storeCING2db']
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if force_redo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if force_retrieve_input:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId, inputDir, archiveType=archiveType, formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC, nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doTalos=doTalos):
nTerror("Failed to validate project read")
return True
if storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db( entryId, ARCHIVE_CASP_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
def testResPlot(self):
actuallyRunProcheck = False
actuallyRunWhatif = False
showValues = False
modelNum = 1 # Only used when simulating data
#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"
ranges = None
if entryId.startswith("2hgh"):
# Compile a NTlist instance with residue objects.
ranges = "2-54,111-136,145-193"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
# 191-193 are bound ZN ions.
elif entryId.startswith("1brv"):
# Truncate from Val171-Glu189 to:
ranges = "176-188"
project = Project( entryId )
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.runDssp()
rangeList = project.molecule.getFixedRangeList(
max_length_range = ResPlot.MAX_WIDTH_IN_RESIDUES, ranges=ranges )
if actuallyRunProcheck:
self.failIf(project.procheck(createPlots=False, runAqua=False) is None)
if actuallyRunWhatif:
self.assertFalse(runWhatif(project))
pointsANGCHK = [] # list per res in rangeList of lists
pointsBNDCHK = []
pointsQUACHK = []
pointsRAMCHK = []
pointsC12CHK = []
pointsBBCCHK = []
resNumb = 0
for resList in rangeList:
for res in resList:
resNumb += 1
# nTdebug(repr(res))
# if random() < 0.2: # Skip a 10%
# continue
whatifResDict = res.setdefault(WHATIF_STR, NTdict())
procheckResDict = res.setdefault(PROCHECK_STR, NTdict())
# if not whatifResDict: # empty dict
# continue
angList = NTlist()
bndList = NTlist()
quaList = NTlist()
ramList = NTlist()
c12List = NTlist()
bbcList = NTlist()
accList = NTlist()
sstList = NTlist()
sstListPossibilities='SH' # secondary structure elements.
for _modelID in range(modelNum):
if not actuallyRunWhatif:
angList.append(random()*10-0) # Simulate abs max of Z-scores.
bndList.append(random()*5+1) # offset by 1 but still want to start from zero?
quaList.append(random()*5+1)
ramList.append(random()*5+1)
c12List.append(random()*5+1)
bbcList.append(random()*5+1)
accList.append(random()*4-2)
if not actuallyRunProcheck:
sstList.append( sstListPossibilities[ int(random()*2)]) # Simulate secondary structure
if not actuallyRunWhatif:
self.assertFalse ( whatifResDict.setDeepByKeys(angList, ANGCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(bndList, BNDCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(quaList, QUACHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(ramList, RAMCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(c12List, C12CHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(bbcList, BBCCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(accList, INOCHK_STR,VALUE_LIST_STR) )
if not actuallyRunProcheck:
self.assertFalse ( procheckResDict.setDeepByKeys(sstList, SECSTRUCT_STR) )
for d in [whatifResDict, procheckResDict]:
checkIDList = d.keys()
for checkID in checkIDList:
if d==whatifResDict:
valueList = d.getDeepByKeys(checkID,VALUE_LIST_STR)
else:
valueList = d.getDeepByKeys(checkID)
if checkID == ANGCHK_STR:
zScore = valueList.average()[0]
pointsANGCHK.append( (resNumb-.5, zScore) )
elif checkID == BNDCHK_STR:
zScore = valueList.average()[0]
pointsBNDCHK.append( (resNumb-.5, zScore) )
elif checkID == QUACHK_STR:
zScore = valueList.average()[0]
pointsQUACHK.append( (resNumb-.5, zScore) )
elif checkID == RAMCHK_STR:
zScore = valueList.average()[0]
pointsRAMCHK.append( (resNumb-.5, zScore) )
elif checkID == C12CHK_STR:
zScore = valueList.average()[0]
pointsC12CHK.append( (resNumb-.5, zScore) )
elif checkID == BBCCHK_STR:
zScore = valueList.average()[0]
pointsBBCCHK.append( (resNumb-.5, zScore) )
# nTdebug("pointsBBCCHK: %s", pointsBBCCHK)
if showValues:
nTdebug("%10s valueList: %-80s" % ( checkID, valueList))
fileNameList =[]
ps = None
r = 0
for resList in rangeList:
r += 1
# nTdebug("resList: %s" % resList)
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (600,600)
nrows = 2
ntPlotList = []
for i in range(nrows):
ntPlotList.append( ps.createSubplot(nrows,1,i+1,useResPlot=True,molecule=project.molecule,resList=resList) )
ps.subplotsAdjust(hspace = .1) # no height spacing between plots.
ps.subplotsAdjust(top = 0.9) # Accommodate icons and res types.
ps.subplotsAdjust(left = 0.15) # Accommodate extra Y axis label.
attr = fontVerticalAttributes()
attr.fontColor = 'blue'
# Left of actual yLabel.
labelAxesExtraList = [
'Backbone',
'Quality',
'Angle',
'',
'' ]
labelAxesList = [
'Ramachandr. Z',
'Chi 1/2. Z',
'Bond max Z',
'Restraint RMSD',
'' ]
for i in range(nrows):
position = (-0.12, 0.5)
ntPlotList[i].labelAxes( position, labelAxesExtraList[i], attributes=attr)
ntPlotList[i].yLabel = labelAxesList[i]
if i != nrows-1:
ntPlotList[i].xLabel = None
plusPoint = pointAttributes( type='plus', size=1.5, color='black' )
circlePoint = pointAttributes( type='circle', size=1.5, color='blue')
plusPoint.lineColor = 'black'
circlePoint.lineColor = 'blue'
length = ntPlotList[0].MAX_WIDTH_IN_RESIDUES
start = (r-1)*length
# pointsBBCCHK = removeNulls(pointsBBCCHK)
# buildin max is overridden by matplotlib
# end = NTmin(start + ntPlot1.MAX_WIDTH_IN_RESIDUES,len(pointsANGCHK))
pointsANGCHKOffset = convertPointsToPlotRange(pointsANGCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsBNDCHKOffset = convertPointsToPlotRange(pointsBNDCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsQUACHKOffset = convertPointsToPlotRange(pointsQUACHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsRAMCHKOffset = convertPointsToPlotRange(pointsRAMCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsC12CHKOffset = convertPointsToPlotRange(pointsC12CHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsBBCCHKOffset = convertPointsToPlotRange(pointsBBCCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsOffsetList = [pointsRAMCHKOffset,
pointsQUACHKOffset,
pointsANGCHKOffset ]
pointsOffsetList2 = [pointsBBCCHKOffset,
pointsC12CHKOffset,
pointsBNDCHKOffset ]
# nTdebug("pointsRAMCHKOffset: %s" % pointsRAMCHKOffset)
# nTdebug("start:end: %s %s" % (start,end))
for i in range(nrows):
if i >= len( pointsOffsetList ):
continue
ntPlotList[i].lines(pointsOffsetList[i], plusPoint)
ntPlotList[i].lines(pointsOffsetList2[i], circlePoint)
ntPlotList[i].autoScaleY( pointsOffsetList[i]+pointsOffsetList2[i] )
if i == 2: # by chance
ntPlotList[i].setYrange((.0, ntPlotList[i].yRange[1]))
ySpaceAxisResTypes = .02 + (nrows-1) * .01
ntPlotList[0].drawResTypes(ySpaceAxis=ySpaceAxisResTypes) # Weirdly can only be called after yRange is set.
for i in range(nrows):
showLabels = False
if i == nrows-1:
showLabels = True
# also sets the grid lines for major. Do last as it won't rescale with plot yet.
ntPlotList[i].drawResNumbers( showLabels=showLabels)
# Draw secondary structure elements and accessibility
# Set x range and major ticker.
# The major ticker determines the grid layout.
# leave space for res types but get it right on top.
# .18 at nrows = 4
# Needs to be done before re-scaling the y axis from [0,1] ???????
ySpaceAxisResIcons = .06 + (nrows-1) * .04
ntPlotList[0].iconBoxYheight = 0.16 * nrows / 3. # .16 at nrows=3
ntPlotList[0].drawResIcons( ySpaceAxis=ySpaceAxisResIcons )
# Set the grid and major tickers
fileNameList.append( 'residuePlotSet%03d.pdf' % r)
ps.hardcopy(fileNameList[r-1])
# end for resList in rangeList:
self.assertFalse( joinPdfPages( fileNameList, 'residuePlotSetAll.pdf' ))
for fileName in fileNameList:
os.unlink( fileName )
