def testNTtreeIndex(self):
mol = Molecule('mol')
mol.addChain('top')
top = mol.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
resList = top.allResidues()
middleValue = resList[len(resList)/2]
for _i in range( 1*10):
# _x = middleValue.sibling(0) # getting myself back should not take time.
_x = middleValue.sibling(1) # this tends to be very expensive
newMol = atom.getParent(level = 3)
self.assertEqual(mol,newMol)
newMol = atom.getMolecule()
self.assertEqual(mol,newMol)
res.removeAtom(atom.name)
newMol = atom.getMolecule()
self.assertEqual(newMol, mol)
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_HTMLfile(self):
"""
Create two html files (project and molecule) that have relative links to each other.
Exercising the machinery in HTMLfile class.
"""
entryId = "test_HTMLfile"
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule)
# initialize project html page
# per item always set 2 top level attributes:
project.htmlLocation = (project.path('index.html'), None)
project.html = HTMLfile(project.htmlLocation[0], project, title = 'Project')
nTdebug("project.htmlLocation[0]: %s" % project.htmlLocation[0])
#create new folders for Molecule/HTML
htmlPath = project.htmlPath()
if os.path.exists(htmlPath):
removedir(htmlPath)
os.makedirs(htmlPath)
nTdebug("htmlPath: %s" % htmlPath)
# initialize molecule html page
for subdir in htmlDirectories.values():
project.mkdir(project.molecule.name, moleculeDirectories.html, subdir)
# NB project.htmlPath is different from project.path
molecule.htmlLocation = (project.htmlPath('indexMolecule.html'), None)
nTdebug("molecule.htmlLocation[0]: %s" % molecule.htmlLocation[0])
molecule.html = HTMLfile(molecule.htmlLocation[0], project,
title = 'Molecule ' + molecule.name)
# nb: destination is a destination obj (eg molecule object) that is to
# have a html attribute that points to an HTMLfile instance.
# In the validate.py code, the source argument is the 'main' section in
# project.html. JFD doesn't understand why.
project.html.insertHtmlLinkInTag('li', section=project.html.main,
source=project, destination=molecule, text='mol ref', id=None)
# rerun for testing.
_link = project.html.findHtmlLocation(project, molecule, id=None)
# self.assertEquals('moleculeName/HTML/indexMolecule.html#_top', link)
project.html.main('ul', openTag=False)
for htmlObj in [ project.html, molecule.html ]:
self.assertFalse(htmlObj.render())
def setupSimplestProject(self):
entryId = 'setupSimplestProject'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
c = molecule.addChain('A')
r1 = c.addResidue('ALA', 1, Nterminal = True)
if r1:
r1.addAllAtoms()
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
return project
def run():
relationName = 'nrgcing_ranges'
fn = os.path.join( '/Users/jd/CMBI/Papers/CING/Data', relationName + '.csv')
nentries = 0
nchains = 0
nsegments = 0
nresidues = 0
nresiduesMin = 999
nresiduesMinEntry = None
r = getRelationFromCsvFile(fn)
columnIdxId = 0
columnIdxRange = 1
for rowIdx in range(r.sizeRows()):
if rowIdx >= 200000:
print "Stopping early."
break
# end if
nentries += 1
pdb_id = r.getValue( rowIdx, columnIdxId)
rangeStr = r.getValue( rowIdx, columnIdxRange)
chain_id = None
# nTdebug( 'pdb_id: %s' % pdb_id)
# nTdebug( 'rangeStr: %s' % rangeStr)
startStopLoL = Molecule.ranges2StartStopLoLStatic(rangeStr)
# nTdebug( 'startStopLoL: %s' % str(startStopLoL) )
nsegments += len(startStopLoL)
for startStopList in startStopLoL:
residueCount = startStopList[2] - startStopList[1] + 1
nresidues += residueCount
if residueCount < nresiduesMin:
nresiduesMin = residueCount
nresiduesMinEntry = pdb_id
# end for
if residueCount < 5:
nTdebug( 'residueCount for %s with range %s and segment %s is %s' % ( pdb_id, rangeStr, str(startStopList), residueCount))
# end for
segmentChainId = startStopList[0]
if segmentChainId != chain_id:
chain_id = segmentChainId
nchains += 1
# end if
# end for
# end for
print "nentries: %s" % nentries
print "nchains: %s" % nchains
print "nsegments: %s" % nsegments
print "nresidues: %s" % nresidues
print "chainsPerEntry: %s" % (nsegments / float(nchains))
print "segmentsPerEntry: %s" % (nsegments / float(nentries))
print "segmentsPerChain: %s" % (nsegments / float(nchains))
print "residuesPerEntry: %s" % (nresidues / float(nentries))
print "residuesPerChain: %s" % (nresidues / float(nchains))
print "residuesPerSegments: %s" % (nresidues / float(nsegments))
print "residuesMin: %s" % nresiduesMin
print "residuesMinEntry: %s" % nresiduesMinEntry
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 upgrade100(project, restore):
"""
Do all things to upgrade project to current configuration
All versions <= 1.00
"""
nTmessage('*** upgrade100: upgrading %s from version %s ***', project, project.version)
verbosity = cing.verbosity
# make sure we get all if we heave debug on
if cing.verbosity < cing.verbosityDebug:
cing.verbosity = cing.verbosityWarning
# Molecules
for molName in project.moleculeNames:
pathName = project.molecules.path(molName)
mol = Molecule.open(pathName)
if mol:
mol.status = 'keep'
project.appendMolecule(mol)
#end if
nTdebug('upgrade100: restored %s', mol)
#end for
# restore the lists
for pl in [project.peaks, project.distances, project.dihedrals, project.rdcs, project.coplanars]:
pl.restore()
#end for
# Now patch talos+
nTmessage('==> upgrade100: talosPlus')
if restoreTalosPlus100(project):
io.error('upgrade100: restoring talosPlus data failed\n')
# Now patch queeny
# nTmessage('==> upgrade100: queeny')
# if restoreQueeny100(project):
# nTerror('upgrade100: restoring queeny data failed')
# project.saveQueeny()
#
# # Now patch shiftx
# if restoreShiftx100(project):
# nTerror('upgrade100: restoring shiftx data failed')
# return None
# project.saveShiftx()
# Plugin registered functions
nTdebug('upgrade100: calling plugins')
project._callPluginRestores()
# save to consolidate
project.save()
cing.verbosity = verbosity
return Project.open(project.name, constants.PROJECT_OLD, restore=restore)
def initBMRB( project, bmrbFile, moleculeName = None ):
"""
Initialize from edited BMRB file
Return molecule instance
"""
mol = Molecule( name=moleculeName )
project.appendMolecule( mol )
error = False
record = None
for record in AwkLike( bmrbFile, minNF = 8, commentString = '#' ):
resName = record.dollar[3]
resNum = record.int(2)
atomName = record.dollar[4]
# shift = record.float(6)
# serror = record.float(7)
# ambig = record.int(8)
res = mol.addResidue( Chain.defaultChainId, resName, resNum, IUPAC )
if (not res):
nTerror( 'Error initBMRB: invalid residue %s %s line %d (%s)\n',
resName, atomName, record.NR, record.dollar[0]
)
error = True
#end if
#end for
error = error or (project.importBMRB( bmrbFile) == None)
if error:
nTmessage( '==> initBMRB: completed with error(s)' )
else:
nTmessage( '==> initBMRB: successfully parsed %d lines from %s', record.NR, record.FILENAME )
#end if
nTmessage("%s", mol.format() )
if error:
return None
return mol
def initBMRB(project, bmrbFile, moleculeName=None):
"""
Initialize from edited BMRB file
Return molecule instance
"""
mol = Molecule(name=moleculeName)
project.appendMolecule(mol)
error = False
record = None
for record in AwkLike(bmrbFile, minNF=8, commentString='#'):
resName = record.dollar[3]
resNum = record.int(2)
atomName = record.dollar[4]
# shift = record.float(6)
# serror = record.float(7)
# ambig = record.int(8)
res = mol.addResidue(Chain.defaultChainId, resName, resNum, IUPAC)
if (not res):
nTerror('Error initBMRB: invalid residue %s %s line %d (%s)\n',
resName, atomName, record.NR, record.dollar[0])
error = True
#end if
#end for
error = error or (project.importBMRB(bmrbFile) == None)
if error:
nTmessage('==> initBMRB: completed with error(s)')
else:
nTmessage('==> initBMRB: successfully parsed %d lines from %s',
record.NR, record.FILENAME)
#end if
nTmessage("%s", mol.format())
if error:
return None
return mol
def initMolecule(self, moleculeName):
"""Initialize new Molecule instance from the tree.
Return Molecule on None on error.
"""
mol = Molecule(name = moleculeName)
# The self.tree contains a tree-like representation of the pdb-records
for ch in self.tree:
chain = mol.addChain(name = ch.name)
for res in ch:
# print '>', ch, res, res.skip, res.db
if not res.skip and res.db != None:
residue = chain.addResidue(res.db.name, res.resNum)
if residue == None:
nTerror("Not adding residue: %s" % res)
continue
residue.addAllAtoms()
#end if
#end for
#end for
# nTdebug('pdbParser.initMolecule: %s', mol)
self.map2molecule(mol)
return mol
def createSimpleFastProject(self):
'create simple fast project'
entryId = 'test'
self.project = Project( entryId )
self.project.removeFromDisk()
self.project = Project.open( entryId, status='new' )
mol = Molecule('test')
self.project.appendMolecule(mol)
c = mol.addChain('A')
self.r1 = c.addResidue('VAL', 1, Nterminal = True)
self.r2 = c.addResidue('VAL', 2)
self.r3 = c.addResidue('GLU', 3)
self.r4 = c.addResidue('TYR', 4)
self.r5 = c.addResidue('PHE', 5)
self.r6 = c.addResidue('GLY', 6)
self.r7 = c.addResidue('ARG', 7)
self.r8 = c.addResidue('LEU', 8, Cterminal = True)
for r in mol.allResidues():
r.addAllAtoms()
mol.updateAll()
def initMolecule(self, moleculeName):
"""Initialize new Molecule instance from the tree.
Return Molecule on None on error.
"""
mol = Molecule(name=moleculeName)
# The self.tree contains a tree-like representation of the pdb-records
for ch in self.tree:
chain = mol.addChain(name=ch.name)
for res in ch:
# print '>', ch, res, res.skip, res.db
if not res.skip and res.db != None:
residue = chain.addResidue(res.db.name, res.resNum)
if residue == None:
nTerror("Not adding residue: %s" % res)
continue
residue.addAllAtoms()
#end if
#end for
#end for
# nTdebug('pdbParser.initMolecule: %s', mol)
self.map2molecule(mol)
return mol
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 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 createSimpleFastProject(self):
'create simple fast project'
entryId = 'test'
self.project = Project(entryId)
self.project.removeFromDisk()
self.project = Project.open(entryId, status='new')
mol = Molecule('test')
self.project.appendMolecule(mol)
c = mol.addChain('A')
self.r1 = c.addResidue('VAL', 1, Nterminal=True)
self.r2 = c.addResidue('VAL', 2)
self.r3 = c.addResidue('GLU', 3)
self.r4 = c.addResidue('TYR', 4)
self.r5 = c.addResidue('PHE', 5)
self.r6 = c.addResidue('GLY', 6)
self.r7 = c.addResidue('ARG', 7)
self.r8 = c.addResidue('LEU', 8, Cterminal=True)
for r in mol.allResidues():
r.addAllAtoms()
mol.updateAll()
def run():
relationName = 'nrgcing_ranges'
fn = os.path.join('/Users/jd/CMBI/Papers/CING/Data', relationName + '.csv')
nentries = 0
nchains = 0
nsegments = 0
nresidues = 0
nresiduesMin = 999
nresiduesMinEntry = None
r = getRelationFromCsvFile(fn)
columnIdxId = 0
columnIdxRange = 1
for rowIdx in range(r.sizeRows()):
if rowIdx >= 200000:
print "Stopping early."
break
# end if
nentries += 1
pdb_id = r.getValue(rowIdx, columnIdxId)
rangeStr = r.getValue(rowIdx, columnIdxRange)
chain_id = None
# nTdebug( 'pdb_id: %s' % pdb_id)
# nTdebug( 'rangeStr: %s' % rangeStr)
startStopLoL = Molecule.ranges2StartStopLoLStatic(rangeStr)
# nTdebug( 'startStopLoL: %s' % str(startStopLoL) )
nsegments += len(startStopLoL)
for startStopList in startStopLoL:
residueCount = startStopList[2] - startStopList[1] + 1
nresidues += residueCount
if residueCount < nresiduesMin:
nresiduesMin = residueCount
nresiduesMinEntry = pdb_id
# end for
if residueCount < 5:
nTdebug(
'residueCount for %s with range %s and segment %s is %s' %
(pdb_id, rangeStr, str(startStopList), residueCount))
# end for
segmentChainId = startStopList[0]
if segmentChainId != chain_id:
chain_id = segmentChainId
nchains += 1
# end if
# end for
# end for
print "nentries: %s" % nentries
print "nchains: %s" % nchains
print "nsegments: %s" % nsegments
print "nresidues: %s" % nresidues
print "chainsPerEntry: %s" % (nsegments / float(nchains))
print "segmentsPerEntry: %s" % (nsegments / float(nentries))
print "segmentsPerChain: %s" % (nsegments / float(nchains))
print "residuesPerEntry: %s" % (nresidues / float(nentries))
print "residuesPerChain: %s" % (nresidues / float(nchains))
print "residuesPerSegments: %s" % (nresidues / float(nsegments))
print "residuesMin: %s" % nresiduesMin
print "residuesMinEntry: %s" % nresiduesMinEntry