def readSummary(self, fix=False):
path = self.path(self.entryName, 'Cing', 'CingSummaryDict.xml')
if not path.exists():
print 'Error Entry.readSummary: file %s does not exist' % path
return None
nTmessage( '==> reading summary from %s', path )
self.cingSummary = xML2obj(path)
if fix:
rog = NTlist( 0, 0, 0 ) # Counts for red, orange, green.
for resname, rogScore in self.cingSummary.CING_residueROG:
print resname, rogScore
if rogScore.isRed():
rog[0] += 1
elif rogScore.isOrange():
rog[1] += 1
else:
rog[2] += 1
#end for
total = reduce(lambda x, y: x+y+0.0, rog) # total expressed as a float because of 0.0
print rog, total
for i, _x in enumerate(rog):
rog[i] = rog[i]*100.0/total
self.cingSummary.cing_red = round(rog[0],1)
self.cingSummary.cing_orange = round(rog[1],1)
self.cingSummary.cing_green = round(rog[2],1)
#end if
#copy the data
for par in cingPars:
if par in self.cingSummary:
self[par] = self.cingSummary[par]
return self.cingSummary
def restoreStereoAssignments( molecule, stereoFileName ):
"""
Restore the stereo assignments from xml stereoFileName,
return count or -1 on error
"""
if not os.path.exists( stereoFileName ):
return -1
stereo = xmlTools.xML2obj(stereoFileName)
if stereo is None:
io.error('restoreStereoAssignment: parsing xml-file "{0}"\n', stereoFileName)
return -1
#end if
count = 0
for nameTuple in stereo:
atm = molecule.decodeNameTuple( nameTuple )
if atm is None:
io.error('restoreStereoAssignment: invalid atom nameTuple ({0})', nameTuple)
else:
atm.stereoAssigned = True
count += 1
#end if
#end for
#nTdebug('Molecule.restoreStereoAssignments: restored %d stereo assignments from "%s\n',count, stereoFileName)
return count
def restoreSequence( molecule, sequenceFile ):
"""Restore sequence from sequenceFile.
Return self or None on error.
"""
if (not os.path.exists( sequenceFile ) ):
io.error('Molecule.restoreSequence: sequenceFile "{0}" not found\n',
sequenceFile
)
return None
#end if
# compatibility
if molecule.content.version < 0.92:
fileObject = open(sequenceFile, 'r')
for line in fileObject:
exec(line)
#end for
fileObject.close()
else:
sequence = xmlTools.xML2obj( sequenceFile )
if sequence is None:
io.error('restoreSequence: error parsing xml-file "{0}"', sequenceFile)
return None
for chainId, resName, resNum, convention in sequence:
molecule.addResidue( chainId, resName, resNum, convention )
#end for
#end if
return molecule
def restoreShiftx100(project):
"""
Restore shiftx results by parsing files.
Return True on error
"""
if project is None:
nTdebug("restoreShiftx100: No project defined")
return True
if project.molecule == None:
return True # Gracefully returns
defs = project.getStatusDict(constants.SHIFTX_KEY)
# Older versions; initialize the required keys of shiftx Status from xml file
if project.version < 0.881:
path = project.validationPath(cdefs.validationsDirectories.shiftx)
if not path:
nTerror('restoreShiftx100: directory "%s" with shiftx data not found', path)
return True
xmlFile = project.path() / 'content.xml'
if not xmlFile.exists():
nTerror('restoreShiftx100: Shiftx results xmlFile "%s" not found', xmlFile)
return True
#end if
shiftxResult = xmlTools.xML2obj(xmlFile)
if not shiftxResult:
nTerror('restoreShiftx100: restoring Shiftx results from xmlFile "%s" failed', xmlFile)
return None
defs.update(shiftxResult)
defs.completed = True
#end if
#update some of the settings
if 'moleculeName' in defs:
del defs['moleculeName']
if 'path' in defs:
defs.directory = disk.Path(defs.path)[-1:]
del defs['path']
else:
defs.directory = constants.SHIFTX_KEY
if 'contenFile' in defs:
del defs['contentFile']
if not defs.completed:
nTdebug('restoreShiftx100: shiftx not completed')
return True
return project.parseShiftx()
def restore(path=None):
if path == None:
path = analysisPath / 'results.xml'
tmp = xML2obj(path)
if not tmp:
return 1
results = ResultsList(dataPath=path[:-1])
for entry in tmp:
# replace keyword
if entry.has_key('programType'):
entry['method'] = entry['programType']
del entry['programType']
if entry['method'] == 'None' and entry['group'] == 'Org':
entry['method'] = 'Original'
results.append(entry)
return results
def openMol_075( path ) :
"""Static method to restore molecule from directory path
implements the <=0.75 storage model
returns Molecule instance or None on error
"""
# old format
content = xmlTools.xML2obj( path=os.path.join( path, NTmolParameters.contentFile ) )
if not content:
io.error('openMol_075: error reading xml file "{0}"\n',
os.path.join( path, NTmolParameters.contentFile )
)
return None
#end if
content.keysformat()
io.debug('openMol_075: content from xml-file: %s', content.format())
mol = molecule.Molecule( name = content.name )
if not mol:
io.error('openMol_075: initializing molecule\n')
return None
#end if
mol.content = content
if content.has_key('sequenceFile') and \
restoreSequence(mol, os.path.join(path, content.sequenceFile)) is None:
return None
if content.has_key('resonanceFile') and \
restoreResonances(mol, os.path.join(path, content.resonanceFile), append=False) < 0:
return None
if content.has_key('stereoFile') and \
restoreStereoAssignments(mol, os.path.join(path, content.stereoFile)) < 0:
return None
if content.has_key('coordinateFile') and \
restoreCoordinates(mol, os.path.join(path, content.coordinateFile), append=False) is None:
return None
mol._check()
mol.updateAll()
return mol
def upgradeProject2Json( name, restore ):
"""Upgrade the project from project.xml to project.json file
Convert several parameters to new Adict types
"""
io.debug('upgradeToJson: restoring {0}\n', name)
root, newName, ext = Project.rootPath(name)
if not root:
io.error('upgradeToJson: unable to open Project "{0}" because root is [{1}]\n', name, root)
return None
if not root.exists():
io.error('upgradeToJson: unable to open Project "{0}" because root [{1}] was not found\n', name, root)
return None
#end if
pfile = root / 'project.xml' # Name in all versions <= 1.0
# Check if we find the xml file
if pfile.exists():
io.message('==> Upgrading cing project; please stand by\n')
#GWV: 20140203: cannot do an update method() -> errors in partioning restraints. Do not understand
pr = xmlTools.xML2obj(pfile)
if pr is None:
io.error('upgradeToJson: parsing from project file "{0}" failed\n', pfile)
return None
try:
# <= 0.75 version have string
pr.version = float(pr.version.strip('abcdefghijklmnopqrtsuvw ()!@#$%^&*').split()[0])
except:
pass
# change to Time object
pr.created = io.Time.fromString(pr.created)
pr.lastSaved = io.Time(disk.modtime(pfile))
# change types of names list
for listName in 'moleculeNames peakListNames distanceListNames dihedralListNames rdcListNames'.split():
#print 'listName>>',listName, (listName in pr)
if listName in pr:
pr[listName] = [n for n in pr[listName]]
# update from old status type
status = Adict()
for key in constants.VALIDATION_KEYS:
sdict = StatusDict(key)
status[key] = sdict
# if not isinstance(sdict, StatusDict):
# sdict = StatusDict(key)
if key in pr.status:
# print 'upgrade2json> key=', key
# not certain if we get dict or NTdict; this circumvent unwanted keys of NTdict
for k,v in pr.status[key].items():
#print 'upgrade2json>> k,v', k,v
sdict[k] = v
#print '>>>\n', sdict.formatItems()
#end if
#end for
#end for
# update the status from old definitions;
for (key, statusName) in [
(constants.SHIFTX_KEY, 'shiftxStatus'),
(constants.PROCHECK_KEY,'procheckStatus'),
(constants.DSSP_KEY, 'dsspStatus'),
(constants.WHATIF_KEY, 'whatifStatus'),
(constants.WATTOS_KEY, 'wattosStatus'),
(constants.VASCO_KEY, 'vascoStatus'),
(constants.X3DNA_KEY, 'x3dnaStatus')
]:
sdict = status[key]
if statusName in pr:
#print 'upgrade2json> statusName=', statusName
# not certain if we get dict or NTdict; this circumvent unwanted keys of NTdict
for k,v in pr[statusName].items():
#print 'upgrade2json>> k,v=', k,v
sdict[k] = v
#print '>>>\n', sdict.formatItems()
#end if
#LEGACY names
pr[statusName] = sdict
#end for
# update some fields if present
for sdict in status.values():
if 'molecule' in sdict and isinstance(sdict['molecule'], tuple):
sdict['molecule'] = pid.Pid.new('Molecule:' + sdict['molecule'][0])
if 'moleculeName' in sdict and isinstance(sdict['molecule'], tuple):
sdict['molecule'] = pid.Pid.new('Molecule:' + sdict['moleculeName'][0])
del sdict['moleculeName']
if 'runVersion' in sdict:
sdict['version'] = sdict['runVersion']
del sdict['runVersion']
if 'smlFile' in sdict:
del sdict['smlFile']
# sdict['date'] = io.Time(1360158182.7) # Wed Feb 6 13:43:02 2013
sdict['date'] = io.Time(pr.lastSaved) # make a copy because otherwise the json handler breaks
sdict['version'] = 0.95 # old version
#end for
# make this the new status dict
pr.status = status
#print '>>>>>\n', pr.status.queeny.formatItems()
pr._save2json()
# have to make the directory because we have not yet fully initialised all directories at this stage
pr._updateProjectPaths()
disk.rename(pfile, pr.path() / cdefs.directories.version1 / 'project.xml' )
#now we should be able to open it again
return Project.open( name, status = constants.PROJECT_OLD, restore = restore )
else:
io.error('upgradeToJson: missing Project file "{0}"\n', pfile)
return None
