def importNmrStar31(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('STAR', ['*.str']),
FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import NMR-STAR 3.1 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
nmrStarObj = NmrStarFormat(self.project, self, verbose=True)
nmrStarObj.readProject(fileName, minimalPrompts=True, version='3.1')
self.eciFrame.updateAll()
return nmrStarObj
def importFullStarProjects(starFileName, projectName, inputDir='.', outputDir='.', guiRoot=None, allowPopups=0,minimalPrompts=1,verbose=1):
'''Returns a full CCPN project rooted in inputDir/projectName that will be created and saved.
Input will be from inputDir/starFileName
Returns False for error.
'''
if not os.path.exists(inputDir):
nTerror("Failed to find inputDir: %s" % inputDir)
return False
starFileNameFull = os.path.join(inputDir, starFileName)
if not os.path.exists(starFileNameFull):
nTerror("Failed to find starFileNameFull: %s" % starFileNameFull)
return False
if not os.path.exists(outputDir):
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
ccpnProject = Implementation.MemopsRoot(name=projectName)
# 'linkAtoms': (True,False,'If set to False (off), unrecognized coordinate atoms will not be linked.'),
keywds = {'minimalPrompts': minimalPrompts, 'allowPopups': allowPopups, 'linkAtoms':0}
formatNmrStarFormat = NmrStarFormat(ccpnProject, guiRoot, verbose=verbose, **keywds)
formatNmrStarFormat.version = '3.1'
entryTitle = 'Project from NMR-STAR for %s' % projectName
entryDetails = "Created by Wim Vranken's FormatConverter embedded in CING"
formatNmrStarFormat.getFullProject( starFileNameFull, title = entryTitle, details = entryDetails, **keywds)
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
# formatNmrStarFormat.linkResonances(
# forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
# globalStereoAssign=1,
# setSingleProchiral=1,
# setSinglePossEquiv=1,
## strucGen=structureGeneration,
# allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
# Catch entries like mentioned in issue
try:
ccpnProject.checkAllValid()
except ApiError:
nTtracebackError()
nTerror("Failed ccpnProject.checkAllValid")
nTerror("See issue: %s%d" % (issueListUrl, 266))
return False
ccpnProject.saveModified()
if not os.path.exists(ccpnProjectPath):
nTerror("Failed to find new CCPN project directory: %s" % ccpnProjectPath)
return False
tgzFileName = projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
return ccpnProject
def importStarChemicalShifts(ccpnProject, inputDir, guiRoot, allowPopups=1, minimalPrompts=0, verbose=1, **presets):
print "JFD: now in importStarChemicalShifts"
# formatCns = CnsFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts, allowPopups=allowPopups, **presets)
formatNmrStarFormat = NmrStarFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts,
allowPopups=allowPopups, **presets)
ccpnShiftListOfList = []
# Actually just one but this is less time to code;-)
globPattern = inputDir + '/*_21.str'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
shiftList = formatNmrStarFormat.readShifts(fn, minimalPrompts=minimalPrompts, verbose=verbose)
if not shiftList:
nTerror("Failed to read")
return True
shiftList.setName(fnBaseName)
ccpnShiftListOfList.append(shiftList)
# Find and print this shiftList in the CCPN data model. Just to check lookup.
shiftList = ccpnProject.currentNmrProject.findFirstMeasurementList(className = 'ShiftList')
print 'ShiftList: [%s]' % shiftList
keywds = getDeepByKeysOrDefault(presets, {}, READ_SHIFTS, KEYWORDS)
if keywds:
nTmessage("In importStarChemicalShifts using keywds...")
nTdebug(str(keywds))
shiftList = getDeepByKeys(ccpnShiftListOfList, 0) # no need to repeat
nTdebug("First shiftList: %s" % shiftList)
if shiftList == None:
nTerror("Failed to get shiftList again.")
return True
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
formatNmrStarFormat.linkResonances(
forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
# strucGen=structureGeneration,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
def writeBmrbChemShiftDeposition(guiParent, chain, chemShiftList, outFile):
proj = chain.root
format = NmrStarFormat(proj, guiParent, verbose=1)
fout = open(outFile, 'w')
resSeq = newline
for residue in chain.sortedResidues():
resSeq += residue.molResidue.chemComp.getCode1Letter()
chopOff = len(resSeq) / 41.0
if chopOff == int(chopOff):
resSeq += newline
fout.write("_Mol_residue_sequence" + newline)
fout.write(";")
fout.write(resSeq + newline)
fout.write(";" + (newline * 2))
fout.write("""
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label""")
fout.write(newline * 2)
count = 0
for residue in chain.sortedResidues():
count += 1
fout.write("%-3d %-3d %3s" %
(residue.seqId, residue.seqCode, residue.ccpCode))
if count / 5.0 == int(count / 5.0):
fout.write(newline)
else:
fout.write(" ")
fout.write("stop_")
fout.write(newline)
fout.write("""
###################################################################
# Chemical Shift Ambiguity Code Definitions #
# #
# Codes Definition #
# #
# 1 Unique #
# 2 Ambiguity of geminal atoms or geminal methyl #
# proton groups #
# 3 Aromatic atoms on opposite sides of the ring #
# (e.g. Tyr HE1 and HE2 protons) #
# 4 Intraresidue ambiguities (e.g. Lys HG and #
# HD protons) #
# 5 Interresidue ambiguities (Lys 12 vs. Lys 27) #
# 9 Ambiguous, specific ambiguity not defined #
# #
###################################################################
# INSTRUCTIONS
# 1) Replace the @-signs with appropriate values.
# 2) Text comments concerning the assignments can be
# supplied in the full deposition.
# 3) Feel free to add or delete rows to the table as needed.
# The row numbers (_Atom_shift_assign_ID values) will be
# re-assigned to sequential values by BMRB
# The atom table chosen for this sequence is:
loop_
_Atom_shift_assign_ID
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
#
#Atom Residue
#shift Seq Residue Atom Atom Shift/ Error/ Ambiguity
#assign code Label Name Type ppm ppm Code
#---------------------------------------------------------------
#""")
fout.write(newline * 2)
# Using code originally written for XEasy output
format.getFormatNamingSystemName = getFormatNamingSystemName
format.writeShifts(outFile,
measurementList=chemShiftList,
chains=[chain],
noWrite=True,
compressResonances=False)
counter = 1
for chemShift in format.measurementFile.chemShifts:
if chemShift.atomName[-1] == '*':
atomName = chemShift.atomName[:-1]
else:
atomName = chemShift.atomName
fout.write("%-6d %-5d %-4s %-5s %-5s %-7.3f %-7.3f %d" %
(counter, chemShift.seqCode, chemShift.resLabel, atomName,
chemShift.atomType, chemShift.value, chemShift.valueError,
chemShift.ambCode))
counter += 1
fout.write(newline)
fout.write(newline)
fout.write("stop_")
fout.write(newline * 2)
fout.close()
return True
def makeChemShiftSelections(guiParent, chains, chemShiftList, verbose=0):
#
# TODO: only NON-EXCHANGABLE hydrogens for sidechain!!! Mark them in ref data?
#
#
# Get the info from the chemical shift list and the relevant chains
#
if not chains or not chemShiftList:
print " ERROR need chains or chemShiftList!"
return False
#
# Set up for all chains...
#
results = {}
for chain in chains:
if chain.molecule.molType not in chemShiftClasses.keys():
continue
chemShiftClassMolType = chemShiftClasses[chain.molecule.molType]
for residue in chain.sortedResidues():
atomSetsDone = []
for atom in residue.sortedAtoms():
atomType = atom.chemAtom.elementSymbol
if atomType not in chemShiftClassMolType.keys():
continue
atomChemShiftClasses = chemShiftClassMolType[atomType]
atomName = atom.name
atomRecognized = 0
for chemShiftClass in atomChemShiftClasses.keys():
(findAtomNames,
ignoreAtomNames) = atomChemShiftClasses[chemShiftClass]
atomFound = 0
if atomName in findAtomNames:
atomFound = 1
elif not findAtomNames:
if atomName not in ignoreAtomNames:
chemAtom = atom.chemAtom
chemAtomSet = chemAtom.chemAtomSet
if chemAtomSet and (chemAtomSet.isEquivalent
or chemAtomSet.isEquivalent
== None):
if chemAtomSet.name not in atomSetsDone:
atomSetsDone.append(chemAtomSet.name)
atomFound = 1
atomRecognized = 1
else:
atomFound = 1
if atomFound:
atomRecognized = 1
if not results.has_key(chemShiftClass):
results[chemShiftClass] = [0, 0]
results[chemShiftClass][0] += 1
if not atomRecognized:
print " Chain atom name %s not found" % atomName
#
# Do per chain... but keep track of all.
#
format = NmrStarFormat(chains[0].root, guiParent, verbose=0)
format.getFormatNamingSystemName = getFormatNamingSystemName
for chain in chains:
if chain.molecule.molType not in chemShiftClasses.keys():
continue
chemShiftClassMolType = chemShiftClasses[chain.molecule.molType]
format.writeShifts('voidFileNotWritten',
measurementList=chemShiftList,
chains=[chain],
noWrite=True,
verbose=False,
individualAtoms=False)
for chemShift in format.measurementFile.chemShifts:
atomType = chemShift.atomType
if atomType not in chemShiftClassMolType.keys():
continue
atomChemShiftClasses = chemShiftClassMolType[atomType]
atomRecognized = 0
for chemShiftClass in atomChemShiftClasses.keys():
(findAtomNames,
ignoreAtomNames) = atomChemShiftClasses[chemShiftClass]
atomFound = 0
if chemShift.atomName in findAtomNames:
atomFound = 1
elif not findAtomNames:
if chemShift.atomName not in ignoreAtomNames:
atomFound = 1
if atomFound:
atomRecognized = 1
results[chemShiftClass][1] += 1
if not atomRecognized:
print " Chemical shift atom name %s not found" % atomName
del format.measurementFile
#
# Print results
#
if verbose:
chemShiftResultClasses = results.keys()
chemShiftResultClasses.sort()
for chemShiftClass in chemShiftResultClasses:
percentage = results[chemShiftClass][1] * 100.0 / results[
chemShiftClass][0]
print " %-20s: %6.2f found (%d/%d total)" % (
chemShiftClass, percentage, results[chemShiftClass][1],
results[chemShiftClass][0])
return results
def importFullStarProjects(starFileName,
projectName,
inputDir='.',
outputDir='.',
guiRoot=None,
allowPopups=0,
minimalPrompts=1,
verbose=1):
'''Returns a full CCPN project rooted in inputDir/projectName that will be created and saved.
Input will be from inputDir/starFileName
Returns False for error.
'''
if not os.path.exists(inputDir):
nTerror("Failed to find inputDir: %s" % inputDir)
return False
starFileNameFull = os.path.join(inputDir, starFileName)
if not os.path.exists(starFileNameFull):
nTerror("Failed to find starFileNameFull: %s" % starFileNameFull)
return False
if not os.path.exists(outputDir):
os.mkdir(outputDir)
os.chdir(outputDir)
ccpnProjectPath = os.path.join(outputDir, projectName)
if os.path.exists(ccpnProjectPath):
shutil.rmtree(ccpnProjectPath)
ccpnProject = Implementation.MemopsRoot(name=projectName)
# 'linkAtoms': (True,False,'If set to False (off), unrecognized coordinate atoms will not be linked.'),
keywds = {
'minimalPrompts': minimalPrompts,
'allowPopups': allowPopups,
'linkAtoms': 0
}
formatNmrStarFormat = NmrStarFormat(ccpnProject,
guiRoot,
verbose=verbose,
**keywds)
formatNmrStarFormat.version = '3.1'
entryTitle = 'Project from NMR-STAR for %s' % projectName
entryDetails = "Created by Wim Vranken's FormatConverter embedded in CING"
formatNmrStarFormat.getFullProject(starFileNameFull,
title=entryTitle,
details=entryDetails,
**keywds)
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
# formatNmrStarFormat.linkResonances(
# forceDefaultChainMapping=1, # may be overwritten by using forceChainMappings.
# globalStereoAssign=1,
# setSingleProchiral=1,
# setSinglePossEquiv=1,
## strucGen=structureGeneration,
# allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
# Catch entries like mentioned in issue
try:
ccpnProject.checkAllValid()
except ApiError:
nTtracebackError()
nTerror("Failed ccpnProject.checkAllValid")
nTerror("See issue: %s%d" % (issueListUrl, 266))
return False
ccpnProject.saveModified()
if not os.path.exists(ccpnProjectPath):
nTerror("Failed to find new CCPN project directory: %s" %
ccpnProjectPath)
return False
tgzFileName = projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
return ccpnProject
def importStarChemicalShifts(ccpnProject,
inputDir,
guiRoot,
allowPopups=1,
minimalPrompts=0,
verbose=1,
**presets):
print "JFD: now in importStarChemicalShifts"
# formatCns = CnsFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts, allowPopups=allowPopups, **presets)
formatNmrStarFormat = NmrStarFormat(ccpnProject,
guiRoot,
verbose=verbose,
minimalPrompts=minimalPrompts,
allowPopups=allowPopups,
**presets)
ccpnShiftListOfList = []
# Actually just one but this is less time to code;-)
globPattern = inputDir + '/*_21.str'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
for fn in fileList:
fnBaseName = os.path.basename(fn).split('.')[0]
shiftList = formatNmrStarFormat.readShifts(
fn, minimalPrompts=minimalPrompts, verbose=verbose)
if not shiftList:
nTerror("Failed to read")
return True
shiftList.setName(fnBaseName)
ccpnShiftListOfList.append(shiftList)
# Find and print this shiftList in the CCPN data model. Just to check lookup.
shiftList = ccpnProject.currentNmrProject.findFirstMeasurementList(
className='ShiftList')
print 'ShiftList: [%s]' % shiftList
keywds = getDeepByKeysOrDefault(presets, {}, READ_SHIFTS, KEYWORDS)
if keywds:
nTmessage("In importStarChemicalShifts using keywds...")
nTdebug(str(keywds))
shiftList = getDeepByKeys(ccpnShiftListOfList, 0) # no need to repeat
nTdebug("First shiftList: %s" % shiftList)
if shiftList == None:
nTerror("Failed to get shiftList again.")
return True
# nmrConstraintStore = shiftList.nmrConstraintStore
# structureGeneration = nmrConstraintStore.findFirstStructureGeneration()
formatNmrStarFormat.linkResonances(
forceDefaultChainMapping=
1, # may be overwritten by using forceChainMappings.
globalStereoAssign=1,
setSingleProchiral=1,
setSinglePossEquiv=1,
# strucGen=structureGeneration,
allowPopups=allowPopups,
minimalPrompts=minimalPrompts,
verbose=verbose,
**keywds)
