def convert(projectName, rootDir):
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name = projectName)
nmrProject = project.newNmrProject(name = project.name)
structureGeneration = nmrProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(project, guiRoot, verbose = 1)
globPattern = authorDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern,fileList))
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
project.saveModified()
tgzFileName = "../"+projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
def importPdbCoords(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB coordinates 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:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = PseudoPdbFormat(self.project, self, verbose=True)
pdbObj.readCoordinates(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return pdbObj
def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern,fileList))
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject, checkValid=True, newPath=ccpnPathNew, removeExisting=True)
def convert(projectName, rootDir):
datasetDir = os.path.join(rootDir, projectName)
nijmegenDir = os.path.join(datasetDir, "Nijmegen")
authorDir = os.path.join(datasetDir, "Authors")
os.chdir(nijmegenDir)
projectPath = os.path.join(nijmegenDir, projectName)
if os.path.exists(projectPath):
shutil.rmtree(projectPath)
project = Implementation.MemopsRoot(name=projectName)
nmrProject = project.newNmrProject(name=project.name)
structureGeneration = nmrProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(project, guiRoot, verbose=1)
globPattern = authorDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
project.saveModified()
tgzFileName = "../" + projectName + ".tgz"
cmd = "tar -czf %s %s" % (tgzFileName, projectName)
do_cmd(cmd)
def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject,
checkValid=True,
newPath=ccpnPathNew,
removeExisting=True)
def importPseudoPdb(ccpnProject, inputDir, guiRoot, allowPopups=1, minimalPrompts=0, verbose=1, **presets):
nTdebug("Using presets %s" % repr(presets))
formatPseudoPdb = PseudoPdbFormat(ccpnProject, guiRoot, verbose=verbose, minimalPrompts=minimalPrompts, allowPopups=allowPopups)
nmrProject = ccpnProject.currentNmrProject
# nmrProject = project.newNmrProject(name=project.name)
structureEnsembleList = ccpnProject.sortedStructureEnsembles()
if len(structureEnsembleList) != 1:
nTerror("Failed to find single structureEnsemble; instead found: %d" % len(structureEnsembleList) )
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("In importPseudoPdb, removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
structureGenerationList = nmrProject.sortedStructureGenerations()
if not structureGenerationList:
nTdebug("No or empty structureGenerationList; creating a new one.")
nmrProject.newStructureGeneration()
structureGenerationList = nmrProject.sortedStructureGenerations()
if len(structureGenerationList) != 1:
nTerror("Failed to find single structureGeneration; instead found: %d" % len(structureGenerationList) )
structureGeneration = structureGenerationList[0]
# structureGeneration = nmrProject.findFirstStructureGeneration()
# structureGeneration = nmrProject.newStructureGeneration()
if not structureGeneration:
nTerror("Failed to find or create structureGeneration")
return True
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
if len(fileList) != 1:
nTerror("Failed to find single PDB file; instead found list: %s" % repr(fileList))
return True
keywds = getDeepByKeysOrDefault(presets, {}, READ_COORDINATES, KEYWORDS)
nTdebug("In importPseudoPdb: from getDeepByKeysOrDefault keywds: %s" % repr(keywds))
reportDifference(ccpnProject, fileList[0])
status = formatPseudoPdb.readCoordinates(fileList, strucGen=structureGeneration, linkAtoms=0, swapFirstNumberAtom=1,
minimalPrompts=minimalPrompts, verbose=verbose, **keywds)
if not status: # can return None or False on error
nTerror("Failed to formatPseudoPdb.readCoordinates")
return True # returns True on error
def replaceCoordinates():
cityList = [ 'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle', 'Utrecht' ]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir,DATA_STR)
dataDividedDir = os.path.join(baseDir,DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join( dataOrgDir, entryCode )
ccpnFile = os.path.join(dataOrgEntryDir, entryCode+".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew, 'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew, 'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " + os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status = 'new')
project.initCcpn(ccpnFolder = ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" % (globPattern,fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject, checkValid=True, newPath=entryCodeNew, removeExisting=True)
def replaceCoordinates():
cityList = [
'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle',
'Utrecht'
]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir, DATA_STR)
dataDividedDir = os.path.join(baseDir, DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join(dataOrgDir, entryCode)
ccpnFile = os.path.join(dataOrgEntryDir, entryCode + ".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew,
'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew,
'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " +
os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status='new')
project.initCcpn(ccpnFolder=ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble(
)
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning(
"No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" %
(globPattern, fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject,
checkValid=True,
newPath=entryCodeNew,
removeExisting=True)