def createTodoList(entryList, cityList, programHoH):
entryListFileName = os.path.join(baseDir, 'list', 'entry_list_todo.csv')
newEntryList = []
for entry in entryList:
for city in cityList:
entryNew = entry + city
programId = getDeepByKeys(programHoH, entry, city)
if programId:
newEntryList.append(entryNew)
writeEntryListToFile(entryListFileName, newEntryList)
def createTodoList(entryList, cityList, programHoH):
entryListFileName = os.path.join(baseDir, 'list', 'entry_list_todo.csv')
newEntryList = []
for entry in entryList:
for city in cityList:
entryNew = entry + city
programId = getDeepByKeys(programHoH, entry, city)
if programId:
newEntryList.append(entryNew)
writeEntryListToFile(entryListFileName, newEntryList)
"""
Collect data needed for nrgcing from RCSB-PDB REST calls.
Execute like:
python $CINGROOT/python/cing/NRG/getRCSB_PDB.py
"""
from cing import cingDirTmp
from cing.Libs.NTutils import * # @UnusedWildImport
from cing.NRG.PDBEntryLists import getPdbEntries
from cing.NRG.PDBEntryLists import writeEntryListToFile
cing.verbosity = cing.verbosityDebug
cingDirTmpTest = os.path.join(cingDirTmp, "getRCSB_PDB")
mkdirs(cingDirTmpTest)
os.chdir(cingDirTmpTest)
testing = False
if testing: # testing with smaller set
pdbList = getPdbEntries(mustHaveExperimentalNmrData=True, onlySolidState=True)
else:
pdbList = getPdbEntries(mustHaveExperimentalNmrData=True)
nTmessage("getPdbEntries exp: %d" % (len(pdbList)))
writeEntryListToFile("hasExpData.csv", pdbList)
from cing.Scripts.doScriptOnEntryList import doScriptOnEntryList
cing.verbosity = cing.verbosityDebug
# parameters for doScriptOnEntryList
startDir = baseDir
cingDirNRG = os.path.join(cingPythonDir, 'cing', 'NRG' )
pythonScriptFileName = os.path.join(cingDirNRG, 'doAnnotateCasdNmr.py')
if False:
entryListFileName = os.path.join(startDir, 'list', 'entry_list_all.csv')
# entryListFileName = os.path.join(startDir, 'list', 'entry_list_redo.csv')
else:
entryListFileName = os.path.join(startDir, 'list', 'entry_list_single.csv')
entryList = 'VpR247Cheshire'.split()
writeEntryListToFile(entryListFileName, entryList)
extraArgList = ()
doScriptOnEntryList(pythonScriptFileName,
entryListFileName,
startDir,
processes_max = 2,
delay_between_submitting_jobs = 2,
max_time_to_wait = 6000,
start_entry_id = 0,
max_entries_todo = 100,
expectPdbEntryList = False,
extraArgList = extraArgList)
def annotateLoop():
"""
from cing.NRG.CaspNmrMassageCcpnProject import baseDir
from cing.NRG.PDBEntryLists import writeEntryListToFile
from cing.Scripts.doScriptOnEntryList import doScriptOnEntryList
cing.verbosity = cing.verbosityDebug
cingDirNRG = os.path.join(cingPythonDir, 'cing', 'NRG' )
pythonScriptFileName = os.path.join(cingDirNRG, 'doAnnotateCaspNmr.py')
if False:
entryListFileName = os.path.join(baseDir, 'list', 'entry_list_all.csv')
# entryListFileName = os.path.join(startDir, 'list', 'entry_list_redo.csv')
else:
entryListFileName = os.path.join(baseDir, 'list', 'entry_list_single.csv')
# entryList = 'T0538Org T0538TS001 T0538TS039'.split()
# entryList = 'T0538Org'.split()
# entryList = 'T0538TS001 T0538TS002 T0538TS257'.split()
entryList = 'T0538TS328'.split()
writeEntryListToFile(entryListFileName, entryList)
extraArgList = ()
doScriptOnEntryList(pythonScriptFileName,
entryListFileName,
baseDir,
processes_max = 2,
delay_between_submitting_jobs = 2,
max_time_to_wait = 6000,
start_entry_id = 0,
max_entries_todo = 100,
expectPdbEntryList = False,
extraArgList = extraArgList)
"""
Collect data needed for nrgcing from RCSB-PDB REST calls.
Execute like:
python $CINGROOT/python/cing/NRG/getRCSB_PDB.py
"""
from cing import cingDirTmp
from cing.Libs.NTutils import * #@UnusedWildImport
from cing.NRG.PDBEntryLists import getPdbEntries
from cing.NRG.PDBEntryLists import writeEntryListToFile
cing.verbosity = cing.verbosityDebug
cingDirTmpTest = os.path.join(cingDirTmp, 'getRCSB_PDB')
mkdirs(cingDirTmpTest)
os.chdir(cingDirTmpTest)
testing = False
if testing: # testing with smaller set
pdbList = getPdbEntries(mustHaveExperimentalNmrData=True,
onlySolidState=True)
else:
pdbList = getPdbEntries(mustHaveExperimentalNmrData=True)
nTmessage("getPdbEntries exp: %d" % (len(pdbList)))
writeEntryListToFile('hasExpData.csv', pdbList)