Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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)
Ejemplo n.º 3
0
"""
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)
Ejemplo n.º 4
0
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():
    """
Ejemplo n.º 5
0
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)
Ejemplo n.º 6
0
"""
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)