def searchPdbEntries(self):
"""
Set the list of matched entries and the dictionary holding the
number of matches. They need to be defined as globals to this module.
Return True on error.
Also searches the PDB and BMRB databases itself.
"""
# modification_time = os.path.getmtime("/Users/jd/.cshrc")
# self.match.d[ "1brv" ] = EntryInfo(time=modification_time)
## following statement is equivalent to a unix command like:
nTdebug("Looking for entries from the PDB database.")
self.entry_list_pdb.addList(getPdbEntries())
if not self.entry_list_pdb:
nTerror("No PDB entries found")
return True
nTmessage("Found %s PDB entries." % len(self.entry_list_pdb))
def searchPdbEntries(self):
"""
Set the list of matched entries and the dictionary holding the
number of matches. They need to be defined as globals to this module.
Return True on error.
Also searches the PDB and BMRB databases itself.
"""
# modification_time = os.path.getmtime("/Users/jd/.cshrc")
# self.match.d[ "1brv" ] = EntryInfo(time=modification_time)
## following statement is equivalent to a unix command like:
nTdebug("Looking for entries from the PDB database.")
self.entry_list_pdb.addList(getPdbEntries())
if not self.entry_list_pdb:
nTerror("No PDB entries found")
return True
nTmessage("Found %s PDB entries." % len(self.entry_list_pdb))
"""
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)
"""
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)
