def _getligprop(self, filename):
""" calculate basic properties from PDBQT ligand
mw, hba, hbd, heavy atoms
"""
try:
lines = hf.getLines(filename)
atoms = hf.getAtoms(lines)
except:
return False, sys.exc_info()[1]
if len(lines) == 0:
return False, "empty file"
if len(atoms) == 0:
return False, "no atoms (INVALID FILE)"
try:
tors = int(lines[-1].split()[1])
except:
return False, "no torsions (INVALID FILE)"
# hb
hba, hbd = [ len(x) for x in hf.findHbAccepDon(atoms) ]
# atypes ( report all types with duplicates, to be used for updating lib types)
atypes = list(set([ x.split()[-1] for x in atoms ]))
# heavy
heavy = len([ x for x in atypes if not x == 'HD' ])
# mw
mw = 0
for a in atypes:
mw += hf.adtypes.get( a, [None,0])[1]
return True, {'tors' : tors, 'heavy' : heavy, 'mw' : mw, 'hba' : hba, 'hbd': hbd, 'atypes': atypes }
def writeLogJson(self, logname, compression = False):
""" write log in json format
"""
if not len(self.results.keys()):
print "cowardly refusing to write an empty file"
return
hf.writejson(logname, self.results, compression)
def upload(self, dirname=None, destpath=None, autoregister=False, overwrite=False, bg=False):
"""upload the library to the remote server $dest path"""
if dirname == None:
dirname = hf.validFilename(self.name())
if dirname == '':
dirname = 'libdir'
self.dprint("warning: lib dirname empty, providing substutute [%s]" % libdir)
if destpath == None:
destpath == self.server.getLibraryPath()
if (self.server == None) or (self.server == 'localhost'):
self._localcopy( dirname, destpath, autoregister, overwrite, bg)
else:
self._remotecopy( dirname, destpath, autoregister, overwrite, bg)
self.updatestatus()
def updateDownloadBigFile(self):
""" update download status of big files transfers"""
if self.checkPending() == False:
return 100.00
#self._counter
try:
self.dprint("checking local size of [%s]" % self._localfile)
curr_size = os.stat(self._localfile).st_size
self.dprint(' found %s' % curr_size)
except:
self.dprint('file checking error [%s]' % sys.exc_info()[1] )
curr_size = 0
pc = hf.percent(curr_size, self._total)
self.dprint("current size [%d/%d] : %2.3f%%" % (curr_size, self._total, pc) )
return pc
def updateDownloadBigFile(self):
""" update download status of big files transfers"""
if self.checkPending() == False:
return 100.00
#self._counter
try:
self.dprint("checking local size of [%s]" % self._localfile)
curr_size = os.stat(self._localfile).st_size
self.dprint(' found %s' % curr_size)
except:
self.dprint('file checking error [%s]' % sys.exc_info()[1])
curr_size = 0
pc = hf.percent(curr_size, self._total)
self.dprint("current size [%d/%d] : %2.3f%%" %
(curr_size, self._total, pc))
return pc
def _remotecopy(self, dirname, destpath, autoregister=False, overwrite=False, bg=True):
""" perform the copy on remote path"""
# generating fullpath
self.path = destpath + '/' + dirname
if self.server.ssh.exists(self.path):
self.dprint('remote library dirname[%s] exist in the path[%s] => [%s]...' % (dirname, destpath, self.path))
if not overwrite:
self.dprint('overwrite not allowed, returning')
return
else:
self.server.ssh.remove([self.path])
# update the ligand destination with split_path
step = self.options['split']
items = sorted(self.items.keys())
total = len(items)
if (not step == None) and (step <= total):
count = 0
for i in items:
self.dprint("updating splitted name [%s] =>" % self.items[i]['fullpath']),
self.items[i]['fullpath'] = '/'.join([hf.splitdir(count, total, step),
self.items[i]['fullpath']])
self.dprint("[%s]" % self.items[i]['fullpath'])
count+=1
transfer_list = []
for i in items:
dest = '/'.join([dirname, self.items[i]['fullpath'] ])
transfer_list.append( [self.items[i]['source'], dest])
# transfer files
mule = self.server.transfer
self.dprint("starting the transfer with the mule[%s]" % mule)
mule.upload(files = transfer_list, remotedestpath=destpath, bg=bg)
self.dprint("mule started... ongoing...")
if autoregister:
if not bg:
libindex = self.path + '/' + 'library.db'
self.saveIndex(libindex)
self.registerLibrary(overwrite)
else:
print "AUTOREGISTER DISABLED! BACKGROUND UPLOAD (TO FIX)"