def __init__(self, docking, filename=None, parser=None):
self.docking = docking
self.filename = filename
if filename:
if not parser:
parser = DlgParser()
self.parser = parser
parser.parse(filename)
#for now, keep info about ad3 vs ad4
self.version = parser.version
self.dlgFile = filename
self.dpo = self._buildDpo(parser.dpfLines)
#if the autodock job did not finish, all models do not exist
#so shorten the expected list of conformations to actual value
if len(parser.modelList)<self.dpo['ga_run']['value']:
self.dpo['ga_run']['value']= len(parser.modelList)
self.output = parser.histogramlines
##???
self.macroStem = self.dpo.receptor_stem
self.macroFile = self.macroStem + '.pdbqs'
if self.parser.version>=4.0:
self.macroFile = self.macroStem + '.pdbqt'
##???
filename = self.dpo['move']['value']
if self.docking and not hasattr(self.docking, 'ligMol'):
ligMol = self._buildInputLig(parser.ligLines, filename=filename)
if ligMol is not None:
ligMol.filename = self.dpo['move']['value']
ligMol.name = os.path.splitext(ligMol.filename)[0]
self.docking.ligMol = ligMol
ligMol.trueLigAtoms = ligMol.allAtoms
if hasattr(self, 'flex_res') and self.flex_res:
self.docking.flex_res = self.flex_res
trueLigAtoms = ligMol.trueLigAtoms
for r in self.flex_res:
if r.name in ligMol.chains.residues.name:
for a in r.atoms:
thisAt = ligMol.allAtoms.get(a.name)
trueLigAtoms = trueLigAtoms - thisAt
ligMol.trueLigAtoms = trueLigAtoms
ligMol.lenNonHAtoms = len(ligMol.trueLigAtoms.get(lambda x: x.element!='H'))
directory = a
if verbose: print 'set directory to ', a
if o in ('-o', '--o'):
outputfilename = a
if verbose: print 'set outputfilename to ', a
if o in ('-v', '--v'):
verbose = True
if verbose: print 'set verbose to ', True
if o in ('-h', '--'):
usage()
sys.exit()
if not directory:
print 'summarize_time: directory must be specified.'
usage()
sys.exit()
p = DlgParser()
dlg_list = glob.glob(directory + '/*.dlg')
for dlg in dlg_list:
p.parse(dlg)
stem = dlg_list[0].split('.')[0]
ostr = '%s: % 12.4f m \n' %(directory, p.total_time)
fptr = open(outputfilename, 'a')
fptr.write(ostr)
fptr.close()
# To execute this command type:
# summarize_time.py -d directory -o outputfilename -v
if o in ('-d', '--d'):
directory = a
if verbose: print 'set directory to ', a
if o in ('-o', '--o'):
outputfilename = a
if verbose: print 'set outputfilename to ', a
if o in ('-v', '--v'):
verbose = True
if verbose: print 'set verbose to ', True
if o in ('-h', '--'):
usage()
sys.exit()
if not directory:
print 'summarize_time: directory must be specified.'
usage()
sys.exit()
p = DlgParser()
dlg_list = glob.glob(directory + '/*.dlg')
for dlg in dlg_list:
p.parse(dlg)
stem = dlg_list[0].split('.')[0]
ostr = '%s: % 12.4f m \n' % (directory, p.total_time)
fptr = open(outputfilename, 'a')
fptr.write(ostr)
fptr.close()
# To execute this command type:
# summarize_time.py -d directory -o outputfilename -v