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