def prepare( self ):
"""
Overrides Executor method.
"""
Executor.prepare( self )
self.__prepareFolder()
## if setGrid hasn't been called yet, create automatic grid
if not self.gsize:
self.setGrid()
if self.protonate:
reducer = Reduce( self.model, verbose=self.verbose,
autocap=self.autocap,
tempdir=self.tempdir, cwd=self.cwd,
log=self.log, debug=self.debug )
if self.verbose:
self.log.add('adding hydrogen atoms to input structure\n')
self.delphimodel = reducer.run()
else:
self.delphimodel = self.model.clone()
self.delphimodel.xplor2amber()
if not os.path.exists( self.f_charges ):
self.__prepareCharges( self.f_charges )
self.delphimodel.writePdb( self.f_pdb )
def prepare(self):
"""
Overrides Executor method.
"""
Executor.prepare(self)
self.__prepareFolder()
## if setGrid hasn't been called yet, create automatic grid
if not self.gsize:
self.setGrid()
if self.protonate:
reducer = Reduce(self.model,
verbose=self.verbose,
autocap=self.autocap,
tempdir=self.tempdir,
cwd=self.cwd,
log=self.log,
debug=self.debug)
if self.verbose:
self.log.add('adding hydrogen atoms to input structure\n')
self.delphimodel = reducer.run()
else:
self.delphimodel = self.model.clone()
self.delphimodel.xplor2amber()
if not os.path.exists(self.f_charges):
self.__prepareCharges(self.f_charges)
self.delphimodel.writePdb(self.f_pdb)
def prepare(self, cleanUp=1):
"""
Overrides Executor method.
"""
Executor.prepare(self)
self.flush() ## important to avoid empty input file
## Write PDB's to disc if needed
self.writeStructures()
