def _run(self):
self.make_workdir()
if self.is_fragment:
parrot = Parrot(self.workdir, self.refmac_hklout, self.seqin,
self.solvent)
parrot.run()
if parrot.error:
self.logger.error('Parrot run failed! {}'.format(parrot.cmd))
return
self.mtz_fname = parrot.expected_output
cad = Cad(self.workdir, self.mtz_fname, 'buccaneer_input.mtz',
self.cad_stdin, self.refmac_hklout)
cad.run()
if cad.error:
self.logger.error('Cad run failed! {}'.format(cad.cmd))
return
original_dir = os.getcwd()
os.chdir(self.workdir)
p = subprocess.Popen(self.cmd, stdout=subprocess.PIPE, shell=True)
self.logcontents = p.communicate()[0]
touch(self.logfile, self.logcontents)
os.chdir(original_dir)
def _run(self):
self.make_workdir()
original_dir = os.getcwd()
os.chdir(self.workdir)
p = subprocess.Popen(self.cmd, stdout=subprocess.PIPE, shell=True)
self.logcontents = p.communicate()[0]
touch(self.logfile, self.logcontents)
os.chdir(original_dir)
def _run(self):
self.make_workdir()
original_dir = os.getcwd()
os.chdir(self.workdir)
mtz2various = Mtz2Various(self.workdir, self.hklin, self.input_hkl,
self.mtz2various_stdin)
mtz2various.run()
if mtz2various.error:
self.logger.error('mtz2various run failed! {}'.format(
mtz2various.cmd))
return
shutil.copyfile(self.xyzin, self.input_pda)
p = subprocess.Popen(self.cmd, stdout=subprocess.PIPE, shell=True)
self.logcontents = p.communicate()[0]
touch(self.logfile, self.logcontents)
os.chdir(original_dir)
def _run(self):
self.make_workdir()
p = subprocess.Popen(self.cmd, stdout=subprocess.PIPE, shell=True)
self.logcontents = p.communicate()[0]
touch(self.logfile, self.logcontents)