def test_tmp_file_9(self):
tmp = tmp_file(delete=False, directory=os.getcwd(), prefix="first", suffix="last")
self.assertTrue(os.path.isfile(tmp))
path, name = os.path.split(tmp)
self.assertEqual(os.getcwd(), path)
self.assertTrue(name.startswith("first"))
self.assertTrue(name.endswith("last"))
os.remove(tmp)
def test_tmp_file_4(self):
tmp = tmp_file(prefix="first")
self.assertTrue(os.path.isfile(tmp))
self.assertTrue(os.path.basename(tmp).startswith("first"))
os.remove(tmp)
def test_tmp_file_3(self):
tmp = tmp_file(directory=os.getcwd())
self.assertTrue(os.path.isfile(tmp))
path, _ = os.path.split(tmp)
self.assertEqual(os.getcwd(), path)
os.remove(tmp)
def test_tmp_file_2(self):
tmp = tmp_file(delete=True)
self.assertFalse(os.path.isfile(tmp))
def test_tmp_file_1(self):
tmp = tmp_file()
self.assertTrue(os.path.isfile(tmp))
os.remove(tmp)
def test_tmp_file_7(self):
tmp = tmp_file(delete=True, stem="middle")
self.assertFalse(os.path.isfile(tmp))
self.assertTrue("middle" in os.path.basename(tmp))
def test_tmp_file_6(self):
tmp = tmp_file(suffix="last")
self.assertTrue(os.path.isfile(tmp))
self.assertTrue(os.path.basename(tmp).endswith("last"))
os.remove(tmp)
def test_tmp_file_5(self):
tmp = tmp_file(stem="middle")
self.assertTrue(os.path.isfile(tmp))
self.assertTrue("middle" in os.path.basename(tmp))
os.remove(tmp)
def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, submit_queue=False, monitor=None):
"""Submit jobs to run in serial or on a cluster
Parameters
----------
results : class
Results from :obj: '_LatticeParameterScore' or :obj: '_AmoreRotationScore'
nproc : int, optional
Number of processors to use [default: 1]
process_all : bool, optional
Terminate MR after a success [default: True]
submit_qtype : str
The cluster submission queue type - currently support SGE and LSF
submit_queue : str
The queue to submit to on the cluster
monitor : str
Returns
-------
file
Output pdb from mr
file
Output hkl from mr - if using phaser
file
Output log file from mr program
file
Output pdb from refinement
file
Output hkl from refinement
file
Output log file from refinement program
"""
if not os.path.isdir(self.output_dir):
os.mkdir(self.output_dir)
run_files = []
sol_cont = SolventContent(self.cell_parameters, self.space_group)
mat_prob = MatthewsProbability(self.cell_parameters, self.space_group)
for result in results:
mr_workdir = os.path.join(self.output_dir, result.pdb_code, 'mr', self.mr_program)
mr_logfile = os.path.join(mr_workdir, '{0}_mr.log'.format(result.pdb_code))
mr_pdbout = os.path.join(mr_workdir, '{0}_mr_output.pdb'.format(result.pdb_code))
mr_hklout = os.path.join(mr_workdir, '{0}_mr_output.mtz'.format(result.pdb_code))
ref_workdir = os.path.join(mr_workdir, 'refine')
ref_hklout = os.path.join(ref_workdir, '{0}_refinement_output.mtz'.format(result.pdb_code))
ref_logfile = os.path.join(ref_workdir, '{0}_ref.log'.format(result.pdb_code))
ref_pdbout = os.path.join(ref_workdir, '{0}_refinement_output.pdb'.format(result.pdb_code))
diff_mapout1 = os.path.join(ref_workdir, '{0}_refmac_2fofcwt.map'.format(result.pdb_code))
diff_mapout2 = os.path.join(ref_workdir, '{0}_refmac_fofcwt.map'.format(result.pdb_code))
if os.path.isfile(ref_logfile):
rp = refmac_parser.RefmacParser(ref_logfile)
if _mr_job_succeeded(rp.final_r_fact, rp.final_r_free):
score = MrScore(pdb_code=result.pdb_code)
if self.mr_program == "molrep":
mp = molrep_parser.MolrepParser(mr_logfile)
score.molrep_score = mp.score
score.molrep_tfscore = mp.tfscore
elif self.mr_program == "phaser":
pp = phaser_parser.PhaserParser(mr_logfile)
score.phaser_tfz = pp.tfz
score.phaser_llg = pp.llg
score.phaser_rfz = pp.rfz
rp = refmac_parser.RefmacParser(ref_logfile)
score.final_r_free = rp.final_r_free
score.final_r_fact = rp.final_r_fact
self._search_results = [score]
return
if isinstance(result, AmoreRotationScore) or isinstance(result, PhaserRotationScore):
pdb_struct = PdbStructure()
pdb_struct.from_file(result.dat_path)
mr_pdbin = os.path.join(self.output_dir, result.pdb_code + ".pdb")
pdb_struct.save(mr_pdbin)
elif isinstance(result, LatticeSearchResult):
pdb_struct = PdbStructure()
pdb_struct.from_file(result.pdb_path)
mr_pdbin = result.pdb_path
else:
raise ValueError("Do not recognize result container")
solvent_content = sol_cont.calculate_from_struct(pdb_struct)
if solvent_content > 30:
solvent_content, n_copies = mat_prob.calculate_content_ncopies_from_struct(pdb_struct)
else:
pdb_struct.keep_first_chain_only()
pdb_struct.save(mr_pdbin)
solvent_content, n_copies = mat_prob.calculate_content_ncopies_from_struct(pdb_struct)
msg = "%s is predicted to be too large to fit in the unit "\
+ "cell with a solvent content of at least 30 percent, "\
+ "therefore MR will use only the first chain"
logger.debug(msg, result.pdb_code)
mr_cmd = [
CMD_PREFIX, "ccp4-python", "-m", self.mr_python_module, "-hklin", self.mtz, "-hklout", mr_hklout,
"-pdbin", mr_pdbin, "-pdbout", mr_pdbout, "-logfile", mr_logfile, "-work_dir", mr_workdir, "-nmol",
n_copies, "-sgalternative", self.sgalternative
]
ref_cmd = [
CMD_PREFIX, "ccp4-python", "-m", self.refine_python_module, "-pdbin", mr_pdbout, "-pdbout", ref_pdbout,
"-hklin", mr_hklout, "-hklout", ref_hklout, "-logfile", ref_logfile, "-work_dir", ref_workdir,
"-refinement_type", self.refine_type, "-ncyc", self.refine_cycles
]
if self.mr_program == "molrep":
mr_cmd += ["-space_group", self.space_group]
elif self.mr_program == "phaser":
mr_cmd += [
"-i",
self.i,
"-sigi",
self.sigi,
"-f",
self.f,
"-sigf",
self.sigf,
"-solvent",
solvent_content,
"-timeout",
self.timeout,
]
if isinstance(result, LatticeSearchResult):
mr_cmd += ['-autohigh', 4.0, '-hires', 5.0]
# ====
# Create a run script - prefix __needs__ to contain mr_program so we can find log
# Leave order of this as SGE does not like scripts with numbers as first char
# ====
prefix, stem = self.mr_program + "_", result.pdb_code
fft_cmd1, fft_stdin1 = self.fft(ref_hklout, diff_mapout1, "2mfo-dfc")
run_stdin_1 = tmp_file(directory=self.output_dir, prefix=prefix, stem=stem, suffix="_1.stdin")
with open(run_stdin_1, 'w') as f_out:
f_out.write(fft_stdin1)
fft_cmd2, fft_stdin2 = self.fft(ref_hklout, diff_mapout2, "mfo-dfc")
run_stdin_2 = tmp_file(directory=self.output_dir, prefix=prefix, stem=stem, suffix="_2.stdin")
with open(run_stdin_2, 'w') as f_out:
f_out.write(fft_stdin2)
ccp4_scr = os.environ["CCP4_SCR"]
if self.tmp_dir:
tmp_dir = os.path.join(self.tmp_dir)
else:
tmp_dir = os.path.join(self.output_dir)
cmd = [
[EXPORT, "CCP4_SCR=" + tmp_dir],
mr_cmd + [os.linesep],
ref_cmd + [os.linesep],
fft_cmd1 + ["<", run_stdin_1, os.linesep],
fft_cmd2 + ["<", run_stdin_2, os.linesep],
[EXPORT, "CCP4_SCR=" + ccp4_scr],
]
run_script = make_script(cmd, directory=self.output_dir, prefix=prefix, stem=stem)
run_log = run_script.rsplit(".", 1)[0] + '.log'
run_files += [(run_script, run_stdin_1, run_stdin_2, run_log, mr_pdbout, mr_logfile, ref_logfile)]
if not self.mute:
logger.info("Running %s Molecular Replacement", self.mr_program)
run_scripts, _, _, _, mr_pdbouts, mr_logfiles, ref_logfiles = zip(*run_files)
j = Job(submit_qtype)
j.submit(
run_scripts,
directory=self.output_dir,
nproc=nproc,
name='simbad_mr',
queue=submit_queue,
permit_nonzero=True)
interval = int(numpy.log(len(run_scripts)) / 3)
interval_in_seconds = interval if interval >= 5 else 5
if process_all:
j.wait(interval=interval_in_seconds, monitor=monitor)
else:
j.wait(interval=interval_in_seconds, monitor=monitor, check_success=mr_succeeded_log)
mr_results = []
for result, mr_logfile, mr_pdbout, ref_logfile in zip(results, mr_logfiles, mr_pdbouts, ref_logfiles):
if not os.path.isfile(mr_logfile):
logger.debug("Cannot find %s MR log file: %s", self.mr_program, mr_logfile)
continue
elif not os.path.isfile(ref_logfile):
logger.debug("Cannot find %s refine log file: %s", self.mr_program, ref_logfile)
continue
elif not os.path.isfile(mr_pdbout):
logger.debug("Cannot find %s output file: %s", self.mr_program, mr_pdbout)
continue
score = MrScore(pdb_code=result.pdb_code)
if self.mr_program == "molrep":
mp = molrep_parser.MolrepParser(mr_logfile)
score.molrep_score = mp.score
score.molrep_tfscore = mp.tfscore
elif self.mr_program == "phaser":
pp = phaser_parser.PhaserParser(mr_logfile)
score.phaser_tfz = pp.tfz
score.phaser_llg = pp.llg
score.phaser_rfz = pp.rfz
if self._dano is not None:
try:
anode = anomalous_util.AnodeSearch(self.mtz, self.output_dir, self.mr_program)
anode.run(result)
a = anode.search_results()
score.dano_peak_height = a.dano_peak_height
score.nearest_atom = a.nearest_atom
except RuntimeError:
logger.debug("RuntimeError: Unable to create DANO map for: %s", result.pdb_code)
except IOError:
logger.debug("IOError: Unable to create DANO map for: %s", result.pdb_code)
if os.path.isfile(ref_logfile):
rp = refmac_parser.RefmacParser(ref_logfile)
score.final_r_free = rp.final_r_free
score.final_r_fact = rp.final_r_fact
else:
logger.debug("Cannot find %s log file: %s", self.refine_program, ref_logfile)
mr_results += [score]
self._search_results = mr_results
def test_check_script_4(self):
ss = tmp_file(delete=False)
with open(ss, "w") as f_out:
f_out.write("sleep 1")
self.assertRaises(PyJobError, Job.check_script, ss)