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fixed docs ... forgot some dependencies
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Felix Simkovic committed Aug 14, 2018
1 parent ea248b8 commit cdcb5bd
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Showing 3 changed files with 71 additions and 82 deletions.
6 changes: 2 additions & 4 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,7 @@

# If set, mock the import system to have external dependencies
autodoc_mock_imports = [
'clipper', 'pandas', 'pyrvapi', 'cctbx.crystal', 'cctbx.uctbx', "morda", 'pyjob', 'pyjob.dispatch',
'pyjob.platform', 'pyjob.misc', 'iotbx', 'iotbx.pdb', 'iotbx.pdb.fetch', 'iotbx.pdb.mining', 'cluster_run',
'mmtbx.scaling.matthews', 'parse_molrep', 'parse_refmac', 'scipy.spatial', 'phaser'
'clipper', 'pyrvapi', 'cctbx', 'morda', 'iotbx', 'mmtbx', 'parse_molrep', 'parse_refmac', 'phaser'
]

# Add any paths that contain templates here, relative to this directory.
Expand Down Expand Up @@ -374,7 +372,7 @@ def setup(app):
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
'python': ('https://docs.python.org/3', None),
'multiprocessing': ('https://docs.python.org/3', None),
'numpy': ('https://docs.scipy.org/doc/numpy/', None),
'pandas': ('https://pandas.pydata.org', None),
'pyjob': ('https://pyjob.readthedocs.io', None),
}
3 changes: 3 additions & 0 deletions docs/doc-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,2 +1,5 @@
enum34
pandas
pyjob >= 0.1.5
sphinx-argparse
sphinx_bootstrap_theme ==0.5.3
144 changes: 66 additions & 78 deletions simbad/mr/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,15 @@ class MrSubmit(object):
If a solution is found and process_all is not set, the queued jobs will be terminated.
"""

def __init__(self, mtz, mr_program, refine_program, refine_type, refine_cycles, output_dir, tmp_dir, timeout,
def __init__(self,
mtz,
mr_program,
refine_program,
refine_type,
refine_cycles,
output_dir,
tmp_dir,
timeout,
sgalternative=None):
"""Initialise MrSubmit class"""
self.input_file = None
Expand Down Expand Up @@ -253,9 +261,9 @@ def timeout(self, timeout):
def get_mtz_info(self, mtz):
"""Get various information from the input MTZ
Parameters
----------
mtz : str
Parameters
----------
mtz : str
Path to the input MTZ
Returns
Expand All @@ -280,8 +288,7 @@ def get_mtz_info(self, mtz):
self._cell_parameters = " ".join(map(str, cell_parameters))

# Extract column labels from input mtz
self._f, self._sigf, self._i, self._sigi, self._dano, self._sigdano, self._free = mtz_util.get_labels(
mtz)
self._f, self._sigf, self._i, self._sigi, self._dano, self._sigdano, self._free = mtz_util.get_labels(mtz)

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
Expand Down Expand Up @@ -324,27 +331,18 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su
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))
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))
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)
Expand All @@ -370,8 +368,7 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su
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")
mr_pdbin = os.path.join(self.output_dir, result.pdb_code + ".pdb")
pdb_struct.save(mr_pdbin)
elif isinstance(result, LatticeSearchResult):
pdb_struct = PdbStructure()
Expand All @@ -394,52 +391,51 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su

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
"-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
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,
"-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
]
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")
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")
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)

Expand All @@ -457,42 +453,40 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su
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_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)]
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)
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)
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)
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)
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)
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)
logger.debug("Cannot find %s output file: %s", self.mr_program, mr_pdbout)
continue

score = MrScore(pdb_code=result.pdb_code)
Expand All @@ -509,26 +503,22 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su

if self._dano is not None:
try:
anode = anomalous_util.AnodeSearch(
self.mtz, self.output_dir, self.mr_program)
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)
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)
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)
logger.debug("Cannot find %s log file: %s", self.refine_program, ref_logfile)
mr_results += [score]

self._search_results = mr_results
Expand Down Expand Up @@ -600,8 +590,7 @@ def summarize(self, csv_file):
if self._dano:
columns += ["dano_peak_height", "nearest_atom"]

summarize_result(self.search_results,
csv_file=csv_file, columns=columns)
summarize_result(self.search_results, csv_file=csv_file, columns=columns)


def _mr_job_succeeded(r_fact, r_free):
Expand All @@ -624,8 +613,7 @@ def mr_succeeded_log(log):
"""
mr_prog, pdb = os.path.basename(log).replace('.log', '').split('_', 1)
refmac_log = os.path.join(os.path.dirname(
log), pdb, "mr", mr_prog, "refine", pdb + "_ref.log")
refmac_log = os.path.join(os.path.dirname(log), pdb, "mr", mr_prog, "refine", pdb + "_ref.log")
if os.path.isfile(refmac_log):
rp = refmac_parser.RefmacParser(refmac_log)
return _mr_job_succeeded(rp.final_r_fact, rp.final_r_free)
Expand Down

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