def molrep(self, f, m, keys=""):
job = Job(self, utils.cbin("molrep"))
job.args += ["-f", f, "-m", m]
if keys:
job.args.append("-i")
job.std_input = keys.strip() + "\nend"
return job
def molrep(self, f, m, keys=""):
job = Job(self, utils.cbin("molrep"))
job.args += ["-f", f, "-m", m]
if keys:
job.args.append("-i")
job.std_input = keys.strip() + "\nend"
return job
def molrep(self, f, m, keys=''):
job = Job(self, utils.cbin('molrep'))
job.args += ['-f', f, '-m', m]
if keys:
job.args.append('-i')
job.std_input = keys.strip() + '\nend'
return job
def find_path():
if os.name == 'nt':
for path in [
"C:/WinCoot/wincoot.bat", # since WinCoot 0.8.8
"C:/WinCoot/runwincoot.bat", # WinCoot prior to 0.8.8
utils.cbin("coot.bat")
]: # CCP4 script added in 2018
if os.path.exists(path):
return path
utils.comment("\nNote: WinCoot not found.\n")
else:
return utils.syspath("coot")
def ccp4_job(workflow, prog, logical=None, ki="", parser=None, add_end=True):
"""Handle traditional convention for arguments of CCP4 programs.
logical - dictionary with where keys are so-called logical names.
ki (string or list of lines) - Keyworded Input to be passed through stdin.
add_end - adds "end" as the last line of stdin
Note: "colin" and "labin" mean the same (column label),
but different programs use different keywords.
"""
job = Job(workflow, utils.cbin(prog))
if logical:
for a in ["hklin", "hklout", "hklref", "xyzin", "xyzout", "libin"]:
if logical.get(a):
job.args += [a.upper(), logical[a]]
lines = ki.splitlines() if isinstance(ki, basestring) else ki
stripped = [a.strip() for a in lines if a and not a.isspace()]
if add_end and not (stripped and stripped[-1].lower() == "end"):
stripped.append("end")
job.std_input = "\n".join(stripped)
job.parser = parser
return job
def ccp4_job(workflow, prog, logical=None, ki="", parser=None, add_end=True):
"""Handle traditional convention for arguments of CCP4 programs.
logical - dictionary with where keys are so-called logical names.
ki (string or list of lines) - Keyworded Input to be passed through stdin.
add_end - adds "end" as the last line of stdin
Note: "colin" and "labin" mean the same (column label),
but different programs use different keywords.
"""
job = Job(workflow, utils.cbin(prog))
if logical:
for a in ["hklin", "hklout", "hklref", "xyzin", "xyzout", "libin"]:
if logical.get(a):
job.args += [a.upper(), logical[a]]
lines = ki.splitlines() if isinstance(ki, basestring) else ki
stripped = [a.strip() for a in lines if a and not a.isspace()]
if add_end and not (stripped and stripped[-1].lower() == "end"):
stripped.append("end")
job.std_input = "\n".join(stripped)
job.parser = parser
return job
def gemmi_blobs(self, hklin, xyzin, sigma=1.0):
job = Job(self, utils.cbin('gemmi'))
job.name += ' ' + 'blobs'
job.args += ['blobs', '--dimple', '--sigma=%g' % sigma, hklin, xyzin]
job.parser = '_gemmi_blobs_parser'
return job