def start(cwd='./', args=['-I']):
ensure_has_cif2cell()
version = jmol_version.split('.')
if len(version) < 3:
version += [0] * (3 - len(version))
#if int(version[0]) < 12 or (int(version[0]) == 12 and int(version[1]) < 3):
if int(version[0]) < 13 or (int(version[0]) == 13 and int(version[1]) == 2
and int(version[2]) < 8):
raise Exception(
"jmol_ext.start_jmol: requires at least jmol version 13.2.8, your version:"
+ str(jmol_version))
command = Command(jmol_path, args, cwd=cwd, stophook=_jmol_stophook)
command.start()
return command
def cif2cell(cwd, args, timeout=30):
ensure_has_cif2cell()
#raise Exception("Debug: cif2cell call!")
#p = subprocess.Popen([cif2cell_path]+args, stdout=subprocess.PIPE,
# stderr=subprocess.PIPE, cwd=cwd)
#print("COMMAND CIF2CELL",args)
out, err, completed = Command(cif2cell_path, args, cwd=cwd).run(timeout)
#print("COMMAND CIF2CELL END",out)
return out, err, completed
def platon(cwd, args, timeout=60):
ensure_has_platon()
#p = subprocess.Popen([platon_path]+args, stdout=subprocess.PIPE,
# stderr=subprocess.PIPE, cwd=cwd)
#out, err = p.communicate()
#print("COMMAND PLATON")
#raise Exception("PLATON")
#print("EXECUTING PLATON",platon_path,args)
out, err, completed = Command(platon_path, args, cwd=cwd).run(timeout)
#print("COMMAND PLATON END", out, err, completed, cwd)
return out, err, completed
def isotropy(cwd, args, inputstr, timeout=30):
ensure_has_isotropy()
#p = subprocess.Popen([cif2cell_path]+args, stdout=subprocess.PIPE,
# stderr=subprocess.PIPE, cwd=cwd)
#print("COMMAND CIF2CELL")
out, err, completed = Command(os.path.join(isotropy_path, 'findsym'),
args,
cwd=cwd,
inputstr=inputstr).run(timeout)
#print("COMMAND CIF2CELL END")
return out, err, completed
def aflow(ioa_in, args, timeout=30):
ioa_in = httk.IoAdapterString.use(ioa_in)
#
#print("COMMAND AFLOW")
#print("SENDING IN",ioa_in.string)
out, err, completed = Command(aflow_path, args, inputstr=ioa_in.string).run(timeout)
#print("COMMAND AFLOW END")
#return out, err
#
#p = subprocess.Popen([aflow_path]+args, stdin=subprocess.PIPE,stdout=subprocess.PIPE,
# stderr=subprocess.PIPE)
#out, err = p.communicate(input=ioa_in.string)
ioa_in.close()
return out, err, completed
def check_works():
global jmol_version, jmol_version_date
if jmol_path == "" or not os.path.exists(jmol_path):
raise ImportError(
"httk.external.jmol imported without access to a jmol binary. jmol path was set to:"
+ str(jmol_path))
out, err, completed = Command(jmol_path, ['-n', '-o'],
cwd='./').run(15, debug=False)
if completed is None or completed != 0:
raise Exception("jmol_ext: Could not execute jmol. Return code:" +
str(completed) + " out:" + str(out) + " err:" +
str(err))
def get_version(results, match):
results['version'] = match.group(1)
results['version_date'] = match.group(2)
# Why do we take os.path.join() of httk.IoAdapterString(out)?
# Trying to do that in Python 3 fails.
# results = micro_pyawk(os.path.join(httk.IoAdapterString(out)), [
# ['^ *Jmol Version: ([^ ]+) +([^ ]+)', None, get_version],
# ], debug=False)
results = micro_pyawk(httk.IoAdapterString(out), [
['^ *Jmol Version: ([^ ]+) +([^ ]+)', None, get_version],
],
debug=False)
if not 'version' in results:
raise Exception(
"jmol_ext: Could not extract version string from jmol -n -o. Return code:"
+ str(completed) + " out:" + str(out) + " err:" + str(err))
jmol_version = results['version']
jmol_version_date = results['version_date']
def run(cwd, args, timeout=None):
ensure_has_cif2cell()
#print("COMMAND JMOL")
out, err, completed = Command(jmol_path, args, cwd=cwd).run(timeout)
#print("COMMMDN JMOL END")
return out, err, completed