def main():
try:
fetch_and_run_jobs_forever()
except KeyboardInterrupt:
sys.exit(1)
except:
email.SendTracebackEmail("webtlsmdrund.py exception")
raise
def main():
try:
daemon_main()
except KeyboardInterrupt:
sys.stdout.write('interrupted, exiting...\n')
raise SystemExit
except:
email.SendTracebackEmail("webtlsmdd.py exception")
raise
def main():
try:
daemon_main()
except:
email.SendTracebackEmail("webtlsmdd.py exception")
raise
def analysis_main(struct_path, opt_dict):
"""Runs the TLS analysis on a structure.
"""
## get source filename split up for use in
## constructing output file names
struct_path = os.path.realpath(struct_path)
directory, filename = os.path.split(struct_path)
basename, ext = os.path.splitext(filename)
## set option vars and defaults
chain_ids = opt_dict.get("-c")
#conf.globalconf.recombination = opt_dict.has_key("-e")
if opt_dict.has_key("-e"):
conf.globalconf.recombination = True
if opt_dict.has_key("-o"):
try:
nsmooth = int(opt_dict["-o"])
except ValueError:
print "[ERROR] -o argument must be an integer"
usage()
conf.globalconf.adp_smoothing = nsmooth
if opt_dict.has_key("-u"):
print opt_dict["-u"]
try:
min_subseg = int(opt_dict["-u"])
except ValueError:
print "[ERROR] -u argument must be an integer"
usage()
conf.globalconf.min_subsegment_size = min_subseg
if opt_dict.has_key("-n"):
try:
num_segs = int(opt_dict["-n"])
except ValueError:
print "[ERROR] -n argument must be an integer"
usage()
conf.globalconf.nparts = num_segs
if opt_dict.has_key("-t"):
tpath, tchain_id = opt_dict["-t"].split(":")
conf.globalconf.target_struct_path = tpath
conf.globalconf.target_struct_chain_id = tchain_id
if opt_dict.has_key("-v"):
conf.globalconf.verbose = True
if opt_dict.has_key("-s"):
conf.globalconf.use_svg = True
if opt_dict.has_key("-k"):
conf.globalconf.skip_jmol = True
if opt_dict.has_key("-x"):
conf.globalconf.webtlsmdd = opt_dict["-x"]
if opt_dict.has_key("-j"):
conf.globalconf.job_id = opt_dict["-j"]
if opt_dict.has_key("-i"):
conf.globalconf.struct_id = opt_dict["-i"]
## set the TLS model to use
if opt_dict.has_key("-m"):
tls_model = opt_dict.get("-m").upper()
if tls_model in ["ANISO", "ISOT", "NLANISO", "NLISOT"]:
conf.globalconf.tls_model = tls_model
else:
print "[ERROR] Invalid TLS Model: %s" % (tls_model)
usage()
## weighting scheme
if opt_dict.has_key("-w"):
val = opt_dict["-w"].upper()
val = val.upper()
if val == "IUISO":
conf.globalconf.weight_model = val
else:
print "[ERROR] Invalid Weight Model: %s" % (val)
usage()
## atoms to include
if opt_dict.has_key("-a"):
val = opt_dict["-a"].upper()
if val not in ["ALL", "MAINCHAIN"]:
usage()
conf.globalconf.include_atoms = val
if opt_dict.has_key("--skip-html"):
conf.globalconf.skip_html = True
if opt_dict.has_key("--generate-jmol-viewer"):
conf.globalconf.generate_jmol_view = True
if opt_dict.has_key("--generate-jmol-animate"):
conf.globalconf.generate_jmol_animate = True
if opt_dict.has_key("--generate-histogram"):
conf.globalconf.generate_histogram = True
if opt_dict.has_key("--user-comment="):
conf.globalconf.user_comment = opt_dict["--user-comment="]
if opt_dict.has_key("--help") or opt_dict.has_key("-h"):
usage()
try:
tlsmd_analysis.TLSMD_Main(struct_file_path=struct_path,
sel_chain_ids=chain_ids,
html_report_dir=opt_dict.get("-r"))
except:
if opt_dict.has_key("-b"):
email.SendTracebackEmail("tlsmd.py traceback")
raise