def chain_type_string(chain_sizes):
listx = []
for c in chain_sizes.split(';'):
chid, length, selected, type = misc.parse_chains(c)
if selected == "1":
listx.append("%s:%s" % (chid, type))
return ";".join(listx)
def chain_type_string(chain_sizes):
listx = []
for c in chain_sizes.split(';'):
chid, length, selected, type = misc.parse_chains(c)
if selected == "1":
listx.append("%s:%s" % (chid, type))
return ";".join(listx)
def get_job(mysql):
"""Remove the top job from the queue file and return it.
"""
## NOTE: This is the very first step in the entire webtlsmdrund.py process
try:
job_id = mysql.get_next_queued_job_id()
except socket.error:
log_write("[ERROR] unable to connect to MySQL")
raise SystemExit
if job_id == "":
return None
## change state of the job and re-load to catch any updates which may
## have occurred
if mysql.job_set_state(job_id, "running") == False:
return None
mysql.job_set_state(job_id, "running")
jdict = mysql.job_get_dict(job_id)
if jdict == None:
return None
## Construct the run command for this job
tlsmd = [conf.TLSMD_PROGRAM_PATH, "-b", "-rANALYSIS"]
## Job ID
tlsmd.append("-j%s" % (job_id))
## override PDB ID
tlsmd.append("-i%s" % (jdict["structure_id"]))
## Jmol/Histogram features
if jdict["generate_jmol_view"] == True:
tlsmd.append("--generate-jmol-viewer")
if jdict["generate_jmol_animate"] == True:
tlsmd.append("--generate-jmol-animate")
if jdict["generate_histogram"] == True:
tlsmd.append("--generate-histogram")
## plot style
if jdict["plot_format"] == "SVG":
tlsmd.append("-s")
## select TLS model
tls_model = jdict["tls_model"]
if tls_model == "ISOT":
tlsmd.append("-mISOT")
else:
tlsmd.append("-mANISO")
## set maximum number of segments
tlsmd.append("-n%s" % (jdict["nparts"]))
## select LSQ weighting
#tlsmd.append("-w%s" % (jdict["weight"]))
## select chain IDs to analyze
cids = []
chains = jdict["chain_sizes"].rstrip(";")
for c in chains.split(';'):
chid, length, selected, type = misc.parse_chains(c)
if selected == "1":
cids.append(chid)
tlsmd.append("-c%s" % (",".join(cids)))
## included atoms
tlsmd.append("-a%s" % (jdict["include_atoms"]))
## input PDB file
tlsmd.append(conf.PDB_FILENAME)
jdict["tlsmd"] = tlsmd
return jdict
def get_job(mysql):
"""Remove the top job from the queue file and return it.
"""
## NOTE: This is the very first step in the entire webtlsmdrund.py process
try:
job_id = mysql.get_next_queued_job_id()
except socket.error:
log_write("[ERROR] unable to connect to MySQL")
raise SystemExit
if job_id == "":
return None
## change state of the job and re-load to catch any updates which may
## have occurred
if mysql.job_set_state(job_id, "running") == False:
return None
mysql.job_set_state(job_id, "running")
jdict = mysql.job_get_dict(job_id)
if jdict == None:
return None
## Construct the run command for this job
tlsmd = [conf.TLSMD_PROGRAM_PATH, "-b", "-rANALYSIS" ]
## Job ID
tlsmd.append("-j%s" % (job_id))
## override PDB ID
tlsmd.append("-i%s" % (jdict["structure_id"]))
## Jmol/Histogram features
if jdict["generate_jmol_view"] == True:
tlsmd.append("--generate-jmol-viewer")
if jdict["generate_jmol_animate"] == True:
tlsmd.append("--generate-jmol-animate")
if jdict["generate_histogram"] == True:
tlsmd.append("--generate-histogram")
## plot style
if jdict["plot_format"] == "SVG":
tlsmd.append("-s")
## select TLS model
tls_model = jdict["tls_model"]
if tls_model == "ISOT":
tlsmd.append("-mISOT")
else:
tlsmd.append("-mANISO")
## set maximum number of segments
tlsmd.append("-n%s" % (jdict["nparts"]))
## select LSQ weighting
#tlsmd.append("-w%s" % (jdict["weight"]))
## select chain IDs to analyze
cids = []
chains = jdict["chain_sizes"].rstrip(";")
for c in chains.split(';'):
chid, length, selected, type = misc.parse_chains(c)
if selected == "1":
cids.append(chid)
tlsmd.append("-c%s" % (",".join(cids)))
## included atoms
tlsmd.append("-a%s" % (jdict["include_atoms"]))
## input PDB file
tlsmd.append(conf.PDB_FILENAME)
jdict["tlsmd"] = tlsmd
return jdict
