def handleNonOpal(weboptions, storage_host):
"""
Handle non opal run.
"""
pdblist, errlist = readPDB(weboptions.pdbfile)
dummydef = Definition()
dummyprot = Protein(pdblist, dummydef)
"""
if len(pdblist) == 0 and len(errlist) == 0:
text = "Unable to find PDB file - Please make sure this is "
text += "a valid PDB file ID!"
#print "Content-type: text/html\n"
print text
sys.exit(2)
elif dummyprot.numAtoms() > MAXATOMS and weboptions["opt"] == True:
text = "<HTML><HEAD>"
text += "<TITLE>PDB2PQR Error</title>"
text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
text += "Due to server limits, we are currently unable to optimize "
text += "proteins of greater than %i atoms on the server (PDB2PQR " % MAXATOMS
text += "found %s atoms in the selected PDB file). If you " % dummyprot.numAtoms()
text += "want to forgo optimization please try the server again.<P>"
text += "Otherwise you may use the standalone version of PDB2PQR that "
text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
text += "PDB2PQR SourceForge project page</a>."
text += "<script type=\"text/javascript\">"
text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
text += "</script>"
text += "<script type=\"text/javascript\">"
text += "try {"
text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
for key in weboptions:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
#print "Content-type: text/html\n"
print text
sys.exit(2)
"""
try:
starttime = time.time()
name = setID(starttime)
#Some job parameters logging.
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
'w')
apbsInputFile.write(str(weboptions["apbs"]))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
'w')
typemapInputFile.write(str(weboptions["typemap"]))
typemapInputFile.close()
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name),
'w')
statusfile.write('running')
statusfile.close()
# Recording CGI run information for PDB2PQR Opal
pdb2pqrLogFile = open(
'%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrLogFile.write(
str(weboptions.getOptions()) + '\n' + str(weboptions.ff))
# str(weboptions.ff)+'\n'+
# str(os.environ["REMOTE_ADDR"]))
pdb2pqrLogFile.close()
pid = os.fork()
if pid:
from PDB2PQR_web import jobutils
redirect = redirector(name, weboptions)
file_list = [
'typemap',
'pdb2pqr_status',
'pdb2pqr_start_time',
]
print('===========')
print(weboptions.getCommandLine())
# for i in weboptions.getRunArguments():
# print(i)
print('===========')
if isinstance(file_list, list):
try:
jobutils.send_to_storage_service(
storage_host, name, file_list,
os.path.join(INSTALLDIR, TMPDIR))
except Exception as err:
with open('storage_err', 'a+') as fin:
fin.write(err)
# print redirector(name, weboptions)
return redirect
sys.exit()
else:
currentdir = os.getcwd()
os.chdir("/")
os.setsid()
os.umask(0)
os.chdir(currentdir)
os.close(1) # not sure if these
os.close(2) # two lines are necessary
pqrpath = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, name, name)
orig_stdout = sys.stdout
orig_stderr = sys.stderr
sys.stdout = open(
'%s%s%s/pdb2pqr_stdout.txt' % (INSTALLDIR, TMPDIR, name), 'w')
sys.stderr = open(
'%s%s%s/pdb2pqr_stderr.txt' % (INSTALLDIR, TMPDIR, name), 'w')
run_arguements = weboptions.getRunArguments()
if weboptions.runoptions.get('ph_calc_method', '') == 'pdb2pka':
run_arguements['ph_calc_options'][
'output_dir'] = '%s%s%s/pdb2pka_output' % (INSTALLDIR,
TMPDIR, name)
header, lines, missedligands = runPDB2PQR(
pdblist,
weboptions.ff,
outname=pqrpath,
commandLine=weboptions.getCommandLine(),
**weboptions.getRunArguments())
sys.stdout.close()
sys.stderr.close()
sys.stdout = orig_stdout
sys.stderr = orig_stderr
endtimefile = open(
'%s%s%s/pdb2pqr_end_time' % (INSTALLDIR, TMPDIR, name), 'w')
endtimefile.write(str(time.time()))
endtimefile.close()
pqrfile = open(pqrpath, "w")
pqrfile.write(header)
whitespace = weboptions.otheroptions['whitespace']
for line in lines:
# Adding whitespaces if --whitespace is in the weboptions
if whitespace:
if line[0:4] == 'ATOM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % string.strip(newline))
elif line[0:6] == 'HETATM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % string.strip(newline))
else:
pqrfile.write("%s\n" % string.strip(line))
pqrfile.close()
if weboptions.otheroptions['apbs']:
from src import inputgen
from src import psize
method = "mg-auto"
size = psize.Psize()
size.parseInput(pqrpath)
size.runPsize(pqrpath)
async = 0 # No async files here!
myinput = inputgen.Input(pqrpath,
size,
method,
async,
potdx=True)
myinput.printInputFiles()
myinput.dumpPickle()
endtime = time.time() - starttime
#createResults(header, input, name, endtime, missedligands)
#logRun(weboptions, endtime, len(lines), weboptions.ff, os.environ["REMOTE_ADDR"])
#printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
if 'ligand' in weboptions:
outputligandfile = open(
'%s%s%s/%s.mol2' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputligandfile.write(weboptions.ligandfilestring)
outputligandfile.close()
outputpdbfile = open(
'%s%s%s/%s.pdb' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputpdbfile.write(weboptions.pdbfilestring)
outputpdbfile.close()
statusfile = open(
'%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('complete\n')
filelist = glob.glob('%s%s%s/%s*' %
(INSTALLDIR, TMPDIR, name, name))
for filename in filelist:
statusfile.write(filename + '\n')
statusfile.close()
'''Upload associated APBS run files to the storage service'''
from PDB2PQR_web import jobutils
jobDir = os.path.join(INSTALLDIR, TMPDIR, name)
sys.stdout = open('%s/debug_forked_stdout.out' % (jobDir), 'a+')
sys.stderr = open('%s/debug_forked_stderr.out' % (jobDir), 'a+')
file_list = os.listdir(jobDir)
if isinstance(file_list, list):
try:
jobutils.send_to_storage_service(
storage_host, name, file_list,
os.path.join(INSTALLDIR, TMPDIR))
except Exception as err:
with open('storage_err', 'a+') as fin:
fin.write(err)
sys.stdout.close()
sys.stderr.close()
#TODO: Better error reporting.
#Also, get forked job to properly write error status on failure.
except StandardError, details:
#except StandardError as details:
print traceback.format_exc()
print sys.exc_info()[0]
#print details
createError(name, details)
def handleNonOpal(weboptions):
"""
Handle non opal run.
"""
pdblist, errlist = readPDB(weboptions.pdbfile)
dummydef = Definition()
dummyprot = Protein(pdblist, dummydef)
if len(pdblist) == 0 and len(errlist) == 0:
text = "Unable to find PDB file - Please make sure this is "
text += "a valid PDB file ID!"
#print "Content-type: text/html\n"
print(text)
sys.exit(2)
elif dummyprot.numAtoms() > MAXATOMS and weboptions["opt"] == True:
text = "<HTML><HEAD>"
text += "<TITLE>PDB2PQR Error</title>"
text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
text += "Due to server limits, we are currently unable to optimize "
text += "proteins of greater than %i atoms on the server (PDB2PQR " % MAXATOMS
text += "found %s atoms in the selected PDB file). If you " % dummyprot.numAtoms()
text += "want to forgo optimization please try the server again.<P>"
text += "Otherwise you may use the standalone version of PDB2PQR that "
text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
text += "PDB2PQR SourceForge project page</a>."
text += "<script type=\"text/javascript\">"
text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
text += "</script>"
text += "<script type=\"text/javascript\">"
text += "try {"
text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
for key in weboptions:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
#print "Content-type: text/html\n"
print(text)
sys.exit(2)
try:
starttime = time.time()
name = setID(starttime)
#Some job parameters logging.
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
apbsInputFile.write(str(weboptions["apbs"]))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
typemapInputFile.write(str(weboptions["typemap"]))
typemapInputFile.close()
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('running')
statusfile.close()
# Recording CGI run information for PDB2PQR Opal
pdb2pqrLogFile = open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrLogFile.write(str(weboptions.getOptions())+'\n'+
str(weboptions.ff)+'\n'+
str(os.environ["REMOTE_ADDR"]))
pdb2pqrLogFile.close()
pid = os.fork()
if pid:
print(redirector(name, weboptions))
sys.exit()
else:
currentdir = os.getcwd()
os.chdir("/")
os.setsid()
os.umask(0)
os.chdir(currentdir)
os.close(1) # not sure if these
os.close(2) # two lines are necessary
pqrpath = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, name, name)
orig_stdout = sys.stdout
orig_stderr = sys.stderr
sys.stdout = open('%s%s%s/pdb2pqr_stdout.txt' % (INSTALLDIR, TMPDIR, name), 'w')
sys.stderr = open('%s%s%s/pdb2pqr_stderr.txt' % (INSTALLDIR, TMPDIR, name), 'w')
run_arguements = weboptions.getRunArguments()
if weboptions.runoptions.get('ph_calc_method', '') == 'pdb2pka':
run_arguements['ph_calc_options']['output_dir']='%s%s%s/pdb2pka_output' % (INSTALLDIR, TMPDIR, name)
header, lines, missedligands, _ = runPDB2PQR(pdblist,
weboptions.ff,
outname = pqrpath,
commandLine = weboptions.getCommandLine(),
**weboptions.getRunArguments())
sys.stdout.close()
sys.stderr.close()
sys.stdout = orig_stdout
sys.stderr = orig_stderr
endtimefile = open('%s%s%s/pdb2pqr_end_time' % (INSTALLDIR, TMPDIR, name), 'w')
endtimefile.write(str(time.time()))
endtimefile.close()
pqrfile = open(pqrpath, "w")
pqrfile.write(header)
whitespace = weboptions.otheroptions['whitespace']
for line in lines:
# Adding whitespaces if --whitespace is in the weboptions
if whitespace:
if line[0:4] == 'ATOM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
elif line[0:6] == 'HETATM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
else:
pqrfile.write("%s\n" % line.strip())
pqrfile.close()
if weboptions.otheroptions['apbs']:
from src import inputgen
from src import psize
method = "mg-auto"
size = psize.Psize()
size.parseInput(pqrpath)
size.runPsize(pqrpath)
async = 0 # No async files here!
myinput = inputgen.Input(pqrpath, size, method, async, potdx=True)
myinput.printInputFiles()
myinput.dumpPickle()
endtime = time.time() - starttime
#createResults(header, input, name, endtime, missedligands)
#logRun(weboptions, endtime, len(lines), weboptions.ff, os.environ["REMOTE_ADDR"])
#printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
if 'ligand' in weboptions:
outputligandfile = open('%s%s%s/%s.mol2' % (INSTALLDIR,TMPDIR, name, name),'w')
outputligandfile.write(weboptions.ligandfilestring)
outputligandfile.close()
outputpdbfile = open('%s%s%s/%s.pdb' % (INSTALLDIR,TMPDIR,name,name),'w')
outputpdbfile.write(weboptions.pdbfilestring)
outputpdbfile.close()
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('complete\n')
filelist = glob.glob('%s%s%s/%s*' % (INSTALLDIR, TMPDIR, name, name))
for filename in filelist:
statusfile.write(filename+'\n')
statusfile.close()
#TODO: Better error reporting.
#Also, get forked job to properly write error status on failure.
except Exception as details:
#except StandardError as details:
print(traceback.format_exc())
print(sys.exc_info()[0])
#print details
createError(name, details)