def makeInputFile(path, name=None):
from AppService_types import ns0
inputFile = ns0.InputFileType_Def("inputFile")
if name is None:
import os.path
name = os.path.basename(path)
inputFile._name = name
f = open(path)
inputFile._contents = f.read()
f.close()
return inputFile
def launchJobNB(self, commandline, inFilesPath, numProcs = None, email = None, \
passwd=None):
""" launchJobNB(commandline, inFilesPath[, numProcs, email, passwd]) -> JobStatus
It invokes the execution of the remote application and return.
commandline: is a string containing the command line that should be executed
inFilesPath: is a list of strings containing relative or absolute path to the
files need to be uploaded for the execution of the application
numProcs: is the number of processors that should be used to run the parallel
application (this option is valid only for parallel applicaiton)
email: is a string containing the email used to send notification when the
application execution will finish
passwd: is a string containing the passwd used to authenticate with the server
@returns: a JobStatus Oject which can be used to monitor its execution"""
inputFiles = []
if inFilesPath != None:
for i in inFilesPath:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
if i.startswith("http:") or i.startswith("https:"):
#this is a URL
inputFile._location = i
elif self.isOpal2():
#use attachment this is opal2 server
if os.name == 'dos' or os.name == 'nt':
inputFile._attachment = open(i, "rb")
else:
inputFile._attachment = open(i, "r")
else:
#it's not a opal2 server don't user attachment
infile = open(i, "r")
inputFile._contents = infile.read()
infile.close()
inputFiles.append(inputFile)
req = launchJobRequest()
req._argList = commandline
req._inputFile = inputFiles
if email:
req._sendNotification = True
req._userEmail = email
if passwd:
req._password = passwd
if numProcs :
req._numProcs = numProcs
jobStatus = self.appServicePort.launchJob(req)
return JobStatus(self, jobStatus._jobID)
def launchJobNB(self, commandline, inFilesPath, numProcs = None, email = None, \
passwd=None):
""" invoke the execution of the remote scientific application
using Opal a return right away
@returns: a jobStatus Oject which can be used to monitor its execution"""
inputFiles = []
if inFilesPath != None:
for i in inFilesPath:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
if i.startswith("http:") or i.startswith("https:"):
#this is a URL
inputFile._location = i
elif self.isOpal2():
#use attachment this is opal2 server
if os.name == 'dos' or os.name == 'nt':
inputFile._attachment = open(i, "rb")
else:
inputFile._attachment = open(i, "r")
else:
#it's not a opal2 server don't user attachment
infile = open(i, "r")
inputFile._contents = infile.read()
infile.close()
inputFiles.append(inputFile)
req = launchJobRequest()
req._argList = commandline
req._inputFile = inputFiles
if email:
req._sendNotification = True
req._userEmail = email
if passwd:
req._password = passwd
if numProcs :
req._numProcs = numProcs
jobStatus = self.appServicePort.launchJob(req)
return JobStatus(self, jobStatus._jobID)
# Instantiate a new non-blocking job request
req = launchJobRequest()
# Set the command-line arguments for the job.
# Use DNA alphabet, and find 3 motifs.
req._argList = "meme crp0.fasta -dna -mod zoops -nmotifs 3"
# Get contents of local file to be used as input
fastaFile = open("./crp0.fasta", "r")
fastaFileContents = fastaFile.read()
fastaFile.close()
# Set name and content of remote input file.
# Only one input file is used, the FASTA file.
inputFiles = []
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = 'crp0.fasta'
inputFile._contents = fastaFileContents
inputFiles.append(inputFile)
req._inputFile = inputFiles
# Launch non-blocking job and retrieve job ID
print "Launching remote MEME job"
resp = appServicePort.launchJob(req)
jobID = resp._jobID
print "Received Job ID:", jobID
# Poll for job status
status = resp._status
print "Polling job status"
while 1:
# preloaded Saccaromyces cerevisiae genome.
#req._argList = "crp0.meme.xml saccharomyces_cerevisiae.na --oc ."
# Get contents of local files to be used as input
fastaFile = open("./crp0.fasta", "r")
fastaFileContents = fastaFile.read()
fastaFile.close()
motifFile = open("./crp0.meme.xml", "r")
motifFileContents = motifFile.read()
motifFile.close()
# Set name and content of remote input file.
# Two input files are used, the motif file
#and the FASTA file.
inputFiles = []
motifInputFile = ns0.InputFileType_Def('inputFile')
motifInputFile._name = 'crp0.meme.xml'
motifInputFile._contents = motifFileContents
inputFiles.append(motifInputFile)
fastaInputFile = ns0.InputFileType_Def('inputFile')
fastaInputFile._name = 'uploaded_db'
fastaInputFile._contents = fastaFileContents
inputFiles.append(fastaInputFile)
req._inputFile = inputFiles
# Launch a non-blocking job
print "Launching non-blocking FIMO job"
resp = appServicePort.launchJob(req)
jobID = resp._jobID
print "Received Job ID:", jobID
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
print "</P>"
print "<script type=\"text/javascript\">"
print "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
print "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
print "</script>"
print "<script type=\"text/javascript\">"
print "try {"
print "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
for key in weboptions:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, weboptions[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
def mainCGI():
"""
Main driver for running PDB2PQR from a web page
"""
global ligandFile, pdbfilestring, templigandstring, ffFileString, name, pdblist, namesFileString, launchJobRequest, AppServiceLocator, pdbfilename, namesfile, fffile, ns0, ligandfilename, pdbfile, namesFile, ffFile
print("Content-type: text/html\n")
import cgi
import cgitb
cgitb.enable()
form = cgi.FieldStorage()
ff = form["FF"].value
input = 0
apbs_input = "INPUT" in form
typemap = "TYPEMAP" in form
neutraln = "NEUTRALN" in form
neutralc = "NEUTRALC" in form
if HAVE_PDB2PQR_OPAL == "1":
have_opal = True
# Opal-specific import statments
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
if have_opal:
options = {"ff": ff}
fffile = None
namesfile = None
else:
options = {"extensions": {}}
if "DEBUMP" in form:
options["debump"] = 1
else:
options["debump"] = 0
if "OPT" in form:
options["opt"] = 1
else:
options["opt"] = 0
if "PROPKA" in form:
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
# print "Content-type: text/html\n"
print(text)
sys.exit(2)
if "PDBID" in form:
pdbfile = getPDBFile(form["PDBID"].value)
pdbfilename = form["PDBID"].value
elif "PDB" in form:
pdbfile = StringIO(form["PDB"].value)
pdbfilename = form["PDB"].filename
pdbfilename = pdbfilename.split(r'[/\\]')[-1]
if "INPUT" in form:
input = 1
options["apbs"] = 1
if "USERFF" in form:
if have_opal:
ffname = form["USERFF"].filename
ffname = ffname.split(r'[/\\]')[-1]
if ffname[-4:] == ".DAT":
ffname = ffname[:-4]
fffile = StringIO(form["USERFF"].value)
namesfile = StringIO(form["USERNAMES"].value)
options["ff"] = ffname
options["userff"] = fffile
options["usernames"] = namesfile
else:
userff = StringIO(form["USERFF"].value)
usernames = StringIO(form["USERNAMES"].value)
options["ff"] = "user-defined"
options["userff"] = userff
options["usernames"] = usernames
if "FFOUT" in form:
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if "CHAIN" in form:
options["chain"] = 1
if "WHITESPACE" in form:
options["whitespace"] = 1
if "TYPEMAP" in form:
options["typemap"] = 1
if "NEUTRALN" in form:
options["neutraln"] = 1
if "NEUTRALC" in form:
options["neutralc"] = 1
if "LIGAND" in form:
if have_opal:
ligandfilename = str(form["LIGAND"].filename)
ligandfilename = ligandfilename.split(r'[/\\]')[-1]
# for Windows-style newline compatibility
templigandfilename = tempfile.mkstemp()[1]
templigandfile = open(templigandfilename, 'w')
templigandfile.write(form["LIGAND"].value)
templigandfile.close()
templigandfile = open(templigandfilename, 'rU')
if have_opal:
options["ligand"] = templigandfile.read()
else:
templigandstring = templigandfile.read() # this variable is used again later to write this file to output
options["ligand"] = StringIO(templigandstring)
templigandfile.close()
if not have_opal:
pdbfilestring = pdbfile.read()
pdblist, errlist = readPDB(StringIO(pdbfilestring))
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 "opt" in options:
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 MAXATOMS atoms on the server (PDB2PQR "
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 options:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
# print "Content-type: text/html\n"
print(text)
sys.exit(2)
try:
if have_opal:
ligandFile = None
ffFile = None
namesFile = None
# else:
starttime = time.time()
name = setID(starttime)
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name), 'w')
apbsInputFile.write(str(apbs_input))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name), 'w')
typemapInputFile.write(str(typemap))
typemapInputFile.close()
if have_opal:
myopts = ""
for key in options:
if key == "opt":
if options[key] == 0:
# user does not want optimization
key = "noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key == "debump":
if options[key] == 0:
# user does not want debumping
key = "nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key == "ph":
val = options[key]
key = "with-ph=%s" % val
elif key == "ffout":
val = options[key]
key = "ffout=%s" % val
elif key == "ligand":
val = ligandfilename
key = "ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFile._contents = options["ligand"]
elif key == "apbs":
key = "apbs-input"
elif key == "chain":
key = "chain"
elif key == "whitespace":
key = "whitespace"
elif key == "typemap":
key = "typemap"
elif key == "ff":
val = options[key]
key = "ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val + ".DAT"
ffFileString = fffile.read()
ffFile._contents = ffFileString
if namesfile:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = val + ".names"
namesFileString = namesfile.read()
namesFile._contents = namesFileString
if key not in ["userff", "usernames"]:
myopts += "--" + str(key) + " "
myopts += str(pdbfilename) + " "
if pdbfilename[-4:] == ".pdb":
myopts += "%s.pqr" % str(pdbfilename[:-4])
else:
myopts += "%s.pqr" % str(pdbfilename)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = pdbfilename
pdbOpalFile._contents = pdbfile.read()
pdbfile.close()
inputFiles.append(pdbOpalFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
if namesFile:
inputFiles.append(namesFile)
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception as e:
printHeader("PDB2PQR Job Submission - Error")
print("<BODY>\n<P>")
print("There was an error with your job submission<br>")
print("</P>")
print("<script type=\"text/javascript\">")
print(
"var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");")
print(
"document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));")
print("</script>")
print("<script type=\"text/javascript\">")
print("try {")
print("var pageTracker = _gat._getTracker(\"UA-11026338-3\");")
for key in options:
print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key]))
print("pageTracker._trackPageview();")
print("} catch(err) {}</script>")
print("</BODY>")
print("</HTML>")
sys.exit(2)
# printHeader("PDB2PQR Job Submission",have_opal,jobid=resp._jobID)
pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print(redirector(name))
if "userff" in options:
options["userff"] = ffFileString
if "usernames" in options:
options["usernames"] = namesFileString
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(str(options) + '\n' + str(ff) + '\n' + str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
else:
# pqrpath = startServer(name)
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('running')
statusfile.close()
pid = os.fork()
if pid:
print(redirector(name))
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)
options["outname"] = pqrpath
options["verbose"] = ""
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')
header, lines, missedligands = runPDB2PQR(pdblist, ff, options)
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)
for line in lines: # type: object
# Adding whitespaces if --whitespace is in the options
if "whitespace" in options.keys() and options["whitespace"] == 1:
if line[0:4] == 'ATOM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
elif line[0:6] == 'HETATM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
else:
pqrfile.write("%s\n" % line.strip())
pqrfile.close()
if input:
from src import inputgen as Inp
from src import psize as Pz
method = "mg-auto"
size = Pz.Psize()
size.parseInput(pqrpath)
size.runPsize(pqrpath)
async = 0 # No async files here!
myinput = Inp.Input(pqrpath, size, method, async)
myinput.printInputFiles()
myinput.dumpPickle()
endtime = time.time() - starttime
# createResults(header, input, name, endtime, missedligands)
logRun(options, endtime, len(lines), ff, os.environ["REMOTE_ADDR"])
# printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
if "LIGAND" in form:
outputligandfile = open('%s%s%s/%s.mol2' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputligandfile.write(templigandstring)
outputligandfile.close()
outputpdbfile = open('%s%s%s/%s.pdb' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputpdbfile.write(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()
except SystemError.StandardError as details:
print(details)
createError(name, details)
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception as e:
printHeader("PDB2PQR Job Submission - Error")
print("<BODY>\n<P>")
print("There was an error with your job submission<br>")
print("</P>")
print("<script type=\"text/javascript\">")
print(
"var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
)
print(
"document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
)
print("</script>")
print("<script type=\"text/javascript\">")
print("try {")
print("var pageTracker = _gat._getTracker(\"UA-11026338-3\");")
for key in weboptions:
print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" %
(key, weboptions[key]))
print("pageTracker._trackPageview();")
print("} catch(err) {}</script>")
print("</BODY>")
print("</HTML>")
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()
pdb2pqrOpalJobIDFile = open(
'%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print(redirector(name, weboptions))
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open(
'%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(
str(weboptions.getOptions()) + '\n' +
str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
except Exception as details:
print(details)
createError(name, details)
def mainCGI():
"""
Opal driver for running PDB2PQR from a web page
"""
serviceURL = OPALURL
cgitb.enable()
form = cgi.FieldStorage()
options = {}
ff = form["FF"].value
options["ff"] = ff
fffile = None
input = 0
if form.has_key("DEBUMP"): options["debump"] = 1
else: options["debump"] = 0
if form.has_key("OPT"): options["opt"] = 1
else: options["opt"] = 0
if form.has_key("PROPKA"):
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
# print "Content-type: text/html\n"
print text
sys.exit(2)
if form.has_key("PDBID"):
filename = form["PDBID"].value
infile = getPDBFile(form["PDBID"].value)
elif form.has_key("PDB"):
filename = form["PDB"].filename
filename=re.split(r'[/\\]',filename)[-1]
infile = StringIO(form["PDB"].value)
if form.has_key("INPUT"):
input = 1
options["apbs"] = 1
if form.has_key("USERFF"):
# userff = StringIO(form["USERFF"].value)
# ff = "user-defined"
# options["userff"] = userff
ffname = form["USERFF"].filename
ffname = re.split(r'[/\\]',ffname)[-1]
fffile = StringIO(form["USERFF"].value)
options["ff"] = ffname
if form.has_key("FFOUT"):
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if form.has_key("CHAIN"):
options["chain"] = 1
if form.has_key("WHITESPACE"):
options["whitespace"] = 1
if form.has_key("LIGAND"):
ligandfilename=str(form["LIGAND"].filename)
ligandfilename=re.split(r'[/\\]',ligandfilename)[-1]
options["ligand"] = StringIO(form["LIGAND"].value)
try:
# starttime = time.time()
# name = setID(starttime)
name = filename
ligandFile=None
ffFile=None
# begin SOAP changes
# need to switch options from a dictionary to something resembling a command line query
# such as --chain
myopts=""
for key in options:
if key=="opt":
if options[key]==0:
# user does not want optimization
key="noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key=="debump":
if options[key]==0:
# user does not want debumping
key="nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key=="ph":
val=options[key]
key="with-ph=%s" % val
elif key=="ffout":
val=options[key]
key="ffout=%s" % val
elif key=="ligand":
val=ligandfilename
key="ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFileTemp = open(options["ligand"], "r")
ligandFileString = ligandFileTemp.read()
ligandFileTemp.close()
ligandFile._contents = ligandFileString
elif key=="apbs":
key="apbs-input"
elif key=="chain":
key="chain"
elif key=="whitespace":
key="whitespace"
elif key=="ff":
val=options[key]
key="ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val
ffFileTemp = open(fffile, "r")
ffFileString = ffFileTemp.read()
ffFileTemp.close()
ffFile._contents = ffFileString
myopts+="--"+str(key)+" "
myopts+=str(filename)+" "
myopts+="%s.pqr" % str(name)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(serviceURL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbFile = ns0.InputFileType_Def('inputFile')
pdbFile._name = filename
pdbFile._contents = infile.read()
infile.close()
inputFiles.append(pdbFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
req._inputFile=inputFiles
try:
resp=appServicePort.launchJob(req)
except Exception, e:
printheader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
print "</P>\n</BODY>"
print "</HTML>"
sys.exit(2)
printheader("PDB2PQR Job Submission",resp._jobID)
def mainCGI():
"""
Main driver for running PDB2PQR from a web page
"""
print "Content-type: text/html\n"
import cgi
import cgitb
cgitb.enable()
form = cgi.FieldStorage()
ff = form["FF"].value
input = 0
apbs_input = form.has_key("INPUT")
typemap = form.has_key("TYPEMAP")
neutraln = form.has_key("NEUTRALN")
neutralc = form.has_key("NEUTRALC")
if HAVE_PDB2PQR_OPAL == "1":
have_opal = True
# Opal-specific import statments
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
if have_opal:
options = {}
options["ff"] = ff
fffile = None
namesfile = None
else:
options = {"extensions": {}}
if form.has_key("DEBUMP"):
options["debump"] = 1
else:
options["debump"] = 0
if form.has_key("OPT"):
options["opt"] = 1
else:
options["opt"] = 0
if form.has_key("PROPKA"):
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
#print "Content-type: text/html\n"
print text
sys.exit(2)
if form.has_key("PDBID"):
pdbfile = getPDBFile(form["PDBID"].value)
pdbfilename = form["PDBID"].value
elif form.has_key("PDB"):
pdbfile = StringIO(form["PDB"].value)
pdbfilename = form["PDB"].filename
pdbfilename = re.split(r'[/\\]', pdbfilename)[-1]
if form.has_key("INPUT"):
input = 1
options["apbs"] = 1
if form.has_key("USERFF"):
if have_opal:
ffname = form["USERFF"].filename
ffname = re.split(r'[/\\]', ffname)[-1]
if ffname[-4:] == ".DAT":
ffname = ffname[:-4]
fffile = StringIO(form["USERFF"].value)
namesfile = StringIO(form["USERNAMES"].value)
options["ff"] = ffname
options["userff"] = fffile
options["usernames"] = namesfile
else:
userff = StringIO(form["USERFF"].value)
usernames = StringIO(form["USERNAMES"].value)
options["ff"] = "user-defined"
options["userff"] = userff
options["usernames"] = usernames
if form.has_key("FFOUT"):
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if form.has_key("CHAIN"):
options["chain"] = 1
if form.has_key("WHITESPACE"):
options["whitespace"] = 1
if form.has_key("TYPEMAP"):
options["typemap"] = 1
if form.has_key("NEUTRALN"):
options["neutraln"] = 1
if form.has_key("NEUTRALC"):
options["neutralc"] = 1
if form.has_key("LIGAND"):
if have_opal:
ligandfilename = str(form["LIGAND"].filename)
ligandfilename = re.split(r'[/\\]', ligandfilename)[-1]
# for Windows-style newline compatibility
templigandfilename = tempfile.mkstemp()[1]
templigandfile = open(templigandfilename, 'w')
templigandfile.write(form["LIGAND"].value)
templigandfile.close()
templigandfile = open(templigandfilename, 'rU')
if have_opal:
options["ligand"] = templigandfile.read()
else:
templigandstring = templigandfile.read(
) # this variable is used again later to write this file to output
options["ligand"] = StringIO(templigandstring)
templigandfile.close()
if not have_opal:
pdbfilestring = pdbfile.read()
pdblist, errlist = readPDB(StringIO(pdbfilestring))
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 "opt" in options:
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 MAXATOMS atoms on the server (PDB2PQR "
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 options:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, options[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
#print "Content-type: text/html\n"
print text
sys.exit(2)
try:
if have_opal:
ligandFile = None
ffFile = None
namesFile = None
#else:
starttime = time.time()
name = setID(starttime)
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
'w')
apbsInputFile.write(str(apbs_input))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
'w')
typemapInputFile.write(str(typemap))
typemapInputFile.close()
if have_opal:
myopts = ""
for key in options:
if key == "opt":
if options[key] == 0:
# user does not want optimization
key = "noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key == "debump":
if options[key] == 0:
# user does not want debumping
key = "nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key == "ph":
val = options[key]
key = "with-ph=%s" % val
elif key == "ffout":
val = options[key]
key = "ffout=%s" % val
elif key == "ligand":
val = ligandfilename
key = "ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFile._contents = options["ligand"]
elif key == "apbs":
key = "apbs-input"
elif key == "chain":
key = "chain"
elif key == "whitespace":
key = "whitespace"
elif key == "typemap":
key = "typemap"
elif key == "ff":
val = options[key]
key = "ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val + ".DAT"
ffFileString = fffile.read()
ffFile._contents = ffFileString
if namesfile:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = val + ".names"
namesFileString = namesfile.read()
namesFile._contents = namesFileString
if key not in ["userff", "usernames"]:
myopts += "--" + str(key) + " "
myopts += str(pdbfilename) + " "
if pdbfilename[-4:] == ".pdb":
myopts += "%s.pqr" % str(pdbfilename[:-4])
else:
myopts += "%s.pqr" % str(pdbfilename)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = pdbfilename
pdbOpalFile._contents = pdbfile.read()
pdbfile.close()
inputFiles.append(pdbOpalFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
if namesFile:
inputFiles.append(namesFile)
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
print "</P>"
print "<script type=\"text/javascript\">"
print "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
print "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
print "</script>"
print "<script type=\"text/javascript\">"
print "try {"
print "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
for key in options:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, options[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
#printHeader("PDB2PQR Job Submission",have_opal,jobid=resp._jobID)
pdb2pqrOpalJobIDFile = open(
'%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print redirector(name)
if options.has_key("userff"):
options["userff"] = ffFileString
if options.has_key("usernames"):
options["usernames"] = namesFileString
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open(
'%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(
str(options) + '\n' + str(ff) + '\n' +
str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
else:
def execApbs(vars=None, argv=None):
""" Executes APBS and regulates checking of job status and retrieval of data if job is successfully completed. """
if argv is None:
# i.e. if it is a local run
argv = sys.argv
webRun = False
else:
webRun = True
custom_service_url = None
if vars != None:
if vars.has_key('service_url'):
custom_service_url = vars['service_url']
vars = initRemoteVars(argv)
if custom_service_url != None:
vars['service_url'] = custom_service_url
global service_url
#*argument parser
# command-line arguments
vars['inFile'] = argv[-1]
# parses input file
if (vars['inFile'].find("/") == -1):
directory = ""
else:
directory = os.path.dirname(vars['inFile']) + '/'
vars['inFile'] = os.path.basename(vars['inFile'])
nprocs = 1
if not vars.has_key('service_url'):
# find out if it's sequential or parallel
tempFile = open(directory + vars['inFile'], 'r')
version_check_flag = True
for line in tempFile:
# remove whitespace
line = line.strip()
if (line[:5] == 'pdime'):
dimension_array = line.split()
nprocs = int(dimension_array[1]) * int(
dimension_array[2]) * int(dimension_array[3])
global parallel_service_url
vars['service_url'] = parallel_service_url
version_check_flag = False
if (line[:5] == 'async'):
vars['service_url'] = service_url
version_check_flag = True
break
if version_check_flag:
vars['service_url'] = service_url
tempFile.close()
else:
version_check_flag = True # Enable version checking for custom defined Opal service as well
service_url = vars['service_url']
# Retrieve a reference to the AppServicePort
#*this is also from the path to the service
appServicePort = AppServiceLocator().getAppServicePort(vars['service_url'])
# Set up remote job launch
req = launchJobRequest()
# Checks version compatibility (but currently only works for sequential calculations)
if version_check_flag:
opal_version = AppServicePortTypeSoapBindingSOAP(
vars['service_url']).getAppMetadata(
getAppMetadataRequest())._usage.split()[-1]
if opal_version != local_version:
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
stderr.write(
"It appears that the remote server version of APBS (%s) does not match\nthe local version (%s)!\n"
% (opal_version, local_version))
stderr.write("Proceed at your own risk!!\n")
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
if webRun:
return False
if (vars.has_key('argList')):
vars['argList'] = vars['argList'] + " " + vars['inFile']
else:
vars['argList'] = vars['inFile']
req._argList = vars['argList']
req._numProcs = nprocs
# append all input files in this manner - in this case we have two of them
inputFiles = []
#*this is where apbs.in is read in
inputFiles.append(ns0.InputFileType_Def('inputFile'))
#*this must be the same as req._argList is defined to be
inputFiles[-1]._name = vars['inFile']
tempFile = open(directory + vars['inFile'], 'r')
inputFiles[-1]._contents = tempFile.read()
tempFile.close()
# this is where the rest of the files to read in are determined
start = False
tempFile = open(directory + vars['inFile'], 'r')
for line in tempFile:
# remove whitespace
line = line.strip()
if (line == "end"):
break
if (start and line.find("#") != 0):
# eliminates lines with just comments
# remove comment
if (line.find("#") != -1):
line = line[:line.find("#")]
# re-remove whitespace (left after comment removal)
line = line.strip()
# remove everything except file name
count = -1
while line[count] != ' ':
count = count - 1
fileName = line[count + 1:]
inputFiles.append(ns0.InputFileType_Def('inputFile'))
inputFiles[-1]._name = fileName
tempFile2 = open(directory + fileName, "r")
inputFiles[-1]._contents = tempFile2.read()
tempFile2.close()
if (line == "read"):
start = True
tempFile.close()
# req's inputFile variable is the array of input files created in the lines directly above
req._inputFile = inputFiles
if vars['typeOfRun'] == 'remote':
appServicePort.launchJob(req)
return [appServicePort, appServicePort.launchJob(req)]
# Launch job, and retrieve job ID
print "Launching remote APBS job"
try:
resp = appServicePort.launchJob(req)
except ZSI.FaultException, errstr:
stderr.write(
"Error! Failed to execute Opal job. Please send the entire output to the APBS development team.\n"
)
stderr.write("%s\n" % errstr.fault.AsSoap())
sys.exit(13)