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main_cgi.py
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main_cgi.py
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"""
Driver for PDB2PQR
This module takes a PDB file as input and performs optimizations
before yielding a new PDB-style file as output.
Ported to Python by Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis
Parsing utilities provided by Nathan A. Baker (Nathan.Baker@pnl.gov)
Pacific Northwest National Laboratory
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific
Northwest National Laboratory, operated by Battelle Memorial Institute,
Pacific Northwest Division for the U.S. Department Energy.;
Paul Czodrowski & Gerhard Klebe, University of Marburg.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Battelle Memorial Institute,
Pacific Northwest National Laboratory, US Department of Energy, or University
of Marburg nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
"""
__date__ = "5 April 2010"
__author__ = "Todd Dolinsky, Nathan Baker, Jens Nielsen, Paul Czodrowski, Jan Jensen, Samir Unni, Yong Huang"
import glob
import os
import time
import re
import sys
import string
from StringIO import StringIO
#import tempfile
#from src import pdb
#from src import structures
#from src import routines
#from src import protein
#from src import server
from src.pdb import readPDB
#from src.utilities import *
#from src.structures import *
from src.definitions import Definition
#from src.forcefield import *
#from src.routines import *
from src.protein import Protein
#from src.server import *
#from src.hydrogens import *
from src import utilities
from src.server import setID, createError
from src.aconf import (STYLESHEET,
WEBSITE,
PDB2PQR_OPAL_URL,
HAVE_PDB2PQR_OPAL,
INSTALLDIR,
TMPDIR,
MAXATOMS,
PDB2PQR_VERSION)
__version__ = PDB2PQR_VERSION
from main import runPDB2PQR
def printHeader(pagetitle,have_opal=None,jobid=None):
"""
Function to print html headers
"""
if jobid:
if have_opal:
print "Location: querystatus.cgi?jobid=%s&typeofjob=opal\n" % (jobid)
else:
print "Location: querystatus.cgi?jobid=%s&typeofjob=local\n" % (jobid)
#print "Content-type: text/html\n"
print "<HTML>"
print "<HEAD>"
print "\t<TITLE>%s</TITLE>" % pagetitle
print "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
print "</HEAD>"
return
def redirector(name, weboptions):
"""
Prints a page which redirects the user to querystatus.cgi and writes starting time to file
"""
redirectWait = 3
utilities.startLogFile(name, 'pdb2pqr_start_time', str(time.time()))
jobid = int(name)
analiticsDict = weboptions.getOptions()
events = {}
events['submission'] = analiticsDict['pdb']+'|'+str(os.environ["REMOTE_ADDR"])
del analiticsDict['pdb']
events['titration'] = str(analiticsDict.get('ph'))
if 'ph' in analiticsDict:
del analiticsDict['ph']
events['apbsInput'] = str(analiticsDict.get('apbs'))
del analiticsDict['apbs']
#Clean up selected extensions output
if 'selectedExtensions' in analiticsDict:
analiticsDict['selectedExtensions'] = ' '.join(analiticsDict['selectedExtensions'])
options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.iteritems())
events['options']=options
eventsScriptString = ''
for event in events:
eventsScriptString += utilities.getEventTrackingString(category='submissionData',
action=event,
label=events[event])
redirectURL = "{website}querystatus.cgi?jobid={jobid}&calctype=pdb2pqr".format(website=WEBSITE,
jobid=jobid)
string = """
<html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<meta http-equiv="Refresh" content="{wait}; url={redirectURL}">
</head>
<body>
You are being automatically redirected to a new location.<br />
If your browser does not redirect you in {wait} seconds, or you do
not wish to wait, <a href="{redirectURL}">click here</a>.
</body>
</html>""".format(trackingscript=utilities.getTrackingScriptString(jobid=jobid),
trackingevents=eventsScriptString, redirectURL=redirectURL, wait=redirectWait)
return string
def sanitizeFileName(fileName):
fileName = re.split(r'[/\\]',fileName)[-1]
fileName = fileName.replace(' ', '_')
fileName = fileName.replace('-', '_')
return fileName
class WebOptionsError(Exception):
pass
class WebOptions(object):
'''Helper class for gathering and querying options selected by the user'''
def __init__(self, form):
'''Gleans all information about the user selected options and uploaded files.
Also validates the user input. Raises WebOptionsError if there is any problems.'''
#options to pass to runPDB2PQR
self.runoptions = {}
#Additional options to pass to google analytics along with the run options.
#These are included in has_key(), __contains__(), and __getitem__() calls.
self.otheroptions = {}
self.runoptions['debump'] = form.has_key("DEBUMP")
self.runoptions['opt'] = form.has_key("OPT")
if form.has_key('FF'):
self.ff = form["FF"].value.lower()
else:
raise WebOptionsError('Force field type missing from form.')
if form.has_key("PDBID") and form["PDBID"].value and form["PDBSOURCE"].value == 'ID':
self.pdbfile = utilities.getPDBFile(form["PDBID"].value)
if self.pdbfile is None:
raise WebOptionsError('The pdb ID provided is invalid.')
self.pdbfilestring = self.pdbfile.read()
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = form["PDBID"].value
elif form.has_key("PDB") and form["PDB"].filename and form["PDBSOURCE"].value == 'UPLOAD':
self.pdbfilestring = form["PDB"].value
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = sanitizeFileName(form["PDB"].filename)
else:
raise WebOptionsError('You need to specify a pdb ID or upload a pdb file.')
if form.has_key("PROPKA"):
if not form.has_key('PH'):
raise WebOptionsError('Please provide a pH value.')
phHelp = 'Please choose a pH between 0.0 and 14.0.'
try:
ph = float(form["PH"].value)
except ValueError:
raise WebOptionsError('The pH value provided must be a number! ' + phHelp)
if ph < 0.0 or ph > 14.0:
text = "The entered pH of %.2f is invalid! " % ph
text += phHelp
raise WebOptionsError(text)
self.runoptions['ph'] = ph
#build propka options
self.runoptions['propkaOptions'] = utilities.createPropkaOptions(ph, True)
self.otheroptions['apbs'] = form.has_key("INPUT")
self.otheroptions['whitespace'] = form.has_key("WHITESPACE")
if self.ff == 'user':
if form.has_key("USERFF") and form["USERFF"].filename:
self.userfffilename = sanitizeFileName(form["USERFF"].filename)
self.userffstring = form["USERFF"].value
self.runoptions['userff'] = StringIO(form["USERFF"].value)
else:
text = "A force field file must be provided if using a user created force field."
raise WebOptionsError(text)
if form.has_key("USERNAMES") and form["USERNAMES"].filename:
self.usernamesfilename = sanitizeFileName(form["USERNAMES"].filename)
self.usernamesstring = form["USERNAMES"].value
self.runoptions['usernames'] = StringIO(form["USERNAMES"].value)
else:
text = "A names file must be provided if using a user created force field."
raise WebOptionsError(text)
if form.has_key("FFOUT") and form["FFOUT"].value != "internal":
self.runoptions['ffout'] = form["FFOUT"].value
self.runoptions['chain'] = form.has_key("CHAIN")
self.runoptions['typemap'] = form.has_key("TYPEMAP")
self.runoptions['neutraln'] = form.has_key("NEUTRALN")
self.runoptions['neutralc'] = form.has_key("NEUTRALC")
if (self.runoptions['neutraln'] or self.runoptions['neutraln']) and \
self.ff != 'parse':
raise WebOptionsError('Neutral N-terminus and C-terminus require the PARSE forcefield.')
if form.has_key("LIGAND") and form['LIGAND'].filename:
self.ligandfilename=sanitizeFileName(form["LIGAND"].filename)
ligandfilestring = form["LIGAND"].value
# for Windows and Mac style newline compatibility for pdb2pka
ligandfilestring = ligandfilestring.replace('\r\n', '\n')
self.ligandfilestring = ligandfilestring.replace('\r', '\n')
self.runoptions['ligand'] = StringIO(self.ligandfilestring)
if self.pdbfilename[-4:]==".pdb":
self.pqrfilename = "%s.pqr" % self.pdbfilename[:-4]
else:
self.pqrfilename = "%s.pqr" % self.pdbfilename
#Always turn on summary and verbose.
self.runoptions['verbose'] = True
self.runoptions['selectedExtensions'] = ['summary']
def getLoggingList(self):
'''Returns a list of options the user has turned on.
Used for logging jobs later in usage.txt'''
results = []
for key in self:
if self[key]:
results.append(key)
return results
def getRunArguments(self):
'''Returns argument suitable for runPDB2PQR'''
return self.runoptions.copy()
def getOptions(self):
'''Returns all options for reporting to Google analytics'''
options = self.runoptions.copy()
options.update(self.otheroptions)
options['ff'] = self.ff
options['pdb'] = self.pdbfilename
#propkaOptions is redundant.
if options.has_key('propkaOptions'):
del options['propkaOptions']
if options.has_key('ligand'):
options['ligand'] = self.ligandfilename
if options.has_key('userff'):
options['userff'] = self.userfffilename
if options.has_key('usernames'):
options['usernames'] = self.usernamesfilename
return options
def getCommandLine(self):
commandLine = []
if not self.runoptions['debump']:
commandLine.append('--nodebump')
if not self.runoptions['opt']:
commandLine.append('--noopt')
if 'ph' in self.runoptions:
commandLine.append('--with-ph=%s' % self.runoptions['ph'])
if self.otheroptions['apbs']:
commandLine.append('--apbs-input')
if self.otheroptions['whitespace']:
commandLine.append('--whitespace')
if 'userff' in self.runoptions and self.ff == 'user':
commandLine.append('--userff=%s' % self.userfffilename)
commandLine.append('--usernames=%s' % self.usernamesfilename)
else:
commandLine.append('--ff=%s' % self.ff)
if 'ffout' in self.runoptions:
commandLine.append('--ffout=%s' % self.runoptions['ffout'])
for o in ('chain', 'typemap', 'neutraln', 'neutralc', 'verbose'):
if self.runoptions[o]:
commandLine.append('--' + o)
if 'ligand' in self.runoptions:
commandLine.append('--ligand=%s' % self.ligandfilename)
for ext in self.runoptions.get('selectedExtensions',[]):
commandLine.append('--%s' % ext)
commandLine.append(self.pdbfilename)
commandLine.append(self.pqrfilename)
return ' '.join(commandLine)
def __contains__(self, item):
'''Helper for checking for the presence of an option'''
return item in self.runoptions or item in self.otheroptions
def has_key(self, item):
'''Helper for checking for the presence of an option'''
return item in self.runoptions or item in self.otheroptions
def __iter__(self):
for key in self.runoptions:
yield key
for key in self.otheroptions:
yield key
def __getitem__(self, key):
return self.runoptions[key] if key in self.runoptions else self.otheroptions[key]
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
from ZSI.TC import String
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)
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 StandardError, details:
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 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 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')
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[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % string.strip(newline))
elif line[0:6] == 'HETATM':
newline = line[0:16] + ' ' + 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()
#TODO: Better error reporting.
#Also, get forked job to properly write error status on failure.
except StandardError as details:
print details
createError(name, details)
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()
try:
weboptions = WebOptions(form)
except WebOptionsError as error:
print(error)
sys.exit(2)
if HAVE_PDB2PQR_OPAL=="1":
handleOpal(weboptions)
else:
handleNonOpal(weboptions)
return