""" 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" __version__ = "1.8" 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) 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 "" print "" print "\t%s" % pagetitle print "\t\n" % STYLESHEET print "" 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 = """ {trackingscript} You are being automatically redirected to a new location.
If your browser does not redirect you in {wait} seconds, or you do not wish to wait, click here. """.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 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 "\n

" print "There was an error with your job submission
" print "

" print "" print "" print "" print "" 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 = "" text += "PDB2PQR Error" text += "" % STYLESHEET text += "

PDB2PQR Error

" 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.

" text += "Otherwise you may use the standalone version of PDB2PQR that " text += "is available from the " text += "PDB2PQR SourceForge project page." text += "" text += "" text += "" #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, **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) 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, 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