Description: Use 2to3 to port from Python2 to Python3 Bug-Debian: https://bugs.debian.org/937262 Author: Andreas Tille Last-Update: Tue, 15 Feb 2022 07:03:38 -0500 --- a/main_cgi.py +++ b/main_cgi.py @@ -53,7 +53,7 @@ import re import sys import string -from StringIO import StringIO +from io import StringIO #import tempfile #from src import pdb @@ -94,16 +94,16 @@ """ if jobid: if have_opal: - print "Location: querystatus.cgi?jobid=%s&typeofjob=opal\n" % (jobid) + print("Location: querystatus.cgi?jobid=%s&typeofjob=opal\n" % (jobid)) else: - print "Location: querystatus.cgi?jobid=%s&typeofjob=local\n" % (jobid) + 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 "" + print("") + print("") + print("\t%s" % pagetitle) + print("\t\n" % STYLESHEET) + print("") return def redirector(name, weboptions): @@ -135,7 +135,7 @@ if 'selectedExtensions' in analiticsDict: analiticsDict['selectedExtensions'] = ' '.join(analiticsDict['selectedExtensions']) - options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.iteritems()) + options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.items()) events['options']=options eventsScriptString = '' @@ -188,31 +188,31 @@ #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") + self.runoptions['debump'] = "DEBUMP" in form + self.runoptions['opt'] = "OPT" in form - if form.has_key('FF'): + if 'FF' in form: 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': + if "PDBID" in form 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': + elif "PDB" in form 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("PKACALCMETHOD"): + if "PKACALCMETHOD" in form: if form["PKACALCMETHOD"].value != 'none': - if not form.has_key('PH'): + if 'PH' not in form: raise WebOptionsError('Please provide a pH value.') phHelp = 'Please choose a pH between 0.0 and 14.0.' @@ -237,11 +237,11 @@ 'sdie': 80, 'pairene': 1.0} - self.otheroptions['apbs'] = form.has_key("INPUT") - self.otheroptions['whitespace'] = form.has_key("WHITESPACE") + self.otheroptions['apbs'] = "INPUT" in form + self.otheroptions['whitespace'] = "WHITESPACE" in form if self.ff == 'user': - if form.has_key("USERFF") and form["USERFF"].filename: + if "USERFF" in form and form["USERFF"].filename: self.userfffilename = sanitizeFileName(form["USERFF"].filename) self.userffstring = form["USERFF"].value self.runoptions['userff'] = StringIO(form["USERFF"].value) @@ -249,7 +249,7 @@ 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: + if "USERNAMES" in form and form["USERNAMES"].filename: self.usernamesfilename = sanitizeFileName(form["USERNAMES"].filename) self.usernamesstring = form["USERNAMES"].value self.runoptions['usernames'] = StringIO(form["USERNAMES"].value) @@ -257,20 +257,20 @@ 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": + if "FFOUT" in form 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") - self.runoptions['drop_water'] = form.has_key("DROPWATER") + self.runoptions['chain'] = "CHAIN" in form + self.runoptions['typemap'] = "TYPEMAP" in form + self.runoptions['neutraln'] = "NEUTRALN" in form + self.runoptions['neutralc'] = "NEUTRALC" in form + self.runoptions['drop_water'] = "DROPWATER" in form 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: + if "LIGAND" in form and form['LIGAND'].filename: self.ligandfilename=sanitizeFileName(form["LIGAND"].filename) ligandfilestring = form["LIGAND"].value # for Windows and Mac style newline compatibility for pdb2pka @@ -313,16 +313,16 @@ options['pdb'] = self.pdbfilename #propkaOptions is redundant. - if options.has_key('ph_calc_options'): + if 'ph_calc_options' in options: del options['ph_calc_options'] - if options.has_key('ligand'): + if 'ligand' in options: options['ligand'] = self.ligandfilename - if options.has_key('userff'): + if 'userff' in options: options['userff'] = self.userfffilename - if options.has_key('usernames'): + if 'usernames' in options: options['usernames'] = self.usernamesfilename return options @@ -437,24 +437,24 @@ try: resp=appServicePort.launchJob(req) - except Exception, e: + except Exception as e: printHeader("PDB2PQR Job Submission - Error") - print "\n

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

" - print "" - print "") + print("" - print "" - print "" + print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])) + print("pageTracker._trackPageview();") + print("} catch(err) {}") + print("") + print("") sys.exit(2) try: @@ -475,7 +475,7 @@ pdb2pqrOpalJobIDFile.write(resp._jobID) pdb2pqrOpalJobIDFile.close() - print redirector(name, weboptions) + print(redirector(name, weboptions)) # Recording CGI run information for PDB2PQR Opal pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w') @@ -483,8 +483,8 @@ str(os.environ["REMOTE_ADDR"])) pdb2pqrOpalLogFile.close() - except StandardError, details: - print details + except Exception as details: + print(details) createError(name, details) def handleNonOpal(weboptions): @@ -500,7 +500,7 @@ 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 + print(text) sys.exit(2) elif dummyprot.numAtoms() > MAXATOMS and weboptions["opt"] == True: text = "" @@ -527,7 +527,7 @@ text += "} catch(err) {}" text += "" #print "Content-type: text/html\n" - print text + print(text) sys.exit(2) try: @@ -558,7 +558,7 @@ pid = os.fork() if pid: - print redirector(name, weboptions) + print(redirector(name, weboptions)) sys.exit() else: currentdir = os.getcwd() @@ -646,10 +646,10 @@ #TODO: Better error reporting. #Also, get forked job to properly write error status on failure. - except StandardError, details: + except Exception as details: #except StandardError as details: - print traceback.format_exc() - print sys.exc_info()[0] + print(traceback.format_exc()) + print(sys.exc_info()[0]) #print details createError(name, details) @@ -657,7 +657,7 @@ """ Main driver for running PDB2PQR from a web page """ - print "Content-type: text/html\n" + print("Content-type: text/html\n") import cgi import cgitb --- a/pdb2pka/NEWligand_topology.py +++ b/pdb2pka/NEWligand_topology.py @@ -7,13 +7,13 @@ import numpy #from sets import Set -from ligandclean.trial_templates import * -from ligandclean.lookuptable import * +from .ligandclean.trial_templates import * +from .ligandclean.lookuptable import * try: - from substruct import Algorithms + from .substruct import Algorithms except ImportError: txt = "Cannot import Algorithms, this may be the result of disabling pdb2pka at configure stage!" - raise ImportError, txt + raise ImportError(txt) from types import * def length(vector): @@ -51,7 +51,7 @@ # Get the likely types from names # trivial_types=['N','O','C','H'] - for atom in self.atoms.keys(): + for atom in list(self.atoms.keys()): if atom[0] in trivial_types: if atom[0]!='H': # Get rid of all the hydrogens self.atoms[atom]['type']=atom[0] @@ -61,9 +61,9 @@ # First approximation: Anything closer than 2.0 A is bonded # self.dists={} - for atom1 in self.atoms.keys(): + for atom1 in list(self.atoms.keys()): self.dists[atom1]={} - for atom2 in self.atoms.keys(): + for atom2 in list(self.atoms.keys()): if atom1==atom2: continue # @@ -79,7 +79,7 @@ # # Get the torsion angles # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() for atom in atoms: self.atoms[atom]['torsions']=self.get_torsions(atom) @@ -128,7 +128,7 @@ # # Get the torsion angles # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() for atom in atoms: self.atoms[atom]['torsions']=self.get_torsions(atom) @@ -149,7 +149,7 @@ # + determine their likely order (e.g. single, double, or triple) # ambs={} - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) for atom_name in atoms: bonds=self.atoms[atom_name]['bonds'] atype=self.atoms[atom_name]['type'] @@ -172,13 +172,13 @@ # valences={'C':4,'O':2,'N':3} for atom in self.atoms: - print atom, self.atoms[atom] + print(atom, self.atoms[atom]) # # ok, now it gets hairy # - print - print 'Guessing sybyl atom types' - for atom in self.atoms.keys(): + print() + print('Guessing sybyl atom types') + for atom in list(self.atoms.keys()): stype=None at=self.atoms[atom] # @@ -218,7 +218,7 @@ # Do some postchecks # - right now only for Carboxylic acids # - for atom in self.atoms.keys(): + for atom in list(self.atoms.keys()): at=self.atoms[atom] if at['sybylType']=='C.2': # @@ -239,11 +239,11 @@ # # All Done # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() - print '\nFinal Sybyl type results' + print('\nFinal Sybyl type results') for atom in atoms: - print atom,self.atoms[atom]['sybylType'] + print(atom,self.atoms[atom]['sybylType']) return # @@ -273,7 +273,7 @@ tps.sort() # To agree with dictionary layout best_fit=2.00 best_type=None - for bond in bond_props.keys(): + for bond in list(bond_props.keys()): if bond[0]==tps[0] and bond[-1]==tps[1]: if abs(dist-bond_props[bond][0]) maching pair of ligand and template atoms # temporary depostion @@ -631,10 +631,10 @@ # loop over all entries for possiblyredundantentries in NonRedundantCliques: if set(possiblyredundantentries).issubset(set(xxxx)): - print NonRedundantCliques + print(NonRedundantCliques) NonRedundantCliques.remove(possiblyredundantentries) NonRedundantCliques.append(xxxx) - print NonRedundantCliques + print(NonRedundantCliques) elif set(xxxx).issubset(set(possiblyredundantentries)): #print "found subset which is not added to the list" pass @@ -665,17 +665,17 @@ for allCl in dict_of_matched_lig_fragments: if dict_of_matched_lig_fragments[allCl]['matchedligatoms'] == NonRedundantCliques[0]: - print "WE MATCHED", dict_of_matched_lig_fragments[allCl]['templatename'] - print "matchedligatoms : ", dict_of_matched_lig_fragments[allCl]['matchedligatoms'] - print "type : ", dict_of_matched_lig_fragments[allCl]['type'] - print "modelpka : ", dict_of_matched_lig_fragments[allCl]['modelpka'] - print "titratableatoms : ", dict_of_matched_lig_fragments[allCl]['titratableatoms'] - print "matching atoms : ", dict_of_matched_lig_fragments[allCl]['matching_atoms'] + print("WE MATCHED", dict_of_matched_lig_fragments[allCl]['templatename']) + print("matchedligatoms : ", dict_of_matched_lig_fragments[allCl]['matchedligatoms']) + print("type : ", dict_of_matched_lig_fragments[allCl]['type']) + print("modelpka : ", dict_of_matched_lig_fragments[allCl]['modelpka']) + print("titratableatoms : ", dict_of_matched_lig_fragments[allCl]['titratableatoms']) + print("matching atoms : ", dict_of_matched_lig_fragments[allCl]['matching_atoms']) # re-run matching to get mutiple titratable sites? # TJD: This is to resolve the bug fix when allCl is None if dict_of_matched_lig_fragments != {}: - print dict_of_matched_lig_fragments[allCl] + print(dict_of_matched_lig_fragments[allCl]) return dict_of_matched_lig_fragments[allCl] else: return {} --- a/pdb2pka/apbs.py +++ b/pdb2pka/apbs.py @@ -20,11 +20,11 @@ # # We need _apbslib.so and apbslib.py # - print - print 'Missing libraries for interfacing with APBS' - print - print 'You need to build APBS with Python support using the CMake variable -DENABLE_PYTHON=ON.' - print + print() + print('Missing libraries for interfacing with APBS') + print() + print('You need to build APBS with Python support using the CMake variable -DENABLE_PYTHON=ON.') + print() sys.exit(0) Python_kb = 1.3806581e-23 @@ -53,7 +53,7 @@ """ Return the error message """ - return `self.value` + return repr(self.value) class runAPBS: @@ -226,7 +226,7 @@ routines.write("Preparing to run %d PBE calculations. \n" % self.nosh.ncalc) - for icalc in xrange(self.nosh.ncalc): + for icalc in range(self.nosh.ncalc): sys.stdout.write("---------------------------------------------\n") self.calc = NOsh_getCalc(self.nosh, icalc) self.mgparm = self.calc.mgparm --- a/pdb2pka/charge_mon.py +++ b/pdb2pka/charge_mon.py @@ -1,4 +1,4 @@ -from Tkinter import * +from tkinter import * class charge_mon(Frame): @@ -56,13 +56,13 @@ self.cv.create_text(0,self.calc,text=self.text,anchor='nw') charges={} for resnum,atomname,charge in charge_list: - if not charges.has_key(resnum): + if resnum not in charges: charges[resnum]=[] charges[resnum].append(charge) # # Sum all charges # - for res in charges.keys(): + for res in list(charges.keys()): non_zero=None sum=0.0 for crg in charges[res]: @@ -77,7 +77,7 @@ # # later=[] - for resid in charges.keys(): + for resid in list(charges.keys()): x_count=self.res_pos[resid] if charges[resid] is None: fill='white' @@ -98,7 +98,7 @@ # for x_count,text,resid in later: self.cv.create_text(x_count,self.calc,text=text,anchor='nw',fill='black') - print '!!Wrong charge: %s %s' %(text,str(resid)) + print('!!Wrong charge: %s %s' %(text,str(resid))) # # Update and increment row # --- a/pdb2pka/example.py +++ b/pdb2pka/example.py @@ -46,7 +46,7 @@ """ Return the error message """ - return `self.value` + return repr(self.value) def getUnitConversion(): """ @@ -97,7 +97,7 @@ if not parseInputFromString(nosh, INPUT): stderr.write("main: Error while parsing input file.\n") - raise APBSError, "Error occurred!" + raise APBSError("Error occurred!") # Load the molecules using Valist_load routine @@ -145,14 +145,14 @@ sys.stdout.write("Preparing to run %d PBE calculations. \n" % nosh.ncalc) - for icalc in xrange(nosh.ncalc): + for icalc in range(nosh.ncalc): sys.stdout.write("---------------------------------------------\n") calc = NOsh_getCalc(nosh, icalc) mgparm = calc.mgparm pbeparm = calc.pbeparm if calc.calctype != 0: sys.stderr.write("main: Only multigrid calculations supported!\n") - raise APBSError, "Only multigrid calculations supported!" + raise APBSError("Only multigrid calculations supported!") for k in range(0, nosh.nelec): if NOsh_elec2calc(nosh,k) >= icalc: @@ -171,7 +171,7 @@ alist, dielXMap, dielYMap, dielZMap, kappaMap, chargeMap, pmgp, pmg) != 1: sys.stderr.write("Error setting up MG calculation!\n") - raise APBSError, "Error setting up MG calculation!" + raise APBSError("Error setting up MG calculation!") # Print problem parameters @@ -183,13 +183,13 @@ if solveMG(nosh, thispmg, mgparm.type) != 1: stderr.write("Error solving PDE! \n") - raise APBSError, "Error Solving PDE!" + raise APBSError("Error Solving PDE!") # Set partition information : Routine setPartMG if setPartMG(nosh, mgparm, thispmg) != 1: sys.stderr.write("Error setting partition info!\n") - raise APBSError, "Error setting partition info!" + raise APBSError("Error setting partition info!") ret, totEnergy[icalc] = energyMG(nosh, icalc, thispmg, 0, totEnergy[icalc], 0.0, 0.0, 0.0) @@ -212,7 +212,7 @@ if nosh.nprint > 0: sys.stdout.write("---------------------------------------------\n") sys.stdout.write("PRINT STATEMENTS\n") - for iprint in xrange(nosh.nprint): + for iprint in range(nosh.nprint): if NOsh_printWhat(nosh, iprint) == NPT_ENERGY: printEnergy(com, nosh, totEnergy, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_FORCE: @@ -283,7 +283,7 @@ # Print out the number of elec statements - print "Number of elecs: ", len(input.elecs) + print("Number of elecs: ", len(input.elecs)) # Let's set the dielectric in the second elec statement @@ -295,4 +295,4 @@ # And print the results! - print "Now we have: ", potentials + print("Now we have: ", potentials) --- a/pdb2pka/graph_cut/create_titration_output.py +++ b/pdb2pka/graph_cut/create_titration_output.py @@ -2,7 +2,7 @@ def create_output(path, curves): file_name_template = "{}_{}_{}.csv" - for key, curve in curves.items(): + for key, curve in list(curves.items()): file_name = file_name_template.format(*key) file_path = os.path.join(path, file_name) --- a/pdb2pka/graph_cut/graph.py +++ b/pdb2pka/graph_cut/graph.py @@ -21,7 +21,7 @@ self._build_nodes() #Create edges going in and out of S and T. - for key, v in self.pc.residue_variables.items(): + for key, v in list(self.pc.residue_variables.items()): prot_instance = v.instances["PROTONATED"] prot_capacity = prot_instance.energyNF / 2.0 prot_node = key+("PROTONATED",) @@ -39,7 +39,7 @@ self.DG.add_edge(deprot_node, "T", capacity=deprot_capacity) #Create all interaction energy edges. - for p, q in combinations(iter(self.pc.residue_variables.items()),2): + for p, q in combinations(iter(list(self.pc.residue_variables.items())),2): p_key, p_residue = p q_key, q_residue = q @@ -91,7 +91,7 @@ """Creates a map of residues to instances based on the """ labeling = {} uncertain = [] - for key, v in self.pc.residue_variables.items(): + for key, v in list(self.pc.residue_variables.items()): prot_node = key+("PROTONATED",) deprot_node = key+("DEPROTONATED",) --- a/pdb2pka/graph_cut/protein_complex.py +++ b/pdb2pka/graph_cut/protein_complex.py @@ -14,7 +14,7 @@ "HIS": {"model_pka": 6.6, "ionizable": 1, "tautomers":{"protonated":("1", "2"), "deprotonated":("1+2",)}}, } all_tautomers = set() -for residue_data in titratable_residue_data.values(): +for residue_data in list(titratable_residue_data.values()): all_tautomers.update(residue_data["tautomers"]["deprotonated"]) all_tautomers.update(residue_data["tautomers"]["protonated"]) state_to_tautomer = {} @@ -77,8 +77,8 @@ return self.instances.get(state) def get_prot_and_deprot_instances(self): #We don't want the placeholder instances - prot = [value for key, value in self.instances.items() if "PROTONATED" not in key and value.protonated] - deprot = [value for key, value in self.instances.items() if "PROTONATED" not in key and not value.protonated] + prot = [value for key, value in list(self.instances.items()) if "PROTONATED" not in key and value.protonated] + deprot = [value for key, value in list(self.instances.items()) if "PROTONATED" not in key and not value.protonated] return prot, deprot def __hash__(self): return hash(self.name) @@ -180,7 +180,7 @@ """After we have loaded the backgroind and desolvation files we need to update the consolidated instances to use the minimum energy of the instances they are meant to replace.""" - for key, residue in self.residue_variables.items(): + for key, residue in list(self.residue_variables.items()): name = key[0] if name == 'HIS': continue @@ -210,7 +210,7 @@ handled_interaction_pairs = set() #See https://docs.python.org/2/library/itertools.html#itertools.combinations - for v, w in combinations(iter(self.residue_variables.items()),2): + for v, w in combinations(iter(list(self.residue_variables.items())),2): v_key, v_residue = v w_key, w_residue = w v_name = v_key[0] @@ -251,7 +251,7 @@ #Now handle HIS. #See https://docs.python.org/2/library/itertools.html#itertools.permutations - for v, w in permutations(iter(self.residue_variables.items()),2): + for v, w in permutations(iter(list(self.residue_variables.items())),2): his_key, his_residue = v other_key, other_residue = w his_name = his_key[0] @@ -292,12 +292,12 @@ #Clean out unused interaction energies self.drop_interaction_pairs(handled_interaction_pairs) - for key, residue in self.residue_variables.items(): + for key, residue in list(self.residue_variables.items()): name = key[0] if name == 'HIS': continue - residue.instances = OrderedDict((k,v) for k,v in residue.instances.items() if "PROTONATED" in k) + residue.instances = OrderedDict((k,v) for k,v in list(residue.instances.items()) if "PROTONATED" in k) def divide_his(self): @@ -373,7 +373,7 @@ # HId <-> HIe.) #See https://docs.python.org/2/library/itertools.html#itertools.product - for v, w in product(iter(self.residue_variables.items()), repeat=2): + for v, w in product(iter(list(self.residue_variables.items())), repeat=2): his_key, his_residue = v other_key, other_residue = w his_name, his_chain, his_location = his_key @@ -535,7 +535,7 @@ ph_multiplier += 1.0 #See https://docs.python.org/2/library/itertools.html#itertools.combinations - for v, w in combinations(iter(self.residue_variables.items()), 2): + for v, w in combinations(iter(list(self.residue_variables.items())), 2): v_key, v_residue = v w_key, w_residue = w is_same_his = (v_key[1:] == w_key[1:] and v_key[0] in ("HId", "HIe") and w_key[0] in ("HId", "HIe")) @@ -544,12 +544,12 @@ if labeling[v_residue].protonated and labeling[w_residue].protonated: ph_multiplier -= 2.0 - for v in self.residue_variables.values(): + for v in list(self.residue_variables.values()): v_instance = labeling[v] energy += v_instance.energyNF if normal_form else v_instance.energy ie = self.normalized_interaction_energies if normal_form else self.interaction_energies - for v, w in combinations(iter(self.residue_variables.values()),2): + for v, w in combinations(iter(list(self.residue_variables.values())),2): v_instance = labeling[v] w_instance = labeling[w] energy += ie[v_instance, w_instance] @@ -562,7 +562,7 @@ return energy def instance_interaction_energy(self, instance, labeling, interaction_energy): - return sum(interaction_energy.get((instance, labeling[x]),0) for x in self.residue_variables.values()) + return sum(interaction_energy.get((instance, labeling[x]),0) for x in list(self.residue_variables.values())) def evaluate_energy_diff(self, residue, labeling, normal_form = False): """Returns the total energy difference between the deprontated and protonated @@ -572,12 +572,12 @@ prot_instance = residue.instances["PROTONATED"] prot_energy = 0 - for x in self.residue_variables.values(): + for x in list(self.residue_variables.values()): prot_energy += ie.get((prot_instance, labeling[x]),0.0) prot_energy += prot_instance.energyNF if normal_form else prot_instance.energy deprot_instance = residue.instances["DEPROTONATED"] - deprot_energy = sum(ie.get((deprot_instance, labeling[x]),0.0) for x in self.residue_variables.values()) + deprot_energy = sum(ie.get((deprot_instance, labeling[x]),0.0) for x in list(self.residue_variables.values())) deprot_energy += deprot_instance.energyNF if normal_form else deprot_instance.energy return prot_energy - deprot_energy @@ -644,8 +644,8 @@ EHd1 = hid_prot_instance.energy EHd0 = hid_deprot_instance.energy - sum_ErHd_a1 = sum(ie.get((labeling_copy[x], hid_prot_instance), 0) for x in self.residue_variables.values()) - sum_ErHd_a0 = sum(ie.get((labeling_copy[x], hid_deprot_instance), 0) for x in self.residue_variables.values()) + sum_ErHd_a1 = sum(ie.get((labeling_copy[x], hid_prot_instance), 0) for x in list(self.residue_variables.values())) + sum_ErHd_a0 = sum(ie.get((labeling_copy[x], hid_deprot_instance), 0) for x in list(self.residue_variables.values())) if normal_form: EHe1 = hie_prot_instance.energyNF @@ -654,8 +654,8 @@ EHe1 = hie_prot_instance.energy EHe0 = hie_deprot_instance.energy - sum_ErHe_a1 = sum(ie.get((labeling_copy[x], hie_prot_instance), 0) for x in self.residue_variables.values()) - sum_ErHe_a0 = sum(ie.get((labeling_copy[x], hie_deprot_instance), 0) for x in self.residue_variables.values()) + sum_ErHe_a1 = sum(ie.get((labeling_copy[x], hie_prot_instance), 0) for x in list(self.residue_variables.values())) + sum_ErHe_a0 = sum(ie.get((labeling_copy[x], hie_deprot_instance), 0) for x in list(self.residue_variables.values())) hsp_hse = EHd1 - EHd0 + sum_ErHd_a1 - sum_ErHd_a0 hsp_hsd = EHe1 - EHe0 + sum_ErHe_a1 - sum_ErHe_a0 @@ -670,7 +670,7 @@ self.normalized_constant_energy = 0.0 #Add the pH to the instances. - for residue in self.residue_variables.values(): + for residue in list(self.residue_variables.values()): residue.instances["DEPROTONATED"].energyNF = residue.instances["DEPROTONATED"].energy # TODO - I'm not sure why this is +pH.... residue.instances["PROTONATED"].energyNF = residue.instances["PROTONATED"].energy + math.log(10)*pH @@ -697,7 +697,7 @@ v_residue = rv[v_key] w_residue = rv[w_key] - for v_instance in v_residue.instances.values(): + for v_instance in list(v_residue.instances.values()): w_instances = list(w_residue.instances.values()) min_energy = min(self.normalized_interaction_energies[v_instance, w_instance] for w_instance in w_instances) @@ -709,11 +709,11 @@ self.normalized_interaction_energies[w_instance, v_instance] -= min_energy #Normalize the instance energies. - for residue in self.residue_variables.values(): - min_energy = min(instance.energyNF for instance in residue.instances.values()) + for residue in list(self.residue_variables.values()): + min_energy = min(instance.energyNF for instance in list(residue.instances.values())) self.normalized_constant_energy += min_energy if min_energy != sys.float_info.max: - for instance in residue.instances.values(): + for instance in list(residue.instances.values()): instance.energyNF -= min_energy @@ -722,11 +722,11 @@ Used primarily for testing.""" self.interaction_energies_for_ph = self.interaction_energies.copy() - for residue in self.residue_variables.values(): + for residue in list(self.residue_variables.values()): residue.instances["DEPROTONATED"].energy_with_ph = residue.instances["DEPROTONATED"].energy residue.instances["PROTONATED"].energy_with_ph = residue.instances["PROTONATED"].energy + math.log(10)*pH - for v, w in combinations(iter(self.residue_variables.items()), 2): + for v, w in combinations(iter(list(self.residue_variables.items())), 2): v_key, v_residue = v w_key, w_residue = w is_same_his = (v_key[1:] == w_key[1:] and v_key[0] in ("HId", "HIe") and w_key[0] in ("HId", "HIe")) --- a/pdb2pka/graph_cut/titration_curve.py +++ b/pdb2pka/graph_cut/titration_curve.py @@ -1,6 +1,6 @@ -from __future__ import print_function -from graph import ProteinGraph -from uncertainty import resolve_uncertainty + +from .graph import ProteinGraph +from .uncertainty import resolve_uncertainty from collections import defaultdict import math from pprint import pprint @@ -23,12 +23,12 @@ normal_form - Dump the normal form part of the state.""" rv = pc.residue_variables ie = pc.normalized_interaction_energies if normal_form else pc.interaction_energies_for_ph - for v_residue in rv.values(): - for v_instance in v_residue.instances.values(): - for w_residue in rv.values(): + for v_residue in list(rv.values()): + for v_instance in list(v_residue.instances.values()): + for w_residue in list(rv.values()): if v_residue == w_residue: continue - for w_instance in w_residue.instances.values(): + for w_instance in list(w_residue.instances.values()): out_file.write(str((v_instance, w_instance)) + " " + str(round(ie[v_instance, w_instance],4)) + '\n') keys = list(pc.residue_variables.keys()) for key in keys: @@ -127,7 +127,7 @@ new_labeling = resolve_uncertainty(protein_complex, labeling, uncertain, verbose=True) curve_values = get_curve_values(protein_complex, new_labeling, pH) - for key, value in curve_values.items(): + for key, value in list(curve_values.items()): curves[key].append((pH, value)) return curves @@ -140,7 +140,7 @@ aH = math.pow(10, -pH) - for key, residue in protein_complex.residue_variables.items(): + for key, residue in list(protein_complex.residue_variables.items()): name, chain, location = key if name in ("HId", "HIe"): --- a/pdb2pka/graph_cut/uncertainty.py +++ b/pdb2pka/graph_cut/uncertainty.py @@ -1,4 +1,4 @@ -from __future__ import print_function + import sys from itertools import product import random --- a/pdb2pka/graph_cut/utils.py +++ b/pdb2pka/graph_cut/utils.py @@ -18,8 +18,8 @@ if flipped_inter_avg is not None: diff = abs(inter_avg - flipped_inter_avg) if diff > 0.0: - print group1_type, group1_chain, group1_loc, group1_state - print group2_type, group2_chain, group2_loc, group2_state + print(group1_type, group1_chain, group1_loc, group1_state) + print(group2_type, group2_chain, group2_loc, group2_state) @@ -50,10 +50,10 @@ res_type = pKa.pKaGroup.name chain = pKa.residue.chainID location = str(pKa.residue.resSeq) - for state, energy in pKa.desolvation.iteritems(): + for state, energy in pKa.desolvation.items(): _process_desolv_or_background_line(protein_complex, res_type, chain, location, state, energy) - for state, energy in pKa.background.iteritems(): + for state, energy in pKa.background.items(): _process_desolv_or_background_line(protein_complex, res_type, chain, location, state, energy) def _process_desolv_or_background_line(protein_complex, res_type, chain, location, state_name, energy): --- a/pdb2pka/inputgen_pKa.py +++ b/pdb2pka/inputgen_pKa.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # $Id$ # @@ -57,7 +57,7 @@ # # Set all the attributes # - for prop in defaults.keys(): + for prop in list(defaults.keys()): setattr(self,prop,defaults[prop]) return @@ -87,7 +87,7 @@ # minmax=[[999.9,-999.9],[999.9,-999.9],[999.9,-999.9]] for coord in coords: - for axis in xrange(3): + for axis in range(3): if coord[axis]minmax[axis][1]: @@ -97,7 +97,7 @@ # center=[0,0,0] extent=[0,0,0] - for axis in xrange(3): + for axis in range(3): extent[axis]=minmax[axis][1]-minmax[axis][0] center[axis]=extent[axis]/2.0+minmax[axis][0] return center,extent @@ -138,7 +138,7 @@ # # Not a known type # - raise 'unknown type',type + raise Exception('unknown type') return def getText_sub(self): --- a/pdb2pka/ligand_topology.py +++ b/pdb2pka/ligand_topology.py @@ -9,7 +9,7 @@ import numpy as Numeric from sets import Set -from ligandclean.trial_templates import * +from .ligandclean.trial_templates import * from types import * def length(vector): @@ -47,7 +47,7 @@ # Get the likely types from names # trivial_types=['N','O','C','H'] - for atom in self.atoms.keys(): + for atom in list(self.atoms.keys()): if atom[0] in trivial_types: if atom[0]!='H': # Get rid of all the hydrogens self.atoms[atom]['type']=atom[0] @@ -57,9 +57,9 @@ # First approximation: Anything closer than 2.0 A is bonded # self.dists={} - for atom1 in self.atoms.keys(): + for atom1 in list(self.atoms.keys()): self.dists[atom1]={} - for atom2 in self.atoms.keys(): + for atom2 in list(self.atoms.keys()): if atom1==atom2: continue # @@ -75,7 +75,7 @@ # # Get the torsion angles # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() for atom in atoms: self.atoms[atom]['torsions']=self.get_torsions(atom) @@ -124,7 +124,7 @@ # # Get the torsion angles # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() for atom in atoms: self.atoms[atom]['torsions']=self.get_torsions(atom) @@ -143,7 +143,7 @@ # + determine their likely order (e.g. single, double, or triple) # ambs={} - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) for atom_name in atoms: bonds=self.atoms[atom_name]['bonds'] atype=self.atoms[atom_name]['type'] @@ -166,13 +166,13 @@ # valences={'C':4,'O':2,'N':3} for atom in self.atoms: - print atom, self.atoms[atom] + print(atom, self.atoms[atom]) # # ok, now it gets hairy # - print - print 'Guessing sybyl atom types' - for atom in self.atoms.keys(): + print() + print('Guessing sybyl atom types') + for atom in list(self.atoms.keys()): stype=None at=self.atoms[atom] # @@ -212,7 +212,7 @@ # Do some postchecks # - right now only for Carboxylic acids # - for atom in self.atoms.keys(): + for atom in list(self.atoms.keys()): at=self.atoms[atom] if at['sybylType']=='C.2': # @@ -233,11 +233,11 @@ # # All Done # - atoms=self.atoms.keys() + atoms=list(self.atoms.keys()) atoms.sort() - print '\nFinal Sybyl type results' + print('\nFinal Sybyl type results') for atom in atoms: - print atom,self.atoms[atom]['sybylType'] + print(atom,self.atoms[atom]['sybylType']) return # @@ -267,7 +267,7 @@ tps.sort() # To agree with dictionary layout best_fit=2.00 best_type=None - for bond in bond_props.keys(): + for bond in list(bond_props.keys()): if bond[0]==tps[0] and bond[-1]==tps[1]: if abs(dist-bond_props[bond][0]) gives a match_list if t[at]['sybylType'] == self.atoms[atom2match]['sybylType'] \ and atom2match not in already_visited: @@ -587,9 +587,9 @@ else: matched_atom_types2(nbat,t) else: - print "sybylType s don't match", atom2match + print("sybylType s don't match", atom2match) # 2nd loop to go over to the neighboured atoms - for at in t.keys(): + for at in list(t.keys()): if atom2match in already_visited: for nbat in self.atoms[atom2match]['bonds']: if nbat in already_visited: @@ -607,7 +607,7 @@ else: matched_atom_types2(nbat,t) - print "\t\t\tlen alrvis %3d" % (len(already_visited)) + print("\t\t\tlen alrvis %3d" % (len(already_visited))) def createsybyllistonthefly(lig_atom): # look in matched_atom_types2 - line 656 @@ -623,7 +623,7 @@ if ent_lig not in already_visited: already_visited.append(ent_lig) # look for matching neighbours - for at in t.keys(): + for at in list(t.keys()): if t[at]['sybylType'] == self.atoms[ent_lig]['sybylType'] and ent_lig not in matchlist: matchlist.append(at) for matches in matchlist: @@ -634,7 +634,7 @@ if putative_next_atom2match not in putative_next_a2m_list: putative_next_a2m_list.append(putative_next_atom2match) else: - print "sybyl neighbours don't match" + print("sybyl neighbours don't match") else: # what's here? pass @@ -645,7 +645,7 @@ def matchatomtypeintemplateandgetliglist(atom2match,t,stored_nbs_of_atom2match=[],been_here_flag=False,\ already_visited=[],hit_list=[]): - print atom2match,"hit_list",hit_list,been_here_flag + print(atom2match,"hit_list",hit_list,been_here_flag) putative_next_a2m_list = [] # we don't want to miss the nbs of a matched atom (see [1]) if atom2match in stored_nbs_of_atom2match: @@ -653,15 +653,15 @@ gothroughallnbsofmatchlistatom(stored_nbs_of_atom2match,t,already_visited,hit_list) # does this really work? - to which position of the routine do we go now? if been_here_flag == True: - print "it's true...", putative_next_a2m_list + print("it's true...", putative_next_a2m_list) for next_at in putative_next_a2m_list: - print "TRUE (been_here_flag)", putative_next_a2m_list + print("TRUE (been_here_flag)", putative_next_a2m_list) matchatomtypeintemplateandgetliglist(next_at,t,been_here_flag=True) matchlist = [] - for at in t.keys(): + for at in list(t.keys()): if t[at]['sybylType'] == self.atoms[atom2match]['sybylType'] and atom2match not in already_visited: already_visited.append(atom2match) - print "we found a match for %4s " %(atom2match) + print("we found a match for %4s " %(atom2match)) matchlist.append(at) # look for sybylnbs of all stored entries in matchlist for entries in matchlist: @@ -669,7 +669,7 @@ if len(Set(t[entries]['sybyl_neighbours']).difference(Set(createsybyllistonthefly(atom2match)))) == 0: hit_list.append(atom2match) stored_nbs_of_atom2match = self.atoms[atom2match]['bonds'] - print "nbs %s of hit %s" %(stored_nbs_of_atom2match,atom2match) + print("nbs %s of hit %s" %(stored_nbs_of_atom2match,atom2match)) for nbs in stored_nbs_of_atom2match: # call itself! # @@ -682,7 +682,7 @@ matchatomtypeintemplateandgetliglist(start_atom,t) # matched_atom_types2(start_atom,t) - for current_template in templates.keys(): + for current_template in list(templates.keys()): match2(templates[current_template],atoms,start_atom=atoms[4]) # start_atom should be 0 # match(templates[current_template],atoms) --- a/pdb2pka/ligandclean/ligff.py +++ b/pdb2pka/ligandclean/ligff.py @@ -1,5 +1,5 @@ from src.forcefield import * -from peoe_PDB2PQR import PEOE as calc_charges +from .peoe_PDB2PQR import PEOE as calc_charges from src.pdb import * from src.definitions import * from pdb2pka import NEWligand_topology @@ -86,7 +86,7 @@ ligand_titratable_groups=X.find_titratable_groups() if verbose: - print "ligand_titratable_groups", ligand_titratable_groups + print("ligand_titratable_groups", ligand_titratable_groups) # # Append the ligand data to the end of the PDB data # @@ -166,7 +166,7 @@ elif ff == "parse": defpath = PARSE_FILE else: - raise ValueError, "Invalid forcefield %s!" % ff + raise ValueError("Invalid forcefield %s!" % ff) if not os.path.isfile(defpath): for path in sys.path: @@ -175,7 +175,7 @@ defpath = testpath break if not os.path.isfile(defpath): - raise ValueError, "Unable to find forcefield %s!" % defpath + raise ValueError("Unable to find forcefield %s!" % defpath) file = open(defpath, 'rU') lines = file.readlines() @@ -268,7 +268,7 @@ "Cl": 1.75} #Add lower case keys to more lenient matching. -ParseRadiiDictLower = dict((key.lower(), value) for key, value in ParseRadiiDict.items()) +ParseRadiiDictLower = dict((key.lower(), value) for key, value in list(ParseRadiiDict.items())) ParseRadiiDict.update(ParseRadiiDictLower) class ligand_charge_handler(MOL2MOLECULE): @@ -289,7 +289,7 @@ #print "newly_calced - net charge %1.4f" %(qqqgesges) #print else: - atoms_last_calc=self.ligand_props.keys() + atoms_last_calc=list(self.ligand_props.keys()) # # Get the atoms presently in the pdb2pqr array # @@ -317,30 +317,30 @@ # for atom in atoms_now: if not atom in atoms_last_calc: - print 'This atom was missing before',atom - print 'If it is a hydrogen for the titratable, we need to create a bond entry!' + print('This atom was missing before',atom) + print('If it is a hydrogen for the titratable, we need to create a bond entry!') # We should be here only if is a titratable for current_atom in atoms_now: # check if it't a titratable H for res_atoms in residue.atoms: if current_atom == res_atoms.name and "titratableH" in dir(res_atoms): - print "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn" - print "been here" + print("nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn") + print("been here") for ResAtoms in residue.atoms: ResAtoms.formalcharge = 0.0 self.recalc_charges(residue) for atom in atoms_last_calc: if not atom in atoms_now: - print 'This atom used to be here, but is now missing',atom + print('This atom used to be here, but is now missing',atom) #self.recalc_charges(residue) xxxnetq = 0.0 for xxx in residue.atoms: - print "after neutralizing %s %1.4f" %(xxx.name, xxx.charge) + print("after neutralizing %s %1.4f" %(xxx.name, xxx.charge)) xxxnetq = xxxnetq+xxx.charge - print '-----------------------' - print "net charge: %1.4f" % (xxxnetq) - print - print + print('-----------------------') + print("net charge: %1.4f" % (xxxnetq)) + print() + print() else: # Yes - nothing to do pass @@ -378,10 +378,10 @@ for at in residue.atoms: # WAS: self.lAtoms: ele = at.sybylType.split('.')[0] charge = at.charge - if ParseRadiiDict.has_key(ele): + if ele in ParseRadiiDict: radius = ParseRadiiDict[ele] else: - raise 'Please check ParseRadiiDict in ligff.py -- radius data not found for',ele + raise Exception('Please check ParseRadiiDict in ligff.py -- radius data not found for %s' % ele) # # Store the radii and charges # --- a/pdb2pka/ligandclean/peoe_PDB2PQR.py +++ b/pdb2pka/ligandclean/peoe_PDB2PQR.py @@ -67,7 +67,7 @@ } #Add lower case keys to more lenient matching. -ChargetermsLower = dict((key.lower(), value) for key, value in Chargeterms.items()) +ChargetermsLower = dict((key.lower(), value) for key, value in list(Chargeterms.items())) Chargeterms.update(ChargetermsLower) def PEOE( atoms, damp=0.778, k=1.56): @@ -87,9 +87,9 @@ abs_qges = 0.0 counter = 0 for a in atoms.atoms: - sybylType = a.sybylType.lower() - if not Chargeterms.has_key(sybylType): - raise KeyError, 'PEOE Error: Atomtype <%s> not known, treating atom %s as dummy' % (a.sybylType, a.name) + sybylType = a.sybylType.lower() + if sybylType not in Chargeterms: + raise KeyError('PEOE Error: Atomtype <%s> not known, treating atom %s as dummy' % (a.sybylType, a.name)) if a.sybylType == 'O.3': a.chi = Chargeterms['O.OH'][0] a.abc = Chargeterms['O.OH'] --- a/pdb2pka/pKaIO_compat.py +++ b/pdb2pka/pKaIO_compat.py @@ -12,7 +12,7 @@ #try: import os -from pKa_utility_functions_compat import * +from .pKa_utility_functions_compat import * class pKaIO: @@ -95,10 +95,10 @@ filename=self.pkafile import string if not filename: - print filename,'is not a filename' + print(filename,'is not a filename') os._exit(0) if not os.path.isfile(filename): - raise 'File does not exist:',filename + raise Exception('File does not exist: %s' % filename) fd=open(filename) lines=fd.readlines() fd.close() @@ -112,7 +112,7 @@ else: raise ValueError('Unknown format') if string.lower(string.strip(lines[1]))!=string.lower('Format 1.0'): - raise 'unknown format: ',lines[1] + raise Exception('unknown format: %s' % lines[1]) # Next line is text linenumber=3 pKa={} @@ -246,13 +246,13 @@ fd.write('%s pKa File\n' %format) fd.write('Format 1.0\n') fd.write(' Group pKa value Model pK dpK dDesolv dBack dElec\n') - groups=data.keys() + groups=list(data.keys()) # Sort accroding to the residue sequence number newgroup ={} for g in groups: newg = g.split('_')[2] newgroup[int(newg),g]=g - newgroupkeys = newgroup.keys() + newgroupkeys = list(newgroup.keys()) newgroupkeys.sort() groups = [] for k in newgroupkeys: @@ -263,7 +263,7 @@ # --------- # for group in groups: - if data.has_key(group): + if group in data: this_data=data[group] fd.write('%15s %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f \n' %(self.WI_res_text(group,format), this_data['pKa'], @@ -295,7 +295,7 @@ filename=self.titcurvfile import string if not os.path.isfile(filename): - raise 'File does not exist:',filename + raise Exception('File does not exist: %s' % filename) fd=open(filename) lines=fd.readlines() fd.close() @@ -307,9 +307,9 @@ elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Titration Curve File'): format='pdb2pka' else: - raise 'Unknown format' + raise Exception('Unknown format') if string.lower(string.strip(lines[1]))!=string.lower('Format 1.0'): - raise 'unknown format: ',lines[1] + raise Exception('unknown format: %s' % lines[1]) phvals=string.split(lines[2]) phstart=string.atof(phvals[0]) phend=string.atof(phvals[1]) @@ -361,27 +361,27 @@ # # Extract some data from the dictionary # - residues=data.keys() - phvals=data[residues[0]].keys() + residues=list(data.keys()) + phvals=list(data[residues[0]].keys()) phvals.sort() for residue in residues: - newpHvals=data[residue].keys() + newpHvals=list(data[residue].keys()) newpHvals.sort() if newpHvals!=phvals: - print phvals - print newpHvals - raise 'Dictionary does not contain identical pH values' + print(phvals) + print(newpHvals) + raise Exception('Dictionary does not contain identical pH values') # # Check that a pKa value is in the pH values # for residue in residues: - if not data[residue].has_key('pKa'): + if 'pKa' not in data[residue]: #print 'No pKa value found. Setting to zero!! - Jens change this!!' data[residue]['pKa']=0.0 # # Find the pH-start, stop and step # - phvals=data[residues[0]].keys() + phvals=list(data[residues[0]].keys()) phvals.sort() phstart=phvals[0] phstop=phvals[-2] @@ -397,13 +397,13 @@ # Start pH, end pH, pH step # fd.write('%6.3f %7.3f %6.3f\n' %(phstart,phstop,phstep)) - residues=data.keys() + residues=list(data.keys()) # Sort accroding to the residue sequence number newresidue ={} for r in residues: newr = r.split('_')[2] newresidue[int(newr),r]=r - newresiduekeys = newresidue.keys() + newresiduekeys = list(newresidue.keys()) newresiduekeys.sort() residues = [] for k in newresiduekeys: @@ -439,11 +439,11 @@ if self.matrix_file: filename=self.matrix_file else: - raise 'No matrix filename given' + raise Exception('No matrix filename given') # import os, string if not os.path.isfile(filename): - raise "File not found",filename + raise Exception("File not found %s" % filename) fd=open(filename) lines=fd.readlines() fd.close() @@ -459,9 +459,9 @@ elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Interaction Matrix File'): format='WHAT IF' else: - raise 'Unknown format' + raise Exception('Unknown format') if not string.strip(lines[1])=='Format 1.0': - raise 'Wrong format',lines[1] + raise Exception('Wrong format %s' % lines[1]) x=1 done=None partners=None @@ -500,7 +500,7 @@ partners=np else: if partners!=np: - raise 'Number of partners changes:',np + raise Exception('Number of partners changes: %s' % np) self.matrix[resid]={} # # Now read all the interactions with the partners @@ -577,7 +577,7 @@ fd=open(filename,'w') fd.write('%s Interaction Matrix File\n' %format) fd.write('Format 1.0\n') - groups=self.matrix.keys() + groups=list(self.matrix.keys()) groups.sort() num_groups=len(groups) @@ -594,7 +594,7 @@ for g in newgroups: newg = g.split('_')[2] newnewgroup[int(newg),g]=g - newnewgroupkeys = newnewgroup.keys() + newnewgroupkeys = list(newnewgroup.keys()) newnewgroupkeys.sort() newgroups = [] for k in newnewgroupkeys: @@ -605,19 +605,19 @@ # --------- # for group in newgroups: - if self.matrix.has_key(group): + if group in self.matrix: fd.write('%s %7.4f\n' %(self.WI_res_text(group,format),float(num_groups))) self.write_section(group,fd,format) written[group]=1 # # Is there a terminal group associated with this residue? # - if self.matrix.has_key('T'+group): + if 'T'+group in self.matrix: fd.write('%s %7.4f\n' %(self.WI_res_text('T'+group),float(num_groups))) self.write_section('T'+group,fd,format) written['T'+group]=1 else: - if self.matrix.has_key('T'+group) and not written.has_key('T'+group): + if 'T'+group in self.matrix and 'T'+group not in written: fd.write('%s %7.4f\n' %(self.WI_res_text('T'+group,format),float(num_groups))) self.write_section('T'+group,fd,format) written['T'+group]=1 @@ -632,19 +632,19 @@ """Write an interaction energy matrix in pdb2pka format""" """At the moment, we just reformat and write a WHAT IF file""" self.matrix={} - for group1 in matrix.keys(): + for group1 in list(matrix.keys()): self.matrix[group1.uniqueid]={} - for tit1 in matrix[group1].keys(): - for state1 in matrix[group1][tit1].keys(): + for tit1 in list(matrix[group1].keys()): + for state1 in list(matrix[group1][tit1].keys()): sub_m=matrix[group1][tit1][state1] - for group2 in sub_m.keys(): - if not self.matrix[group1.uniqueid].has_key(group2.uniqueid): + for group2 in list(sub_m.keys()): + if group2.uniqueid not in self.matrix[group1.uniqueid]: self.matrix[group1.uniqueid][group2.uniqueid]=[] - for tit2 in sub_m[group2].keys(): - for state2 in sub_m[group2][tit2].keys(): + for tit2 in list(sub_m[group2].keys()): + for state2 in list(sub_m[group2][tit2].keys()): self.matrix[group1.uniqueid][group2.uniqueid].append(sub_m[group2][tit2][state2]) - for group1 in self.matrix.keys(): - for group2 in self.matrix[group1].keys(): + for group1 in list(self.matrix.keys()): + for group2 in list(self.matrix[group1].keys()): sum=0.0 for val in self.matrix[group1][group2]: sum=sum+val @@ -657,7 +657,7 @@ # def write_section(self,group,fd,format): - groups_tmp=self.matrix[group].keys() + groups_tmp=list(self.matrix[group].keys()) groups2=[] for group_x in groups_tmp: if group_x[0]=='T': @@ -670,7 +670,7 @@ for g in groups2: newg = g.split('_')[2] newgroup[int(newg),g]=g - newgroupkeys = newgroup.keys() + newgroupkeys = list(newgroup.keys()) newgroupkeys.sort() groups2 = [] for k in newgroupkeys: @@ -678,19 +678,19 @@ written={} for group2 in groups2: - if self.matrix[group].has_key(group2): + if group2 in self.matrix[group]: fd.write('%s %7.4f\n' %(self.WI_res_text(group2,format),self.matrix[group][group2][0])) fd.write('%7.4f\n%7.4f\n%7.4f\n'%(self.matrix[group][group2][1],self.matrix[group][group2][2],self.matrix[group][group2][3])) written[group2]=1 # # Is there a terminal group associated with this residue? # - if self.matrix[group].has_key('T'+group2): + if 'T'+group2 in self.matrix[group]: fd.write('%s %7.4f\n' %(self.WI_res_text('T'+group2,format),self.matrix[group]['T'+group2][0])) fd.write('%7.4f\n%7.4f\n%7.4f\n'%(self.matrix[group]['T'+group2][1],self.matrix[group]['T'+group2][2],self.matrix[group]['T'+group2][3])) written['T'+group2]=1 else: - if self.matrix[group].has_key('T'+group2) and not written.has_key('T'+group2): + if 'T'+group2 in self.matrix[group] and 'T'+group2 not in written: fd.write('%s %7.4f\n' %(self.WI_res_text('T'+group2,format),self.matrix[group]['T'+group2][0])) fd.write('%7.4f\n%7.4f\n%7.4f\n'%(self.matrix[group]['T'+group2][1],self.matrix[group]['T'+group2][2],self.matrix[group]['T'+group2][3])) written['T'+group2]=1 @@ -706,14 +706,14 @@ if self.desolv_file: filename=self.desolv_file else: - raise 'No desolv filename given' + raise Exception('No desolv filename given') # # # This subroutine reads a DESOLV file # import os, string if not os.path.isfile(filename): - raise "File not found",filename + raise Exception("File not found %s" % filename) fd=open(filename) lines=fd.readlines() fd.close() @@ -729,7 +729,7 @@ elif string.strip(lines[0])=='pdb2pka Desolvation Energy File': format='pdb2pka' else: - raise Exception,'Unknown format:'+string.strip(lines[0]) + raise Exception('Unknown format:'+string.strip(lines[0])) # # Call the generic read routine # @@ -748,11 +748,11 @@ if self.backgr_file: filename=self.backgr_file else: - raise 'No matrix filename given' + raise Exception('No matrix filename given') # import os, string if not os.path.isfile(filename): - raise "File not found",filename + raise Exception("File not found %s" % filename) fd=open(filename) lines=fd.readlines() fd.close() @@ -768,7 +768,7 @@ elif string.strip(lines[0])=='pdb2pka Background Energy File': format='pdb2pka' else: - raise Exception,'Unknown format:'+string.strip(lines[0]) + raise Exception('Unknown format:'+string.strip(lines[0])) # # Call the generic read routine # @@ -830,13 +830,13 @@ fd=open(filename,'w') fd.write('%s Desolvation Energy File\n' %format) fd.write('Format 1.0\n') - groups=self.desolv.keys() + groups=list(self.desolv.keys()) # Sort accroding to the residue sequence number newgroup ={} for g in groups: newg = g.split('_')[2] newgroup[int(newg),g]=g - newgroupkeys = newgroup.keys() + newgroupkeys = list(newgroup.keys()) newgroupkeys.sort() groups = [] for k in newgroupkeys: @@ -846,7 +846,7 @@ # --------- # for group in groups: - if self.desolv.has_key(group): + if group in self.desolv: fd.write('%s %7.4f\n' %(self.WI_res_text(group,format),float(self.desolv[group]))) written[group]=1 fd.write('End of file\n') @@ -863,13 +863,13 @@ fd=open(filename,'w') fd.write('%s Background Energy File\n' %format) fd.write('Format 1.0\n') - groups=self.backgr.keys() + groups=list(self.backgr.keys()) # Sort accroding to the residue sequence number newgroup ={} for g in groups: newg = g.split('_')[2] newgroup[int(newg),g]=g - newgroupkeys = newgroup.keys() + newgroupkeys = list(newgroup.keys()) newgroupkeys.sort() groups = [] for k in newgroupkeys: @@ -879,7 +879,7 @@ # --------- # for group in groups: - if self.backgr.has_key(group): + if group in self.backgr: fd.write('%s %7.4f\n' %(self.WI_res_text(group,format),float(self.backgr[group]))) written[group]=1 fd.write('End of file\n') @@ -955,4 +955,4 @@ line='TERMINAL GROUP:\n'+line return line else: - raise Exception,'Unknown format:'+format + raise Exception('Unknown format:'+format) --- a/pdb2pka/pKa_utility_functions_compat.py +++ b/pdb2pka/pKa_utility_functions_compat.py @@ -163,7 +163,7 @@ def istitratable(uniqueid): import string type=string.split(uniqueid,':')[-1] - if acidbase.has_key(type): + if type in acidbase: return 1 else: return None --- a/pdb2pka/pMC_mult.py +++ b/pdb2pka/pMC_mult.py @@ -25,7 +25,7 @@ if (name == "thisown"): return self.this.own() method = class_type.__swig_getmethods__.get(name,None) if method: return method(self) - raise AttributeError,name + raise AttributeError(name) def _swig_repr(self): try: strthis = "proxy of " + self.this.__repr__() @@ -34,7 +34,7 @@ import types try: - _object = types.ObjectType + _object = object _newclass = 1 except AttributeError: class _object : pass @@ -47,7 +47,7 @@ __setattr__ = lambda self, name, value: _swig_setattr(self, PySwigIterator, name, value) __swig_getmethods__ = {} __getattr__ = lambda self, name: _swig_getattr(self, PySwigIterator, name) - def __init__(self): raise AttributeError, "No constructor defined" + def __init__(self): raise AttributeError("No constructor defined") __repr__ = _swig_repr __swig_destroy__ = _pMC_mult.delete_PySwigIterator __del__ = lambda self : None; --- a/pdb2pka/pka_help.py +++ b/pdb2pka/pka_help.py @@ -28,14 +28,14 @@ # # Call our little C++ module # - import pMC_mult + from . import pMC_mult FAST=pMC_mult.MC(intpkas,linear,acidbase,state_counter,is_charged) FAST.set_MCsteps(int(mcsteps)) - print 'Calculating intrinsic pKa value' + print('Calculating intrinsic pKa value') pKavals=FAST.calc_pKas(phstart,phend,phstep) count=0 intpka=pKavals[0] - print 'Simulated intrinsic pKa value: %5.2f' %intpka + print('Simulated intrinsic pKa value: %5.2f' %intpka) count=1 # # Get the charges @@ -57,8 +57,8 @@ if pKavals[count+1]==999.0 and pKavals[count+2]==-999.0: count=count+2 else: - print 'Something is wrong' - print pKavals[count:count+30] + print('Something is wrong') + print(pKavals[count:count+30]) raise Exception('Incorrect data format from pMC_mult') return intpka @@ -73,7 +73,7 @@ ##check if the record is not a water in which case we will print a warning from src.aa import WAT if not record.resName in WAT.water_residue_names: - print "Warning!: HETATM record %s " % record.resName + "%s that is not a water is being dropped\n " % record.element + print("Warning!: HETATM record %s " % record.resName + "%s that is not a water is being dropped\n " % record.element) ##raw_input("Press enter to continue...") continue if isinstance(record, (ATOM, ANISOU, SIGUIJ, SIGATM)): --- a/pdb2pka/pka_old.py +++ b/pdb2pka/pka_old.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # pKa calculations with APBS # @@ -12,9 +12,9 @@ debug=False import optparse import sys, os -from pKa_base import * +from .pKa_base import * -print __file__ +print(__file__) import os try: file_name=__file__ @@ -55,7 +55,7 @@ from src.routines import * from src.protein import * from src.server import * -from StringIO import * +from io import * from src.hydrogens import * @@ -63,11 +63,11 @@ # # Print usage guidelines # - print 'Usage: pka.py --ff --lig --pdie --maps <1 for using provided 3D maps; 2 for genereting new maps>' - print '--xdiel --ydiel --zdiel --kappa ' - print '--smooth ' - print 'Force field can be amber, charmm and parse' - print + print('Usage: pka.py --ff --lig --pdie --maps <1 for using provided 3D maps; 2 for genereting new maps>') + print('--xdiel --ydiel --zdiel --kappa ') + print('--smooth ') + print('Force field can be amber, charmm and parse') + print() return # @@ -83,9 +83,9 @@ routines: The routines object as generated by PDB2PQR forcefield: The forcefield object as generated by PDB2PQR """ - print - print 'PDB2PQR pKa calculations' - print + print() + print('PDB2PQR pKa calculations') + print() import optparse parser = optparse.OptionParser() @@ -252,7 +252,7 @@ # # remove hydrogen atoms # - import pka_help + from . import pka_help pka_help.remove_hydrogens(pdbfilename) # # Get the PDBfile @@ -268,11 +268,11 @@ # sys.exit(2) if len(errlist) != 0 and verbose: - print "Warning: %s is a non-standard PDB file.\n" %pdbfilename - print errlist + print("Warning: %s is a non-standard PDB file.\n" %pdbfilename) + print(errlist) if verbose: - print "Beginning PDB2PQR...\n" + print("Beginning PDB2PQR...\n") # # Read the definition file # @@ -301,12 +301,12 @@ if os.path.isfile(ligand): ligfd=open(ligand, 'rU') else: - print 'skipping ligand',ligand + print('skipping ligand',ligand) continue # # Read the ligand into Paul's code # - from ligandclean import ligff + from .ligandclean import ligff myProtein, myDefinition, Lig = ligff.initialize(myDefinition, ligfd, pdblist, verbose) # # Create the ligand definition from the mol2 data @@ -387,9 +387,9 @@ # Print something for some reason? # if verbose: - print "Created protein object -" - print "\tNumber of residues in protein: %s" % myProtein.numResidues() - print "\tNumber of atoms in protein : %s" % myProtein.numAtoms() + print("Created protein object -") + print("\tNumber of residues in protein: %s" % myProtein.numResidues()) + print("\tNumber of atoms in protein : %s" % myProtein.numAtoms()) # # Set up all other routines # @@ -440,8 +440,8 @@ templist = [] Lig.make_up2date(residue) net_charge=0.0 - print 'Ligand',residue - print 'Atom\tCharge\tRadius' + print('Ligand',residue) + print('Atom\tCharge\tRadius') for atom in residue.getAtoms(): if atom.mol2charge: atom.ffcharge=atom.mol2charge @@ -455,7 +455,7 @@ # Assign radius # atom.radius = Lig.ligand_props[atom.name]["radius"] - print '%s\t%6.4f\t%6.4f' %(atom.name,atom.ffcharge,atom.radius) + print('%s\t%6.4f\t%6.4f' %(atom.name,atom.ffcharge,atom.radius)) if atom in misslist: misslist.pop(misslist.index(atom)) templist.append(atom) @@ -480,7 +480,7 @@ # # Print the net charge # - print 'Net charge for ligand %s is: %5.3f' %(residue.name,net_charge) + print('Net charge for ligand %s is: %5.3f' %(residue.name,net_charge)) # # Temporary fix; if ligand was successful, pull all ligands from misslist # Not sure if this is needed at all here ...? (Jens wrote this) @@ -492,9 +492,9 @@ misslist.remove(atom) if verbose: - print "Created protein object (after processing myRoutines) -" - print "\tNumber of residues in protein: %s" % myProtein.numResidues() - print "\tNumber of atoms in protein : %s" % myProtein.numAtoms() + print("Created protein object (after processing myRoutines) -") + print("\tNumber of residues in protein: %s" % myProtein.numResidues()) + print("\tNumber of atoms in protein : %s" % myProtein.numAtoms()) # # Create the APBS input file # @@ -503,17 +503,17 @@ method="" split=0 - import inputgen_pKa + from . import inputgen_pKa igen = inputgen_pKa.inputGen(pdbfilename) # # For convenience # igen.pdie = pdie - print 'Setting protein dielectric constant to ',igen.pdie + print( 'Setting protein dielectric constant to ',igen.pdie) igen.sdie=options.sdie igen.maps=maps if maps==1: - print "Using dielectric and mobile ion-accessibility function maps in PBE" + print( "Using dielectric and mobile ion-accessibility function maps in PBE") if xdiel: igen.xdiel = xdiel else: @@ -533,7 +533,7 @@ usage(2) sys.exit(0) - print 'Setting dielectric function maps: %s, %s, %s'%(igen.xdiel,igen.ydiel,igen.zdiel) + print('Setting dielectric function maps: %s, %s, %s'%(igen.xdiel,igen.ydiel,igen.zdiel)) if kappa: igen.kappa = kappa @@ -542,7 +542,7 @@ usage(2) sys.exit(0) - print 'Setting mobile ion-accessibility function map to: ',igen.kappa + print('Setting mobile ion-accessibility function map to: ',igen.kappa) if sd: xdiel_smooth, ydiel_smooth, zdiel_smooth = smooth(xdiel,ydiel,zdiel) @@ -561,7 +561,7 @@ if __name__ == "__main__": (protein, routines, forcefield,apbs_setup, ligand_titratable_groups, maps, sd), options = startpKa() - import pka_routines + from . import pka_routines mypkaRoutines = pka_routines.pKaRoutines(protein, routines, forcefield, apbs_setup, maps, sd, pdbfile_name, options=options) @@ -579,7 +579,7 @@ # # What should we do? # - print 'Doing full pKa calculation' + print('Doing full pKa calculation') mypkaRoutines.runpKa() # state=1 --- a/pdb2pka/pka_routines.py +++ b/pdb2pka/pka_routines.py @@ -10,21 +10,21 @@ debug=False import os import sys -import pKaIO_compat -from pKa_base import * -import cPickle -import pMC_mult +from . import pKaIO_compat +from .pKa_base import * +import pickle +from . import pMC_mult import math import copy import string -from graph_cut.utils import create_protein_complex_from_matrix, process_desolv_and_background, curve_for_one_group -from graph_cut.titration_curve import get_titration_curves -from graph_cut.create_titration_output import create_output +from .graph_cut.utils import create_protein_complex_from_matrix, process_desolv_and_background, curve_for_one_group +from .graph_cut.titration_curve import get_titration_curves +from .graph_cut.create_titration_output import create_output if debug: - from Tkinter import * - from charge_mon import * + from tkinter import * + from .charge_mon import * CM=charge_mon() else: @@ -32,7 +32,7 @@ import shutil -from pka_help import is_sameatom, titrate_one_group +from .pka_help import is_sameatom, titrate_one_group from src.errors import PDB2PKAError # @@ -56,7 +56,7 @@ from src.hydrogens import hydrogenRoutines, hydrogenAmbiguity #import ligandclean.ligff -from apbs import runAPBS +from .apbs import runAPBS # @@ -124,7 +124,7 @@ if os.path.isfile(self.state_files): raise ValueError('Target directory is a file! Aborting.') - for output_file in self.output_files.values(): + for output_file in list(self.output_files.values()): if os.path.isfile(output_file): os.remove(output_file) @@ -161,7 +161,7 @@ def insert_new_titratable_group(self,ligand_titratable_groups): """Insert the new titratable groups in to self.pkagroups""" group_type=ligand_titratable_groups['type'] - if self.pKagroups.has_key(group_type): + if group_type in self.pKagroups: # # Now modify the group so that it will correspond to the group # we have in the ligand @@ -190,7 +190,7 @@ # # Change the name of the atom that the H is bound to # - if atom_map.has_key(conformation.boundatom): + if conformation.boundatom in atom_map: conformation.boundatom=atom_map[conformation.boundatom] # # Change the name of the hydrogen @@ -201,7 +201,7 @@ # And then for the individual atom names # for atom in conformation.atoms: - if atom_map.has_key(atom.name): + if atom.name in atom_map: atom.name=atom_map[atom.name] elif atom.name==oldhname: atom.name=conformation.hname @@ -316,7 +316,7 @@ ambiguity = pKa.amb titgroup='%s:%s:%s' %(residue.chainID, string.zfill(residue.resSeq,4),pKaGroup.name) - if not potentialDifference.has_key(titgroup): + if titgroup not in potentialDifference: potentialDifference[titgroup]={} for atom in self.protein.getAtoms(): if atom.name in ['N','H','C']: @@ -402,12 +402,12 @@ # Loop over each titration # self.all_potentials={} - if not self.matrix.has_key(pKa): + if pKa not in self.matrix: self.matrix[pKa]={} self.all_potentials[pKa]={} # for titration in pKaGroup.DefTitrations: - if not self.matrix[pKa].has_key(titration): + if titration not in self.matrix[pKa]: self.matrix[pKa][titration]={} self.all_potentials[pKa][titration]={} # @@ -472,7 +472,7 @@ # if os.path.isfile(intene_file_name): with open(intene_file_name) as fd: - savedict=cPickle.load(fd) + savedict=pickle.load(fd) # # pKD? # @@ -480,7 +480,7 @@ try: sys.stdout.flush() with open(allpots_file_name) as fd: - allsavedict=cPickle.load(fd) + allsavedict=pickle.load(fd) read_allpots=1 except EOFError: self.routines.write('\n') @@ -518,12 +518,12 @@ # # Loop over each titration # - if not energies.has_key(pKa): + if pKa not in energies: energies[pKa]={} all_potentials[pKa]={} # for titration in pKaGroup.DefTitrations: - if not energies[pKa].has_key(titration): + if titration not in energies[pKa]: energies[pKa][titration]={} all_potentials[pKa][titration]={} # @@ -549,10 +549,10 @@ # # Check if we have values for this calculation already # - if savedict.has_key(name): + if name in savedict: energies[pKa][titration][state]= savedict[name] if mode=='pKD': - if allsavedict.has_key(name): + if name in allsavedict: all_potentials[pKa][titration][state]=allsavedict[name] continue # @@ -675,10 +675,10 @@ # if calculated_energy: with open(intene_file_name,'w') as fd: - cPickle.dump(savedict,fd) + pickle.dump(savedict,fd) if mode=='pKD' and not read_allpots: with open(allpots_file_name,'w') as fd: - cPickle.dump(allsavedict,fd) + pickle.dump(allsavedict,fd) return energies,all_potentials # @@ -728,8 +728,8 @@ create_output(self.titcurves_dir, curves) pka_values, pH_values = self.find_pka_and_pH(curves) - print pka_values - print pH_values + print(pka_values) + print(pH_values) self.ph_at_0_5 = pH_values ln10=math.log(10) @@ -812,7 +812,7 @@ # X.desolv={} X.backgr={} - for name in pkas.keys(): + for name in list(pkas.keys()): X.desolv[name]=pkas[name]['desolv'] X.backgr[name]=pkas[name]['backgr'] @@ -842,7 +842,7 @@ adjacent_data_points = 5 - for name, curve in curves.iteritems(): + for name, curve in curves.items(): bad_curve = False curve_calc_point = 0.5 @@ -854,7 +854,7 @@ #Check to see if we never cross 0.5 or -0.5 at all if all(charge_side) or not any(charge_side): warning = "WARNING: UNABLE TO CACLCULATE PKA FOR {name}\n".format(name=name) - print warning, + print(warning, end=' ') self.warnings.append(warning) pKa_results[name] = pKa_value continue @@ -865,11 +865,11 @@ if (True,False) not in side_pairs: warning = "WARNING: {name} DOES NOT EXHIBIT Henderson-Hasselbalch BEHAVIOR\n".format(name=name) - print warning, + print(warning, end=' ') self.warnings.append(warning) warning = "WARNING: {name} TITRATION CURVE IS BACKWARDS\n".format(name=name, calc=curve_calc_point) - print warning, + print(warning, end=' ') self.warnings.append(warning) cross_index = charge_side.index(True) bad_curve = True @@ -880,10 +880,10 @@ #(False, True) means we've crossed back over the line and therefore our PKA value is in question. if (True,False) in side_pairs and (False,True) in side_pairs: warning = "WARNING: {name} DOES NOT EXHIBIT Henderson-Hasselbalch BEHAVIOR\n".format(name=name) - print warning, + print(warning, end=' ') self.warnings.append(warning) warning = "WARNING: {name} TITRATION CURVE CROSSES {calc} AT LEAST TWICE\n".format(name=name, calc=curve_calc_point) - print warning, + print(warning, end=' ') self.warnings.append(warning) bad_curve = True @@ -899,11 +899,11 @@ pH_results[name] = ph_at_0_5 except ZeroDivisionError: warning = "WARNING: UNABLE TO CACLCULATE pH FOR {name}, Divide by zero.\n".format(name=name) - print warning, + print(warning, end=' ') self.warnings.append(warning) if not bad_curve: - print "{name} exhibits Henderson-Hasselbalch behavior.".format(name=name) + print("{name} exhibits Henderson-Hasselbalch behavior.".format(name=name)) #Calc pKa value start = max(0, prevous_cross_index-adjacent_data_points) @@ -915,7 +915,7 @@ pKa_value = sum(pkas)/float(len(pkas)) except ZeroDivisionError: warning = "WARNING: UNABLE TO CACLCULATE PKA FOR {name}, Divide by zero.\n".format(name=name) - print warning, + print(warning, end=' ') self.warnings.append(warning) @@ -1191,7 +1191,7 @@ # intpka=titrate_one_group(name='%s' %(pKa.residue),intpkas=intpKas,is_charged=is_charged,acidbase=acidbase) curve = curve_for_one_group(pKa) pka_values, _ = self.find_pka_and_pH(curve) - intpka = pka_values.values()[0] + intpka = list(pka_values.values())[0] pKa.simulated_intrinsic_pKa=intpka return @@ -1241,7 +1241,7 @@ backgroundname = os.path.join(self.state_files,'background_interaction_energies.pickle') if os.path.isfile(backgroundname): with open(backgroundname) as fd: - savedict=cPickle.load(fd) + savedict=pickle.load(fd) else: savedict={} @@ -1270,7 +1270,7 @@ # Set the name for this energy # name='%s_%s_%s_%s' %(titration.name,pKa.residue.chainID,pKa.residue.resSeq,self.get_state_name(titration.name,state)) - if savedict.has_key(name): + if name in savedict: pKa.background[self.get_state_name(titration.name,state)] = savedict[name] continue # @@ -1416,10 +1416,10 @@ # Dump the pickle file # with open(backgroundname,'w') as fd: - cPickle.dump(savedict,fd) + pickle.dump(savedict,fd) with open(self.output_files['background_interaction_energies_file_path'] , 'w') as f: - keys = savedict.keys() + keys = list(savedict.keys()) keys.sort() for key in keys: value = savedict[key] @@ -1442,7 +1442,7 @@ desolvname=os.path.join(self.state_files, 'desolvation_energies.pickle') if os.path.isfile(desolvname): with open(desolvname) as fd: - savedict=cPickle.load(fd) + savedict=pickle.load(fd) else: savedict={} # @@ -1503,7 +1503,7 @@ residue.stateboolean[self.get_state_name(titration.name, state)] = True name='%s_%s_%s_%s' %(titration.name,pKa.residue.chainID,pKa.residue.resSeq,self.get_state_name(titration.name,state)) # - if savedict.has_key(name): + if name in savedict: pKa.desolvation[self.get_state_name(titration.name,state)] = savedict[name] continue self.routines.write("---------> Calculating desolvation energy for residue %s state %s in solvent\n" %(residue.name,self.get_state_name(titration.name,state))) @@ -1570,10 +1570,10 @@ # Dump a pickle file # with open(desolvname,'w') as fd: - cPickle.dump(savedict,fd) + pickle.dump(savedict,fd) with open(self.output_files['desolvation_energies_file_path'], 'w') as f: - keys = savedict.keys() + keys = list(savedict.keys()) keys.sort() for key in keys: value = savedict[key] @@ -1803,7 +1803,7 @@ # center={} extent={} - for axis in minmax.keys(): + for axis in list(minmax.keys()): extent[axis]=minmax[axis][1]-minmax[axis][0] center[axis]=extent[axis]/2.0+minmax[axis][0] return [center['x'],center['y'],center['z']] @@ -1852,9 +1852,9 @@ if found==len(atomlist): break if abs(totphi)<0.01 or abs(totcrg)<0.01: - print 'total abs phi',totphi - print 'total abs crg',totcrg - print 'net charge ',netcrg + print('total abs phi',totphi) + print('total abs crg',totcrg) + print('net charge ',netcrg) PDB2PKAError( 'Something is rotten') return energy @@ -1881,7 +1881,7 @@ # Yes! # with open(result_file,'rb') as fd: - potentials=cPickle.load(fd) + potentials=pickle.load(fd) loaded=True # # Run calc again if needed @@ -1895,7 +1895,7 @@ self.APBS=None if save_results: with open(result_file,'wb') as fd: - cPickle.dump(potentials,fd) + pickle.dump(potentials,fd) return potentials @@ -1932,7 +1932,7 @@ text = "Could not find radius for atom %s" % atomname text += " in residue %s %i" % (residue.name, residue.resSeq) text += " while attempting to set radius!" - raise ValueError, text + raise ValueError(text) # # ------------------------------------ # @@ -1959,7 +1959,7 @@ text = "Could not find charge for atom %s" % atomname text += " in residue %s %i" % (residue.name, residue.resSeq) text += " while attempting to set charge!" - raise ValueError, text + raise ValueError(text) return # # ---------------------------- @@ -2038,8 +2038,8 @@ charge, radius = self.forcefield.getParams1(residue, atomname) initialmap[atomname] = charge if charge is None: - print atomname,charge - print residue.isCterm + print(atomname,charge) + print(residue.isCterm) raise PDB2PKAError('Charge on atom is None') sum+=charge if abs(sum)<0.001: @@ -2061,7 +2061,7 @@ charge, radius = self.forcefield.getParams1(residue, atomname) sum=sum+charge - if initialmap.has_key(atomname): + if atomname in initialmap: initcharge = initialmap[atomname] if charge != initcharge: if not atomname in atomnames: @@ -2072,7 +2072,7 @@ # # Check that no atoms were removed # - for atom in initialmap.keys(): + for atom in list(initialmap.keys()): if not atom in residue.get('map'): atomnames.append(atom) # @@ -2148,8 +2148,8 @@ # Did we add anything? # if added is None and sum>0.001: - print sum - print atomnames + print(sum) + print(atomnames) PDB2PKAError('Could not find integer charge state') # # Did we just want a neutral state identification? @@ -2162,7 +2162,7 @@ # No, we wanted the atomnames # if atomnames==[]: - print 'Did not find any atoms for ',residue.resSeq + print('Did not find any atoms for ',residue.resSeq) PDB2PKAError('Something wrong with charges') for atomname in atomnames: @@ -2192,7 +2192,7 @@ self.routines.write("Finding Titratable groups....\n") sys.stdout.flush() # - pKagroupList=self.pKagroups.keys() + pKagroupList=list(self.pKagroups.keys()) # for chain in self.protein.getChains(): for residue in chain.get("residues"): @@ -2263,7 +2263,7 @@ if amb == None: text = "Could not find hydrogen ambiguity " text += "for titratable group %s!" % group - raise ValueError, text + raise ValueError(text) return amb # @@ -2288,7 +2288,7 @@ 'CTR01c': '1', 'CTR01t': '2', 'CTR02c': '3', 'CTR02t': '4', 'CTR-': '0'} filename = TITRATIONFILE if not os.path.isfile(TITRATIONFILE): - raise ValueError, "Could not find TITRATION.DAT!" + raise ValueError("Could not find TITRATION.DAT!") titration_file = open(filename) @@ -2306,18 +2306,18 @@ line = titration_file.readline() if line[:8] != 'Residue:': text = "Wrong line found when looking for 'Residue'" - raise ValueError, "%s: %s" % (text, line) + raise ValueError("%s: %s" % (text, line)) resname = string.strip(string.split(line)[1]) line = titration_file.readline() if line[:10] != 'Grouptype:': text = "Wrong line found when looking for 'Grouptype'" - raise ValueError, "%s: %s" % (text, line) + raise ValueError("%s: %s" % (text, line)) type = string.lower(string.strip(string.split(line)[1])) if type != 'acid' and type != 'base': - raise ValueError, 'Group type must be acid or base!' + raise ValueError('Group type must be acid or base!') line = titration_file.readline() while 1: @@ -2334,7 +2334,7 @@ if line[:11] != 'Transition:': text = "Wrong line found when looking for 'Transition:'" - raise ValueError, "%s: %s" % (text, line) + raise ValueError("%s: %s" % (text, line)) split=string.split(line[11:],'->') for number in string.split(split[0], ','): @@ -2353,7 +2353,7 @@ # if line[:10]!='Model_pKa:': text = "Wrong line found when looking for 'Model_pKa'" - raise ValueError, "%s: %s" % (text, line) + raise ValueError("%s: %s" % (text, line)) modelpKa = float(string.split(line)[1]) @@ -2401,7 +2401,7 @@ # def smooth(xdiel,ydiel,zdiel): - print '\nSmooting dielectric constant using Gaussian filter:\n' + print('\nSmooting dielectric constant using Gaussian filter:\n') diel=[xdiel,ydiel,zdiel] for d in diel: @@ -2441,18 +2441,18 @@ - print "These should pass without issue" - print "Run acid curve" + print("These should pass without issue") + print("Run acid curve") routines = pKaRoutines(None, None, None, None, '', maps = None, sd =None, restart=False, pairene=1.0, test_mode=True) routines.find_pH_at_0_5('zero_to_neg_one curve base', zero_to_neg_one, False) - print "Run base curve" + print("Run base curve") routines.find_pH_at_0_5('one_to_zero curve acid', one_to_zero, True) - print "These should print warnings" + print("These should print warnings") all_zero_curve = dict((ph,0.0) for ph in ph_list) - print "Run all zero curves" + print("Run all zero curves") routines.find_pH_at_0_5('All zero curve acid', all_zero_curve, False) routines.find_pH_at_0_5('All zero curve base', all_zero_curve, True) @@ -2492,9 +2492,9 @@ routines.find_pH_at_0_5('negative_interpolation_curve acid', negative_interpolation_curve, False) - print 'Accumulated warnings:' + print('Accumulated warnings:') pprint(routines.warnings) - print 'ph values:' + print('ph values:') pprint(routines.ph_at_0_5) --- a/pdb2pka/prepare_pKa_ligand.py +++ b/pdb2pka/prepare_pKa_ligand.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # Take a mol2 file as input, convert to SMILES, search pka_lig_tool database and produce @@ -70,8 +70,8 @@ def read_mol2(self,mol2lines): """Parse the mol2 lines""" - import StringIO, string - mol2fileobj=StringIO.StringIO(string.join(mol2lines)) + import io, string + mol2fileobj=io.StringIO(string.join(mol2lines)) # # Use the mol2 parser in pdb2pqr # @@ -121,18 +121,18 @@ def search_pka_ligtool(self,smiles): """Search the pka_lig_tool database for a ligand match""" - import StringIO, urllib + import io, urllib.request, urllib.parse, urllib.error # # Get the XML data from the server # - args=urllib.urlencode({'smiles':smiles}) + args=urllib.parse.urlencode({'smiles':smiles}) thisurl= url %(server,args) - f=urllib.urlopen(thisurl) + f=urllib.request.urlopen(thisurl) text=f.read() - output = StringIO.StringIO(text) - print text - print smiles + output = io.StringIO(text) + print(text) + print(smiles) return text # # Parse the XML @@ -141,39 +141,39 @@ xmldoc = minidom.parse(output) ligands = xmldoc.firstChild - print 'Search-type was: %s'%ligands.attributes['Type'].value + print('Search-type was: %s'%ligands.attributes['Type'].value) for ligand in ligands.childNodes: atoms = ligand.getElementsByTagName('Atoms')[0] mol2 = ligand.getElementsByTagName('mol2')[0] - print '*'*50 - print 'Found ligand \"%s\"'%ligand.attributes['Name'].value - print - print 'mol2 file' - print '-'*50 - print mol2.firstChild.data - print - print ' Atoms and associated pKa values' - print '-'*50 + print('*'*50) + print('Found ligand \"%s\"'%ligand.attributes['Name'].value) + print() + print('mol2 file') + print('-'*50) + print(mol2.firstChild.data) + print() + print(' Atoms and associated pKa values') + print('-'*50) for atom in atoms.childNodes: - print '%4s %4s %-6s'%(atom.attributes['Name'].value, + print('%4s %4s %-6s'%(atom.attributes['Name'].value, atom.attributes['Number'].value, - atom.attributes['Type'].value) + atom.attributes['Type'].value)) pkas = atom.firstChild if pkas: for pka in pkas.childNodes: - print ' Value: ',pka.attributes['Value'].value - print ' Temperature: ',pka.attributes['Temperature'].value - print ' pH: ',pka.attributes['pH'].value - print ' Solvent: ',pka.attributes['Solvent'].value - print ' Salt type: ',pka.attributes['Salt_type'].value - print ' Salt conc.: ',pka.attributes['Salt_conc.'].value - print ' Titratable group: ',pka.attributes['Titratable_group'].value - print ' Most bio. rel.: ',pka.attributes['Most_bio._relavent'].value - print ' Reference: ',pka.attributes['Reference'].value - print ' Comment: ',pka.attributes['Comment'].value + print(' Value: ',pka.attributes['Value'].value) + print(' Temperature: ',pka.attributes['Temperature'].value) + print(' pH: ',pka.attributes['pH'].value) + print(' Solvent: ',pka.attributes['Solvent'].value) + print(' Salt type: ',pka.attributes['Salt_type'].value) + print(' Salt conc.: ',pka.attributes['Salt_conc.'].value) + print(' Titratable group: ',pka.attributes['Titratable_group'].value) + print(' Most bio. rel.: ',pka.attributes['Most_bio._relavent'].value) + print(' Reference: ',pka.attributes['Reference'].value) + print(' Comment: ',pka.attributes['Comment'].value) - print '*'*50 + print('*'*50) return def get_allhyd_state(self): @@ -187,10 +187,10 @@ if __name__=='__main__': - print - print 'Get pKa values and structures of protonation states for a ligand' - print 'Chresten Soendergaard, Paul Czodrowski, Jens Erik Nielsen 2006-2010' - print + print() + print('Get pKa values and structures of protonation states for a ligand') + print('Chresten Soendergaard, Paul Czodrowski, Jens Erik Nielsen 2006-2010') + print() import sys, os from optparse import OptionParser parser = OptionParser(usage='%prog [options] ',version='%prog 1.0') @@ -228,7 +228,7 @@ break # if mol2file: - print mol2file + print(mol2file) fd=open(mol2file) mol2lines=fd.readlines() fd.close() @@ -241,11 +241,11 @@ except: import sys failed.append([mol2file,sys.exc_info()[0]]) - print 'FAILED' - print sys.exc_info()[0] - print failed - print 'OK',len(ok) - print 'FAILED',len(failed) + print('FAILED') + print(sys.exc_info()[0]) + print(failed) + print('OK',len(ok)) + print('FAILED',len(failed)) --- a/pka.py +++ b/pka.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # pKa calculations with APBS # @@ -28,11 +28,11 @@ # # Print usage guidelines # - print 'Usage: pka.py --ff --lig --pdie --maps <1 for using provided 3D maps; 2 for genereting new maps>' - print '--xdiel --ydiel --zdiel --kappa ' - print '--smooth ' - print 'Force field can be amber, charmm and parse' - print + print('Usage: pka.py --ff --lig --pdie --maps <1 for using provided 3D maps; 2 for genereting new maps>') + print('--xdiel --ydiel --zdiel --kappa ') + print('--smooth ') + print('Force field can be amber, charmm and parse') + print() return # @@ -48,9 +48,9 @@ routines: The routines object as generated by PDB2PQR forcefield: The forcefield object as generated by PDB2PQR """ - print - print 'PDB2PQR pKa calculations' - print + print() + print('PDB2PQR pKa calculations') + print() parser = optparse.OptionParser() @@ -184,7 +184,7 @@ try: ligand = open(options.ligand, 'rU') except IOError: - print 'Unable to find ligand file %s! Skipping...' % options.ligand + print('Unable to find ligand file %s! Skipping...' % options.ligand) #Set up the protien object #In the standalone version of pdb2pka this is redundent but needed so we emulate the @@ -193,8 +193,8 @@ pdbfile = getPDBFile(input_path) pdblist, errlist = readPDB(pdbfile) if len(errlist) != 0 and verbose: - print "Warning: %s is a non-standard PDB file.\n" %input_path - print errlist + print("Warning: %s is a non-standard PDB file.\n" %input_path) + print(errlist) # # Read the definition file # @@ -278,7 +278,7 @@ pdblist, errlist = readPDB(pdbfile) if verbose: - print "Beginning PDB2PKA...\n" + print("Beginning PDB2PKA...\n") # # Read the definition file # @@ -304,9 +304,9 @@ # Print something for some reason? # if verbose: - print "Created protein object -" - print "\tNumber of residues in protein: %s" % myProtein.numResidues() - print "\tNumber of atoms in protein : %s" % myProtein.numAtoms() + print("Created protein object -") + print("\tNumber of residues in protein: %s" % myProtein.numResidues()) + print("\tNumber of atoms in protein : %s" % myProtein.numAtoms()) # # Set up all other routines # @@ -357,8 +357,8 @@ templist = [] Lig.make_up2date(residue) net_charge=0.0 - print 'Ligand',residue - print 'Atom\tCharge\tRadius' + print('Ligand',residue) + print('Atom\tCharge\tRadius') for atom in residue.getAtoms(): if atom.mol2charge: atom.ffcharge=atom.mol2charge @@ -372,7 +372,7 @@ # Assign radius # atom.radius = Lig.ligand_props[atom.name]["radius"] - print '%s\t%6.4f\t%6.4f' %(atom.name,atom.ffcharge,atom.radius) + print('%s\t%6.4f\t%6.4f' %(atom.name,atom.ffcharge,atom.radius)) if atom in misslist: misslist.pop(misslist.index(atom)) templist.append(atom) @@ -397,7 +397,7 @@ # # Print the net charge # - print 'Net charge for ligand %s is: %5.3f' %(residue.name,net_charge) + print('Net charge for ligand %s is: %5.3f' %(residue.name,net_charge)) # # Temporary fix; if ligand was successful, pull all ligands from misslist # Not sure if this is needed at all here ...? (Jens wrote this) @@ -410,9 +410,9 @@ misslist.remove(atom) if verbose: - print "Created protein object (after processing myRoutines) -" - print "\tNumber of residues in protein: %s" % myProtein.numResidues() - print "\tNumber of atoms in protein : %s" % myProtein.numAtoms() + print("Created protein object (after processing myRoutines) -") + print("\tNumber of residues in protein: %s" % myProtein.numResidues()) + print("\tNumber of atoms in protein : %s" % myProtein.numAtoms()) # # Create the APBS input file # @@ -427,11 +427,11 @@ # For convenience # igen.pdie = pdie - print 'Setting protein dielectric constant to ',igen.pdie + print('Setting protein dielectric constant to ',igen.pdie) igen.sdie=sdie igen.maps=maps if maps==1: - print "Using dielectric and mobile ion-accessibility function maps in PBE" + print("Using dielectric and mobile ion-accessibility function maps in PBE") if xdiel: igen.xdiel = xdiel else: @@ -445,14 +445,14 @@ else: raise PDB2PKAError("Z dielectric map is missing\n") - print 'Setting dielectric function maps: %s, %s, %s'%(igen.xdiel,igen.ydiel,igen.zdiel) + print('Setting dielectric function maps: %s, %s, %s'%(igen.xdiel,igen.ydiel,igen.zdiel)) if kappa: igen.kappa = kappa else: raise PDB2PKAError("Mobile ion-accessibility map is missing\n") - print 'Setting mobile ion-accessibility function map to: ',igen.kappa + print('Setting mobile ion-accessibility function map to: ',igen.kappa) if sd: xdiel_smooth, ydiel_smooth, zdiel_smooth = smooth(xdiel,ydiel,zdiel) @@ -475,6 +475,6 @@ mypkaRoutines = pka_routines.pKaRoutines(protein, routines, forcefield, apbs_setup, output_dir, maps, sd, restart=not options.resume, pairene=options.pairene) - print 'Doing full pKa calculation' + print('Doing full pKa calculation') mypkaRoutines.runpKa() --- a/propka30/Source/bonds.py +++ b/propka30/Source/bonds.py @@ -38,7 +38,7 @@ #------------------------------------------------------------------------------------------------------- import pickle,sys,os,math -from lib import pka_print +from .lib import pka_print class bondmaker: @@ -250,9 +250,9 @@ # apply table information on pi-electrons for atom in ligand.atoms: - if atom.name in self.number_of_pi_electrons_in_bonds_ligands.keys(): + if atom.name in list(self.number_of_pi_electrons_in_bonds_ligands.keys()): atom.number_of_pi_electrons_in_double_and_triple_bonds = self.number_of_pi_electrons_in_bonds_ligands[atom.name] - if atom.name in self.number_of_pi_electrons_in_conjugate_bonds_in_ligands.keys(): + if atom.name in list(self.number_of_pi_electrons_in_conjugate_bonds_in_ligands.keys()): atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds = self.number_of_pi_electrons_in_conjugate_bonds_in_ligands[atom.name] # just in case any protein residues are included @@ -360,7 +360,7 @@ # assign bonds - keys = self.boxes.keys() + keys = list(self.boxes.keys()) for key in keys: self.find_bonds_for_atoms(self.boxes[key]) @@ -374,7 +374,7 @@ for by in [y-1,y,y+1]: for bz in [z-1,z,z+1]: key = self.box_key(bx,by,bz) - if key in self.boxes.keys(): + if key in list(self.boxes.keys()): self.boxes[key].append(atom) #pka_print(atom,'->',key,':',len(self.boxes[key])) --- a/propka30/Source/calculator.py +++ b/propka30/Source/calculator.py @@ -38,7 +38,7 @@ #------------------------------------------------------------------------------------------------------- import math, random, string -from lib import pka_print +from .lib import pka_print def InterAtomDistance(atom1, atom2): @@ -218,7 +218,7 @@ dV = 0.00 volume = 0.00 min_distance_4th = pow(2.75, 4) - for chainID in atoms.keys(): + for chainID in list(atoms.keys()): for key in atoms[chainID]["keys"]: for atom in atoms[chainID][key]: if atom.element != "H": @@ -273,7 +273,7 @@ local_cutoff = 0.00 residue.Nmass = 0 residue.Nlocl = 0 - for chainID in atoms.keys(): + for chainID in list(atoms.keys()): for key in atoms[chainID]["keys"]: for atom in atoms[chainID][key]: if atom.element != "H": @@ -312,7 +312,7 @@ Nlocl_his6 = 0 residue.Nmass = 0 residue.Nlocl = 0 - for chainID in atoms.keys(): + for chainID in list(atoms.keys()): for key in atoms[chainID]["keys"]: for atom in atoms[chainID][key]: HYDROGEN_ATOM = ( (atom.name[0] == 'H') or (atom.name[0] in string.digits and atom.name[1] == 'H') ) --- a/propka30/Source/chain.py +++ b/propka30/Source/chain.py @@ -37,10 +37,10 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import math, sys -import lib +from . import lib pka_print = lib.pka_print -import mutate -from residue import Residue +from . import mutate +from .residue import Residue class Chain: --- a/propka30/Source/compare.py +++ b/propka30/Source/compare.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import sys, math, string -from lib import int2roman, convertResidueCode, pka_print +from .lib import int2roman, convertResidueCode, pka_print def compareFoldingContributions(target=None, template=None, options=None): @@ -48,7 +48,7 @@ 4. calculate the difference 5. printout sorted result """ - from mutate import readAlignmentFiles + from .mutate import readAlignmentFiles # checking that pKa values are available checkDonePKA(target, template) @@ -77,7 +77,7 @@ make a list of pdbcodes in 'alignment' """ names = [name] - for key in alignment.keys(): + for key in list(alignment.keys()): if key not in names: names.append(key) @@ -115,8 +115,8 @@ """ str = str[:-1] pka_print(str) - for key1 in alignment.keys(): - for key2 in alignment[key1].keys(): + for key1 in list(alignment.keys()): + for key2 in list(alignment[key1].keys()): str = " %s 100 %s 0" % (key2, "%") index = 0 for code in alignment[key1][key2]['sequence']: --- a/propka30/Source/corresponding_atoms.py +++ b/propka30/Source/corresponding_atoms.py @@ -40,7 +40,7 @@ #------------------------------------------------------------------------------------------------------- import sys -from lib import residueList, atomList, pka_print +from .lib import residueList, atomList, pka_print # NOTE: --- a/propka30/Source/coupled_residues.py +++ b/propka30/Source/coupled_residues.py @@ -38,7 +38,7 @@ #------------------------------------------------------------------------------------------------------- import math -from lib import pka_print +from .lib import pka_print max_intrinsic_pKa_diff = 2.0 min_interaction_energy = 0.5 --- a/propka30/Source/debug.py +++ b/propka30/Source/debug.py @@ -37,10 +37,10 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import string -import lib -import calculator as calculate +from . import lib +from . import calculator as calculate -from lib import pka_print +from .lib import pka_print def interactionMatrix(interaction): @@ -69,9 +69,9 @@ printing out all information in resInfo """ pka_print("in resInfo:") - for key1 in resInfo.keys(): + for key1 in list(resInfo.keys()): pka_print(" --- %s ---" % (key1)) - for key2 in resInfo[key1].keys(): + for key2 in list(resInfo[key1].keys()): pka_print(key2, resInfo[key1][key2]) @@ -162,9 +162,9 @@ """ Prints out alignment information for debugging """ - for key in alignment.keys(): + for key in list(alignment.keys()): pka_print( " --- %s ---" % (key) ) - for key2 in alignment[key].keys(): + for key2 in list(alignment[key].keys()): pka_print("%s %5d%2s" % (alignment[key][key2]["name"], alignment[key][key2]["resNumb"], alignment[key][key2]["chainID"])) pka_print("%s\n" % (alignment[key][key2]["sequence"])) --- a/propka30/Source/determinants.py +++ b/propka30/Source/determinants.py @@ -38,12 +38,12 @@ #------------------------------------------------------------------------------------------------------- import math, time -import iterative -import lib -from lib import pka_print +from . import iterative +from . import lib +from .lib import pka_print #import debug -import calculator as calculate -from determinant import Determinant +from . import calculator as calculate +from .determinant import Determinant def setDeterminants(propka_residues, version=None, options=None): --- a/propka30/Source/iterative.py +++ b/propka30/Source/iterative.py @@ -37,11 +37,11 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import math, time -import calculator as calculate -import lib +from . import calculator as calculate +from . import lib pka_print = lib.pka_print #import debug -from determinant import Determinant +from .determinant import Determinant # Some library functions for the interative pKa determinants --- a/propka30/Source/lib.py +++ b/propka30/Source/lib.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -40,7 +40,7 @@ import string, sys, copy, math -import output +from . import output def loadOptions(): @@ -199,7 +199,7 @@ if filename not in options.alignment: options.alignment.append( filename ) else: - for code in mutation.keys(): + for code in list(mutation.keys()): filename = "%s.pir" % ( extractName(code) ) if filename not in options.alignment: options.alignment.append( filename ) @@ -762,7 +762,7 @@ numerals = { 1 : "I", 4 : "IV", 5 : "V", 9 : "IX", 10 : "X", 40 : "XL", 50 : "L", 90 : "XC", 100 : "C", 400 : "CD", 500 : "D", 900 : "CM", 1000 : "M" } result = "" - for value, numeral in sorted(numerals.items(), reverse=True): + for value, numeral in sorted(list(numerals.items()), reverse=True): while number >= value: result += numeral number -= value --- a/propka30/Source/ligand.py +++ b/propka30/Source/ligand.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -40,7 +40,7 @@ import sys, pdb, protonate, lib, bonds -from vector_algebra import * +from .vector_algebra import * pka_print = lib.pka_print all_sybyl_types = [ @@ -185,7 +185,7 @@ atom.residue = self #self.remove_ions() - self.configuration_keys = atoms[0].configurations.keys() + self.configuration_keys = list(atoms[0].configurations.keys()) # create ligand residue objects self.ligand_residues = [] @@ -265,7 +265,7 @@ for atom in self.atoms: # check if we already have assigned a name to this atom if hasattr(atom, 'sybyl_assigned'): - print(atom.resName, atom.numb, atom.name, 'alreadyassigned') + print((atom.resName, atom.numb, atom.name, 'alreadyassigned')) continue # find some properties of the atom @@ -312,7 +312,7 @@ if atom.get_element() == 'C': # check for amide - if 'O' in bonded_elements.values() and 'N' in bonded_elements.values(): + if 'O' in list(bonded_elements.values()) and 'N' in list(bonded_elements.values()): self.set_type(atom, 'C.2') for b in atom.bonded_atoms: if b.get_element() == 'N': --- a/propka30/Source/mutate.py +++ b/propka30/Source/mutate.py @@ -38,10 +38,10 @@ #------------------------------------------------------------------------------------------------------- import math, os, sys, re -import lib +from . import lib pka_print = lib.pka_print -import output -import pdb +from . import output +from . import pdb #import debug @@ -119,7 +119,7 @@ best_mutation = "WT" dG_ref = proteins["WT"][0] pka_print("%8s %6s\n%8.2lf %6.2lf %s" % ("dG_fold", "ddG_fold", dG_ref, dG_ref-dG_ref, "WT")) - for label in proteins.keys(): + for label in list(proteins.keys()): if label != "WT": dG_mut, protein, full_mutation = proteins[label] pka_print("%8.2lf %6.2lf %s" % (dG_mut, dG_mut-dG_ref, label)) @@ -163,7 +163,7 @@ """ returning a new protein, mutation approach determined from options.mutator """ - from protein import Protein + from .protein import Protein pka_print("mutator: %s" % (options.mutator.label)) pka_print("type: %s\n" % (options.mutator.type)) @@ -174,9 +174,9 @@ alignment = readAlignmentFiles(filenames=options.alignment, mesophile=protein.name, options=options) pdbcode, rest = splitStringMutationInTwo(mutation) if pdbcode == None: - mutation = remakeStringMutation(mutation, protein.atoms.keys()) + mutation = remakeStringMutation(mutation, list(protein.atoms.keys())) else: - mutation = remakeStringMutation(mutation, protein.atoms.keys(), atoms[pdbcode].keys()) + mutation = remakeStringMutation(mutation, list(protein.atoms.keys()), list(atoms[pdbcode].keys())) dict_mutation = recastIntoDictionary(mutation, alignment=alignment, protein=protein) elif isinstance(mutation, dict): # this is already in dictionary-format @@ -233,7 +233,7 @@ print out the mutation in formatted form """ pka_print(" ----- mutation ----- \n", " residue rmsd") - for key in mutation.keys(): + for key in list(mutation.keys()): pka_print(" %s %6.2lf" % (mutation[key]['label'], mutation[key]['rmsd'])) @@ -325,7 +325,7 @@ # store it as alignment-pairs in 'alignments' - for key in alignment.keys(): + for key in list(alignment.keys()): if re.search(mesophile, key): """ do nothing, this matches the mesophile """ # pka_print("match, don't do \"%s\" \"%s\":" % (mesophile, key)) @@ -359,7 +359,7 @@ get the translation for the 'back-tracking' in the 'alignment-mutation' """ rmsd = 0.00; number_of_atoms = 0; translation = [0.00, 0.00, 0.00] - for key in backbone.keys(): + for key in list(backbone.keys()): number_of_atoms += 1 atom1, atom2 = backbone[key] dX = atom2.x - atom1.x; @@ -381,7 +381,7 @@ creating a copy of the atoms dictionary """ newAtoms = {} - for chainID in atoms.keys(): + for chainID in list(atoms.keys()): # creating new chain dictionary newAtoms[chainID] = {'keys': []} for key in atoms[chainID]['keys']: @@ -402,7 +402,7 @@ newAtoms = copyAtomsDictionary(atoms=protein.atoms, options=options) configs = [ protein.configurations[0] ] - for key in mutation.keys(): + for key in list(mutation.keys()): singleMutateAtomsDictionary(atoms=newAtoms, template=atoms, @@ -476,7 +476,7 @@ newAtoms[chainID] = {"keys": []} for key in protein.atoms[chainID]["keys"]: atomList = [] - if key in mutation.keys(): + if key in list(mutation.keys()): # adding residue from thermophile data code = mutation[key]['pdb'] key1 = mutation[key]['template'] @@ -530,7 +530,7 @@ elif isinstance(generic_mutation, list): mutation_list = generic_mutation elif isinstance(generic_mutation, dict): - for key in generic_mutation.keys(): + for key in list(generic_mutation.keys()): chainID1 = generic_mutation[key]['target'][-1] code1, resName = lib.convertResidueCode(resName=generic_mutation[key]['target'][:3]) resNumb = int(generic_mutation[key]['target'][3:7]) @@ -718,7 +718,7 @@ if isinstance(mutations, dict): mutation[ keys[i] ] = mutations[ keys[i] ] elif isinstance(mutations, list): - for key in mutations[i].keys(): + for key in list(mutations[i].keys()): mutation[ key ] = mutations[i][ key ] else: short += "N" @@ -826,7 +826,7 @@ label = "" if isinstance(generic_mutation, dict): - for key in generic_mutation.keys(): + for key in list(generic_mutation.keys()): code1, resName = lib.convertResidueCode(resName=key[:3]) code2, resName = lib.convertResidueCode(resName=generic_mutation[key]['label'][:3]) label += "/%s%d%s" % (code1, int(key[3:7]), code2) @@ -900,7 +900,7 @@ new[target_label]['target'] = target_label mutation = new elif isinstance(mutation, dict): - for key in mutation.keys(): + for key in list(mutation.keys()): mutation[key]['target'] = key if "label" not in mutation[key] and "template" in mutation[key]: # generating new label @@ -917,7 +917,7 @@ rmsd_new = 0.00 rmsd_old = 0.00 number_of_points = len(position['target']) - for key in position['target'].keys(): + for key in list(position['target'].keys()): for i in range(3): rmsd_new += pow( (position['new'][key][i] - position['target'][key][i]), 2) rmsd_old += pow( (position['old'][key][i] - position['target'][key][i]), 2) @@ -1010,8 +1010,8 @@ """ This routine overlaps two residues based on an array of atom labels, 'center' """ - from corresponding_atoms import makeCorrespondingAtomNames - from rotate import rotatePosition, translatePosition, makeCrossProduct, calculateVectorLength, \ + from .corresponding_atoms import makeCorrespondingAtomNames + from .rotate import rotatePosition, translatePosition, makeCrossProduct, calculateVectorLength, \ makeScalarProduct, generateRandomDisplacement, generateRandomRotation, rotateAtoms, translateAtoms # create copy of target @@ -1022,7 +1022,7 @@ dR = [None, None, None] center = ['CA'] - for key in mutation.keys(): + for key in list(mutation.keys()): # mutate the new atoms dictionary (position unchanged) singleMutateAtomsDictionary(atoms=newAtoms, @@ -1076,7 +1076,7 @@ # initializing iterations: copy over 'template' to 'new' & 'old' chainNumb = ord("A") center = [] - for name in position['template'].keys(): + for name in list(position['template'].keys()): center.append(name) position['new'][name] = [position['template'][name][0], position['template'][name][1], position['template'][name][2]] position['old'][name] = [position['template'][name][0], position['template'][name][1], position['template'][name][2]] @@ -1101,7 +1101,7 @@ if rmsd_new < rmsd_old: # pka_print("REMARK update structure (iter %3d (%8.3lf%8.3lf))" % (iter, rmsd_new, rmsd_old)) chainNumb += 1 - for name in position['old'].keys(): + for name in list(position['old'].keys()): for i in range(3): position['old'][name][i] = position['new'][name][i] if False: @@ -1111,7 +1111,7 @@ rotateAtoms(newAtoms[target_chainID][label], axis, theta, center=center) translateAtoms(newAtoms[target_chainID][label], dR) else: - for name in position['new'].keys(): + for name in list(position['new'].keys()): for i in range(3): position['new'][name][i] = position['old'][name][i] @@ -1172,7 +1172,7 @@ atoms[pdbcode] = pdb.readPDB(filename=pdbcode) else: # extracting pdbcode if mutation is in dictionary format - for key in mutation.keys(): + for key in list(mutation.keys()): pdbcode = mutation[key]['pdb'] if pdbcode not in atoms: atoms[pdbcode] = pdb.readPDB(filename=pdbcode) @@ -1201,10 +1201,10 @@ translate = dictionary for translating target and template residues to the origin center = array with atom names in 'position-dictionary': used for 'rotation-center' """ - from rotate import rotatePosition, translatePosition, makeCrossProduct, calculateVectorLength, makeScalarProduct, generateRandomDisplacement, generateRandomRotation + from .rotate import rotatePosition, translatePosition, makeCrossProduct, calculateVectorLength, makeScalarProduct, generateRandomDisplacement, generateRandomRotation # start mutations - for label in mutation.keys(): + for label in list(mutation.keys()): pka_print("%s ==> %s" % (label, mutation[label]['template'])) @@ -1219,10 +1219,10 @@ # debug printout if False: - for key in position['target'].keys(): + for key in list(position['target'].keys()): Rx, Ry, Rz = position['target'][key] pka_print("ATOM 669 %-3s %s A 89 %8.3lf%8.3lf%8.3lf" % (key, original_residue.resName, Rx, Ry, Rz)) - for key in position['template'].keys(): + for key in list(position['template'].keys()): Rx, Ry, Rz = position['template'][key] pka_print("ATOM 669 %-3s GLU B 89 %8.3lf%8.3lf%8.3lf" % ("H", Rx, Ry, Rz)) @@ -1238,7 +1238,7 @@ # debug printout if False: - for key in position['template'].keys(): + for key in list(position['template'].keys()): Rx, Ry, Rz = position['template'][key] pka_print("ATOM 669 %-3s GLU C 89 %8.3lf%8.3lf%8.3lf" % ("H", Rx, Ry, Rz)) @@ -1258,12 +1258,12 @@ # debug printout if False: - for key in position['template'].keys(): + for key in list(position['template'].keys()): Rx, Ry, Rz = position['template'][key] pka_print("ATOM 669 %-3s GLU B 89 %8.3lf%8.3lf%8.3lf" % ("H", Rx, Ry, Rz)) # initializing iterations: copy over 'template' to 'new' & 'old' - for key in position['template'].keys(): + for key in list(position['template'].keys()): position['new'][key] = [position['template'][key][0], position['template'][key][1], position['template'][key][2]] position['old'][key] = [position['template'][key][0], position['template'][key][1], position['template'][key][2]] @@ -1281,7 +1281,7 @@ if rmsd_new < rmsd_old: # pka_print("REMARK update structure (iter %3d (%8.3lf%8.3lf))" % (iter, rmsd_new, rmsd_old)) chainNumb += 1 - for key in position['old'].keys(): + for key in list(position['old'].keys()): for i in range(3): position['old'][key][i] = position['new'][key][i] if False: @@ -1292,7 +1292,7 @@ copied_residue.translate(dR) else: # pka_print("no update (iter %3d (%8.3lf%8.3lf))" % (iter, rmsd_new, rmsd_old)) - for key in position['new'].keys(): + for key in list(position['new'].keys()): for i in range(3): position['new'][key][i] = position['old'][key][i] --- a/propka30/Source/output.py +++ b/propka30/Source/output.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import sys -import lib +from . import lib revision = 182 @@ -63,7 +63,7 @@ filename = "%s.pdb" % (protein.name) file = open(filename, 'w') if options.verbose: - print("writing pdbfile %s" % (filename)) + print(("writing pdbfile %s" % (filename))) close_file = True else: # don't close the file, it was opened in a different place @@ -156,7 +156,7 @@ filename = "%s.pka" % (protein.name) file = open(filename, 'w') if verbose == True: - print("writing pkafile %s" % (filename)) + print(("writing pkafile %s" % (filename))) # writing propka header str = "%s\n" % ( getPropkaHeader() ) @@ -213,7 +213,7 @@ # geting the determinants section str = getDeterminantSection(protein) if verbose: - print(str[:-1]) + print((str[:-1])) str = getSummarySection(protein) if verbose: --- a/propka30/Source/parameters.py +++ b/propka30/Source/parameters.py @@ -37,10 +37,10 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import math -import lib +from . import lib pka_print = lib.pka_print import sys, os -from calculator import calculate +from .calculator import calculate def pKa_mod(resName): @@ -668,7 +668,7 @@ 'TRP': "TRP"} - if resName in resType.keys(): + if resName in list(resType.keys()): return resType[resName] else: return None @@ -1019,7 +1019,7 @@ if resName in Q: return Q[resName] - elif resName in self.ions.keys(): + elif resName in list(self.ions.keys()): return self.ions[resName] else: return 0.00 @@ -1046,9 +1046,9 @@ 'GLN': "AMD", 'TRP': "TRP"} - if resName in resType.keys(): + if resName in list(resType.keys()): return resType[resName] - elif resName in self.ions.keys(): + elif resName in list(self.ions.keys()): return 'LIG' else: return None --- a/propka30/Source/parameters_new.py +++ b/propka30/Source/parameters_new.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- -from lib import pka_print +from .lib import pka_print def resName2Type(resName=None): """ @@ -368,7 +368,7 @@ # updating parameter matrix to full matrix - keys = parameters.keys() + keys = list(parameters.keys()) for key1 in keys: for key2 in keys: if key2 not in parameters[key1]: --- a/propka30/Source/parameters_std.py +++ b/propka30/Source/parameters_std.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- -from lib import pka_print +from .lib import pka_print def resName2Type(resName=None): """ @@ -362,7 +362,7 @@ # updating side-chain parameter matrix to full matrix - keys = parameters.keys() + keys = list(parameters.keys()) for key1 in keys: for key2 in keys: if key2 not in parameters[key1]: --- a/propka30/Source/pdb.py +++ b/propka30/Source/pdb.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import string, sys, copy -import lib +from . import lib pka_print = lib.pka_print excluded_resNames = ["H2O", "HOH", "SO4", "PO4", "PEG", "EPE", "NAG", "TRS"] @@ -109,8 +109,8 @@ for chainID in sorted( atoms.keys() ): for key in atoms[chainID]["keys"]: for atom in atoms[chainID][key]: - str = "%s%4d %4s%3d%7s" % (atom.resName, atom.resNumb, atom.name, len(atom.configurations.keys()), atom.type) - for key in atom.configurations.keys(): + str = "%s%4d %4s%3d%7s" % (atom.resName, atom.resNumb, atom.name, len(list(atom.configurations.keys())), atom.type) + for key in list(atom.configurations.keys()): str += "%5s" % (key) pka_print(str) @@ -361,7 +361,7 @@ self.x += vector[0] self.y += vector[1] self.z += vector[2] - for key in self.configurations.keys(): + for key in list(self.configurations.keys()): for i in range(3): self.configurations[key][i] += vector[i] @@ -405,14 +405,14 @@ self.z = self.configurations[key][2] elif len(self.configurations) == 1: # get single key if only one configuration: saving back-bone protonation when previous residue doesn't have 'key' - for default_key in self.configurations.keys(): + for default_key in list(self.configurations.keys()): break self.x = self.configurations[default_key][0] self.y = self.configurations[default_key][1] self.z = self.configurations[default_key][2] elif True: # get single key if only one configuration: saving back-bone protonation when previous residue doesn't have 'key' - for default_key in self.configurations.keys(): + for default_key in list(self.configurations.keys()): if key[:-2] == default_key[:-2]: break self.x = self.configurations[default_key][0] @@ -421,7 +421,7 @@ else: resLabel = "%-3s%4d%2s" % (self.resName, self.resNumb, self.chainID) keys = "" - for item in self.configurations.keys(): keys += "%5s" % (item) + for item in list(self.configurations.keys()): keys += "%5s" % (item) pka_print("configuration '%s' not found in '%s' atom '%s' [%s]" % (key, resLabel, self.name, keys)) sys.exit(8) --- a/propka30/Source/protein.py +++ b/propka30/Source/protein.py @@ -37,15 +37,15 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import math, sys, os, time, string -import lib +from . import lib pka_print = lib.pka_print -import determinants -import pdb +from . import determinants +from . import pdb #import debug -import output -import coupled_residues -import calculator as calculate -from chain import Chain +from . import output +from . import coupled_residues +from . import calculator as calculate +from .chain import Chain @@ -290,7 +290,7 @@ """ protonates the protein according to given scheme """ - from protonator import makeProtonator + from .protonator import makeProtonator please = makeProtonator(scheme=scheme) self.removeHydrogens() @@ -317,7 +317,7 @@ """ # create a default version if not provided if version == None: - import version + from . import version version = version.makeVersion(label=options.version_label) if len(self.configurations) == 1: @@ -408,25 +408,25 @@ pka_print(str) # get the average pKa properties by dividing the sum with number of configurations, len(configuration keys) - from determinants import Determinant + from .determinants import Determinant for residue in pka_residues: residue_key = residue.label sum_pka = 0.00; sum_Nmass = 0.00; sum_Emass = 0.00; sum_Nlocl = 0.00; sum_Elocl = 0.00 - for key in pkas[residue_key].keys(): + for key in list(pkas[residue_key].keys()): sum_pka += pkas[residue_key][key] sum_Nmass += Nmass[residue_key][key] sum_Emass += Emass[residue_key][key] sum_Nlocl += Nlocl[residue_key][key] sum_Elocl += Elocl[residue_key][key] - residue.pKa_pro = sum_pka/len( pkas[residue_key].keys() ) - residue.Nmass = sum_Nmass/len( pkas[residue_key].keys() ) - residue.Emass = sum_Emass/len( pkas[residue_key].keys() ) - residue.Nlocl = sum_Nlocl/len( pkas[residue_key].keys() ) - residue.Elocl = sum_Elocl/len( pkas[residue_key].keys() ) + residue.pKa_pro = sum_pka/len( list(pkas[residue_key].keys()) ) + residue.Nmass = sum_Nmass/len( list(pkas[residue_key].keys()) ) + residue.Emass = sum_Emass/len( list(pkas[residue_key].keys()) ) + residue.Nlocl = sum_Nlocl/len( list(pkas[residue_key].keys()) ) + residue.Elocl = sum_Elocl/len( list(pkas[residue_key].keys()) ) residue.determinants = [[], [], []] for type in range(3): - for key in determinants[residue_key][type].keys(): - value = determinants[residue_key][type][key] / len( pkas[residue_key].keys() ) + for key in list(determinants[residue_key][type].keys()): + value = determinants[residue_key][type][key] / len( list(pkas[residue_key].keys()) ) if abs(value) > 0.005: # <-- removing determinant that appears as 0.00 newDeterminant = Determinant(key, value) residue.determinants[type].append(newDeterminant) @@ -774,7 +774,7 @@ """ mutates the protein according to 'mutation' using 'method' """ - import mutate + from . import mutate newProtein = mutate.makeMutatedProtein(self, mutation=mutation, atoms=atoms, options=options) return newProtein @@ -784,7 +784,7 @@ """ permutes multiple mutations and determins the most stable combination; note, you need the version for stability calculations """ - import mutate + from . import mutate best_mutation = mutate.optimizeMutationDeterminants(self, mutation=mutation, atoms=atoms, alignment=alignment, version=version, options=options) return best_mutation @@ -794,7 +794,7 @@ """ permutes multiple mutations and determins the most stable combination; note, you need the version for stability calculations """ - import mutate + from . import mutate best_mutation = mutate.optimizeMultipleMutations(self, mutations=mutations, atoms=atoms, alignment=None, version=version, options=options) return best_mutation @@ -914,7 +914,7 @@ file.write(str) # set 'protein' based on pdbcode - for protein in experiment.keys(): + for protein in list(experiment.keys()): str = "%s" % (protein) #pka_print(str) #str += " %s" % (experiment[protein]['pdb']) @@ -925,7 +925,7 @@ # setting a list of labels to work with if labels == None or labels == "ALL": labels = [] - for label in experiment[protein].keys(): + for label in list(experiment[protein].keys()): labels.append(label) # iterating that list @@ -961,7 +961,7 @@ """ Reads necessary information about residues (includes ions) """ - from parameters_new import resName2Type, getQs, pKa_mod + from .parameters_new import resName2Type, getQs, pKa_mod resInfo = {} # reading residue information from parameters.py resInfo['resType'] = resName2Type() @@ -970,7 +970,7 @@ resInfo['type'] = {'C- ': "C-terminus", 'N+ ': "N-terminus"} # setting up 'type' = 'amino-acid' for residues - for resName in resInfo['resType'].keys(): + for resName in list(resInfo['resType'].keys()): if resName not in resInfo['type']: resInfo['type'][resName] = "amino-acid" --- a/propka30/Source/protonate.py +++ b/propka30/Source/protonate.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -39,9 +39,9 @@ #------------------------------------------------------------------------------------------------------- -from vector_algebra import * -import bonds, pdb -from lib import pka_print +from .vector_algebra import * +from . import bonds, pdb +from .lib import pka_print class Protonate: """ Protonates atoms using VSEPR theory """ --- a/propka30/Source/protonator.py +++ b/propka30/Source/protonator.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -40,11 +40,11 @@ import sys, math -from vector_algebra import * -import bonds as bonds -import pdb as pdb +from .vector_algebra import * +from . import bonds as bonds +from . import pdb as pdb -from lib import pka_print +from .lib import pka_print def makeProtonator(scheme=None): @@ -201,7 +201,7 @@ X1, X2, X3 = atoms H = X1.makeCopy(name=name, element='H') - for key in H.configurations.keys(): + for key in list(H.configurations.keys()): for atom in [H, X1, X2, X3]: atom.setConfiguration(key) @@ -227,7 +227,7 @@ X1, X2, X3 = atoms H = X1.makeCopy(name=name, element='H') - for key in H.configurations.keys(): + for key in list(H.configurations.keys()): for atom in [H, X1, X2, X3]: atom.setConfiguration(key) @@ -253,7 +253,7 @@ X1, X2, X3 = atoms H = X2.makeCopy(name=name, element='H') - for key in H.configurations.keys(): + for key in list(H.configurations.keys()): for atom in [H, X1, X2, X3]: atom.setConfiguration(key) --- a/propka30/Source/residue.py +++ b/propka30/Source/residue.py @@ -40,8 +40,8 @@ import string import math import copy -import lib -from pdb import Atom +from . import lib +from .pdb import Atom pka_print = lib.pka_print class Residue: @@ -107,7 +107,7 @@ self.type = "ligand" # setting the number of configurations for this residue - for key in atom.configurations.keys(): + for key in list(atom.configurations.keys()): if key not in self.configurations: self.configurations.append(key) @@ -792,7 +792,7 @@ atom.x += translation[0] atom.y += translation[1] atom.z += translation[2] - for key in atom.configurations.keys(): + for key in list(atom.configurations.keys()): for i in range(3): atom.configurations[key][i] += translation[i] @@ -801,7 +801,7 @@ """ rotate residue theta radians around axis with center=center """ - from rotate import generalRotationMatrix + from .rotate import generalRotationMatrix translate = [0.00, 0.00, 0.00] number_of_atoms = 0 for atom in self.atoms: @@ -839,7 +839,7 @@ atom.z = new_position[2] # rotate configuration - for key in atom.configurations.keys(): + for key in list(atom.configurations.keys()): for xyz in range(3): new_position[xyz] = translate[xyz] for i in range(3): @@ -855,7 +855,7 @@ """ making a copy of this residue """ - from protein import getResidueParameters + from .protein import getResidueParameters if chainID == None: chainID = self.chainID if resNumb == None: resNumb = self.resNumb --- a/propka30/Source/rotate.py +++ b/propka30/Source/rotate.py @@ -40,7 +40,7 @@ import math, os, sys, random -from lib import pka_print +from .lib import pka_print def generateCorrespondingAtoms(): @@ -183,7 +183,7 @@ """ translates the position according to 'translation' """ - for key in position.keys(): + for key in list(position.keys()): for i in range(3): position[key][i] += translation[i] @@ -200,7 +200,7 @@ translate[i] += position[key][i]/len(center) # translate to rotation center - for key in position.keys(): + for key in list(position.keys()): for i in range(3): position[key][i] -= translate[i] @@ -209,7 +209,7 @@ # do the actual rotation new_position = [None, None, None] - for key in position.keys(): + for key in list(position.keys()): # rotate for xyz in range(3): new_position[xyz] = translate[xyz] @@ -270,7 +270,7 @@ atom.z = new_position[2] # rotate configuration - for key in atom.configurations.keys(): + for key in list(atom.configurations.keys()): for xyz in range(3): new_position[xyz] = translate[xyz] for i in range(3): --- a/propka30/Source/vector_algebra.py +++ b/propka30/Source/vector_algebra.py @@ -37,7 +37,7 @@ # Journal of Chemical Theory and Computation, 7, 525-537 (2011) #------------------------------------------------------------------------------------------------------- import math, sys -import lib +from . import lib pka_print = lib.pka_print @@ -275,9 +275,9 @@ # store vectors for all configurations of atoms if atom1!=0: - self.keys = lib.get_sorted_configurations(atom1.configurations.keys()) + self.keys = lib.get_sorted_configurations(list(atom1.configurations.keys())) if atom2!=0: - keys2 = lib.get_sorted_configurations(atom2.configurations.keys()) + keys2 = lib.get_sorted_configurations(list(atom2.configurations.keys())) if self.keys != keys2: pka_print("ERROR: Inequivalent configurations for atoms, please correct your pdbfile to single configuration") pka_print("%s\n%s" % (atom1, atom2)) --- a/propka30/Source/version.py +++ b/propka30/Source/version.py @@ -38,9 +38,9 @@ #------------------------------------------------------------------------------------------------------- import math -import lib +from . import lib import sys, os -import calculator as calculate +from . import calculator as calculate pka_print = lib.pka_print @@ -413,7 +413,7 @@ if resType == None: # doing it for all residues #pka_print("changing back-bone parameters") - for key in self.BackBoneParameters.keys(): + for key in list(self.BackBoneParameters.keys()): self.BackBoneParameters[key][0] = dpka str = " %s: %6.2lf " % (key, self.BackBoneParameters[key][0]) str += "[%5.2lf,%5.2lf]" % (self.BackBoneParameters[key][1][0], self.BackBoneParameters[key][1][1]) @@ -434,9 +434,9 @@ """ if resType == None: # doing it for all residues - for key1 in self.SideChainParameters.keys(): + for key1 in list(self.SideChainParameters.keys()): #pka_print("changing side-chain parameters for resType \"%s\"" % (key1)) - for key2 in self.SideChainParameters[key1].keys(): + for key2 in list(self.SideChainParameters[key1].keys()): self.SideChainParameters[key1][key2][0] = dpka str = " %s: %6.2lf " % (key2, self.SideChainParameters[key1][key2][0]) str += "[%5.2lf,%5.2lf]" % (self.SideChainParameters[key1][key2][1][0], self.SideChainParameters[key1][key2][1][1]) @@ -445,7 +445,7 @@ # doing it just for residue 'key1' key1 = resType #pka_print("changing side-chain parameters for resType \"%s\"" % (key1)) - for key2 in self.SideChainParameters[key1].keys(): + for key2 in list(self.SideChainParameters[key1].keys()): self.SideChainParameters[key1][key2][0] = dpka self.SideChainParameters[key2][key1][0] = dpka str = " %s: %6.2lf " % (key2, self.SideChainParameters[key1][key2][0]) @@ -457,7 +457,7 @@ """ setting the Coulomb model, and its parameters. If parameter is not defined, it will take the default from 'parameters.py' """ - import parameters_new as parameters + from . import parameters_new as parameters coulomb_parameters = parameters.getCoulombParameters() if label not in coulomb_parameters: pka_print("do not accept Coulomb model \"%s\\n" % (label)) @@ -494,7 +494,7 @@ """ setting the desolvation model, and its parameters """ - import parameters_new as parameters + from . import parameters_new as parameters desolvation_parameters = parameters.getDesolvationParameters() if label not in desolvation_parameters: pka_print("do not accept solvation model \"%s\\n" % (label)) @@ -661,7 +661,7 @@ """ Rules of action for version Jan01 """ - import parameters_std as parameters + from . import parameters_std as parameters self.name = "Jan01" self.Nmin = 300 @@ -750,7 +750,7 @@ """ Rules of action for version Jan15 """ - import parameters_std as parameters + from . import parameters_std as parameters self.name = "Jan15" self.Nmin = 300 @@ -839,7 +839,7 @@ """ Rules of action for version May13 """ - import parameters_std as parameters + from . import parameters_std as parameters self.name = "May13" self.coulomb_cutoff = 7.00 @@ -869,7 +869,7 @@ """ Rules of action for version Dec18 """ - import parameters_std as parameters + from . import parameters_std as parameters self.name = "Dec18" self.Nmin = 300 @@ -925,7 +925,7 @@ """ Rules of action for version Dec19 """ - import parameters_std as parameters + from . import parameters_std as parameters self.name = "Dec19" self.Nmin = 300 @@ -981,7 +981,7 @@ """ Rules of action for version Aug24 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Aug24" self.Nmin = 280 @@ -1009,7 +1009,7 @@ """ Rules of action for version Aug30 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Aug30" self.Nmin = 280 @@ -1037,7 +1037,7 @@ """ Rules of action for version Aug31 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Aug31" self.Nmin = 280 @@ -1065,7 +1065,7 @@ """ Rules of action for version Sep05 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Sep05" self.Nmin = 280 @@ -1093,7 +1093,7 @@ """ Rules of action for version Sep06 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Sep06" self.Nmin = 280 @@ -1121,7 +1121,7 @@ """ Rules of action for version Sep07 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Sep07" self.Nmin = 280 @@ -1149,7 +1149,7 @@ """ Rules of action for version Sep08 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Sep08" self.Nmin = 280 @@ -1177,7 +1177,7 @@ """ Rules of action for version Oct13, based on Sep07 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Oct13" self.Nmin = 280 @@ -1239,7 +1239,7 @@ if resName in Q: return Q[resName] - elif resName in self.ions.keys(): + elif resName in list(self.ions.keys()): return self.ions[resName] else: return 0.00 @@ -1266,9 +1266,9 @@ 'GLN': "AMD", 'TRP': "TRP"} - if resName in resType.keys(): + if resName in list(resType.keys()): return resType[resName] - elif resName in self.ions.keys(): + elif resName in list(self.ions.keys()): return 'LIG' else: return None @@ -1309,7 +1309,7 @@ """ Rules of action for version Oct14 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Oct14" self.Nmin = 280 @@ -1337,7 +1337,7 @@ """ Rules of action for version Oct14 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Nov28" self.Nmin = 280 @@ -1365,7 +1365,7 @@ """ Rules of action for version Nov29 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Nov29" self.Nmin = 280 @@ -1393,7 +1393,7 @@ """ Rules of action for version Nov30 """ - import parameters_new as parameters + from . import parameters_new as parameters self.name = "Nov30" self.Nmin = 280 --- a/propka30/experiment.py +++ b/propka30/experiment.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public --- a/propka30/propka.py +++ b/propka30/propka.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -41,7 +41,7 @@ import string, re, sys, os, math -import Source.lib as lib +from Source import lib from Source.protein import Protein --- a/propka30/propka_det.py +++ b/propka30/propka_det.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -39,8 +39,8 @@ #------------------------------------------------------------------------------------------------------- import string, re, sys, os, math -import Source.version as propka -import Source.lib as lib +from Source import version as propka +from Source import lib from Source.protein import Protein from Source.mutate import makeCompositeAtomsDictionary --- a/propka30/propka_gui.py +++ b/propka30/propka_gui.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -39,8 +39,8 @@ #------------------------------------------------------------------------------------------------------- import string, re, sys, os, math -import Source.version as propka -import Source.lib as lib +from Source import version as propka +from Source import lib from Source.protein import Protein from Source.mutate import makeCompositeAtomsDictionary pka_print = lib.pka_print --- a/propka30/propka_mut.py +++ b/propka30/propka_mut.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -40,11 +40,11 @@ import string, re, sys, os, math -import Source.lib as lib -import Source.mutate as mutate +from Source import lib +from Source import mutate from Source.protein import Protein from Source.pdb import readPDB -import Source.version as propka +from Source import version as propka pka_print = lib.pka_print --- a/propka30/propka_pdb.py +++ b/propka30/propka_pdb.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # * This library is free software; you can redistribute it and/or # * modify it under the terms of the GNU Lesser General Public @@ -40,7 +40,7 @@ import string, re, sys, os, math -import Source.lib as lib +from Source import lib from Source.protein import Protein --- a/querystatus.py +++ b/querystatus.py @@ -9,7 +9,7 @@ import sys import cgi import cgitb -import os,shutil,glob,string,time,urllib +import os,shutil,glob,string,time,urllib.request,urllib.parse,urllib.error from datetime import timedelta from src.server import * from src.aconf import * @@ -72,7 +72,7 @@ out_f.write(origin_line) - for x in xrange(3): + for x in range(3): split_line = in_f.readline().split() grid_dims = [float(item) for item in split_line[-3:]] @@ -146,7 +146,7 @@ # construct soap request try: status=appServicePort.queryStatus(queryStatusRequest(jobid)) - except Exception, e: + except Exception as e: return ["error"] if status._code == 4: return ["error"] @@ -170,16 +170,16 @@ Main method for determining the query page output """ logopts = {} - print "Content-type: text/html\n\n" + print("Content-type: text/html\n\n") calctype = form["calctype"].value # prints version error, if it exists if form["jobid"].value == 'False': - print printheader("%s Job Status Page" % calctype.upper()) + print(printheader("%s Job Status Page" % calctype.upper())) progress = "version_mismatch" runtime = 0 elif form["jobid"].value == 'notenoughmem': - print printheader("%s Job Status Page" % calctype.upper()) + print(printheader("%s Job Status Page" % calctype.upper())) progress = "not_enough_memory" runtime = 0 else: @@ -194,7 +194,7 @@ string+= "\t\t\n" % (WEBSITE, TMPDIR, form["jobid"].value) string+= "\t\n" string+= "\n" - print string + print(string) return # prepares for Opal query, if necessary @@ -283,18 +283,18 @@ resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (WEBSITE, form["jobid"].value) if progress == "complete": - print printheader("%s Job Status Page" % calctype.upper(), jobid=form["jobid"].value) + print(printheader("%s Job Status Page" % calctype.upper(), jobid=form["jobid"].value)) elif progress == "error": - print printheader("%s Job Status Page - Error" % calctype.upper(),0, jobid=form["jobid"].value) + print(printheader("%s Job Status Page - Error" % calctype.upper(),0, jobid=form["jobid"].value)) elif progress == "running": # job is not complete, refresh in 30 seconds - print printheader("%s Job Status Page" % calctype.upper(), refresh, jobid=form["jobid"].value) + print(printheader("%s Job Status Page" % calctype.upper(), refresh, jobid=form["jobid"].value)) - print "\n

" - print "

" - print '
' - print "

Status:" + print("\n

") + print("

") + print('
') + print("

Status:") color = "FA3434" image = WEBSITE+"images/red_x.png" @@ -306,12 +306,12 @@ color = "ffcc00" image = WEBSITE+"images/yellow_exclamation.png" - print "%s" % (color, progress) - print "
" % image - print "

" - print "Run time: " + str(timedelta(seconds=round(runtime))) + '
' - print "Current time: %s
" % time.asctime() - print "

\n
\n

" + print("%s" % (color, progress)) + print("
" % image) + print("

") + print("Run time: " + str(timedelta(seconds=round(runtime))) + '
') + print("Current time: %s
" % time.asctime()) + print("

\n
\n

") if progress == "complete": if calctype=="pdb2pqr": @@ -325,8 +325,8 @@ resp = appServicePort.getOutputs(getOutputsRequest(jobid)) filelist = resp._outputFile - print "Here are the results:

    " - print "
  • Input files
      " + print("Here are the results:
        ") + print("
      • Input files
          ") if calctype=="pdb2pqr": # this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension @@ -335,26 +335,26 @@ file_name = filelist[i]._name if ((len(file_name) == 4 and '.' not in file_name) or (file_name.lower().endswith(".pdb") and "pdb2pka_output" not in file_name)): - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) if file_name.lower().endswith((".mol", ".mol2", ".names", ".dat")) and "pdb2pka_output" not in file_name: - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) else: - print "
        • %s.pdb
          • " % (WEBSITE, TMPDIR, jobid, jobid, jobid) + print("
        • %s.pdb
          • " % (WEBSITE, TMPDIR, jobid, jobid, jobid)) elif calctype=="apbs": if have_opal: for i in range(0,len(filelist)): if filelist[i]._name == "apbsinput.in" or filelist[i]._name[-4:] == ".pqr": - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) else: - print "
        • apbsinput.in
          • " % (WEBSITE, TMPDIR, jobid) - print "
        • %s.pqr
          • " % (WEBSITE, TMPDIR, jobid, jobid, jobid) + print("
        • apbsinput.in
          • " % (WEBSITE, TMPDIR, jobid)) + print("
        • %s.pqr
          • " % (WEBSITE, TMPDIR, jobid, jobid, jobid)) - print "
        • " - print "
      • Output files
          " + print("
        • ") + print("
      • Output files
          ") queryString = [str(os.environ["REMOTE_ADDR"])] # Getting PDB2PQR run log info @@ -369,17 +369,17 @@ if have_opal: for i in range(0,len(filelist)): if filelist[i]._name.endswith((".propka", "-typemap.html")): - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) if filelist[i]._name.endswith(".in") and "pdb2pka_output" not in filelist[i]._name: - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) if filelist[i]._name.endswith(".pqr") and not filelist[i]._name.endswith("background_input.pqr"): - print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) + print("
        • %s
          • " % (filelist[i]._url, filelist[i]._name)) #Get the first line of the summary file. if filelist[i]._name.endswith(".summary"): - f=urllib.urlopen(filelist[i]._url) + f=urllib.request.urlopen(filelist[i]._url) summaryLine = f.readline().strip() #logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine queryString.append(summaryLine) @@ -403,7 +403,7 @@ continue outputfilelist.append('%s%s' % (jobid, extension)) for outputfile in outputfilelist: - print "
        • %s
          • " % (WEBSITE, TMPDIR, jobid, outputfile, outputfile) + print("
        • %s
          • " % (WEBSITE, TMPDIR, jobid, outputfile, outputfile)) logopts['queryPDB2PQR'] = '|'.join(queryString) @@ -417,7 +417,7 @@ currentpath = os.getcwd() zipjobid = filelist[i]._name.split("-")[0] dxfilename = '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name) - urllib.urlretrieve(filelist[i]._url, dxfilename) + urllib.request.urlretrieve(filelist[i]._url, dxfilename) os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid)) # making both the dx file and the compressed file (.gz) available in the directory syscommand = 'cp %s dxbkupfile' % (filelist[i]._name) @@ -444,8 +444,8 @@ os.chdir(currentpath) outputcubefilezip = cubefilebasename+".gz" - print "
        • %s
          • " % (WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip) - print "
        • %s
          • " % (WEBSITE, TMPDIR, zipjobid, outputcubefilezip, outputcubefilezip) + print("
        • %s
          • " % (WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip)) + print("
        • %s
          • " % (WEBSITE, TMPDIR, zipjobid, outputcubefilezip, outputcubefilezip)) else: outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid)) @@ -472,7 +472,7 @@ createcube(dxfile, pqrfilename, cubefilename) - print "
        • %s
          • " % (WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip)) + print("
        • %s
          • " % (WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip))) outputcubefilelist = glob.glob('%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, jobid, jobid)) for cubefile in outputcubefilelist: @@ -489,7 +489,7 @@ os.chdir(currentpath) outputcubefilezip = cubefile+".gz" - print "
        • %s
          • " % (WEBSITE, TMPDIR, jobid, os.path.basename(outputcubefilezip), os.path.basename(outputcubefilezip)) + print("
        • %s
          • " % (WEBSITE, TMPDIR, jobid, os.path.basename(outputcubefilezip), os.path.basename(outputcubefilezip))) logopts['queryAPBS'] = '|'.join(queryString) @@ -501,22 +501,22 @@ outputfilelist.append((filelist[i]._url, os.path.basename(filelist[i]._name))) #print "
        • %s
          • " % (filelist[i]._url, filelist[i]._name) if outputfilelist: - print "
        • " - print "
      • PDB2PKA files
          " + print("
        • ") + print("
      • PDB2PKA files
          ") for outputfile in outputfilelist: - print "
        • %s
          • " % (outputfile[0], outputfile[1]) + print("
        • %s
          • " % (outputfile[0], outputfile[1])) else: outputfilelist = glob.glob('%s%s%s/pdb2pka_output/*.DAT' % (INSTALLDIR, TMPDIR, jobid)) outputfilelist.extend(glob.glob('%s%s%s/pdb2pka_output/*.txt' % (INSTALLDIR, TMPDIR, jobid))) outputfilelist = [os.path.basename(outputfile) for outputfile in outputfilelist] if outputfilelist: - print "
        • " - print "
      • PDB2PKA files
          " + print("
        • ") + print("
      • PDB2PKA files
          ") for outputfile in outputfilelist: - print "
        • %s
          • " % (WEBSITE, TMPDIR, jobid, outputfile, outputfile) + print("
        • %s
          • " % (WEBSITE, TMPDIR, jobid, outputfile, outputfile)) - print "
        • " - print "
      • Runtime and debugging information
          " + print("
        • ") + print("
      • Runtime and debugging information
      " + print("
") #if have_opal: @@ -552,17 +552,17 @@ # print "
  • %s
    • " % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype=="pdb2pqr" and apbs_input and HAVE_APBS: - print "

    Click here to run APBS with your results.

    " % nexturl + print("

    Click here to run APBS with your results.

    " % nexturl) elif calctype=="apbs": #print "

    Click here to visualize your results in Jmol.

    " % nexturl - print "

    Visualize your results online:" - print "

    " % (url_3dmol, url_jmol) + print("

    Visualize your results online:") + print("

    " % (url_3dmol, url_jmol)) elif progress == "error": - print "There was an error with your query request. This page will not refresh." + print("There was an error with your query request. This page will not refresh.") - print "" - print "
  • Runtime and debugging information
      " + print("
    • ") + print("
  • Runtime and debugging information
    • " + print("") if have_opal: - print "
    If your job has been running for a prolonged period of time and failed with no reason listed in the standard out or standard error, then the job probably timed out and was terminated by the system.
    " + print("
    If your job has been running for a prolonged period of time and failed with no reason listed in the standard out or standard error, then the job probably timed out and was terminated by the system.
    ") - print '
    If you are having trouble running PDB2PQR on the webserver, please download the command line version of PDB2PQR and run the job from there.' + print('
    If you are having trouble running PDB2PQR on the webserver, please download the command line version of PDB2PQR and run the job from there.') elif progress == "running": - print "Page will refresh in %d seconds
    " % refresh - print "
    " + print("Page will refresh in %d seconds
    " % refresh) + print("
    ") if not have_opal: - print "" - print "
  • Runtime and debugging information
      " + print("
    • ") + print("
  • Runtime and debugging information
    • " + print("
  • Program output (stdout)
    • " % stdouturl) + print("
  • Program errors and warnings (stderr)
    • " % stderrurl) + print("") - print "Your results will appear at this page. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours)." % resultsurl + print("Your results will appear at this page. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours)." % resultsurl) elif progress == "version_mismatch": - print "The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed" + print("The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed") - print "

    " - print "" - print "
    " - print "" - print "" + print("") + print(" ") + print("") + print("") -if __name__ == "__main__" and os.environ.has_key("REQUEST_METHOD"): +if __name__ == "__main__" and "REQUEST_METHOD" in os.environ: """ Determine if called from command line or CGI """ refresh=30 - if not form.has_key("jobid") and form["calctype"].value=="pdb2pqr": - print "Content-type: text/html\n\n" - print printheader("PDB2PQR Job Status - Error") + if "jobid" not in form and form["calctype"].value=="pdb2pqr": + print("Content-type: text/html\n\n") + print(printheader("PDB2PQR Job Status - Error")) text="\n" text+="\t

    Missing jobid field

    \n" text+="\t

    Your request url is missing the jobid field

    \n" @@ -632,7 +632,7 @@ text += "pageTracker._trackPageview();" text += "} catch(err) {}" text+="\n" - print text + print(text) sys.exit(2) --- a/pdb2pka/substruct/Algorithms.cpp +++ b/pdb2pka/substruct/Algorithms.cpp @@ -136,7 +136,7 @@ for (int i=0; i