Changes to work on Python 3

pdbfixer.py

@@ -116,7 +116,7 @@ class PDBFixer(object):
         templatesPath = os.path.join(os.path.dirname(__file__), 'templates')
         templatesPath = os.path.join(os.path.dirname(__file__), 'templates')
         for file in os.listdir(templatesPath):
         for file in os.listdir(templatesPath):
             templatePdb = app.PDBFile(os.path.join(templatesPath, file))
             templatePdb = app.PDBFile(os.path.join(templatesPath, file))
-            name = templatePdb.topology.residues().next().name
+            name = next(templatePdb.topology.residues()).name
             self.templates[name] = templatePdb
             self.templates[name] = templatePdb
         
         
     def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
     def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
@@ -256,7 +256,7 @@ class PDBFixer(object):
             newResidue = chain.topology.addResidue(residueName, chain)
             newResidue = chain.topology.addResidue(residueName, chain)
             translate = startPosition+(endPosition-startPosition)*(i+1.0)/(len(residueNames)+1.0)
             translate = startPosition+(endPosition-startPosition)*(i+1.0)/(len(residueNames)+1.0)
             templateAtoms = list(template.topology.atoms())
             templateAtoms = list(template.topology.atoms())
-            if newResidue == chain.residues().next():
+            if newResidue == next(chain.residues()):
                 templateAtoms = [atom for atom in templateAtoms if atom.name not in ('P', 'OP1', 'OP2')]
                 templateAtoms = [atom for atom in templateAtoms if atom.name not in ('P', 'OP1', 'OP2')]
             for atom in templateAtoms:
             for atom in templateAtoms:
                 newAtom = chain.topology.addAtom(atom.name, atom.element, newResidue)
                 newAtom = chain.topology.addAtom(atom.name, atom.element, newResidue)
@@ -443,7 +443,7 @@ class PDBFixer(object):
             
             
             # Set any previously existing atoms to be massless, they so won't move.
             # Set any previously existing atoms to be massless, they so won't move.
             
             
-            for atom in existingAtomMap.itervalues():
+            for atom in existingAtomMap.values():
                 system.setParticleMass(atom.index, 0.0)
                 system.setParticleMass(atom.index, 0.0)
             
             
             # If any heavy atoms were omitted, add them back to avoid steric clashes.
             # If any heavy atoms were omitted, add them back to avoid steric clashes.

ui.py

@@ -5,9 +5,14 @@ from pdbfixer import PDBFixer, substitutions, proteinResidues, dnaResidues, rnaR
 import uiserver
 import uiserver
 import webbrowser
 import webbrowser
 import os.path
 import os.path
-import urllib2
 import gzip
 import gzip
-from cStringIO import StringIO
+from io import BytesIO
+try:
+    from urllib.request import urlopen
+    from io import StringIO
+except:
+    from urllib2 import urlopen
+    from cStringIO import StringIO
 
 
 def loadHtmlFile(name):
 def loadHtmlFile(name):
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
@@ -25,16 +30,16 @@ def startPageCallback(parameters, handler):
     global fixer
     global fixer
     if 'type' in parameters:
     if 'type' in parameters:
         if parameters.getfirst('type') == 'local':
         if parameters.getfirst('type') == 'local':
-            pdb = PdbStructure(parameters['pdbfile'].value.splitlines())
+            pdb = PdbStructure(parameters['pdbfile'].value.decode().splitlines())
             fixer = PDBFixer(pdb)
             fixer = PDBFixer(pdb)
             displayDeleteChainsPage()
             displayDeleteChainsPage()
         else:
         else:
             id = parameters.getfirst('pdbid')
             id = parameters.getfirst('pdbid')
             url = "ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb"+id.lower()+".ent.gz"
             url = "ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb"+id.lower()+".ent.gz"
             try:
             try:
-                response = urllib2.urlopen(url)
-                content = gzip.GzipFile(fileobj=StringIO(response.read())).read()
-                pdb = PdbStructure(content.splitlines())
+                response = urlopen(url)
+                content = gzip.GzipFile(fileobj=BytesIO(response.read())).read()
+                pdb = PdbStructure(content.decode().splitlines())
                 fixer = PDBFixer(pdb)
                 fixer = PDBFixer(pdb)
                 displayDeleteChainsPage()
                 displayDeleteChainsPage()
             except:
             except:
@@ -160,7 +165,7 @@ def displayConvertResiduesPage():
 def displayMissingAtomsPage():
 def displayMissingAtomsPage():
     uiserver.setCallback(missingAtomsPageCallback)
     uiserver.setCallback(missingAtomsPageCallback)
     fixer.findMissingAtoms()
     fixer.findMissingAtoms()
-    allResidues = list(set(fixer.missingAtoms.iterkeys()).union(fixer.missingTerminals.iterkeys()))
+    allResidues = list(set(fixer.missingAtoms.keys()).union(fixer.missingTerminals.keys()))
     allResidues.sort(key=lambda x: x.index)
     allResidues.sort(key=lambda x: x.index)
     if len(allResidues) == 0:
     if len(allResidues) == 0:
         fixer.addMissingAtoms()
         fixer.addMissingAtoms()

uiserver.py

 from threading import Thread
 from threading import Thread
-from SocketServer import ThreadingMixIn
-from BaseHTTPServer import HTTPServer, BaseHTTPRequestHandler
-from urlparse import parse_qs
 import cgi
 import cgi
+import sys
+try:
+    from socketserver import ThreadingMixIn
+    from http.server import HTTPServer, BaseHTTPRequestHandler
+    from urllib.parse import parse_qs
+except:
+    from SocketServer import ThreadingMixIn
+    from BaseHTTPServer import HTTPServer, BaseHTTPRequestHandler
+    from urlparse import parse_qs
 
 
 class _Handler(BaseHTTPRequestHandler):
 class _Handler(BaseHTTPRequestHandler):
     def do_GET(self):
     def do_GET(self):
@@ -40,6 +46,8 @@ class _Handler(BaseHTTPRequestHandler):
         self.send_header("Content-type", type)
         self.send_header("Content-type", type)
         self.send_header("Content-length", str(len(response)))
         self.send_header("Content-length", str(len(response)))
         self.end_headers()
         self.end_headers()
+        if sys.version_info.major > 2:
+            response = bytes(response, 'UTF-8')
         self.wfile.write(response)
         self.wfile.write(response)
     
     
     def sendDownload(self, download, filename):
     def sendDownload(self, download, filename):
@@ -49,6 +57,8 @@ class _Handler(BaseHTTPRequestHandler):
         self.send_header("Content-length", str(len(download)))
         self.send_header("Content-length", str(len(download)))
         self.send_header("Content-Disposition", 'attachment; filename="%s"' % filename)
         self.send_header("Content-Disposition", 'attachment; filename="%s"' % filename)
         self.end_headers()
         self.end_headers()
+        if sys.version_info.major > 2:
+            download = bytes(download, 'UTF-8')
         self.wfile.write(download)
         self.wfile.write(download)
 
 
 class _ThreadingHTTPServer(ThreadingMixIn, HTTPServer):
 class _ThreadingHTTPServer(ThreadingMixIn, HTTPServer):