Merge branch 'master' of https://github.com/SimTk/pdbfixer

Conflicts:
	pdbfixer/ui.py

.travis.yml

 language: c
+
+env:
+    matrix:
+        - CONDA_PY=2.7
+        - CONDA_PY=3.3
+        - CONDA_PY=3.4
+
 install:
     - sudo apt-get update -qq
     - sudo apt-get install -qq python-dev python-pip python-yaml g++ ftp

pdbfixer/__init__.py

-from pdbfixer import PDBFixer
+from __future__ import absolute_import
+from .pdbfixer import PDBFixer
+

pdbfixer/pdbfixer.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.1"
 
@@ -207,7 +208,7 @@ class PDBFixer(object):
             self.source = url
             file = urlopen(url)
             # Read contents all at once and split into lines, since urlopen doesn't like it when we read one line at a time over the network.
-            contents = file.read()
+            contents = file.read().decode('utf-8')
             lines = contents.split('\n')
             file.close()
             structure = PdbStructure(lines)
@@ -1025,8 +1026,7 @@ class PDBFixer(object):
 def main():
     if len(sys.argv) < 2:
         # Display the UI.
-        
-        import ui
+        from . import ui
         ui.launchUI()
     else:
         # Run in command line mode.

pdbfixer/ui.py

-import simtk.openmm.app as app
-import simtk.unit as unit
-from pdbfixer import PDBFixer, substitutions, proteinResidues, dnaResidues, rnaResidues
-import uiserver
+from __future__ import absolute_import
+
 import webbrowser
 import os.path
-import gzip
 import time
-from io import BytesIO
+
+import simtk.openmm.app as app
+import simtk.unit as unit
+
+from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues
+from . import uiserver
+
 try:
     from urllib.request import urlopen
     from io import StringIO
@@ -26,7 +29,7 @@ def loadImageFile(name):
     if name not in cachedImages:
         imagePath = os.path.join(os.path.dirname(__file__), 'images')
         file = os.path.join(imagePath, name)
-        cachedImages[name] = open(file).read()
+        cachedImages[name] = open(file, 'rb').read()
     return cachedImages[name]
 
 def controlsCallback(parameters, handler):
@@ -58,8 +61,15 @@ def startPageCallback(parameters, handler):
             id = parameters.getfirst('pdbid')
             try:
                 fixer = PDBFixer(pdbid=id)
-            except:
-                handler.sendResponse(header+"Unable to download the PDB file. This may indicate an invalid PDB identifier, or an error in network connectivity."+loadHtmlFile("error.html"))
+            except Exception as e:
+                import traceback
+                print(traceback.format_exc())
+                handler.sendResponse(
+                    header + "<p>Unable to download the PDB file. " +
+                    "This may indicate an invalid PDB identifier, " +
+                    "or an error in network connectivity.</p>" +
+                    "<p>{}</p>".format(e) +
+                    loadHtmlFile("error.html"))
         displayDeleteChainsPage()
 
 def deleteChainsPageCallback(parameters, handler):

pdbfixer/uiserver.py

@@ -46,7 +46,7 @@ class _Handler(BaseHTTPRequestHandler):
         self.send_header("Content-type", type)
         self.send_header("Content-length", str(len(response)))
         self.end_headers()
-        if sys.version_info.major > 2:
+        if sys.version_info.major > 2 and isinstance(response, str):
             response = bytes(response, 'UTF-8')
         self.wfile.write(response)
     

tests/test_build_and_simulate.py

 
+from __future__ import print_function
 import pdbfixer
 import simtk.openmm 
 
@@ -79,7 +80,7 @@ def simulate(pdbcode, pdb_filename):
 
     del context, integrator
 
-    print "Simulation completed: potential = %.3f kcal/mol" % potential
+    print("Simulation completed: potential = %.3f kcal/mol" % potential)
 
     return
 
@@ -105,8 +106,8 @@ def test_build_and_simulate():
     failures = list()
         
     for pdbcode in pdbcodes_to_build:
-        print "------------------------------------------------"
-        print pdbcode
+        print("------------------------------------------------")
+        print(pdbcode)
 
         output_pdb_filename = 'output.pdb'
 
@@ -152,14 +153,14 @@ def test_build_and_simulate():
 
         except Watchdog:
             message = "timed out in stage %s" % stage
-            print message
+            print(message)
             failures.append((pdbcode, Exception(message)))
 
         except Exception as e:
-            print "EXCEPTION DURING BUILD"
+            print("EXCEPTION DURING BUILD")
             #import traceback
             #print traceback.print_exc()
-            print str(e)
+            print(str(e))
             failures.append((pdbcode, e))
         
         watchdog.stop()
@@ -173,14 +174,14 @@ def test_build_and_simulate():
                 
             except Watchdog:
                 message = "timed out in simulation"
-                print message
+                print(message)
                 failures.append((pdbcode, Exception(message)))
 
             except Exception as e:
-                print "EXCEPTION DURING SIMULATE"
+                print("EXCEPTION DURING SIMULATE")
                 #import traceback
                 #print traceback.print_exc()
-                print str(e)
+                print(str(e))
                 failures.append((pdbcode, e))
         
             watchdog.stop()
@@ -189,21 +190,21 @@ def test_build_and_simulate():
         # Clean up.
         os.remove(output_pdb_filename)
 
-    print "------------------------------------------------"
+    print("------------------------------------------------")
 
     if len(failures) != 0:
-        print ""
-        print "SUMMARY OF FAILURES:"
-        print ""
+        print("")
+        print("SUMMARY OF FAILURES:")
+        print("")
         for failure in failures:
             (pdbcode, exception) = failure
-            print "%6s : %s" % (pdbcode, str(exception))
-        print ""
+            print("%6s : %s" % (pdbcode, str(exception)))
+        print("")
 
         raise Exception("Build test failed on one or more PDB files.")
     
     else:
-        print "All tests succeeded."
+        print("All tests succeeded.")
 
 if __name__ == '__main__':
     test_build_and_simulate()