Removed debug code.

.travis.yml

@@ -10,9 +10,8 @@ install:
     
     
 script:
 script:
     - python setup.py install
     - python setup.py install
-#    - nosetests tests/test_build.py
-#    - nosetests tests/test_simulate.py
-    - python tests/test_build.py
+    - nosetests tests/test_build.py
+    - nosetests tests/test_simulate.py
 
 
 after_script:
 after_script:
     - pyflakes pdbfixer/*.py
     - pyflakes pdbfixer/*.py

tests/test_build.py

@@ -7,7 +7,7 @@ import sys
 def test_build():
 def test_build():
     # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
     # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
     pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
     pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
-    pdbcodes = ['1VII'] # DEBUG
+    pdbcodes = ['1VII'] # DEBUG: just use one
 
 
     # Set up PDB retrieval.
     # Set up PDB retrieval.
     pdblist = PDBList(server=PDBList.alternative_download_url)
     pdblist = PDBList(server=PDBList.alternative_download_url)
@@ -35,34 +35,22 @@ def test_build():
         positiveIon = 'Na+'
         positiveIon = 'Na+'
         negativeIon = 'Cl-'
         negativeIon = 'Cl-'
 
 
-        print "Running PDBFixer..."
         infile = open(input_pdb_filename)
         infile = open(input_pdb_filename)
         outfile = open(output_pdb_filename, 'w')
         outfile = open(output_pdb_filename, 'w')
 
 
         try:
         try:
-            print "Creating PDBFixer..."
             fixer = PDBFixer(PdbStructure(infile))
             fixer = PDBFixer(PdbStructure(infile))
-            print "Finding missing residues..."
             fixer.findMissingResidues()
             fixer.findMissingResidues()
-            print "Finding nonstandard residues..."
             fixer.findNonstandardResidues()
             fixer.findNonstandardResidues()
-            print "Replacing nonstandard residues..."
             fixer.replaceNonstandardResidues()
             fixer.replaceNonstandardResidues()
-            print "Finding missing atoms..."
             fixer.findMissingAtoms()
             fixer.findMissingAtoms()
-            print "Adding missing atoms..."
             fixer.addMissingAtoms()
             fixer.addMissingAtoms()
-            print "Removing heterogens..."
             fixer.removeHeterogens(False)
             fixer.removeHeterogens(False)
-            print "Adding missing hydrogens..."
             fixer.addMissingHydrogens(pH)
             fixer.addMissingHydrogens(pH)
             #fixer.addSolvent(box*unit.nanometer, positiveIon, negativeIon, ionic*unit.molar)
             #fixer.addSolvent(box*unit.nanometer, positiveIon, negativeIon, ionic*unit.molar)
-            print "Writing PDB file..."
             app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
             app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
             infile.close()
             infile.close()
             outfile.close()
             outfile.close()
-            print "Done."fg
-            
             
             
             # Delete input file.
             # Delete input file.
             os.remove(input_pdb_filename)
             os.remove(input_pdb_filename)
@@ -75,4 +63,3 @@ def test_build():
     if not success:
     if not success:
         raise Exception("build test failed on one or more PDB files.")
         raise Exception("build test failed on one or more PDB files.")
 
 
-test_build()

tests/test_simulate.py

@@ -4,20 +4,37 @@ from pdbfixer.pdbfixer import *
 import os
 import os
 import sys
 import sys
 
 
-pdbcodes = ['1PGB', '1VII']
+def test_build():
+    # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
+    pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
+    pdbcodes = ['1VII'] # DEBUG: just use one
 
 
-for pdbcode in pdbcodes:
-    pdblist = PDBList()
+    # Set up PDB retrieval.
+    pdblist = PDBList(server=PDBList.alternative_download_url)
+
+    success = True
+
+    for pdbcode in pdbcodes:
+        print pdbcode
+
+        try:
+            print "Attempting to retrieve PDB code '%s' from %s..." % (pdbcode, PDBList.alternative_download_url)
             input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.')
             input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.')
+        except Exception as e:
+            print str(e)
+            print "Could not download PDB code '%s'" % pdbcode
+            continue
+
         output_pdb_filename = 'output.pdb'
         output_pdb_filename = 'output.pdb'
 
 
+        # PDB setup parameters.
+        # TODO: Try several combinations?
         pH = 7.0
         pH = 7.0
         ionic = 50.0 * unit.millimolar
         ionic = 50.0 * unit.millimolar
         box = 10.0 * unit.angstrom
         box = 10.0 * unit.angstrom
         positiveIon = 'Na+'
         positiveIon = 'Na+'
         negativeIon = 'Cl-'
         negativeIon = 'Cl-'
 
 
-    print "Running PDBFixer..."
         infile = open(input_pdb_filename)
         infile = open(input_pdb_filename)
         outfile = open(output_pdb_filename, 'w')
         outfile = open(output_pdb_filename, 'w')
 
 
@@ -41,10 +58,8 @@ for pdbcode in pdbcodes:
 
 
         except Exception as e:
         except Exception as e:
             print str(e)
             print str(e)
-        sys.exit(1)
-
-
-# Signal success.
-sys.exit(0)
+            success = False
 
 
+    if not success:
+        raise Exception("build test failed on one or more PDB files.")