Rename "Tests" directory for consistency.

tests/pkacalc_test.py

@@ -0,0 +1,98 @@
+"""Reproduce tests from original PROPKA."""
+import os
+import re
+from subprocess import call
+import sys
+import unittest
+import logging
+import propka.lib
+import propka.molecular_container
+
+
+# This error tolerance was chosen to make Ubuntu 18.04 pass under Windows 
+# Subsystem Linux.
+ACCEPTABLE_ERROR = 0.001
+
+
+def run_propka(args):
+    """Run PROPKA.
+
+    Args:
+        args:  command-line arguments for PROPKA
+    """
+    options = propka.lib.loadOptions()
+    raise NotImplementedError("Need to incorporated command-line arguments")
+    pdbfiles = options.filenames
+
+    for pdbfile in pdbfiles:
+        my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+        my_molecule.calculate_pka()
+        my_molecule.write_pka()
+
+
+# Setting this up as a direct translation of the original runtest.py script
+# that will be run as part of 'python setup.py test'. This takes on the
+# order of 10s to run.
+
+class SystemTest(unittest.TestCase):
+    """
+    Run the program and compare against reference results.
+    """
+    def test_pka_calc(self):
+        pdbs = ['1FTJ-Chain-A',
+                '1HPX',
+                '4DFR']
+
+        test_dir = os.path.dirname(__file__)
+        base_dir = os.path.dirname(test_dir)
+
+        executable = os.path.join(base_dir, "scripts", "propka31.py")
+
+        env = { "PYTHONPATH" : base_dir }
+
+        for pdb in pdbs:
+            input_filename = os.path.join(test_dir, "pdb", pdb + ".pdb")
+            output_filename = os.path.join(test_dir, pdb + ".out")
+
+            output_file = open(output_filename, "w")
+            call([sys.executable, executable, input_filename],
+                    stdout=output_file, env=env)
+            output_file.close()
+
+            # Check pka predictions.
+            ref = open(os.path.join(test_dir, "results", pdb + ".dat"))
+            output = open(output_filename)
+
+            atpka = False
+            errors = []
+            for line in output:
+                if not atpka:
+                    # Start testing pka values.
+                    if "model-pKa" in line:
+                        atpka = True
+                    continue
+
+                m = re.search('([0-9]+\.[0-9]+)', line)
+                if not m:
+                    break
+
+                expected_value = float(ref.readline())
+                value = float(m.group(0))
+                value_error = (value-expected_value)/expected_value
+
+                if abs(value_error) > ACCEPTABLE_ERROR:
+                    logging.error(value_error)
+                    identity = line[:m.start()].strip()
+                    errors.append("%12s  %8.2f    %8.2f" %
+                            (identity, expected_value, value))
+
+            os.remove("%s.pka" % pdb)
+            os.remove("%s.propka_input" % pdb)
+
+            ref.close()
+            output.close()
+
+            if errors:
+                error_header = "       Group  Expected  Calculated\n"
+                self.fail("Unexpected pKa values:\n" + error_header +
+                          "\n".join(errors))