Merge branch 'master' into nathan/delint

README.md

@@ -56,7 +56,7 @@ Calculate using pdb file
 
 ## Testing (for developers)
 
-Please run `Tests/pkacalc_test.py` via `unittest` or `pytest` after changes before pushing commits.
+Please run `Tests/pkacalc_test.py` via `unittest` or `pytest` as well as `python Tests/runtest.py` after changes before pushing commits.
 
 ## References / Citations
 

Tests/runtest.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+""" Run test for test pdbs """
+
+from __future__ import division
+from __future__ import print_function
+
+from subprocess import call
+import os, re
+import sys
+
+if __name__ == "__main__":
+    # A list of input structures and command-line arguments to be passed in
+    # to PROPKA for each:
+    pdbs = [('1FTJ-Chain-A', []),
+            ('1HPX', []),
+            ('4DFR', []),
+            ('3SGB', []),
+            ('3SGB-subset', ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139']),
+            ('1HPX-warn', ['--quiet']),
+           ]
+
+    for pdb, args in pdbs:
+        print('')
+        print('RUNNING '+pdb)
+
+        # Run pka calculation
+        fh = open(pdb + '.out', 'w')
+        cmd = [sys.executable, '../scripts/propka31.py','pdb/%s.pdb' % pdb] + args
+        ret = call(cmd, stdout=fh, stderr=fh)
+        if ret != 0:
+            print(" ERR:")
+            print(" Failed to execute PROPKA on %s" % pdb)
+            print(" See: %s.out" % pdb)
+            sys.exit(1)
+
+        # Test pka predictions
+        result_file = 'results/%s.dat' % pdb
+        if not os.path.isfile(result_file):
+            print(" ERR:")
+            print(" file not found: %s" % result_file)
+            sys.exit(1)
+
+        result = open(result_file,'r')
+        atpka = False
+        for line in open(pdb+'.pka', 'r').readlines():
+            if not atpka:
+                if "model-pKa" in line:
+                    # test pka
+                    atpka = True
+                    continue
+                else:
+                    continue
+            if "-" in line:
+                # done testing
+                atpka = False
+                continue
+
+            expected_value = float(result.readline())
+            m = re.search('([0-9]+\.[0-9]+)', line)
+            value = float(m.group(0))
+
+            if value != expected_value:
+                print(" ERR:")
+                print(line)
+                print(" %s should be: %s" % (value, expected_value))
+                sys.exit(1)
+