Merge pull request #37 from Electrostatics/nathan/argpase

Fix error when using PROPKA with PDB2PQR

.gitignore

@@ -1,5 +1,5 @@
 
 # Compiled python files
 *.py[cod]
-
+# PIP stuff
-
+*.egg-info

README.md

@@ -36,10 +36,16 @@ directory:
 
     python setup.py install --user --install-scripts ~/bin
 
+For the purposes of testing or development, you may prefer to install PROPKA as
+an editable module via PIP by running
+```
+pip install -e .
+```
+from within a virtual environment (e.g., via [virtualenv](https://pypi.org/project/virtualenv/)).
 
 ## Requirements
 
-* Python 2.7 or higher or Python 3.1 or higher 
+* Python 3.1 or higher 
 
 ## Getting started
 
@@ -56,7 +62,8 @@ Calculate using pdb file
 
 ## Testing (for developers)
 
-Please run `Tests/runtest.py/` after changes before pushing commits.
+Please see [`tests/README.md`](tests/README.md) for testing instructions.
+Please run these tests after making changes to the code and _before_ pushing commits.
 
 ## References / Citations
 

Tests/hybrid36.py

@@ -1,57 +0,0 @@
-import unittest
-
-import propka.hybrid36 as hybrid36
-
-class Hybrid36Test(unittest.TestCase):
-    def testDecode(self):
-        test_values = {
-            "99999": 99999,
-            "A0000": 100000,
-            "0": 0,
-            "9": 9,
-            "A": 10,
-            "  ZZZZY": 43770014,
-            "ZZZZZ": 43770015, # ZZZZZ - A0000 + 100000
-            "a0000": 43770016,
-            "zzzzz": 87440031,
-            "zzzzy": 87440030,
-            "99": 99,
-            "A0": 100,
-            "ZZ": 1035,
-            "zz": 1971,
-            "-99999": -99999,
-            "-A0000": -100000,
-            "-0": 0,
-            "-9": -9,
-            "-A": -10,
-            "-ZZZZY": -43770014,
-            "-ZZZZZ": -43770015, # ZZZZZ - A0000 + 100000
-            "-a0000": -43770016,
-            "-zzzzz": -87440031,
-            "-zzzzy": -87440030,
-            "-99": -99,
-            "-A0": -100,
-            "-ZZ": -1035,
-            "-zz": -1971,
-            "PROPKA": 954495146,
-            "A001Z": 100071,
-            "B0000": 1779616,
-        }
-
-        for k, v in test_values.iteritems():
-            self.assertEqual(hybrid36.decode(k), v)
-
-    def testErrors(self):
-        test_values = [
-            "99X99",
-            "X9-99",
-            "XYZa",
-            "",
-            "-",
-            "!NotOk",
-        ]
-
-        for v in test_values:
-            with self.assertRaises(ValueError) as e:
-                hybrid36.decode(v)
-            self.assertTrue(v in str(e.exception))

Tests/pkacalc_test.py

@@ -1,80 +0,0 @@
-
-import os
-import re
-from subprocess import call
-import sys
-import unittest
-import logging
-
-
-# This error tolerance was chosen to make Ubuntu 18.04 pass under Windows 
-# Subsystem Linux.
-ACCEPTABLE_ERROR = 0.001
-
-
-# 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))

Tests/runtest.py

@@ -1,68 +0,0 @@
-#!/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)
-

propka/lib.py

@@ -185,8 +185,12 @@ def build_parser(parser=None):
     group.add_argument("-p", "--parameters", dest="parameters",
                        default=pkg_resources.resource_filename(__name__, "propka.cfg"),
                        help="set the parameter file [%(default)s]")
+    try:
         group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
                            help="logging level verbosity", default="INFO")
+    except argparse.ArgumentError:
+        # It is possible that --log-level has already been set by APBS
+        pass
     group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0,
                        help="setting pH-value used in e.g. stability calculations [7.0]")
     group.add_argument("-w", "--window", dest="window", nargs=3, type=float,
@@ -210,17 +214,21 @@ def build_parser(parser=None):
                              "ligand bond orders"))
     group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
                        help="Keep protons in input file", default=False)
+    group.add_argument("-q", "--quiet", action="store_const", const="WARNING",
+                       dest="log_level", help="supress non-warning messages")
     group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
                        help="Protonate all atoms (will not influence pKa calculation)",
                        default=False)
     return parser
 
 
-def loadOptions(*args):
+def loadOptions(args):
     """
     Load the arguments parser with options. Note that verbosity is set as soon
     as this function is invoked.
 
+    Arguments:
+        args:  list of arguments
     Returns:
         argparse namespace
     """
@@ -235,7 +243,7 @@ def loadOptions(*args):
         # command line
         options = parser.parse_args()
     else:
-        options = parser.parse_args(list(args))
+        options = parser.parse_args(args)
 
     # adding specified filenames to arguments
     options.filenames.append(options.input_pdb)

requirements.txt

@@ -0,0 +1 @@
+pytest

setup.py

@@ -56,5 +56,6 @@ See http://propka.org/ for the PROPKA web server.
             ],
         },
       zip_safe=True,
-      test_suite="Tests",
+      python_requires='>=3',
+      test_suite="tests",
 )

tests/README.md

@@ -0,0 +1,15 @@
+# Testing PROPKA
+
+These tests assume that PROPKA is installed as a module on your system.
+If you are running in a virtual environment and want to make changes to your
+code, module installation accomplished by
+```
+pip install -e .
+```
+from the top level of the PROPKA source directory.
+
+Once PROPKA is available as a module, the tests can be run by
+```
+python -m pytest tests
+```
+either in the top-level directory or `tests` subdirectory.

tests/regression_test.py

@@ -0,0 +1,144 @@
+"""Tests for PROPKA 3.1"""
+import logging
+import os
+import re
+from pathlib import Path
+import pytest
+import pandas as pd
+import propka.lib
+import propka.molecular_container
+
+
+_LOGGER = logging.getLogger(__name__)
+
+
+# Maximum error set by number of decimal places in pKa output as well as need
+# to make unmodified code work on WSL Ubuntu 18.04
+MAX_ERR = 0.01
+
+
+# This directory
+TEST_DIR = Path("tests")
+# Location for test PDBs
+PDB_DIR = Path("pdb")
+# Location for results for comparing output (allow running from tests/ and ../tests/)
+RESULTS_DIR = Path("tests/results")
+if not RESULTS_DIR.is_dir():
+    _LOGGER.warning("Switching to sub-directory")
+    RESULTS_DIR = Path("results")
+# Arguments to add to all tests
+DEFAULT_ARGS = []
+
+
+def get_test_dirs():
+    """Get locations of test files.
+
+    Returns:
+        dictionary with test file locations.
+    """
+    path_dict = {}
+    for key, path in [("pdbs", PDB_DIR), ("results", RESULTS_DIR)]:
+        test_path = TEST_DIR / path
+        if test_path.is_dir():
+            path_dict[key] = test_path
+        else:
+            test_path = path
+            if test_path.is_dir():
+                path_dict[key] = test_path
+            else:
+                errstr = "Can't find %s test files in %s" % (key, [TEST_DIR / path, path])
+                raise FileNotFoundError(errstr)
+    return path_dict
+
+
+def run_propka(options, pdb_path, tmp_path):
+    """Run PROPKA software.
+
+    Args:
+        options:  list of PROPKA options
+        pdb_path:  path to PDB file
+        tmp_path:  path for working directory
+    """
+    options += [str(pdb_path)]
+    args = propka.lib.loadOptions(options)
+    try:
+        _LOGGER.warning("Working in tmpdir %s because of PROPKA file output; need to fix this.",
+                        tmp_path)
+        cwd = Path.cwd()
+        os.chdir(tmp_path)
+        molecule = propka.molecular_container.Molecular_container(str(pdb_path), args)
+        molecule.calculate_pka()
+        molecule.write_pka()
+    except Exception as err:
+        raise err
+    finally:
+        os.chdir(cwd)
+
+
+def compare_output(pdb, tmp_path, ref_path):
+    """Compare results of test with reference.
+
+    Args:
+        pdb:  PDB filename stem
+        tmp_path:  temporary directory
+        ref_path:  path with reference results
+    Raises:
+        ValueError if results disagree.
+    """
+    ref_data = []
+    with open(ref_path, "rt") as ref_file:
+        for line in ref_file:
+            ref_data.append(float(line))
+
+    test_data = []
+    pka_path = Path(tmp_path) / ("%s.pka" % pdb)
+    with open(pka_path, "rt") as pka_file:
+        at_pka = False
+        for line in pka_file:
+            if not at_pka:
+                if "model-pKa" in line:
+                    at_pka = True
+            elif line.startswith("---"):
+                at_pka = False
+            else:
+                m = re.search(r'([0-9]+\.[0-9]+)', line)
+                value = float(m.group(0))
+                test_data.append(value)
+
+    df = pd.DataFrame({"reference": ref_data, "test": test_data})
+    df["difference"] = df["reference"] - df["test"]
+    max_err = df["difference"].abs().max()
+    if max_err > MAX_ERR:
+        errstr = "Error in test (%g) exceeds maximum (%g)" % (max_err, MAX_ERR)
+        raise ValueError(errstr)
+
+
+@pytest.mark.parametrize("pdb, options", [
+    pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
+    pytest.param('1HPX', [], id="1HPX: no options"),
+    pytest.param('4DFR', [], id="4DFR: no options"),
+    pytest.param('3SGB', [], id="3SGB: no options"),
+    pytest.param('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"], 
+        id="3SGB: --titrate_only"),
+    pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")])
+def test_regression(pdb, options, tmp_path):
+    """Basic regression test of PROPKA functionality."""
+    path_dict = get_test_dirs()
+    ref_path = path_dict["results"] / ("%s.dat" % pdb)
+    if ref_path.is_file():
+        ref_path = ref_path.resolve()
+    else:
+        _LOGGER.warning("Missing results file for comparison: %s", ref_path)
+        ref_path = None
+    pdb_path = path_dict["pdbs"] / ("%s.pdb" % pdb)
+    if pdb_path.is_file():
+        pdb_path = pdb_path.resolve()
+    else:
+        errstr = "Missing PDB file: %s" % pdb_path
+        raise FileNotFoundError(errstr)
+    tmp_path = Path(tmp_path).resolve()
+
+    run_propka(options, pdb_path, tmp_path)
+    if ref_path is not None:
+        compare_output(pdb, tmp_path, ref_path)