PROPKA testing working with pytest.

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)