Add tests for Jess output comparing to output from CLI

pyjess/tests/__init__.py

@@ -1,12 +1,14 @@
 from . import (
-    test_atom, 
+    test_atom,
+    test_jess,
     test_molecule,
-    test_tess_atom, 
+    test_tess_atom,
     test_tess_template
 )
 
 def load_tests(loader, suite, pattern):
     suite.addTests(loader.loadTestsFromModule(test_atom))
+    suite.addTests(loader.loadTestsFromModule(test_jess))
     suite.addTests(loader.loadTestsFromModule(test_molecule))
     suite.addTests(loader.loadTestsFromModule(test_tess_atom))
     suite.addTests(loader.loadTestsFromModule(test_tess_template))

pyjess/tests/data/template_01.qry

@@ -0,0 +1 @@
+../../../vendor/jess/examples/template_01.qry

pyjess/tests/data/template_02.qry

@@ -0,0 +1 @@
+../../../vendor/jess/examples/template_02.qry

pyjess/tests/test_jess.py

@@ -0,0 +1,45 @@
+import unittest
+
+from .._jess import Template, Molecule, Jess
+from .utils import files
+from . import data
+
+
+class TestAtom(unittest.TestCase):
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    def test_query(self):
+
+        with files(data).joinpath("template_01.qry").open() as f:
+            template = Template.load(f) 
+            jess = Jess([template])
+
+        with files(data).joinpath("pdb1lnb.pdb").open() as f:
+            molecule = Molecule.load(f)
+
+        hits = list(jess.query(molecule, 1, 2, 2))
+        self.assertEqual(len(hits), 1)
+        self.assertAlmostEqual(hits[0].rmsd, 0.555, places=3)
+        self.assertAlmostEqual(hits[0].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[0].log_evalue, -2.10, places=1)
+
+        hits = list(jess.query(molecule, 2, 5, 3))
+        self.assertEqual(len(hits), 2)
+        self.assertAlmostEqual(hits[0].rmsd, 0.555, places=3)
+        self.assertAlmostEqual(hits[0].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[0].log_evalue, -2.10, places=1)
+        self.assertAlmostEqual(hits[1].rmsd, 1.440, places=3)
+        self.assertAlmostEqual(hits[1].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[1].log_evalue, 0.12, places=1)
+
+        hits = list(jess.query(molecule, 2, 5, 5))
+        self.assertEqual(len(hits), 3)
+        self.assertAlmostEqual(hits[0].rmsd, 0.555, places=3)
+        self.assertAlmostEqual(hits[0].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[0].log_evalue, -2.10, places=1)
+        self.assertAlmostEqual(hits[1].rmsd, 1.440, places=3)
+        self.assertAlmostEqual(hits[1].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[1].log_evalue, 0.12, places=1)
+        self.assertAlmostEqual(hits[2].rmsd, 1.644, places=3)
+        self.assertAlmostEqual(hits[2].determinant, 1.0, places=3)
+        self.assertAlmostEqual(hits[2].log_evalue, 0.63, places=1)

pyjess/tests/utils.py

@@ -0,0 +1,7 @@
+try:
+    from importlib.resources import files
+except ImportError:
+    try:
+        from importlib_resources import files # type: ignore
+    except ImportError:
+        files = None # type: ignore