fixes to get atom selector and pdb reader tests working

MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py

@@ -475,6 +475,8 @@ def __init__(
 
         self._parent = None
 
+        self.element = ATOMS_DATABASE[self._symbol]["element"]
+
         for k, v in kwargs.items():
             try:
                 setattr(self, k, v)
@@ -523,6 +525,8 @@ def restore_bonds(self, atom_dict: dict[str, Atom]) -> List[Tuple[int, int]]:
         return [(self.index, other.index) for other in self._bonds]
 
     def __eq__(self, other):
+        if not isinstance(other, _ChemicalEntity):
+            return False
         if not self._index == other._index:
             return False
         if not self._symbol == other._symbol:
@@ -1823,6 +1827,10 @@ def serialize(self, h5_contents: dict[str, list[list[str]]]) -> tuple[str, int]:
 
         return "nucleotide_chains", len(h5_contents["nucleotide_chains"]) - 1
 
+    @property
+    def nucleotides(self):
+        return self._nucleotides
+
     def set_nucleotides(self, nucleotides: list[Nucleotide]) -> None:
         """
         Sets the provided Nucleotide objects as the nucleotides making up this chain, and creates bonds between them.

MDANSE/Src/MDANSE/Framework/Selectors/Macromolecule.py

@@ -55,5 +55,11 @@ def select(self, macromolecules):
                 m = Macromolecule.lookup.get(ce.__class__, None)
                 if m in macromolecules:
                     sel.update([at for at in ce.atom_list])
+                if (isinstance(ce, Protein)
+                        and "peptide_chain" in macromolecules):
+                    for ce2 in ce.peptide_chains:
+                        m = Macromolecule.lookup.get(ce2.__class__, None)
+                        if m in macromolecules:
+                            sel.update([at for at in ce.atom_list])
 
         return sel

MDANSE/Tests/UnitTests/select_atoms.py

@@ -0,0 +1,3 @@
+selection = [
+    at for at in chemicalSystem.atom_list if at.element.strip().lower() == "phosphorus"
+]

MDANSE/Tests/UnitTests/TestAtomSelector.py → MDANSE/Tests/UnitTests/test_atom_selector.py

@@ -44,13 +44,54 @@
 
 @author: Eric C. Pellegrini
 """
-
+import os
 import unittest
-
-from MDANSE.Framework.Selectors import *
+from MDANSE.Framework.Selectors import All
+from MDANSE.Framework.Selectors import Amine
+from MDANSE.Framework.Selectors import Ammonium
+from MDANSE.Framework.Selectors import AtomElement
+from MDANSE.Framework.Selectors import AtomFullName
+from MDANSE.Framework.Selectors import AtomIndex
+from MDANSE.Framework.Selectors import AtomName
+from MDANSE.Framework.Selectors import AtomPicked
+from MDANSE.Framework.Selectors import AtomSymbol
+from MDANSE.Framework.Selectors import Backbone
+from MDANSE.Framework.Selectors import CarboHydrogen
+from MDANSE.Framework.Selectors import CarbonAlpha
+from MDANSE.Framework.Selectors import ChainName
+from MDANSE.Framework.Selectors import HeteroHydrogen
+from MDANSE.Framework.Selectors import Hydroxyl
+from MDANSE.Framework.Selectors import Macromolecule
+from MDANSE.Framework.Selectors import Methyl
+from MDANSE.Framework.Selectors import MoleculeIndex
+from MDANSE.Framework.Selectors import MoleculeName
+from MDANSE.Framework.Selectors import NitroHydrogen
+from MDANSE.Framework.Selectors import NucleotideBase
+from MDANSE.Framework.Selectors import NucleotideSugar
+from MDANSE.Framework.Selectors import NucleotideType
+from MDANSE.Framework.Selectors import OxyHydrogen
+from MDANSE.Framework.Selectors import Peptide
+from MDANSE.Framework.Selectors import Phosphate
+from MDANSE.Framework.Selectors import PythonScript
+from MDANSE.Framework.Selectors import ResidueClass
+from MDANSE.Framework.Selectors import ResidueName
+from MDANSE.Framework.Selectors import ResidueType
+from MDANSE.Framework.Selectors import SideChain
+from MDANSE.Framework.Selectors import Sulphate
+from MDANSE.Framework.Selectors import SulphurHydrogen
+from MDANSE.Framework.Selectors import Thiol
+from MDANSE.Framework.Selectors import WithinShell
 from MDANSE.IO.PDBReader import PDBReader
 
 
+pbd_2vb1 = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), "Data", "2vb1.pdb")
+pbd_1gip = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), "Data", "1gip.pdb")
+select_atoms_script = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), "select_atoms.py")
+
+
 class TestAtomsSelector(unittest.TestCase):
     """ """
 
@@ -61,10 +102,10 @@ def setUpClass(cls):
         """
         super(TestAtomsSelector, cls).setUpClass()
 
-        reader = PDBReader("../../Data/PDB/2vb1.pdb")
+        reader = PDBReader(pbd_2vb1)
         cls._proteinChemicalSystem = reader.build_chemical_system()
 
-        reader = PDBReader("../../Data/PDB/1gip.pdb")
+        reader = PDBReader(pbd_1gip)
         cls._nucleicAcidChemicalSystem = reader.build_chemical_system()
 
     def test_all(self):
@@ -93,7 +134,7 @@ def test_atom_element(self):
 
     def test_atom_full_name(self):
         selector = AtomFullName.AtomFullName(self._proteinChemicalSystem)
-        selection = selector.select([".LYS1.N", ".VAL2.O"])
+        selection = selector.select(["...LYS1.N", "...VAL2.O"])
         self.assertEqual(len(selection), 2)
 
         selection = list(selector.select(["*"]))
@@ -146,7 +187,7 @@ def test_backbone(self):
 
     def test_carbo_hydrogens(self):
         selector = CarboHydrogen.CarboHydrogen(self._proteinChemicalSystem)
-        selection = selector.select([".LYS1.HB2", ".LYS1.HB3"])
+        selection = selector.select(["...LYS1.HB2", "...LYS1.HB3"])
         self.assertEqual(len(selection), 2)
 
         selection = list(selector.select(["*"]))
@@ -170,7 +211,7 @@ def test_chain_name(self):
     def test_hetero_hydrogen(self):
         selector = HeteroHydrogen.HeteroHydrogen(self._proteinChemicalSystem)
 
-        selection = selector.select([".SER24.HG"])
+        selection = selector.select(["...SER24.HG"])
         self.assertEqual(len(selection), 1)
 
         selection = selector.select(["*"])
@@ -179,7 +220,7 @@ def test_hetero_hydrogen(self):
     def test_hydroxyl(self):
         selector = Hydroxyl.Hydroxyl(self._proteinChemicalSystem)
 
-        selection = selector.select([".SER24.HG"])
+        selection = selector.select(["...SER24.HG"])
         self.assertEqual(len(selection), 1)
 
         selection = selector.select(["*"])
@@ -197,7 +238,7 @@ def test_macromolecule(self):
     def test_methyl(self):
         selector = Methyl.Methyl(self._proteinChemicalSystem)
 
-        selection = selector.select([".VAL29.1HG1", ".VAL29.1HG2"])
+        selection = selector.select(["...VAL29.1HG1", "...VAL29.1HG2"])
         self.assertEqual(len(selection), 2)
 
         selection = selector.select(["*"])
@@ -221,15 +262,15 @@ def test_molecule_name(self):
         selection = selector.select([""])
         self.assertEqual(len(selection), 1960)
 
-        selection = selector.select(["WAT9709"])
+        selection = selector.select(["WAT_9709"])
         self.assertEqual(len(selection), 3)
 
         selection = selector.select(["*"])
         self.assertEqual(len(selection), 30714)
 
     def test_nitro_hydrogens(self):
         selector = NitroHydrogen.NitroHydrogen(self._proteinChemicalSystem)
-        selection = selector.select([".LYS1.HT1", ".LYS1.HT2", ".LYS1.HT3"])
+        selection = selector.select(["...LYS1.HT1", "...LYS1.HT2", "...LYS1.HT3"])
         self.assertEqual(len(selection), 3)
 
         selection = list(selector.select(["*"]))
@@ -275,7 +316,7 @@ def test_nucleotide_type(self):
     def test_oxy_hydrogen(self):
         selector = OxyHydrogen.OxyHydrogen(self._proteinChemicalSystem)
 
-        selection = selector.select([".THR118.HG1"])
+        selection = selector.select(["...THR118.HG1"])
         self.assertEqual(len(selection), 1)
 
         selection = selector.select(["*"])
@@ -297,7 +338,7 @@ def test_phosphate(self):
 
     def test_python_script(self):
         selector = PythonScript.PythonScript(self._nucleicAcidChemicalSystem)
-        selection = selector.select(["./Tests/UnitTests/select_atoms.py"])
+        selection = selector.select([select_atoms_script])
         self.assertEqual(len(selection), 22)
 
     def test_residue_class(self):
@@ -312,7 +353,7 @@ def test_residue_class(self):
     def test_residue_name(self):
         selector = ResidueName.ResidueName(self._proteinChemicalSystem)
 
-        selection = selector.select([".LYS1"])
+        selection = selector.select(["...LYS1"])
         self.assertEqual(len(selection), 24)
 
         selection = selector.select(["*"])

MDANSE/Tests/UnitTests/TestPDBReader.py → MDANSE/Tests/UnitTests/test_pdb_reader.py

@@ -44,14 +44,16 @@
 
 @author: Eric C. Pellegrini
 """
-
+import os
 import unittest
-
 import numpy
-
 from MDANSE.IO.PDBReader import PDBReader
 
 
+pbd_2vb1 = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), "data", "2vb1.pdb")
+
+
 class TestPDBReader(unittest.TestCase):
     """
     Unittest for the geometry-related functions
@@ -61,7 +63,7 @@ def test_reader(self):
         with self.assertRaises((IOError, AttributeError)):
             reader = PDBReader("xxxxx.pdb")
 
-        reader = PDBReader("../../Data/Trajectories/CHARMM/2vb1.pdb")
+        reader = PDBReader(pbd_2vb1)
 
         chemicalSystem = reader.build_chemical_system()
 
@@ -81,14 +83,3 @@ def test_reader(self):
         self.assertAlmostEqual(conf.variables["coordinates"][-1, 0], 2.4937)
         self.assertAlmostEqual(conf.variables["coordinates"][-1, 1], 3.9669)
         self.assertAlmostEqual(conf.variables["coordinates"][-1, 2], -0.5209)
-
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestPDBReader))
-    return s
-
-
-if __name__ == "__main__":
-    unittest.main(verbosity=2)