Test all PDBSelectors with mmCIF files

modules/atom/test/input/atomtype.cif

@@ -0,0 +1,29 @@
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM   1 C  CA . ALA A  1  1 ? 953.312  704.510 700.259 1.00 84.31  ? 1 ALA A CA 1
+ATOM   2 C  CB . GLN A  1  2 ? 862.521  620.909 612.377 1.00 10.00  ? 2 GLN A CA 1 
+ATOM   3 C  C  . GLN A  1  3 ? 862.521  620.909 612.377 1.00 10.00  ? 3 GLN A CA 1 
+ATOM   4 O  O  . ALA A  1  4 ? 953.312  704.510 700.259 1.00 84.31  ? 4 ALA A CA 1
+ATOM   5 N  N  . GLN A  1  5 ? 862.521  620.909 612.377 1.00 10.00  ? 5 GLN A CA 1 
+ATOM   6 P  P  . DG  B  2  1 ? 862.521  620.909 612.377 1.00 10.00  ? 6 DG  B P  1 
+HETATM 7 CA CA . CA  C  3  . ? 862.521  620.909 612.377 1.00 10.00  ? 7 CA  C CA 1 

modules/atom/test/input/water.cif

@@ -0,0 +1,26 @@
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM   1 C CA . ALA A  1  1 ? 953.312  704.510 700.259 1.00 84.31  ? 1 ALA A CA 1
+ATOM   2 H HA . ALA A  1  2 ? 953.312  704.510 700.259 1.00 84.31  ? 2 ALA A HA 1
+HETATM 3 O O  . HOH B  2  . ? 862.521  620.909 612.377 1.00 10.00  ? 3 HOH B O  1 
+HETATM 4 O O  . HOH B  2  . ? 862.521  620.909 612.377 1.00 10.00  ? 4 HOH B O  1 

modules/atom/test/test_mmcif.py

@@ -200,6 +200,164 @@ def test_atom_selector(self):
         self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
                          [68, 287, 287, 287, 287])
 
+    def test_calpha_selector(self):
+        """Check CAlphaPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.CAlphaPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Only residue 1 contains a C-alpha (residue 6 is calcium, should
+        # be rejected)
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1])
+
+    def test_cbeta_selector(self):
+        """Check CBetaPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.CBetaPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Only residue 2 contains a C-beta
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [2])
+
+    def test_atom_type_selector(self):
+        """Check AtomTypePDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.AtomTypePDBSelector(['CA', 'O']))
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue 1 is C-alpha; residue 4 is O; residue 7 is "CA" (calcium)
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 4, 7])
+
+    def test_residue_type_selector(self):
+        """Check ResidueTypePDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.ResidueTypePDBSelector(['ALA']))
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residues 1 and 4 are ALA
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 4])
+
+    def test_c_selector(self):
+        """Check CPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.CPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Only residue 3 contains a C atom
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [3])
+
+    def test_n_selector(self):
+        """Check NPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.NPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Only residue 5 contains a N atom
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [5])
+
+    def test_p_selector(self):
+        """Check PPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.PPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Only residue 6 contains a P atom
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [6])
+
+    def test_all_selector(self):
+        """Check AllPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('nonalttest.cif'), m,
+                                 IMP.atom.AllPDBSelector())
+        # All alternative locations should be selected
+        self.assertEqual(len(IMP.atom.get_leaves(mp)), 6)
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.AllPDBSelector())
+        # Both ATOM and HETATM records should be selected
+        self.assertEqual(len(IMP.atom.get_leaves(mp)), 7)
+
+    def test_water_selector(self):
+        """Check WaterPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('water.cif'), m,
+                                 IMP.atom.WaterPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residues 3, 4 are waters
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [3, 4])
+
+    def test_hydrogen_selector(self):
+        """Check HydrogenPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('water.cif'), m,
+                                 IMP.atom.HydrogenPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue 2 only contains hydrogen
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [2])
+
+    def test_non_water_non_hydrogen_selector(self):
+        """Check NonWaterNonHydrogenPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('water.cif'), m,
+                                 IMP.atom.NonWaterNonHydrogenPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue 1 contains CA (not water or hydrogen)
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1])
+
+    def test_non_hydrogen_selector(self):
+        """Check NonHydrogenPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('water.cif'), m,
+                                 IMP.atom.NonHydrogenPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue 1 contains CA, 3 and 4 are water oxygens
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 3, 4])
+
+    def test_non_water_selector(self):
+        """Check NonWaterPDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('water.cif'), m,
+                                 IMP.atom.NonWaterPDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 2])
+
+    def test_backbone_selector(self):
+        """Check BackbonePDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('atomtype.cif'), m,
+                                 IMP.atom.BackbonePDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue 2 is excluded because it only contains CB (non-backbone);
+        # residue 6 is excluded because its "CA" is calcium, not C-alpha
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 3, 4, 5])
+
     def test_chain_selector(self):
         """Check reading single chain from an mmCIF file"""
         m = IMP.Model()