Test adding files containing nonpolymers

ihmwg · Feb 13, 2024 · 51e1a4f · 51e1a4f
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diff --git a/test/input/mini_nonpoly.cif b/test/input/mini_nonpoly.cif
@@ -0,0 +1,82 @@
+data_model
+_entry.id model
+_struct.entry_id model
+_struct.pdbx_model_details .
+_struct.pdbx_structure_determination_methodology integrative
+_struct.title .
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/IHM-dictionary/9be59e1/ihm-extension.dic
+_audit_conform.dict_name ihm-extension.dic
+_audit_conform.dict_version 1.24
+#
+loop_
+_chem_comp.id
+_chem_comp.type
+_chem_comp.name
+_chem_comp.formula
+_chem_comp.formula_weight
+HEM non-polymer 'PROTOPORPHYRIN IX CONTAINING FE' 'C34 H32 Fe N4 O4' 616.499
+#
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 non-polymer man Heme 616.499 2 .
+#
+#
+loop_
+_pdbx_entity_nonpoly.entity_id
+_pdbx_entity_nonpoly.name
+_pdbx_entity_nonpoly.comp_id
+1 Heme HEM
+#
+#
+loop_
+_struct_asym.id
+_struct_asym.entity_id
+_struct_asym.details
+A 1 'First heme'
+B 1 'Second heme'
+#
+#
+loop_
+_pdbx_nonpoly_scheme.asym_id
+_pdbx_nonpoly_scheme.entity_id
+_pdbx_nonpoly_scheme.mon_id
+_pdbx_nonpoly_scheme.ndb_seq_num
+_pdbx_nonpoly_scheme.pdb_seq_num
+_pdbx_nonpoly_scheme.auth_seq_num
+_pdbx_nonpoly_scheme.auth_mon_id
+_pdbx_nonpoly_scheme.pdb_strand_id
+_pdbx_nonpoly_scheme.pdb_ins_code
+A 1 HEM 1 100 100 HEM A .
+B 1 HEM 1 200 200 HEM B .
+#
+#
+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_seq_id
+_atom_site.auth_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.label_asym_id
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.label_entity_id
+_atom_site.auth_asym_id
+_atom_site.auth_comp_id
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_PDB_model_num
+_atom_site.ihm_model_id
+HETATM 1 FE FE . HEM . 100 ? A 0 0 0 . 1 A HEM . 1 1
+HETATM 2 FE FE . HEM . 200 ? B 10.000 10.000 10.000 . 1 B HEM . 1 1
diff --git a/test/input/mini_nonpoly_add.cif b/test/input/mini_nonpoly_add.cif
@@ -0,0 +1,82 @@
+data_model
+_entry.id model
+_struct.entry_id model
+_struct.pdbx_model_details .
+_struct.pdbx_structure_determination_methodology integrative
+_struct.title .
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/IHM-dictionary/9be59e1/ihm-extension.dic
+_audit_conform.dict_name ihm-extension.dic
+_audit_conform.dict_version 1.24
+#
+loop_
+_chem_comp.id
+_chem_comp.type
+_chem_comp.name
+_chem_comp.formula
+_chem_comp.formula_weight
+HEM non-polymer 'PROTOPORPHYRIN IX CONTAINING FE' 'C34 H32 Fe N4 O4' 616.499
+#
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 non-polymer man Heme 616.499 2 .
+#
+#
+loop_
+_pdbx_entity_nonpoly.entity_id
+_pdbx_entity_nonpoly.name
+_pdbx_entity_nonpoly.comp_id
+1 Heme HEM
+#
+#
+loop_
+_struct_asym.id
+_struct_asym.entity_id
+_struct_asym.details
+A 1 'First heme'
+B 1 'Second heme'
+#
+#
+loop_
+_pdbx_nonpoly_scheme.asym_id
+_pdbx_nonpoly_scheme.entity_id
+_pdbx_nonpoly_scheme.mon_id
+_pdbx_nonpoly_scheme.ndb_seq_num
+_pdbx_nonpoly_scheme.pdb_seq_num
+_pdbx_nonpoly_scheme.auth_seq_num
+_pdbx_nonpoly_scheme.auth_mon_id
+_pdbx_nonpoly_scheme.pdb_strand_id
+_pdbx_nonpoly_scheme.pdb_ins_code
+A 1 HEM 1 100 100 HEM A .
+B 1 HEM 1 800 800 HEM B .
+#
+#
+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_seq_id
+_atom_site.auth_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.label_asym_id
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.label_entity_id
+_atom_site.auth_asym_id
+_atom_site.auth_comp_id
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_PDB_model_num
+_atom_site.ihm_model_id
+HETATM 1 FE FE . HEM . 100 ? A 0 0 0 . 1 A HEM . 1 1
+HETATM 2 FE FE . HEM . 800 ? B 10.000 10.000 10.000 . 1 B HEM . 1 1
diff --git a/test/test_make_mmcif.py b/test/test_make_mmcif.py
@@ -148,6 +148,51 @@ def test_add_polymers(self):
         self.assertEqual(s.title, 'Auto-generated system')
         os.unlink('output.cif')
 
+    @unittest.skipIf(sys.version_info[0] < 3, "make-mmcif.py needs Python 3")
+    def test_add_non_polymers(self):
+        """Check that make-mmcif combines non-polymer information"""
+        # mini_nonpoly.cif contains two hemes A, B
+        incif = utils.get_input_file_name(TOPDIR, 'mini_nonpoly.cif')
+        # mini_nonpoly_add.cif also contains A, B; A has the same author
+        # provided residue number as mini_nonpoly.cif but B is different
+        # (so should be renamed C when we add)
+        addcif = utils.get_input_file_name(TOPDIR, 'mini_nonpoly_add.cif')
+        subprocess.check_call([sys.executable, MAKE_MMCIF, incif,
+                               '--add', addcif])
+        with open('output.cif') as fh:
+            s, = ihm.reader.read(fh)
+        self.assertEqual(len(s.entities), 1)
+        self.assertEqual(len(s.asym_units), 3)
+        self.assertEqual(len(s.state_groups), 2)
+        # Model from mini_nonpoly.cif
+        self.assertEqual(len(s.state_groups[0]), 1)
+        self.assertEqual(len(s.state_groups[0][0]), 1)
+        self.assertEqual(len(s.state_groups[0][0][0]), 1)
+        m = s.state_groups[0][0][0][0]
+        self.assertEqual(m.protocol.name, 'modeling')
+        self.assertEqual(m.assembly.name, 'Modeled assembly')
+        chain_a, chain_b, = m.representation
+        self.assertIs(chain_a.asym_unit, s.asym_units[0])
+        self.assertIs(chain_b.asym_unit, s.asym_units[1])
+        for chain in chain_a, chain_b:
+            self.assertIsInstance(chain, ihm.representation.AtomicSegment)
+            self.assertFalse(chain.rigid)
+        # Model from mini_nonpoly_add.cif
+        self.assertEqual(len(s.state_groups[1]), 1)
+        self.assertEqual(len(s.state_groups[1][0]), 1)
+        self.assertEqual(len(s.state_groups[1][0][0]), 1)
+        m = s.state_groups[1][0][0][0]
+        self.assertEqual(m.protocol.name, 'modeling')
+        self.assertEqual(m.assembly.name, 'Modeled assembly')
+        chain_a, chain_c, = m.representation
+        self.assertIs(chain_a.asym_unit, s.asym_units[0])
+        self.assertIs(chain_c.asym_unit, s.asym_units[2])
+        for chain in chain_a, chain_c:
+            self.assertIsInstance(chain, ihm.representation.AtomicSegment)
+            self.assertFalse(chain.rigid)
+        self.assertEqual(s.title, 'Auto-generated system')
+        os.unlink('output.cif')
+
 
 if __name__ == '__main__':
     unittest.main()