Added test for create_non_poly with initializers

include/cif++/model.hpp

@@ -216,6 +216,14 @@ class atom
 		set_location(loc);
 	}
 
+	/// \brief rotate the coordinates of this atom by \a q around point \a p
+	void rotate(quaternion q, point p)
+	{
+		auto loc = get_location();
+		loc.rotate(q, p);
+		set_location(loc);
+	}
+
 	/// \brief Translate and rotate the position of this atom by \a t and \a q
 	void translate_and_rotate(point t, quaternion q)
 	{

src/model.cpp

@@ -2335,18 +2335,19 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
 	{
 		auto atom_id = atom_site.get_unique_id("");
 
-		atom.set_value("name", atom_id);
+		atom.set_value("id", atom_id);
 		atom.set_value("label_asym_id", asym_id);
 		atom.set_value("auth_asym_id", asym_id);
 		atom.set_value("label_entity_id", entity_id);
 
 		atom.set_value_if_empty({"group_PDB", "HETATM"});
 		atom.set_value_if_empty({"label_comp_id", comp_id});
-		atom.set_value_if_empty({"label_seq_id", ""});
+		atom.set_value_if_empty({"label_seq_id", "."});
 		atom.set_value_if_empty({"auth_comp_id", comp_id});
 		atom.set_value_if_empty({"auth_seq_id", 1});
 		atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
 		atom.set_value_if_empty({"label_alt_id", ""});
+		atom.set_value_if_empty({"occupancy", 1.0, 2});
 
 		auto row = atom_site.emplace(atom.begin(), atom.end());
 

src/pdb/cif2pdb.cpp

@@ -3372,7 +3372,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 	auto &atom_site = db["atom_site"];
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
 	auto &entity = db["entity"];
-	auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
+	// auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
 	// auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
 	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];
 

test/model-test.cpp

@@ -202,6 +202,123 @@ _atom_type.symbol   C
 
 // --------------------------------------------------------------------
 
+BOOST_AUTO_TEST_CASE(create_nonpoly_2)
+{
+    cif::VERBOSE = 1;
+
+	cif::file file;
+	file.load_dictionary("mmcif_pdbx.dic");
+	file.emplace("TEST");	// create a datablock
+	
+	cif::mm::structure structure(file);
+
+	cif::file lig("HEM.cif");
+	auto &chem_comp_atom = lig["HEM"]["chem_comp_atom"];
+
+	std::vector<cif::row_initializer> atoms;
+
+	for (const auto &[type_symbol, label_atom_id, Cartn_x, Cartn_y, Cartn_z] :
+		chem_comp_atom.rows<std::string,std::string,float,float,float>(
+				"type_symbol", "atom_id", "model_Cartn_x", "model_Cartn_y", "model_Cartn_z"))
+	{
+		atoms.emplace_back(cif::row_initializer{
+			{ "type_symbol", type_symbol },
+			{ "label_atom_id", label_atom_id },
+			{ "auth_atom_id", label_atom_id },
+			{ "Cartn_x", Cartn_x },
+			{ "Cartn_y", Cartn_y },
+			{ "Cartn_z", Cartn_z }
+		});
+
+		if (atoms.size() == 4)
+			break;
+	}
+
+	std::string entity_id = structure.create_non_poly_entity("HEM");
+	structure.create_non_poly(entity_id, atoms);
+
+	auto expected = R"(
+data_TEST
+# 
+_pdbx_nonpoly_scheme.asym_id         A 
+_pdbx_nonpoly_scheme.ndb_seq_num     1 
+_pdbx_nonpoly_scheme.entity_id       1 
+_pdbx_nonpoly_scheme.mon_id          HEM 
+_pdbx_nonpoly_scheme.pdb_seq_num     1 
+_pdbx_nonpoly_scheme.auth_seq_num    1 
+_pdbx_nonpoly_scheme.pdb_mon_id      HEM 
+_pdbx_nonpoly_scheme.auth_mon_id     HEM 
+_pdbx_nonpoly_scheme.pdb_strand_id   A 
+_pdbx_nonpoly_scheme.pdb_ins_code    . 
+#
+loop_
+_atom_site.id
+_atom_site.auth_asym_id
+_atom_site.label_alt_id
+_atom_site.label_asym_id
+_atom_site.label_atom_id
+_atom_site.label_comp_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.type_symbol
+_atom_site.group_PDB
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+1 A ? A CHA HEM 1 . C HETATM ? 2.748 -19.531 39.896 1.00 ? 1 HEM CHA 1
+2 A ? A CHB HEM 1 . C HETATM ? 3.258 -17.744 35.477 1.00 ? 1 HEM CHB 1
+3 A ? A CHC HEM 1 . C HETATM ? 1.703 -21.9   33.637 1.00 ? 1 HEM CHC 1
+4 A ? A CHD HEM 1 . C HETATM ? 1.149 -23.677 38.059 1.00 ? 1 HEM CHD 1
+#
+_chem_comp.id               HEM
+_chem_comp.type             NON-POLYMER
+_chem_comp.name             'PROTOPORPHYRIN IX CONTAINING FE'
+_chem_comp.formula          'C34 H32 Fe N4 O4'
+_chem_comp.formula_weight   616.487000
+#
+_pdbx_entity_nonpoly.entity_id   1
+_pdbx_entity_nonpoly.name        'PROTOPORPHYRIN IX CONTAINING FE'
+_pdbx_entity_nonpoly.comp_id     HEM
+#
+_entity.id                 1
+_entity.type               non-polymer
+_entity.pdbx_description   'PROTOPORPHYRIN IX CONTAINING FE'
+_entity.formula_weight     616.487000
+#
+_struct_asym.id                            A
+_struct_asym.entity_id                     1
+_struct_asym.pdbx_blank_PDB_chainid_flag   N
+_struct_asym.pdbx_modified                 N
+_struct_asym.details                       ?
+#
+_atom_type.symbol   C
+)"_cf;
+
+	expected.load_dictionary("mmcif_pdbx.dic");
+
+	if (not (expected.front() == structure.get_datablock()))
+	{
+		BOOST_TEST(false);
+		std::cout << expected.front() << std::endl
+				<< std::endl
+				<< structure.get_datablock() << std::endl;
+		
+
+		expected.save("/tmp/a");
+		file.save("/tmp/b");
+	}
+}
+
+
+// --------------------------------------------------------------------
+
 BOOST_AUTO_TEST_CASE(test_atom_id)
 {
 	auto data = R"(

test/unit-v2-test.cpp

@@ -3104,4 +3104,3 @@ _date    today
 
 	BOOST_TEST(db == db2);
 }
-