mmCIF writer unitest, entities start at 1

modules/io/tests/CMakeLists.txt

@@ -15,6 +15,7 @@ set(OST_IO_UNIT_TESTS
   tests.cc
   test_star_parser.cc
   test_mmcif_reader.cc
+  test_mmcif_writer.cc
   test_mmcif_info.cc
   test_io_img.cc
   test_exceptions.cc

modules/io/tests/test_mmcif_writer.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2024 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include <ost/platform.hh>
+#include <ost/conop/conop.hh>
+#include <ost/mol/mol.hh>
+#include <ost/io/mol/mmcif_writer.hh>
+
+using namespace ost;
+using namespace ost::io;
+
+BOOST_AUTO_TEST_SUITE( io );
+
+conop::CompoundLibPtr SetDefaultCompoundLib() {
+  // return NULL if not successful, else return newly set default lib
+  // REQ: OST_ROOT to be set
+  char * ost_root = getenv("OST_ROOT");
+  if (!ost_root) return conop::CompoundLibPtr();
+  SetPrefixPath(ost_root);
+  String lib_path = GetSharedDataPath() + "/compounds.chemlib";
+  conop::CompoundLibPtr compound_lib = conop::CompoundLib::Load(lib_path);
+  if (compound_lib) {
+    conop::Conopology::Instance().SetDefaultLib(compound_lib);
+  }
+  return compound_lib;
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_writer_entity1)
+{
+  BOOST_TEST_MESSAGE("  Running mmcif_writer_entity1 tests...");
+
+  /*
+    Make sure molecular entities in mmCIF files written by OST start counting
+    at ID 1. This is not enforced by the mmCIF format definition, but common
+    practice.
+   */
+
+  // Create tiny entity
+  mol::EntityHandle ent=mol::CreateEntity();
+  mol::XCSEditor edi=ent.EditXCS();
+  mol::ChainHandle ch=edi.InsertChain("A");
+  mol::ResidueHandle r=edi.AppendResidue(ch, "GLY");
+  mol::AtomHandle a=edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5),
+                                   "C");
+  a.SetOccupancy(1.0);
+  a.SetBFactor(128.0);
+  edi.SetChainType(ch, mol::CHAINTYPE_UNKNOWN);
+
+  // Create mmCIF stream
+  MMCifWriter writer;
+  writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+  std::stringstream out;
+  writer.Write("test", out);
+
+  // Check if entity starts with 1, either by reading mmCIF or "grep"
+  String s=out.str();
+  BOOST_CHECK_EQUAL(
+                    s.substr(0, 53),
+                    "data_test\nloop_\n_entity.id\n_entity.type\n1 non-polymer"
+                    );
+
+  BOOST_TEST_MESSAGE("  done.");
+}
+
+BOOST_AUTO_TEST_SUITE_END();