diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 23a361a6dacdb0b42c889c38b8b11def18232ad2..18df1a76670555dd6532141c400f7a00a9ecc983 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -878,7 +878,7 @@ namespace {
}
}
- bool all_hetatm = entity_info.type == "non-polymer";
+ bool all_hetatm = entity_info.type != "polymer";
for(auto at: at_list) {
// group_PDB
if(at.IsHetAtom() || all_hetatm) {
diff --git a/modules/io/tests/test_mmcif_writer.cc b/modules/io/tests/test_mmcif_writer.cc
index 8e4d3d3bb073a613866cf3535b85b089137ec1a8..ec1559d21f154d4c8dc68ed439fde47f07a5db6a 100644
--- a/modules/io/tests/test_mmcif_writer.cc
+++ b/modules/io/tests/test_mmcif_writer.cc
@@ -34,17 +34,104 @@ 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");
+ 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);
+ 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_force_hetatm)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_force_hetatm tests...");
+ /*
+ Make sure that atoms set to HETATM are written as HETATM. There is some
+ logic in place to deal with HETAM for mmcif_conform=false, check that this
+ is working.
+ */
+ // Create small entity
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ mol::ResidueHandle r1=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r1, "N", geom::Vec3(1, 1, 1), "N", 1.0, 0.0, true);
+ edi.InsertAtom(r1, "C", geom::Vec3(4, 1, 2), "C", 1.0, 0.0, true);
+ mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r2, "N", geom::Vec3(5, 2, 3), "N", 1.0, 0.0, true);
+ edi.InsertAtom(r2, "C", geom::Vec3(4, 1, 1), "C", 1.0, 0.0, true);
+ mol::ResidueHandle r3=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r3, "N", geom::Vec3(5, 2, 2), "N", 1.0, 0.0, true);
+ edi.InsertAtom(r3, "C", geom::Vec3(4, 1, 0), "C", 1.0, 0.0, true);
+ edi.SetChainType(ch, mol::CHAINTYPE_UNKNOWN);
+ // make sure we have a proper polypeptide
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
+ BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
+ BOOST_CHECK_EQUAL(mol::InSequence(r2, r3), true);
+
+ // Create mmCIF stream
+ MMCifWriter writer;
+ writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ std::stringstream out;
+ writer.Write("test", out);
+
+ String s=out.str();
+ // make sure the entity is a polymer
+ BOOST_CHECK_NE(s.find("_entity.id\n_entity.type\n1 polymer"), String::npos);
+ // check all atom records to be HETATMs
+ for(auto i: ch.GetAtomList()){
+ BOOST_CHECK_NE(s.find("HETATM "+
+ i.GetElement()+" "+
+ i.GetName()+" "+
+ i.GetResidue().GetName()),
+ String::npos);
+ }
+
+ // check that ATOM is written, if HETATM is not set
+ // Create small entity
+ ent=mol::CreateEntity();
+ edi=ent.EditXCS();
+ ch=edi.InsertChain("A");
+ r1=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r1, "N", geom::Vec3(1, 1, 1), "N");
+ edi.InsertAtom(r1, "C", geom::Vec3(4, 1, 2), "C");
+ r2=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r2, "N", geom::Vec3(5, 2, 3), "N");
+ edi.InsertAtom(r2, "C", geom::Vec3(4, 1, 1), "C");
+ r3=edi.AppendResidue(ch, "GLY");
+ edi.InsertAtom(r3, "N", geom::Vec3(5, 2, 2), "N");
+ edi.InsertAtom(r3, "C", geom::Vec3(4, 1, 0), "C");
+ edi.SetChainType(ch, mol::CHAINTYPE_UNKNOWN);
+ // make sure we have a proper polypeptide
+ heu_proc.Process(ent);
+ BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
+ BOOST_CHECK_EQUAL(mol::InSequence(r2, r3), true);
+
+ // Create mmCIF stream
+ writer=MMCifWriter();
+ writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ out=std::stringstream();
+ writer.Write("test", out);
+
+ s=out.str();
+ // make sure the entity is a polymer
+ BOOST_CHECK_NE(s.find("_entity.id\n_entity.type\n1 polymer"), String::npos);
+ // check all atom records to be ATOMs
+ for(auto i: ch.GetAtomList()){
+ BOOST_CHECK_NE(s.find("ATOM "+
+ i.GetElement()+" "+
+ i.GetName()+" "+
+ i.GetResidue().GetName()),
+ String::npos);
+ }
+
+ BOOST_TEST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_writer_entity1)
{
BOOST_TEST_MESSAGE(" Running mmcif_writer_entity1 tests...");
@@ -59,8 +146,7 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_entity1)
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", 1.0, 128.0);
+ edi.InsertAtom(r, "CA", geom::Vec3(32.0, -128.0, -2.5), "C");
edi.SetChainType(ch, mol::CHAINTYPE_UNKNOWN);
// Create mmCIF stream
@@ -83,7 +169,7 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
/*
Go for small polymers that are not polymer... the story of 2 amino acids (to
be handled like RCSB as 2 separated chains) plus how the same thing works
- for nucleic acids and branched molecules (sugars).
+ for nucleic acids.
*/
// Polypeptide: 2aa in a chain are 2 separated entities for RCSB (check 1E8K)
@@ -209,8 +295,9 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
// Create mmCIF stream
- writer = MMCifWriter();
+ writer=MMCifWriter();
writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ out=std::stringstream();
writer.Write("test", out);
s=out.str();
@@ -230,7 +317,112 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
String::npos);
}
- // 3AXH, 1A4G
+ BOOST_TEST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_writer_small_sugars)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_writer_small_sugars tests...");
+ /*
+ While RCSB marks dipeptides and dinucleotides as non-ploymers, sugarse are
+ marked branched as soon as there are 2 connected.
+ */
+ // Branched: 2 sugars connected (check RCSB 3AXH)
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ edi.SetChainType(ch, mol::CHAINTYPE_OLIGOSACCHARIDE);
+ // GLC
+ mol::ResidueHandle r1=edi.AppendResidue(ch, "GLC");
+ r1.SetChemClass(mol::ChemClass('Y'));
+ edi.InsertAtom(r1, "C1", geom::Vec3(-17.103, -7.005, -18.605), "C");
+ edi.InsertAtom(r1, "C2", geom::Vec3(-18.238, -7.769, -17.910), "C");
+ edi.InsertAtom(r1, "C3", geom::Vec3(-18.607, -9.018, -18.701), "C");
+ edi.InsertAtom(r1, "C4", geom::Vec3(-18.909, -8.623, -20.136), "C");
+ edi.InsertAtom(r1, "C5", geom::Vec3(-17.692, -7.925, -20.738), "C");
+ edi.InsertAtom(r1, "C6", geom::Vec3(-17.985, -7.413, -22.123), "C");
+ edi.InsertAtom(r1, "O1", geom::Vec3(-15.956, -7.805, -18.503), "O");
+ edi.InsertAtom(r1, "O2", geom::Vec3(-17.855, -8.167, -16.612), "O");
+ edi.InsertAtom(r1, "O3", geom::Vec3(-19.758, -9.617, -18.139), "O");
+ edi.InsertAtom(r1, "O4", geom::Vec3(-19.249, -9.772, -20.895), "O");
+ edi.InsertAtom(r1, "O5", geom::Vec3(-17.381, -6.775, -19.989), "O");
+ edi.InsertAtom(r1, "O6", geom::Vec3(-19.210, -6.695, -22.028), "O");
+ // GLC
+ mol::ResidueHandle r2=edi.AppendResidue(ch, "GLC");
+ r2.SetChemClass(mol::ChemClass('Y'));
+ edi.InsertAtom(r2, "C1", geom::Vec3(-20.076, -6.111, -23.424), "C");
+ edi.InsertAtom(r2, "C2", geom::Vec3(-21.506, -5.777, -22.960), "C");
+ edi.InsertAtom(r2, "C3", geom::Vec3(-22.102, -7.005, -22.273), "C");
+ edi.InsertAtom(r2, "C4", geom::Vec3(-22.152, -8.101, -23.352), "C");
+ edi.InsertAtom(r2, "C5", geom::Vec3(-20.802, -8.397, -24.036), "C");
+ edi.InsertAtom(r2, "C6", geom::Vec3(-21.027, -9.040, -25.414), "C");
+ edi.InsertAtom(r2, "O2", geom::Vec3(-21.398, -4.714, -22.066), "O");
+ edi.InsertAtom(r2, "O3", geom::Vec3(-23.396, -6.675, -21.796), "O");
+ edi.InsertAtom(r2, "O4", geom::Vec3(-22.738, -9.283, -22.830), "O");
+ edi.InsertAtom(r2, "O5", geom::Vec3(-20.007, -7.236, -24.284), "O");
+ edi.InsertAtom(r2, "O6", geom::Vec3(-21.528, -8.081, -26.325), "O");
+
+ // Connect the two sugars
+ edi.Connect(r1.FindAtom("O6"), r2.FindAtom("C1"));
+
+ // Create mmCIF stream
+ MMCifWriter writer;
+ writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ std::stringstream out;
+ writer.Write("test", out);
+
+ String s=out.str();
+ // Check that the mmCIF output contains 2 non-polymer entities
+ BOOST_CHECK_NE(s.find("loop_\n_entity.id\n_entity.type\n1 branched"),
+ String::npos);
+ // Check that atoms are HETATMs since non-poly
+ for(auto i: ch.GetAtomList()){
+ BOOST_CHECK_NE(s.find("HETATM "+
+ i.GetElement()+" "+
+ i.GetName()+" "+
+ i.GetResidue().GetName()),
+ String::npos);
+ }
+
+ // Non-poly: single sugar (check RCSB 1BDG)
+ ent=mol::CreateEntity();
+ edi=ent.EditXCS();
+ ch=edi.InsertChain("A");
+ edi.SetChainType(ch, mol::CHAINTYPE_OLIGOSACCHARIDE);
+ // GLC
+ r1=edi.AppendResidue(ch, "GLC");
+ r1.SetChemClass(mol::ChemClass('Y'));
+ edi.InsertAtom(r1, "C1", geom::Vec3(-17.103, -7.005, -18.605), "C");
+ edi.InsertAtom(r1, "C2", geom::Vec3(-18.238, -7.769, -17.910), "C");
+ edi.InsertAtom(r1, "C3", geom::Vec3(-18.607, -9.018, -18.701), "C");
+ edi.InsertAtom(r1, "C4", geom::Vec3(-18.909, -8.623, -20.136), "C");
+ edi.InsertAtom(r1, "C5", geom::Vec3(-17.692, -7.925, -20.738), "C");
+ edi.InsertAtom(r1, "C6", geom::Vec3(-17.985, -7.413, -22.123), "C");
+ edi.InsertAtom(r1, "O1", geom::Vec3(-15.956, -7.805, -18.503), "O");
+ edi.InsertAtom(r1, "O2", geom::Vec3(-17.855, -8.167, -16.612), "O");
+ edi.InsertAtom(r1, "O3", geom::Vec3(-19.758, -9.617, -18.139), "O");
+ edi.InsertAtom(r1, "O4", geom::Vec3(-19.249, -9.772, -20.895), "O");
+ edi.InsertAtom(r1, "O5", geom::Vec3(-17.381, -6.775, -19.989), "O");
+ edi.InsertAtom(r1, "O6", geom::Vec3(-19.210, -6.695, -22.028), "O");
+
+ // Create mmCIF stream
+ writer=MMCifWriter();
+ writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ out = std::stringstream();
+ writer.Write("test", out);
+
+ s=out.str();
+ // Check that the mmCIF output contains 2 non-polymer entities
+ BOOST_CHECK_NE(s.find("loop_\n_entity.id\n_entity.type\n1 non-polymer"),
+ String::npos);
+ // Check that atoms are HETATMs since non-poly
+ for(auto i: ch.GetAtomList()){
+ BOOST_CHECK_NE(s.find("HETATM "+
+ i.GetElement()+" "+
+ i.GetName()+" "+
+ i.GetResidue().GetName()),
+ String::npos);
+ }
BOOST_TEST_MESSAGE(" done.");
}