diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 495e79a8c7d554f39025ffb705fc61bd2f77f6dc..23a361a6dacdb0b42c889c38b8b11def18232ad2 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -878,9 +878,10 @@ namespace {
}
}
+ bool all_hetatm = entity_info.type == "non-polymer";
for(auto at: at_list) {
// group_PDB
- if(at.IsHetAtom()) {
+ if(at.IsHetAtom() || all_hetatm) {
at_data[0] = ost::io::StarWriterValue::FromString("HETATM");
} else {
at_data[0] = ost::io::StarWriterValue::FromString("ATOM");
@@ -1182,8 +1183,25 @@ namespace {
String poly_type = poly_types[i];
if(poly_chains[i]->size() <= 2) {
// must have length of at least 3 to be polymer
+ // feed them as separate non-polymers
type = "non-polymer";
poly_type = "";
+ String branch_type = "";
+ for(auto r: *poly_chains[i]) {
+ T tmp;
+ tmp.push_back(r);
+ String chain_name = chain_name_gen.Get();
+ int entity_id = SetupEntity(chain_name,
+ type,
+ poly_type,
+ branch_type,
+ tmp,
+ false,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
+ tmp);
+ }
+ continue;
}
String branch_type = "";
String chain_name = chain_name_gen.Get();
diff --git a/modules/io/tests/test_mmcif_writer.cc b/modules/io/tests/test_mmcif_writer.cc
index 353ba674788071d362c78b42035bfe823785cd4b..8661a7327983badb4c0d3df44beb9eb073000030 100644
--- a/modules/io/tests/test_mmcif_writer.cc
+++ b/modules/io/tests/test_mmcif_writer.cc
@@ -20,10 +20,11 @@
#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/conop/heuristic.hh>
#include <ost/io/mol/mmcif_writer.hh>
+#include <ost/mol/mol.hh>
+#include <ost/platform.hh>
using namespace ost;
using namespace ost::io;
@@ -47,7 +48,6 @@ conop::CompoundLibPtr SetDefaultCompoundLib() {
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
@@ -60,9 +60,7 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_entity1)
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);
+ "C", 1.0, 128.0);
edi.SetChainType(ch, mol::CHAINTYPE_UNKNOWN);
// Create mmCIF stream
@@ -73,10 +71,90 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_entity1)
// 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_CHECK_NE(s.find("_entity.id\n_entity.type\n1 non-polymer"),
+ String::npos);
+
+ BOOST_TEST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_writer_poly_vs_non_poly)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_writer_poly_vs_non_poly tests...");
+ /*
+ 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).
+ */
+
+ // Polypeptide: 2aa in a chain are 2 separated entities for RCSB (check 1E8K)
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor edi=ent.EditXCS();
+ mol::ChainHandle ch=edi.InsertChain("A");
+ edi.SetChainType(ch, mol::CHAINTYPE_POLY_PEPTIDE_L);
+ // ALA
+ mol::ResidueHandle r1=edi.AppendResidue(ch, "ALA"); // is_hetatm=false
+ edi.InsertAtom(r1, "N", geom::Vec3(44.987, 17.389, 12.362), "N", 0.81,
+ 25.57);
+ edi.InsertAtom(r1, "CA", geom::Vec3(45.936, 16.434, 12.890), "C", 0.81,
+ 28.21);
+ edi.InsertAtom(r1, "C", geom::Vec3(47.196, 17.227, 13.152), "C", 0.81,
+ 33.78);
+ edi.InsertAtom(r1, "O", geom::Vec3(47.506, 18.153, 12.401), "O", 0.81,
+ 23.02);
+ edi.InsertAtom(r1, "CB", geom::Vec3(46.244, 15.293, 11.961), "C", 0.81,
+ 29.85);
+ // PRO
+ mol::ResidueHandle r2=edi.AppendResidue(ch, "PRO"); // is_hetatm=false
+ edi.InsertAtom(r2, "N", geom::Vec3(47.953, 16.910, 14.229), "N", 0.81,
+ 32.19 );
+ edi.InsertAtom(r2, "CA", geom::Vec3(47.673, 15.829, 15.187), "C", 0.81,
+ 33.89 );
+ edi.InsertAtom(r2, "C", geom::Vec3(46.564, 16.052, 16.233), "C", 0.81,
+ 37.97 );
+ edi.InsertAtom(r2, "O", geom::Vec3(46.059, 17.169, 16.417), "O", 0.81,
+ 34.43 );
+ edi.InsertAtom(r2, "CB", geom::Vec3(49.054, 15.755, 15.880), "C", 0.81,
+ 36.60 );
+ edi.InsertAtom(r2, "CG", geom::Vec3(49.357, 17.213, 16.030), "C", 0.81,
+ 34.77 );
+ edi.InsertAtom(r2, "CD", geom::Vec3(49.098, 17.714, 14.637), "C", 0.81,
+ 34.62 );
+ edi.InsertAtom(r2, "OXT", geom::Vec3(46.144, 15.129, 16.950), "O", 0.81,
+ 34.03 );
+ conop::HeuristicProcessor heu_proc;
+ // Make sure that the two residues r1, r2 are actually connected
+ heu_proc.Process(ent);
+ BOOST_CHECK_EQUAL(mol::InSequence(r1, r2), true);
+
+ // Create mmCIF stream
+ MMCifWriter writer;
+ writer.SetStructure(ent, SetDefaultCompoundLib(), false);
+ std::stringstream out;
+ writer.Write("test", out);
+
+ // Check that the mmCIF output contains 2 non-polymer entities
+ String s=out.str();
+ BOOST_CHECK_NE(
+ s.find("loop_\n_entity.id\n_entity.type\n1 non-polymer\n2 non-polymer"),
+ String::npos);
+ BOOST_CHECK_NE(
+ s.find("loop_\n_struct_asym.id\n_struct_asym.entity_id\nA 1\nB 2"),
+ String::npos);
+ BOOST_CHECK_NE(s.find("HETATM N N ALA"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CA ALA"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C C ALA"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM O O ALA"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CB ALA"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM N N PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CA PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C C PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM O O PRO "), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CB PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CG PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM C CD PRO"), String::npos);
+ BOOST_CHECK_NE(s.find("HETATM O OXT PRO"), String::npos);
+
+ // write mmCIF, check atoms are marked HETATM
BOOST_TEST_MESSAGE(" done.");
}