diff --git a/modules/io/pymod/export_omf_io.cc b/modules/io/pymod/export_omf_io.cc
index b50392dc09ce99de19489f493d1908d681501cd8..fb98237b0ffbb2e5c6e5cd6d00ceceeefde080dd 100644
--- a/modules/io/pymod/export_omf_io.cc
+++ b/modules/io/pymod/export_omf_io.cc
@@ -73,6 +73,7 @@ void export_omf_io() {
.def("GetAU", &OMF::GetAU)
.def("GetAUChain", &OMF::GetAUChain)
.def("GetBU", &OMF::GetBU)
+ .def("GetName", &OMF::GetName)
.def("GetChainNames", &wrap_get_chain_names)
.def("GetPositions", &OMF::GetPositions, return_value_policy<reference_existing_object>(),(arg("cname")))
.def("GetBFactors", &OMF::GetBFactors, return_value_policy<reference_existing_object>(),(arg("cname")))
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index ddaf3d59114f1cd6157ef31ef0b0cfc294a276ab..973595161ed6295631bf6e26593d9984b81b7d1e 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -808,6 +808,26 @@ namespace{
RunLengthEncoding(transformed_sec_structures, run_length_encoded);
Dump(stream, run_length_encoded);
}
+
+ void DumpName(std::ostream& stream, const String& name) {
+ if(name.size() > std::numeric_limits<uint8_t>::max()) {
+ std::stringstream ss;
+ ss << "Max name size that can be dumped is ";
+ ss << std::numeric_limits<uint8_t>::max << ". ";
+ ss << "got: "<<name<<std::endl;
+ throw ost::Error(ss.str());
+ }
+ uint8_t size = name.size();
+ stream.write(reinterpret_cast<char*>(&size), sizeof(uint8_t));
+ stream.write(reinterpret_cast<const char*>(&name[0]), size*sizeof(char));
+ }
+
+ void LoadName(std::istream& stream, String& name) {
+ uint8_t size;
+ stream.read(reinterpret_cast<char*>(&size), sizeof(uint8_t));
+ name.resize(size);
+ stream.read(reinterpret_cast<char*>(&name[0]), size*sizeof(uint8_t));
+ }
}
@@ -3358,7 +3378,9 @@ OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent,
uint8_t options) {
OMFPtr omf(new OMF);
+ omf->name_ = ent.GetName();
omf->options_ = options;
+ omf->version_ = OMF_VERSION;
//////////////////////////////////////////////////////////////////////////////
// Generate kind of a "mini compound library"... Eeach unique residue gets //
@@ -3538,6 +3560,7 @@ String OMF::ToString() const {
ost::mol::EntityHandle OMF::GetAU() const{
ost::mol::EntityHandle ent = mol::CreateEntity();
+ ent.SetName(name_);
ost::mol::XCSEditor ed = ent.EditXCS(mol::BUFFERED_EDIT);
for(auto it = chain_data_.begin(); it!=chain_data_.end(); ++it) {
@@ -3563,6 +3586,9 @@ ost::mol::EntityHandle OMF::GetAUChain(const String& name) const{
throw ost::Error("No chain of name " + name);
}
ost::mol::EntityHandle ent = mol::CreateEntity();
+ std::stringstream ss;
+ ss << name_ << " " << name;
+ ent.SetName(ss.str());
ost::mol::XCSEditor ed = ent.EditXCS(mol::BUFFERED_EDIT);
ost::mol::ChainHandle ch = ed.InsertChain(name);
this->FillChain(ch, ed, chain_data_.at(name));
@@ -3576,6 +3602,9 @@ ost::mol::EntityHandle OMF::GetBU(int bu_idx) const{
const BioUnitDefinition& bu = biounit_definitions_[bu_idx];
ost::mol::EntityHandle ent = mol::CreateEntity();
+ std::stringstream ss;
+ ss << name_ << " " << bu_idx;
+ ent.SetName(ss.str());
ost::mol::XCSEditor ed = ent.EditXCS(mol::BUFFERED_EDIT);
std::vector<String> au_chain_names;
@@ -3634,9 +3663,10 @@ void OMF::ToStream(std::ostream& stream) const {
// We set it to the current version...
// If you loaded a structure from a previous version and you dump it again,
// the version will be updated.
- uint32_t version = OMF_VERSION;
+ uint32_t version = version_;
stream.write(reinterpret_cast<char*>(&version), sizeof(uint32_t));
stream.write(reinterpret_cast<const char*>(&options_), sizeof(uint8_t));
+ DumpName(stream, name_);
if(OptionSet(DEFAULT_PEPLIB)) {
// no need to dump the residue definitions from default lib
@@ -3678,6 +3708,7 @@ void OMF::FromStream(std::istream& stream) {
if(version_ > 1) {
stream.read(reinterpret_cast<char*>(&options_), sizeof(uint8_t));
+ LoadName(stream, name_);
}
if(OptionSet(DEFAULT_PEPLIB)) {
diff --git a/modules/io/src/mol/omf.hh b/modules/io/src/mol/omf.hh
index e049e53482d65124b85c26e8a1b3b969c767c858..f5bb8b9966b0b5c74d9d114f745f212c16b52799 100644
--- a/modules/io/src/mol/omf.hh
+++ b/modules/io/src/mol/omf.hh
@@ -190,6 +190,9 @@ public:
// data access without requirement of generating a full
// OpenStructure entity
+
+ String GetName() const { return name_; }
+
std::vector<String> GetChainNames() const;
const geom::Vec3List& GetPositions(const String& cname) const;
@@ -210,6 +213,7 @@ private:
const ChainDataPtr data,
geom::Mat4 transform = geom::Mat4()) const;
+ String name_;
std::vector<ResidueDefinition> residue_definitions_;
std::vector<BioUnitDefinition> biounit_definitions_;
std::map<String, ChainDataPtr> chain_data_;
diff --git a/modules/io/tests/test_io_omf.py b/modules/io/tests/test_io_omf.py
index 840d9f42d75794620b8e45b312a90ed826f2b232..1ed14044a23919d8f9624254a7d270db2d815a8d 100644
--- a/modules/io/tests/test_io_omf.py
+++ b/modules/io/tests/test_io_omf.py
@@ -78,7 +78,13 @@ def compare_bonds(ent1, ent2):
def compare_ent(ent1, ent2, at_occupancy_thresh = 0.01,
at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
skip_ss=False, skip_cnames = False, skip_bonds = False,
- skip_rnums=False):
+ skip_rnums=False, bu_idx = None):
+ if bu_idx is not None:
+ if ent1.GetName() + ' ' + str(bu_idx) != ent2.GetName():
+ return False
+ else:
+ if ent1.GetName() != ent2.GetName():
+ return False
chain_names_one = [ch.GetName() for ch in ent1.chains]
chain_names_two = [ch.GetName() for ch in ent2.chains]
if skip_cnames:
@@ -109,6 +115,7 @@ class TestOMF(unittest.TestCase):
self.ent = ent
self.seqres = seqres
self.info = info
+ self.ent.SetName("This is a name 123")
def test_AU(self):
omf = io.OMF.FromMMCIF(self.ent, self.info)
@@ -220,15 +227,15 @@ class TestOMF(unittest.TestCase):
# - skip_bonds: Thats qualified atom name based. PDBize used rnums
# and insertion codes for waters...
# - skip_rnums: Again, insertion codes for waters...
- self.assertTrue(compare_ent(omf_loaded.GetBU(0),
- info.GetBioUnits()[0].PDBize(ent),
+ self.assertTrue(compare_ent(info.GetBioUnits()[0].PDBize(ent),
+ omf_loaded.GetBU(0),
skip_cnames=True, skip_bonds=True,
- skip_rnums=True))
+ skip_rnums=True, bu_idx = 0))
- self.assertTrue(compare_ent(omf_loaded.GetBU(1),
- info.GetBioUnits()[1].PDBize(ent),
+ self.assertTrue(compare_ent(info.GetBioUnits()[1].PDBize(ent),
+ omf_loaded.GetBU(1),
skip_cnames=True, skip_bonds=True,
- skip_rnums=True))
+ skip_rnums=True, bu_idx = 1))
# no check for the full guy... problem: PDBize throws all water
# molecules in the same chain, whereas OMF keeps them separate