diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 758862eeb797c966b2336edd499ba00a930b065a..da1bed9d710d3ec33a4c7dfc16cbc02f6812348e 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -179,6 +179,23 @@ of the annotation available.
:type cif_chain_id: :class:`str`
:returns: atom_site.auth_asym_id as :class:`str`
+ .. method:: AddPDBCMMCifhainTr(pdb_chain_id, cif_chain_id)
+
+ Set up a translation for a certain PDB chain name to the mmCIF chain name.
+
+ :param pdb_chain_id: atom_site.label_asym_id
+ :type pdb_chain_id: :class:`str`
+ :param cif_chain_id: atom_site.auth_asym_id
+ :type cif_chain_id: :class:`str`
+
+ .. method:: GetPDBMMCifChainTr(pdb_chain_id)
+
+ Get the translation of a certain PDB chain name to the mmCIF chain name.
+
+ :param pdb_chain_id: atom_site.auth_asym_id
+ :type pdb_chain_id: :class:`str`
+ :returns: atom_site.label_asym_id as :class:`str`
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
@@ -813,4 +830,4 @@ of the annotation available.
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
.. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
-.. LocalWords: auth GetMMCifPDBChainTr
+.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index f94c257e647a6499992dea5172169a029ddd8d85..f2527066afca1d2d715c97dcc1413276eafa7a6b 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -282,6 +282,8 @@ void export_mmcif_io()
.def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
.def("AddMMCifPDBChainTr", &MMCifInfo::AddMMCifPDBChainTr)
.def("GetMMCifPDBChainTr", &MMCifInfo::GetMMCifPDBChainTr)
+ .def("AddPDBMMCifChainTr", &MMCifInfo::AddPDBMMCifChainTr)
+ .def("GetPDBMMCifChainTr", &MMCifInfo::GetPDBMMCifChainTr)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 140676fe6c409c03e2da8a427c2a502da2a936c3..29f0db7463188068b3584a49457126d7ec1601d0 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -40,6 +40,24 @@ String MMCifInfo::GetMMCifPDBChainTr(String cif) const
return tr_it->second;
}
+void MMCifInfo::AddPDBMMCifChainTr(String pdb, String cif)
+{
+ std::map<String, String>::iterator tr_it = pdb_2_cif_chain_id_.find(pdb);
+ if (tr_it != pdb_2_cif_chain_id_.end()) {
+ throw IOException("PDB chain id '"+ pdb +"' is already mapped to '"+
+ tr_it->second+"'.");
+ }
+ pdb_2_cif_chain_id_.insert(std::pair<String, String>(pdb, cif));
+}
+
+String MMCifInfo::GetPDBMMCifChainTr(String pdb) const
+{
+ std::map<String, String>::const_iterator tr_it =
+ pdb_2_cif_chain_id_.find(pdb);
+ if (tr_it == pdb_2_cif_chain_id_.end()) { return ""; }
+ return tr_it->second;
+}
+
void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
{
// find citation
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 68aa79befa08c11015178075d7daceea3d86c051..3eebf54b2369947c9d007e616c4d33c2f968750c 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -22,6 +22,7 @@
#include <vector>
#include <map>
#include <boost/shared_ptr.hpp>
+#include <ost/seq/sequence_list.hh>
#include <ost/geom/geom.hh>
#include <ost/string_ref.hh>
#include <ost/io/module_config.hh>
@@ -783,6 +784,18 @@ public:
/// \return chain name as used in the PDB file (auth_asym_id)
String GetMMCifPDBChainTr(String cif) const;
+ /// \brief Add a new PDB/ mmCIF chain name tuple.
+ ///
+ /// \param pdb chain name as used by the PDB file (auth_asym_id)
+ /// \param cif chain name as used in the mmCIF file (label_asym_id)
+ void AddPDBMMCifChainTr(String pdb, String cif);
+
+ /// \brief Get a CIF chain name for a PDB chain name
+ ///
+ /// \param pdb chain name as used by the mmCIF file (auth_asym_id)
+ /// \return chain name as used in the PDB file (label_asym_id)
+ String GetPDBMMCifChainTr(String pdb) const;
+
/// \brief Add a biounit
///
/// \param bu biounit to be added
@@ -861,6 +874,7 @@ private:
std::vector<MMCifInfoTransOpPtr> transops_;
MMCifInfoStructRefs struct_refs_;
std::map<String, String> cif_2_pdb_chain_id_;
+ std::map<String, String> pdb_2_cif_chain_id_;
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 6f35d4a2f206286578d20339fff710a1d0d1a2eb..762939ca817800366ee487ffadef9da493f5103a 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -500,8 +500,6 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
// store entity id
chain_id_pairs_.push_back(std::pair<mol::ChainHandle,String>(curr_chain_,
columns[indices_[LABEL_ENTITY_ID]].str()));
- // store mmCIF - PDB chain name mapping
- info_.AddMMCifPDBChainTr(cif_chain_name, auth_chain_name);
}
assert(curr_chain_.IsValid());
} else if (chain_id_pairs_.back().second != // unit test
@@ -1541,6 +1539,7 @@ void MMCifReader::OnEndData()
// process chain types
std::vector<std::pair<mol::ChainHandle, String> >::const_iterator css;
MMCifEntityDescMap::const_iterator edm_it;
+ String pdb_auth_chain_name;
for (css = chain_id_pairs_.begin(); css != chain_id_pairs_.end(); ++css) {
edm_it = entity_desc_map_.find(css->second);
@@ -1550,6 +1549,9 @@ void MMCifReader::OnEndData()
if (edm_it->second.seqres.length() > 0) {
seqres_.AddSequence(seq::CreateSequence(css->first.GetName(),
edm_it->second.seqres));
+ pdb_auth_chain_name = css->first.GetStringProp("pdb_auth_chain_name");
+ info_.AddMMCifPDBChainTr(css->first.GetName(), pdb_auth_chain_name);
+ info_.AddPDBMMCifChainTr(pdb_auth_chain_name, css->first.GetName());
} else if (edm_it->second.type!=mol::CHAINTYPE_WATER) {
// mark everything that doesn't have SEQRES as ligand and isn't of type
// water as ligand
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index d5a1ac1a465edbbe121d173b4167244adf804b27..65e4fdaecb42ec54fb50d3c579f24ba8b7ae8adb 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -208,6 +208,11 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
BOOST_CHECK("B" == info.GetMMCifPDBChainTr("A"));
BOOST_CHECK("" == info.GetMMCifPDBChainTr("C"));
+ info.AddPDBMMCifChainTr("A", "B");
+ BOOST_CHECK_THROW(info.AddPDBMMCifChainTr("A", "B"), IOException);
+ BOOST_CHECK("B" == info.GetPDBMMCifChainTr("A"));
+ BOOST_CHECK("" == info.GetPDBMMCifChainTr("C"));
+
BOOST_MESSAGE(" done.");
}
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index ce890cf9d3be305019cbc431726433df8a06beee..68b2fbb5769c6e735ec7e30cb7311f002f9b3346 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -168,10 +168,10 @@ ATOM C CB ILE A 13 . 1 21.236 34.463 16.492 1.00 22.67 . 13 21 ? A
ATOM C CG1 ILE A 13 . 1 20.478 33.469 17.371 1.00 22.14 . 13 22 ? A
ATOM C CG2 ILE A 13 . 1 21.357 33.986 15.016 1.00 21.75 . 13 23 ? A
# - - - - data truncated for brevity - - - -
-HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? A
-HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? A
-HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? A
-HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? A
+HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? C
+HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? C
+HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? C
+HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? C
# - - - - data truncated for brevity - - - -
# chain to be ignored by 'restrict_chains' feature
ATOM N N ILE Z 1 . 1 23.664 33.855 16.884 1.00 22.08 . 1 17 ? Z