Added translation from mmCIF chain name to traditional PDB chain name.

modules/io/doc/mmcif.rst

@@ -160,6 +160,25 @@ of the annotation available.
 
   .. method:: GetStructDetails()
 
+  .. method:: AddMMCifPDBChainTr(cif_chain_id, pdb_chain_id)
+
+    Set up a translation for a certain mmCIF chain name to the traditional PDB
+    chain name.
+
+    :param cif_chain_id: atom_site.label_asym_id
+    :type cif_chain_id: :class:`str`
+    :param pdb_chain_id: atom_site.auth_asym_id
+    :type pdb_chain_id: :class:`str`
+
+  .. method:: GetMMCifPDBChainTr(cif_chain_id)
+
+    Get the translation of a certain mmCIF chain name to the traditional PDB
+    chain name.
+
+    :param cif_chain_id: atom_site.label_asym_id
+    :type cif_chain_id: :class:`str`
+    :returns: atom_site.auth_asym_id as :class:`str`
+
 .. class:: MMCifInfoCitation
 
   This stores citation information from an input file.
@@ -793,4 +812,5 @@ 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
+..  LocalWords:  biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
+..  LocalWords:  auth GetMMCifPDBChainTr

modules/io/pymod/export_mmcif_io.cc

@@ -280,6 +280,8 @@ void export_mmcif_io()
     .def("GetStructDetails", &MMCifInfo::GetStructDetails)
     .def("SetObsoleteInfo", &MMCifInfo::SetObsoleteInfo)
     .def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
+    .def("AddMMCifPDBChainTr", &MMCifInfo::AddMMCifPDBChainTr)
+    .def("GetMMCifPDBChainTr", &MMCifInfo::GetMMCifPDBChainTr)
     .add_property("citations", make_function(&MMCifInfo::GetCitations,
                                    return_value_policy<copy_const_reference>()))
     .add_property("biounits", make_function(&MMCifInfo::GetBioUnits,

modules/io/src/mol/mmcif_info.cc

@@ -22,6 +22,24 @@
 
 namespace ost { namespace io {
 
+void MMCifInfo::AddMMCifPDBChainTr(String cif, String pdb)
+{
+  std::map<String, String>::iterator tr_it = cif_2_pdb_chain_id_.find(cif);
+  if (tr_it != cif_2_pdb_chain_id_.end()) {
+    throw IOException("mmCIF chain id '"+ cif +"' is already mapped to '"+
+                      tr_it->second+"'.");
+  }
+  cif_2_pdb_chain_id_.insert(std::pair<String, String>(cif, pdb));
+}
+
+String MMCifInfo::GetMMCifPDBChainTr(String cif) const
+{
+  std::map<String, String>::const_iterator tr_it =
+    cif_2_pdb_chain_id_.find(cif);
+  if (tr_it == cif_2_pdb_chain_id_.end()) { return ""; }
+  return tr_it->second;
+}
+
 void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
 {
   // find citation

modules/io/src/mol/mmcif_info.hh

@@ -771,6 +771,18 @@ public:
   /// \return experiment resolution
   Real GetResolution() const { return resolution_; }
 
+  /// \brief Add a new mmCIF/ PDB chain name tuple.
+  ///
+  /// \param cif chain name as used by the mmCIF file (label_asym_id)
+  /// \param pdb chain name as used in the PDB file (auth_asym_id)
+  void AddMMCifPDBChainTr(String cif, String pdb);
+
+  /// \brief Get a PDB chain name for a CIF chain name
+  ///
+  /// \param cif chain name as used by the mmCIF file (label_asym_id)
+  /// \return chain name as used in the PDB file (auth_asym_id)
+  String GetMMCifPDBChainTr(String cif) const;
+
   /// \brief Add a biounit
   ///
   /// \param bu biounit to be added
@@ -848,6 +860,7 @@ private:
   std::vector<MMCifInfoBioUnit>  biounits_;   ///< list of biounits
   std::vector<MMCifInfoTransOpPtr> transops_;
 	MMCifInfoStructRefs            struct_refs_;
+  std::map<String, String> cif_2_pdb_chain_id_;
 };
 
 

modules/io/src/mol/mmcif_reader.cc

@@ -500,6 +500,8 @@ 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

modules/io/tests/test_mmcif_info.cc

@@ -202,7 +202,12 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
   #else
   BOOST_CHECK_CLOSE(info.GetResolution(), 1.9f, 0.001f);
   #endif
- 
+
+  info.AddMMCifPDBChainTr("A", "B");
+  BOOST_CHECK_THROW(info.AddMMCifPDBChainTr("A", "B"), IOException);
+  BOOST_CHECK("B" == info.GetMMCifPDBChainTr("A"));
+  BOOST_CHECK("" == info.GetMMCifPDBChainTr("C"));
+
   BOOST_MESSAGE("  done.");
 }