From d39bdc88deb61db3345f2af5ae661bad0687cc57 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 19 Jul 2012 14:31:46 +0200
Subject: [PATCH] Added translation from mmCIF chain name to traditional PDB
chain name.
---
modules/io/doc/mmcif.rst | 22 +++++++++++++++++++++-
modules/io/pymod/export_mmcif_io.cc | 2 ++
modules/io/src/mol/mmcif_info.cc | 18 ++++++++++++++++++
modules/io/src/mol/mmcif_info.hh | 13 +++++++++++++
modules/io/src/mol/mmcif_reader.cc | 2 ++
modules/io/tests/test_mmcif_info.cc | 7 ++++++-
6 files changed, 62 insertions(+), 2 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 855ed0ea2..758862eeb 100644
--- a/modules/io/doc/mmcif.rst
+++ b/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
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 6654393be..f94c257e6 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/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,
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index c8565a2e8..140676fe6 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/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
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index b240e5a1c..68aa79bef 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/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_;
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 2bcdee810..6f35d4a2f 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/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
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 3d2674797..d5a1ac1a4 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/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.");
}
--
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