diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index da840874e29de801134a25a648a83eca6911499a..c5a0a164587a328253cf8a970a5bf557084daf38 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -34,6 +34,13 @@ of the annotation available.
Also available as :meth:`GetCitations`.
+ .. attribute:: method
+
+ Stores the experimental method used to create the structure.
+
+ Also available as :meth:`GetMethod`. May also be modified by
+ :meth:`SetMethod`.
+
.. method:: AddCitation(citation)
Add a citation to the citation list of an info object.
@@ -54,6 +61,14 @@ of the annotation available.
See :attr:`citations`
+ .. method:: SetMethod(method)
+
+ See :attr:`method`
+
+ .. method:: GetMethod()
+
+ See :attr:`method`
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 4e1a7e60af45d51fa8b03c2ab92c887eb5f42374..06cba8423ca595ae9c6e7f5889704eca888c33ab 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -106,8 +106,11 @@ void export_mmcif_io()
.def("AddCitation", &MMCifInfo::AddCitation)
.def("GetCitations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
+ .def("SetMethod", &MMCifInfo::SetMethod)
+ .def("GetMethod", &MMCifInfo::GetMethod)
.def("AddAuthorsToCitation", &MMCifInfo::AddAuthorsToCitation)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
+ .add_property("method", &MMCifInfo::GetMethod, &MMCifInfo::SetMethod)
;
}
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 70624d4f74eb0356f8f618cc2d496357451fa90e..37e8969754d1e31d6d6559669e8ea195cb562f3b 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -245,7 +245,7 @@ private:
class DLLEXPORT_OST_IO MMCifInfo {
public:
/// \brief Create an info object.
- MMCifInfo() {};
+ MMCifInfo(): exptl_method_("") {};
/// \brief Add an item to the list of citations
///
@@ -269,10 +269,24 @@ public:
return citations_;
}
+ /// \brief Set an experimental method.
+ ///
+ /// \param method Method description
+ void SetMethod(String method) { exptl_method_ = method; }
+
+ /// \brief Get an experimental method.
+ ///
+ /// \return Method description
+ const StringRef GetMethod() const
+ {
+ return StringRef(exptl_method_.c_str(), exptl_method_.length());
+ }
+
//protected:
private:
// members
+ String exptl_method_;
std::vector<MMCifInfoCitation> citations_; ///< list of citations
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 5b85c1340ec990377e9f66deea17ea5620f2ecfe..9f99c0b6e625fba1d24fb5a0b3ab58948aaff8b2 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -196,9 +196,13 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
this->TryStoreIdx(AUTHOR_NAME, "name", header);
this->TryStoreIdx(ORDINAL, "ordinal", header);
cat_available = true;
- } /*
-else if (header.GetCategory()=="pdbx_struct_assembly") {
- } else if (header.GetCategory()=="struct_conf") {
+ } else if (header.GetCategory() == "exptl") {
+ category_ = EXPTL;
+ // mandatory items
+ this->TryStoreIdx(CITATION_ID, "entry_id", header);
+ this->TryStoreIdx(METHOD, "method", header);
+ cat_available = true;
+ } /* else if (header.GetCategory()=="struct_conf") {
}*/
category_counts_[category_]++;
return cat_available;
@@ -704,6 +708,11 @@ void MMCifParser::ParseCitationAuthor(const std::vector<StringRef>& columns)
}
}
+void MMCifParser::ParseExptl(const std::vector<StringRef>& columns)
+{
+ info_.SetMethod(columns[indices_[METHOD]].str());
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -728,6 +737,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing citation_author entry")
this->ParseCitationAuthor(columns);
break;
+ case EXPTL:
+ LOG_TRACE("processing exptl entry")
+ this->ParseExptl(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index ecd9f31a39a0982dc8d0f5f65f8001056bbce00f..1376abee23cfafc16e7eb0ad33685263a282fd36 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -226,6 +226,11 @@ protected:
/// \param columns data row
void ParseCitationAuthor(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif exptl information
+ ///
+ /// \param columns data row
+ void ParseExptl(const std::vector<StringRef>& columns);
+
private:
/// \enum magic numbers of this class
typedef enum {
@@ -293,6 +298,12 @@ private:
ORDINAL ///< position in author list
} CitationAuthorItems;
+ /// \enum items of the exptl category
+ typedef enum {
+ EXPTL_ENTRY_ID, ///< identifier
+ METHOD ///< method of the experiment
+ } ExptlItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -300,6 +311,7 @@ private:
ENTITY_POLY,
CITATION,
CITATION_AUTHOR,
+ EXPTL,
DONT_KNOW
} MMCifCategory;
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 47c52b7ece410092f5e4f46464680f143be3af1f..fd5671262c892b25029cbc49790d0f6977c7a93c 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -47,6 +47,7 @@ class TestPDB(unittest.TestCase):
self.assertEquals(s2[0], 'Foo')
i = io.MMCifInfo()
+ i.SetMethod('Deep-Fry')
i.AddCitation(c)
s.append('Bar')
i.AddAuthorsToCitation('ID', s)
@@ -58,6 +59,8 @@ class TestPDB(unittest.TestCase):
self.assertEquals(al[0], 'Foo')
self.assertEquals(al[1], 'Bar')
+ self.assertEquals(i.GetMethod(), 'Deep-Fry')
+
if __name__== '__main__':
unittest.main()
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 97346d7ff5ee6b6bbc090822497b3d391a634da9..d5e1aa3d4c5f405de7a98e8c6f0a9fbeb338d5de 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -79,4 +79,17 @@ BOOST_AUTO_TEST_CASE(mmcif_info_citation)
BOOST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_info)
+{
+ BOOST_MESSAGE(" Running mmcif_info tests...");
+
+ MMCifInfo info = MMCifInfo();
+
+ info.SetMethod("Cooking.");
+ BOOST_CHECK(info.GetMethod() == StringRef("Cooking.", 8));
+
+ BOOST_MESSAGE(" done.");
+}
+
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index d534e834a072416f086dc85cd5e8201483424d12..42b44d38ff547f45227e9218021fd97f3d59acae 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -664,6 +664,10 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
BOOST_MESSAGE(" done.");
+ BOOST_MESSAGE(" reading data fields which should not fail...");
+ BOOST_CHECK(mmcif_p.GetInfo().GetMethod().str() == "Deep-fry");
+ BOOST_MESSAGE(" done.");
+
BOOST_MESSAGE(" done.");
}
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index 2d2322af617a75d450de0f054869b5dbe5d38830..6ada7db03d34b2131f5afc4e824780679235eb73 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -43,6 +43,9 @@ _citation_author.name
primary 3 'Van Hummel, J.F.'
primary 2 'McCheese, B.M.'
+_exptl.entry_id experiment1
+_exptl.method 'Deep-fry'
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol