diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index a99538686572a7c8e934d392b835fd87b8ed2e00..d0b8ffba1f98e6cffb6ac1bf5a1106ae7bf99f87 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -28,6 +28,8 @@ The following categories of a mmCIF file are considered by the parser:
* ``pdbx_struct_assembly``: Used for :class:`MMCifInfoBioUnit`.
* ``pdbx_struct_assembly_gen``: Used for :class:`MMCifInfoBioUnit`.
* ``pdbx_struct_oper_list``: Used for :class:`MMCifInfoBioUnit`.
+* ``struct``: Details about a structure, stored in
+ :class:`MMCifInfoStructDetails`.
Info Classes
@@ -76,6 +78,13 @@ of the annotation available.
Also available as :meth:`GetOperations`. May also be modified by
:meth:`AddOperation`.
+ .. attribute:: struct_details
+
+ Stores details about the structure.
+
+ Also available as :meth:`GetStructDetails`. May also be modified by
+ :meth:`SetStructDetails`.
+
.. method:: AddCitation(citation)
Add a citation to the citation list of an info object.
@@ -131,6 +140,12 @@ of the annotation available.
See :attr:`operations`
+ .. method:: SetStructDetails(details)
+
+ See :attr:`struct_details`
+
+ .. method:: GetStructDetails()
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
@@ -428,3 +443,129 @@ of the annotation available.
.. method:: AddOperations(list of operations)
See :attr:`operations`
+
+.. class:: MMCifInfoStructDetails
+
+ Holds details about the structure.
+
+ .. attribute:: entry_id
+
+ Identifier for a curtain data block. If not provided, resembles an empty
+ string.
+
+ Also available as :meth:`GetEntryID`. May also be modified by
+ :meth:`SetEntryID`.
+
+ .. attribute:: title
+
+ Set a title for the structure.
+
+ Also available as :meth:`GetTitle`. May also be modified by
+ :meth:`SetTitle`.
+
+ .. attribute:: casp_flag
+
+ Tells whether this structure was target in some competition.
+
+ Also available as :meth:`GetCASPFlag`. May also be modified by
+ :meth:`SetCASPFlag`.
+
+ .. attribute:: descriptor
+
+ Descriptor for an NDB structure or the unstructured content of a PDB COMPND
+ record.
+
+ Also available as :meth:`GetDescriptor`. May also be modified by
+ :meth:`SetDescriptor`.
+
+ .. attribute:: mass
+
+ Molecular mass of a molecule.
+
+ Also available as :meth:`GetMass`. May also be modified by
+ :meth:`SetMass`.
+
+ .. attribute:: mass_method
+
+ Method used to determine the molecular weight.
+
+ Also available as :meth:`GetMassMethod`. May also be modified by
+ :meth:`SetMassMethod`.
+
+ .. attribute:: model_details
+
+ Details about how the structure was determined.
+
+ Also available as :meth:`GetModelDetails`. May also be modified by
+ :meth:`SetModelDetails`.
+
+ .. attribute:: model_type_details
+
+ Details about how the type of the structure.
+
+ Also available as :meth:`GetModelTypeDetails`. May also be modified by
+ :meth:`SetModelTypeDetails`.
+
+ .. method:: GetEntryID()
+
+ See :attr:`entry_id`
+
+ .. method:: SetEntryID(id)
+
+ See :attr:`entry_id`
+
+ .. method:: GetTitle()
+
+ See :attr:`title`
+
+ .. method:: SetTitle(title)
+
+ See :attr:`title`
+
+ .. method:: GetCASPFlag()
+
+ See :attr:`casp_flag`
+
+ .. method:: SetCASPFlag(flag)
+
+ See :attr:`casp_flag`
+
+ .. method:: GetDescriptor()
+
+ See :attr:`descriptor`
+
+ .. method:: SetDescriptor(descriptor)
+
+ See :attr:`descriptor`
+
+ .. method:: GetMass()
+
+ See :attr:`mass`
+
+ .. method:: SetMass(mass)
+
+ See :attr:`mass`
+
+ .. method:: GetMassMethod()
+
+ See :attr:`mass_method`
+
+ .. method:: SetMassMethod(method)
+
+ See :attr:`mass_method`
+
+ .. method:: GetModelDetails()
+
+ See :attr:`model_details`
+
+ .. method:: SetModelDetails(details)
+
+ See :attr:`model_details`
+
+ .. method:: GetModelTypeDetails()
+
+ See :attr:`model_type_details`
+
+ .. method:: SetModelTypeDetails(details)
+
+ See :attr:`model_type_details`
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 6da2ac02afaf8bb56ead9adac83e3360a23a2238..9034c8c16fe7d8c785e5579665b9afcac1ed0a04 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -161,6 +161,42 @@ void export_mmcif_io()
.def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
;
+ class_<MMCifInfoStructDetails>("MMCifInfoStructDetails", init<>())
+ .def("SetEntryID", &MMCifInfoStructDetails::SetEntryID)
+ .def("GetEntryID", &MMCifInfoStructDetails::GetEntryID)
+ .def("SetTitle", &MMCifInfoStructDetails::SetTitle)
+ .def("GetTitle", &MMCifInfoStructDetails::GetTitle)
+ .def("SetCASPFlag", &MMCifInfoStructDetails::SetCASPFlag)
+ .def("GetCASPFlag", &MMCifInfoStructDetails::GetCASPFlag)
+ .def("SetDescriptor", &MMCifInfoStructDetails::SetDescriptor)
+ .def("GetDescriptor", &MMCifInfoStructDetails::GetDescriptor)
+ .def("SetMass", &MMCifInfoStructDetails::SetMass)
+ .def("GetMass", &MMCifInfoStructDetails::GetMass)
+ .def("SetMassMethod", &MMCifInfoStructDetails::SetMassMethod)
+ .def("GetMassMethod", &MMCifInfoStructDetails::GetMassMethod)
+ .def("SetModelDetails", &MMCifInfoStructDetails::SetModelDetails)
+ .def("GetModelDetails", &MMCifInfoStructDetails::GetModelDetails)
+ .def("SetModelTypeDetails", &MMCifInfoStructDetails::SetModelTypeDetails)
+ .def("GetModelTypeDetails", &MMCifInfoStructDetails::GetModelTypeDetails)
+ .add_property("entry_id", &MMCifInfoStructDetails::GetEntryID,
+ &MMCifInfoStructDetails::SetEntryID)
+ .add_property("title", &MMCifInfoStructDetails::GetTitle,
+ &MMCifInfoStructDetails::SetTitle)
+ .add_property("casp_flag", &MMCifInfoStructDetails::GetCASPFlag,
+ &MMCifInfoStructDetails::SetCASPFlag)
+ .add_property("descriptor", &MMCifInfoStructDetails::GetDescriptor,
+ &MMCifInfoStructDetails::SetDescriptor)
+ .add_property("mass", &MMCifInfoStructDetails::GetMass,
+ &MMCifInfoStructDetails::SetMass)
+ .add_property("mass_method", &MMCifInfoStructDetails::GetMassMethod,
+ &MMCifInfoStructDetails::SetMassMethod)
+ .add_property("model_details", &MMCifInfoStructDetails::GetModelDetails,
+ &MMCifInfoStructDetails::SetModelDetails)
+ .add_property("model_type_details",
+ &MMCifInfoStructDetails::GetModelTypeDetails,
+ &MMCifInfoStructDetails::SetModelTypeDetails)
+;
+
class_<MMCifInfo>("MMCifInfo", init<>())
.def("AddCitation", &MMCifInfo::AddCitation)
.def("GetCitations", make_function(&MMCifInfo::GetCitations,
@@ -176,6 +212,8 @@ void export_mmcif_io()
.def("AddOperation", &MMCifInfo::AddOperation)
.def("GetOperations", make_function(&MMCifInfo::GetOperations,
return_value_policy<copy_const_reference>()))
+ .def("SetStructDetails", &MMCifInfo::SetStructDetails)
+ .def("GetStructDetails", &MMCifInfo::GetStructDetails)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
@@ -185,5 +223,7 @@ void export_mmcif_io()
&MMCifInfo::SetResolution)
.add_property("operations", make_function(&MMCifInfo::GetOperations,
return_value_policy<copy_const_reference>()))
+ .add_property("struct_details", &MMCifInfo::GetStructDetails,
+ &MMCifInfo::SetStructDetails)
;
}
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index b8b0aba50c34d60dff7607874322580c70c4c75a..3e9400194f8c65e735bf5207330a5807b1fd0b12 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -27,6 +27,129 @@
namespace ost { namespace io {
+class DLLEXPORT_OST_IO MMCifInfoStructDetails {
+public:
+ /// \brief Create a details object.
+ MMCifInfoStructDetails(): entry_id_(""), title_(""), casp_flag_('\0'),
+ descriptor_(""), mass_(0.0), mass_method_(""), model_details_(""),
+ model_type_details_("") {};
+
+ /// \brief Set id.
+ ///
+ /// \param id id
+ void SetEntryID(String id) { entry_id_ = id; }
+ /// \brief Get id.
+ ///
+ /// \return id
+ String GetEntryID() const { return entry_id_; }
+
+ /// \brief Set CASP flag.
+ ///
+ /// \param flag flag
+ void SetCASPFlag(char flag) { casp_flag_ = flag; }
+ /// \brief Get CASP flag.
+ ///
+ /// \return flag
+ char GetCASPFlag() const { return casp_flag_; }
+
+ /// \brief Set descriptor.
+ ///
+ /// \param desc descriptor for an NDB structure or PDB COMPND record
+ void SetDescriptor(String desc) { descriptor_ = desc; }
+ /// \brief Get CASP flag.
+ ///
+ /// \return flag
+ String GetDescriptor() const { return descriptor_; }
+
+ /// \brief Set mass.
+ ///
+ /// \param mass molecular mass
+ void SetMass(Real mass) { mass_ = mass; }
+ /// \brief Get molecular weight.
+ ///
+ /// \return mass
+ Real GetMass() const { return mass_; }
+
+ /// \brief Set the method how the molecular weight was detected.
+ ///
+ /// \param method detection method
+ void SetMassMethod(String method) { mass_method_ = method; }
+ /// \brief Get the method how the molecular weight was determined.
+ ///
+ /// \return method
+ String GetMassMethod() const { return mass_method_; }
+
+ /// \brief Set the description about the production of this structure.
+ ///
+ /// \param desc explaination
+ void SetModelDetails(String desc) { model_details_ = desc; }
+ /// \brief Get the details how the structure was determined.
+ ///
+ /// \return details
+ String GetModelDetails() const { return model_details_; }
+
+ /// \brief Set a description for the type of the structure model.
+ ///
+ /// \param desc explaination
+ void SetModelTypeDetails(String desc) { model_type_details_ = desc; }
+ /// \brief Get the description for the type of the structure model.
+ ///
+ /// \return details
+ String GetModelTypeDetails() const { return model_type_details_; }
+
+ /// \brief Set a title for the data block.
+ ///
+ /// \param title title
+ void SetTitle(String title) { title_ = title; }
+ /// \brief Get the title of the structure model.
+ ///
+ /// \return title
+ String GetTitle() const { return title_; }
+
+ bool operator==(const MMCifInfoStructDetails& sd) const {
+ if (this->entry_id_ != sd.entry_id_) {
+ return false;
+ }
+ if (this->casp_flag_ != sd.casp_flag_) {
+ return false;
+ }
+ if (this->descriptor_ != sd.descriptor_) {
+ return false;
+ }
+ if (this->mass_ != sd.mass_) {
+ return false;
+ }
+ if (this->mass_method_ != sd.mass_method_) {
+ return false;
+ }
+ if (this->model_details_ != sd.model_details_) {
+ return false;
+ }
+ if (this->model_type_details_ != sd.model_type_details_) {
+ return false;
+ }
+ if (this->title_ != sd.title_) {
+ return false;
+ }
+
+ return true;
+ }
+
+ bool operator!=(const MMCifInfoStructDetails& sd) const {
+ return !this->operator == (sd);
+ }
+
+private:
+ String entry_id_;
+ String title_;
+ char casp_flag_;
+ String descriptor_;
+ Real mass_;
+ String mass_method_;
+ String model_details_;
+ String model_type_details_;
+};
+
class DLLEXPORT_OST_IO MMCifInfoTransOp {
public:
/// \brief Create an operation
@@ -156,6 +279,31 @@ public:
if (this->chains_ != bu.chains_) {
return false;
}
+ if (this->operations_.size() == bu.operations_.size()) {
+ std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator th_ops_it;
+ std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator bu_ops_it;
+ std::vector<MMCifInfoTransOpPtr>::const_iterator th_op_it;
+ std::vector<MMCifInfoTransOpPtr>::const_iterator bu_op_it;
+
+ for (th_ops_it = this->operations_.begin(),
+ bu_ops_it = bu.operations_.begin();
+ th_ops_it != this->operations_.end();
+ ++th_ops_it, ++bu_ops_it) {
+ if (th_ops_it->size() == bu_ops_it->size()) {
+ for (th_op_it = th_ops_it->begin(), bu_op_it = bu_ops_it->begin();
+ th_op_it != th_ops_it->end();
+ ++th_op_it, ++bu_op_it) {
+ if (*th_op_it != *bu_op_it) {
+ return false;
+ }
+ }
+ } else {
+ return false;
+ }
+ }
+ } else {
+ return false;
+ }
return true;
}
@@ -468,12 +616,29 @@ public:
return transops_;
}
+ /// \brief Add a set of structure details
+ ///
+ /// \param details info block to be added
+ void SetStructDetails(MMCifInfoStructDetails details)
+ {
+ struct_details_ = details;
+ }
+
+ /// \brief Get the list of details about structures.
+ ///
+ /// \return vector of MMCifInfoStructDetails objects
+ const MMCifInfoStructDetails GetStructDetails() const
+ {
+ return struct_details_;
+ }
+
//protected:
private:
// members
String exptl_method_;
Real resolution_;
+ MMCifInfoStructDetails struct_details_; ///< mmCIF struct category
std::vector<MMCifInfoCitation> citations_; ///< list of citations
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 45275c6b09244de827918083990f05fa000087c2..213187e258882f3e30a37003b6e295e2cd4fdf46 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -245,6 +245,21 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
indices_[MATRIX_3_2] = header.GetIndex("matrix[3][2]");
indices_[MATRIX_3_3] = header.GetIndex("matrix[3][3]");
cat_available = true;
+ } else if (header.GetCategory() == "struct") {
+ category_ = STRUCT;
+ // mandatory items
+ this->TryStoreIdx(STRUCT_ENTRY_ID, "entry_id", header);
+ // optional items
+ indices_[PDBX_CASP_FLAG] = header.GetIndex("pdbx_CASP_flag");
+ indices_[PDBX_DESCRIPTOR] = header.GetIndex("pdbx_descriptor");
+ indices_[PDBX_FORMULA_WEIGHT] = header.GetIndex("pdbx_formula_weight");
+ indices_[PDBX_FORMULA_WEIGHT_METHOD]
+ = header.GetIndex("pdbx_formula_weight_method");
+ indices_[PDBX_MODEL_DETAILS] = header.GetIndex("pdbx_model_details");
+ indices_[PDBX_MODEL_TYPE_DETAILS]
+ = header.GetIndex("pdbx_model_type_details");
+ indices_[STRUCT_TITLE] = header.GetIndex("title");
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -946,6 +961,48 @@ void MMCifParser::ParsePdbxStructOperList(const std::vector<StringRef>& columns)
info_.AddOperation(op);
}
+void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
+{
+ MMCifInfoStructDetails details = MMCifInfoStructDetails();
+
+ details.SetEntryID(columns[indices_[STRUCT_ENTRY_ID]].str());
+
+ if (indices_[STRUCT_TITLE] != -1) {
+ details.SetTitle(columns[indices_[STRUCT_TITLE]].str());
+ }
+
+ if ((indices_[PDBX_CASP_FLAG] != -1) &&
+ (columns[indices_[PDBX_CASP_FLAG]][0] != '?')) {
+ details.SetCASPFlag(columns[indices_[PDBX_CASP_FLAG]][0]);
+ }
+
+ if (indices_[PDBX_DESCRIPTOR] != -1) {
+ details.SetDescriptor(columns[indices_[PDBX_DESCRIPTOR]].str());
+ }
+
+ if (indices_[PDBX_FORMULA_WEIGHT] != -1) {
+ details.SetMass(this->TryGetReal(columns[indices_[PDBX_FORMULA_WEIGHT]],
+ "struct.pdbx_formula_weight"));
+ }
+
+ if (indices_[PDBX_FORMULA_WEIGHT_METHOD] != -1) {
+ details.SetMassMethod(columns[indices_[PDBX_FORMULA_WEIGHT_METHOD]].str());
+ }
+
+ if ((indices_[PDBX_MODEL_DETAILS] != -1) &&
+ (columns[indices_[PDBX_MODEL_DETAILS]][0] != '?')) {
+ details.SetModelDetails(columns[indices_[PDBX_MODEL_DETAILS]].str());
+ }
+
+ if ((indices_[PDBX_MODEL_TYPE_DETAILS] != -1) &&
+ (columns[indices_[PDBX_MODEL_TYPE_DETAILS]][0] != '?')) {
+ details.SetModelTypeDetails(
+ columns[indices_[PDBX_MODEL_TYPE_DETAILS]].str());
+ }
+
+ info_.SetStructDetails(details);
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -990,6 +1047,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing pdbx_struct_oper_list entry")
this->ParsePdbxStructOperList(columns);
break;
+ case STRUCT:
+ LOG_TRACE("processing struct entry")
+ this->ParseStruct(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 568350bbaf71e102286d2afe186a929873404438..740a93132c2dfa8ec4aee0d795ee0d875cb1a777 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -51,6 +51,7 @@ namespace ost { namespace io {
/// \li pdbx_struct_assembly
/// \li pdbx_struct_assembly_gen
/// \li pdbx_struct_oper_list
+/// \li struct
class DLLEXPORT_OST_IO MMCifParser : public StarParser {
public:
/// \brief create a MMCifParser
@@ -264,6 +265,10 @@ protected:
/// \param columns data row
void ParsePdbxStructOperList(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif struct information
+ ///
+ /// \param columns data row
+ void ParseStruct(const std::vector<StringRef>& columns);
private:
/// \enum magic numbers of this class
@@ -377,6 +382,18 @@ private:
MATRIX_3_3 ///< matrix component
} PdbxStructOperListItems;
+ /// \enum items of the struct category
+ typedef enum {
+ STRUCT_ENTRY_ID, ///< name of the structure
+ PDBX_CASP_FLAG, ///< CASP/ CASD-NMR/ other contest target
+ PDBX_DESCRIPTOR, ///< descriptor for NDB structure/ PDB COMPND record
+ PDBX_FORMULA_WEIGHT, ///< mass in daltons
+ PDBX_FORMULA_WEIGHT_METHOD, ///< how mass was determined
+ PDBX_MODEL_DETAILS, ///< methodology
+ PDBX_MODEL_TYPE_DETAILS, ///< type of structure model
+ STRUCT_TITLE ///< title for the data block
+ } StructItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -389,6 +406,7 @@ private:
PDBX_STRUCT_ASSEMBLY,
PDBX_STRUCT_ASSEMBLY_GEN,
PDBX_STRUCT_OPER_LIST,
+ STRUCT,
DONT_KNOW
} MMCifCategory;
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index d6d669aa96b5cb5e0f2ab784685b40f8a25bc36d..64caccbe1d6ee51b9faa2e7583a8740d188b70d3 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -103,6 +103,38 @@ class TestMMCifInfo(unittest.TestCase):
oll = b.GetOperations()
self.assertEquals(oll[0][0].GetID(), '1')
+ def test_mmcifinfo_structdetails(self):
+ d = io.MMCifInfoStructDetails()
+
+ d.SetEntryID('1BAR')
+ d.SetTitle('A Title')
+ d.SetCASPFlag('N')
+ d.SetDescriptor('FooBar')
+ d.SetMass(1.0)
+ d.SetMassMethod('Good Guess')
+ d.SetModelDetails('Created with SwissModel')
+ d.SetModelTypeDetails('Average')
+ self.assertEquals(d.GetEntryID(), '1BAR')
+ self.assertEquals(d.GetTitle(), 'A Title')
+ self.assertEquals(d.GetCASPFlag(), 'N')
+ self.assertEquals(d.GetDescriptor(), 'FooBar')
+ self.assertEquals(d.GetMass(), 1.0)
+ self.assertEquals(d.GetMassMethod(), 'Good Guess')
+ self.assertEquals(d.GetModelDetails(), 'Created with SwissModel')
+ self.assertEquals(d.GetModelTypeDetails(), 'Average')
+
+ i = io.MMCifInfo()
+ i.SetStructDetails(d)
+ self.assertEquals(i.GetStructDetails().GetEntryID(), '1BAR')
+ self.assertEquals(i.GetStructDetails().GetTitle(), 'A Title')
+ self.assertEquals(i.GetStructDetails().GetCASPFlag(), 'N')
+ self.assertEquals(i.GetStructDetails().GetDescriptor(), 'FooBar')
+ self.assertEquals(i.GetStructDetails().GetMass(), 1.0)
+ self.assertEquals(i.GetStructDetails().GetMassMethod(), 'Good Guess')
+ self.assertEquals(i.GetStructDetails().GetModelDetails(),
+ 'Created with SwissModel')
+ self.assertEquals(i.GetStructDetails().GetModelTypeDetails(), 'Average')
+
if __name__== '__main__':
unittest.main()
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 238b71cdc95c7264ecf4c4642da746ec7e75c49b..2c0b7b3e9e3bd38db83c6c92a321fedef3fa1df2 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -129,6 +129,37 @@ BOOST_AUTO_TEST_CASE(mmcif_info_transoperation)
BOOST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_info_structdetails)
+{
+ BOOST_MESSAGE(" Running mmcif_info_structdetails tests...");
+
+ MMCifInfoStructDetails sd = MMCifInfoStructDetails();
+
+ sd.SetEntryID("1BAR");
+ sd.SetTitle("More than a structure");
+ sd.SetCASPFlag('Y');
+ sd.SetDescriptor("ADENYLATE KINASE");
+ sd.SetMass(1.0);
+ sd.SetMassMethod("Good Guess");
+ sd.SetModelDetails("Even more guessing");
+ sd.SetModelTypeDetails("MINIMIZED AVERAGE");
+
+ BOOST_CHECK(sd.GetEntryID() == "1BAR");
+ BOOST_CHECK(sd.GetTitle() == "More than a structure");
+ BOOST_CHECK(sd.GetCASPFlag() == 'Y');
+ BOOST_CHECK(sd.GetDescriptor() == "ADENYLATE KINASE");
+ BOOST_CHECK_CLOSE(sd.GetMass(), 1.0f, 0.001f);
+ BOOST_CHECK(sd.GetMassMethod() == "Good Guess");
+ BOOST_CHECK(sd.GetModelDetails() == "Even more guessing");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "MINIMIZED AVERAGE");
+
+ MMCifInfo info = MMCifInfo();
+ info.SetStructDetails(sd);
+ BOOST_CHECK(info.GetStructDetails() == sd);
+
+ BOOST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_info)
{
BOOST_MESSAGE(" Running mmcif_info tests...");
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 6ae040448b1d63f0ac4d91a15a2965cde816a420..14adae17dbf60ffe24a5fa92a7a9595ceb965489 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -59,11 +59,13 @@ public:
using MMCifParser::ParsePdbxStructAssemblyGen;
using MMCifParser::ParsePdbxStructAssembly;
using MMCifParser::ParsePdbxStructOperList;
+ using MMCifParser::ParseStruct;
using MMCifParser::TryStoreIdx;
using MMCifParser::SetReadSeqRes;
using MMCifParser::SetReadCanonicalSeqRes;
using MMCifParser::ClearState;
using MMCifParser::ConvertSEQRES;
+ using MMCifParser::GetInfo;
};
BOOST_AUTO_TEST_SUITE( io );
@@ -729,6 +731,44 @@ BOOST_AUTO_TEST_CASE(mmcif_biounit_tests)
BOOST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_struct_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ std::vector<StringRef> columns;
+
+ tmmcif_h.SetCategory(StringRef("struct", 6));
+ tmmcif_h.Add(StringRef("entry_id", 8));
+ tmmcif_h.Add(StringRef("pdbx_CASP_flag", 14));
+ tmmcif_h.Add(StringRef("pdbx_model_details", 18));
+ tmmcif_h.Add(StringRef("pdbx_model_type_details", 23));
+ tmmcif_h.Add(StringRef("pdbx_formula_weight", 19));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ columns.push_back(StringRef("1BAR", 4));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("?", 1));
+ columns.push_back(StringRef("1.0", 3));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStruct(columns));
+
+ MMCifInfoStructDetails sd = MMCifInfoStructDetails();
+ sd = tmmcif_p.GetInfo().GetStructDetails();
+
+ BOOST_CHECK(sd.GetCASPFlag() == '\0');
+ BOOST_CHECK(sd.GetModelDetails() == "");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "");
+
+ columns.pop_back();
+ columns.push_back(StringRef("A", 1));
+ BOOST_CHECK_THROW(tmmcif_p.ParseStruct(columns), IOException);
+
+ BOOST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
{
BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
@@ -835,6 +875,15 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
MMCifInfoBioUnit bu = mmcif_p.GetInfo().GetBioUnits().back();
BOOST_CHECK(bu.GetOperations().back().back()->GetType() ==
"identity operation");
+ MMCifInfoStructDetails sd = mmcif_p.GetInfo().GetStructDetails();
+ BOOST_CHECK(sd.GetEntryID() == "1BAR");
+ BOOST_CHECK(sd.GetTitle() == "A Title");
+ BOOST_CHECK(sd.GetCASPFlag() == 'Y');
+ BOOST_CHECK(sd.GetDescriptor() == "ADENYLATE KINASE");
+ BOOST_CHECK_CLOSE(sd.GetMass(), 1.0f, 0.001f);
+ BOOST_CHECK(sd.GetMassMethod() == "Good Guess");
+ BOOST_CHECK(sd.GetModelDetails() == "Even better guessing");
+ BOOST_CHECK(sd.GetModelTypeDetails() == "Guess");
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 b10009871d934a8ece41ad4e2c1fcc1a07ed661e..cf3b4c75192b01316625877d21852c2b7dc5e968 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -85,6 +85,15 @@ _pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 23.3000000000
# biounit end
+_struct.entry_id 1BAR
+_struct.title 'A Title'
+_struct.pdbx_CASP_flag Y
+_struct.pdbx_descriptor 'ADENYLATE KINASE'
+_struct.pdbx_formula_weight 1.0
+_struct.pdbx_formula_weight_method 'Good Guess'
+_struct.pdbx_model_details 'Even better guessing'
+_struct.pdbx_model_type_details 'Guess'
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol