Now parsing resolution from MMCif files.

modules/io/doc/mmcif.rst

@@ -41,6 +41,13 @@ of the annotation available.
     Also available as :meth:`GetMethod`. May also be modified by
     :meth:`SetMethod`.
 
+  .. attribute:: resolution
+
+    Stores the resolution of the crystal structure.
+
+    Also available as :meth:`GetResolution`. May also be modified by
+    :meth:`SetResolution`.
+
   .. method:: AddCitation(citation)
 
     Add a citation to the citation list of an info object.
@@ -69,6 +76,14 @@ of the annotation available.
 
     See :attr:`method`
 
+  .. method:: SetResolution(resolution)
+
+    See :attr:`resolution`
+
+  .. method:: GetResolution()
+
+    See :attr:`resolution`
+
 .. class:: MMCifInfoCitation
 
   This stores citation information from an input file.

modules/io/pymod/export_mmcif_io.cc

@@ -108,9 +108,13 @@ void export_mmcif_io()
                                    return_value_policy<copy_const_reference>()))
     .def("SetMethod", &MMCifInfo::SetMethod)
     .def("GetMethod", &MMCifInfo::GetMethod)
+    .def("SetResolution", &MMCifInfo::SetResolution)
+    .def("GetResolution", &MMCifInfo::GetResolution)
     .def("AddAuthorsToCitation", &MMCifInfo::AddAuthorsToCitation)
     .add_property("citations", make_function(&MMCifInfo::GetCitations,
                                    return_value_policy<copy_const_reference>()))
     .add_property("method", &MMCifInfo::GetMethod, &MMCifInfo::SetMethod)
+    .add_property("resolution", &MMCifInfo::GetResolution,
+                  &MMCifInfo::SetResolution)
   ;
 }

modules/io/src/mol/mmcif_info.hh

@@ -245,7 +245,7 @@ private:
 class DLLEXPORT_OST_IO MMCifInfo {
 public:
   /// \brief Create an info object.
-  MMCifInfo(): exptl_method_("") {};
+  MMCifInfo(): exptl_method_(""), resolution_(0.0f) {};
 
   /// \brief Add an item to the list of citations
   ///
@@ -282,11 +282,22 @@ public:
     return StringRef(exptl_method_.c_str(), exptl_method_.length());
   }
 
+  /// \brief Set resolution.
+  ///
+  /// \param res experiment resolution
+  void SetResolution(Real res) { resolution_ = res; }
+
+  /// \brief Get resolution.
+  ///
+  /// \return experiment resolution
+  Real GetResolution() const { return resolution_; }
+
 //protected:
 
 private:
   // members
   String exptl_method_;
+  Real resolution_;
   std::vector<MMCifInfoCitation> citations_; ///< list of citations
 };
 

modules/io/src/mol/mmcif_reader.cc

@@ -193,17 +193,23 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
     category_ = CITATION_AUTHOR;
     // mandatory items
     this->TryStoreIdx(AUTHOR_CITATION_ID, "citation_id", header);
-    this->TryStoreIdx(AUTHOR_NAME, "name", header);
-    this->TryStoreIdx(ORDINAL, "ordinal", header);
+    this->TryStoreIdx(AUTHOR_NAME,        "name", header);
+    this->TryStoreIdx(ORDINAL,            "ordinal", header);
     cat_available = true;
   } else if (header.GetCategory() == "exptl") {
     category_ = EXPTL;
     // mandatory items
     this->TryStoreIdx(CITATION_ID, "entry_id", header);
-    this->TryStoreIdx(METHOD, "method", header);
+    this->TryStoreIdx(METHOD,      "method", header);
     cat_available = true;
-  } /* else if (header.GetCategory()=="struct_conf") {
-  }*/
+  } else if (header.GetCategory() == "refine") {
+    category_ = REFINE;
+    // mandatory items
+    this->TryStoreIdx(REFINE_ENTRY_ID, "entry_id", header);
+    this->TryStoreIdx(LS_D_RES_HIGH,   "ls_d_res_high", header);
+    this->TryStoreIdx(LS_D_RES_LOW,    "ls_d_res_low", header);
+    cat_available = true;
+  }
   category_counts_[category_]++;
   return cat_available;
 }
@@ -713,6 +719,12 @@ void MMCifParser::ParseExptl(const std::vector<StringRef>& columns)
   info_.SetMethod(columns[indices_[METHOD]].str());
 }
 
+void MMCifParser::ParseRefine(const std::vector<StringRef>& columns)
+{
+  info_.SetResolution(this->TryGetReal(columns[indices_[LS_D_RES_HIGH]],
+                                       "refine.ls_d_res_high"));
+}
+
 void MMCifParser::OnDataRow(const StarLoopDesc& header, 
                             const std::vector<StringRef>& columns)
 {
@@ -741,6 +753,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
     LOG_TRACE("processing exptl entry")
     this->ParseExptl(columns);
     break;
+  case REFINE:
+    LOG_TRACE("processing refine entry")
+    this->ParseRefine(columns);
+    break;
   default:
     throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
                        "Uncatched category '"+ header.GetCategory() +"' found.",

modules/io/src/mol/mmcif_reader.hh

@@ -231,6 +231,11 @@ protected:
   /// \param columns data row
   void ParseExptl(const std::vector<StringRef>& columns);
 
+  /// \brief Fetch MMCif refine information
+  ///
+  /// \param columns data row
+  void ParseRefine(const std::vector<StringRef>& columns);
+
 private:
   /// \enum magic numbers of this class
   typedef enum {
@@ -304,6 +309,13 @@ private:
     METHOD                        ///< method of the experiment
   } ExptlItems;
 
+  /// \enum items of the refine category
+  typedef enum {
+    REFINE_ENTRY_ID,
+    LS_D_RES_HIGH,
+    LS_D_RES_LOW
+  } RefineItems;
+
   /// \enum categories of the mmcif format
   typedef enum {
     ATOM_SITE,
@@ -312,6 +324,7 @@ private:
     CITATION,
     CITATION_AUTHOR,
     EXPTL,
+    REFINE,
     DONT_KNOW
   } MMCifCategory;
 

modules/io/tests/test_io_mmcif.py

@@ -48,6 +48,7 @@ class TestPDB(unittest.TestCase):
 
     i = io.MMCifInfo()
     i.SetMethod('Deep-Fry')
+    i.SetResolution(2.0)
     i.AddCitation(c)
     s.append('Bar')
     i.AddAuthorsToCitation('ID', s)
@@ -60,6 +61,7 @@ class TestPDB(unittest.TestCase):
     self.assertEquals(al[1], 'Bar')
 
     self.assertEquals(i.GetMethod(), 'Deep-Fry')
+    self.assertEquals(i.GetResolution(), 2.0)
 
 if __name__== '__main__':
     unittest.main()

modules/io/tests/test_mmcif_info.cc

@@ -86,7 +86,10 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
   MMCifInfo info = MMCifInfo();
 
   info.SetMethod("Cooking.");
+  info.SetResolution(1.9f);
+
   BOOST_CHECK(info.GetMethod() == StringRef("Cooking.", 8));
+  BOOST_CHECK_CLOSE(info.GetResolution(), 1.9f, 0.001f);
 
   BOOST_MESSAGE("  done.");
 }

modules/io/tests/test_mmcif_reader.cc

@@ -54,6 +54,7 @@ public:
   using MMCifParser::ParseEntity;
   using MMCifParser::ParseEntityPoly;
   using MMCifParser::ParseCitation;
+  using MMCifParser::ParseRefine;
   using MMCifParser::TryStoreIdx;
   using MMCifParser::SetReadSeqRes;
   using MMCifParser::SetReadCanonicalSeqRes;
@@ -567,6 +568,42 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_author_tests)
   BOOST_MESSAGE("  done.");
 }
 
+BOOST_AUTO_TEST_CASE(mmcif_refine_tests)
+{
+  BOOST_MESSAGE("  Running mmcif_refine_tests...");
+  BOOST_MESSAGE("         positive test...");
+  {
+    mol::EntityHandle eh = mol::CreateEntity();
+    std::ifstream s("testfiles/mmcif/atom_site.mmcif");
+    IOProfile profile;
+    MMCifParser mmcif_p(s, eh, profile);
+    BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+    BOOST_CHECK_CLOSE(mmcif_p.GetInfo().GetResolution(), 2.0f, 0.001f);
+  }
+  BOOST_MESSAGE("         done.");
+  BOOST_MESSAGE("         capturing fishy data lines...");
+  {
+    mol::EntityHandle eh;
+    TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+    StarLoopDesc tmmcif_h;
+    std::vector<StringRef> columns;
+    
+    tmmcif_h.SetCategory(StringRef("refine", 6));
+    tmmcif_h.Add(StringRef("entry_id", 8));
+    tmmcif_h.Add(StringRef("ls_d_res_high", 13));
+    tmmcif_h.Add(StringRef("ls_d_res_low", 12));
+    tmmcif_p.OnBeginLoop(tmmcif_h);
+    
+    columns.push_back(StringRef("1Foo", 4));
+    columns.push_back(StringRef("Foo", 3));
+    columns.push_back(StringRef("1", 1));
+    
+    BOOST_CHECK_THROW(tmmcif_p.ParseRefine(columns), IOException);
+  }
+  BOOST_MESSAGE("         done.");
+  BOOST_MESSAGE("  done.");
+}
+
 BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
 {
   BOOST_MESSAGE("  Running mmcif_parseatomident tests...");
@@ -585,7 +622,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
   //StringRef atom_name;
 
   BOOST_MESSAGE("          testing valid line");
-  //tmmcif_p.ParseAtomIdent(columns, chain_name, res_name);
+  //tmmcif_p.ParseAtomIdent();
   BOOST_MESSAGE("          done.");
   // negative
   //cols.push_back(StringRef("ATOM", 4));

modules/io/tests/testfiles/mmcif/atom_site.mmcif

@@ -46,6 +46,10 @@ _citation_author.name
 _exptl.entry_id           experiment1
 _exptl.method             'Deep-fry'
 
+_refine.entry_id       '1BAR'
+_refine.ls_d_res_high  2.0
+_refine.ls_d_res_low   1.5
+
 loop_
 _atom_site.group_PDB
 _atom_site.type_symbol