diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 756669d51900524a126e654685df79963f054cc7..0c15c3767167c9245acd645b4b7ceff2d1991640 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -80,6 +80,7 @@ void MMCifParser::ClearState()
authors_map_.clear();
bu_origin_map_.clear();
bu_assemblies_.clear();
+ secstruct_list_.clear();
}
void MMCifParser::SetRestrictChains(const String& restrict_chains)
@@ -260,6 +261,20 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
= header.GetIndex("pdbx_model_type_details");
indices_[STRUCT_TITLE] = header.GetIndex("title");
cat_available = true;
+ } else if (header.GetCategory() == "struct_conf") {
+ category_ = STRUCT_CONF;
+ // mandatory items
+ this->TryStoreIdx(BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+ this->TryStoreIdx(BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+ this->TryStoreIdx(BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
+ this->TryStoreIdx(CONF_TYPE_ID, "conf_type_id", header);
+ this->TryStoreIdx(END_LABEL_ASYM_ID, "end_label_asym_id", header);
+ this->TryStoreIdx(END_LABEL_COMP_ID, "end_label_comp_id", header);
+ this->TryStoreIdx(END_LABEL_SEQ_ID, "end_label_seq_id", header);
+ this->TryStoreIdx(STRUCT_CONF_ID, "id", header);
+ // optional items
+ indices_[BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -1008,6 +1023,34 @@ void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
info_.SetStructDetails(details);
}
+void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
+{
+ StringRef chain_name;
+ int s_res_num;
+ int e_res_num;
+ // fetch start and end
+ s_res_num = this->TryGetInt(columns[indices_[BEG_LABEL_SEQ_ID]],
+ "struct_conf.beg_label_seq_id"); // unit test
+ e_res_num = this->TryGetInt(columns[indices_[END_LABEL_SEQ_ID]],
+ "struct_conf.end_label_seq_id"); // unit test
+ if(auth_chain_id_) { // unit test both ways
+ if (indices_[BEG_AUTH_ASYM_ID] != -1) { // unit test
+ chain_name = columns[indices_[BEG_AUTH_ASYM_ID]];
+ } else { // unit test
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "foo",
+ this->GetCurrentLinenum()));
+ }
+ } else { // unit test
+ chain_name = columns[indices_[BEG_LABEL_ASYM_ID]];
+ }
+ MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
+ to_res_num(e_res_num, ' '),
+ chain_name.str(),
+ columns[indices_[CONF_TYPE_ID]].str()};
+ secstruct_list_.push_back(hse);
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -1056,6 +1099,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing struct entry")
this->ParseStruct(columns);
break;
+ case STRUCT_CONF:
+ LOG_TRACE("processing struct_conf entry")
+ this->ParseStructConf(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1064,6 +1111,18 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
}
}
+void MMCifParser::AssignSecStructure(mol::EntityHandle ent)
+{
+ // for each helix, take chain
+ // check for overlaps (visual artifacts)
+ // assign helix to chain
+
+ // for all strands
+ // take chain
+ // check for overlaps
+ // assign strand to chain
+}
+
void MMCifParser::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -1155,6 +1214,8 @@ void MMCifParser::OnEndData()
}
bu_assemblies_.clear();
+ // create secondary structure from struct_conf info
+
LOG_INFO("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index ee63212a7cfc184fcf1fb8000477a391aae6e14f..5bb2aeffd3bf7dab04a3ebd7ac8485bbb0bd04d0 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -270,6 +270,14 @@ protected:
/// \param columns data row
void ParseStruct(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif struct_conf (secondary structure) information
+ ///
+ /// \param columns data row
+ void ParseStructConf(const std::vector<StringRef>& columns);
+
+ /// \brief Transform data from struct_conf entry into secondary structure
+ void AssignSecStructure(mol::EntityHandle ent);
+
private:
/// \enum magic numbers of this class
typedef enum {
@@ -394,6 +402,19 @@ private:
STRUCT_TITLE ///< title for the data block
} StructItems;
+ /// \enum items of the struct_conf category
+ typedef enum {
+ BEG_AUTH_ASYM_ID, ///< Starting residue, points to atom_site.auth_asym_id
+ BEG_LABEL_ASYM_ID, ///< Starting residue, points to atom_site.label_asym_id
+ BEG_LABEL_COMP_ID, ///< Starting residue, points to atom_site.label_comp_id
+ BEG_LABEL_SEQ_ID, ///< Starting residue, points to atom_site.label_seq_id
+ CONF_TYPE_ID, ///< Pointer to struct_conf_type.id
+ END_LABEL_ASYM_ID, ///< Ending residue, points to atom_site.label_asym_id
+ END_LABEL_COMP_ID, ///< Ending residue, points to atom_site.label_comp_id
+ END_LABEL_SEQ_ID, ///< Ending residue, points to atom_site.label_seq_id
+ STRUCT_CONF_ID, ///< Unique identifier
+ } StructConfItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -407,6 +428,7 @@ private:
PDBX_STRUCT_ASSEMBLY_GEN,
PDBX_STRUCT_OPER_LIST,
STRUCT,
+ STRUCT_CONF,
DONT_KNOW
} MMCifCategory;
@@ -429,6 +451,15 @@ private:
typedef std::map<String, std::pair<std::vector<int>, std::vector<String> > >
MMCifCitationAuthorMap;
+ /// \struct store struct_conf info (secondary structure)
+ typedef struct {
+ mol::ResNum start;
+ mol::ResNum end;
+ String chain_name;
+ String type;
+ } MMCifHSEntry;
+ typedef std::vector<MMCifHSEntry> MMCifHSVector;
+
// members
MMCifCategory category_;
int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
@@ -457,6 +488,7 @@ private:
MMCifCitationAuthorMap authors_map_;
MMCifBioUAssemblyVector bu_assemblies_;
std::map<String, String> bu_origin_map_; ///< pdbx_struct_assembly.details
+ MMCifHSVector secstruct_list_; ///< for storing struct_conf sec.struct. data
};
}}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index bff617cca9871872389e3495c76fa82040857303..99876427785ea3d741f081394d0036a4256df38d 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -724,8 +724,6 @@ BOOST_AUTO_TEST_CASE(mmcif_biounit_tests)
tmmcif_h.Add(StringRef("matrix[3][2]", 12));
tmmcif_h.Add(StringRef("matrix[3][3]", 12));
-
-
tmmcif_p.OnBeginLoop(tmmcif_h);
columns.pop_back();
@@ -940,6 +938,8 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
BOOST_CHECK_EQUAL(rs->GetNumber().GetNum(), i);
}
+ // add checking of struct_conf info, here
+
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" reading data fields which should not fail...");
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index cf3b4c75192b01316625877d21852c2b7dc5e968..fdc059e508ab95ddb82f9c6d7290bf84cf6b0fbb 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -94,6 +94,27 @@ _struct.pdbx_formula_weight_method 'Good Guess'
_struct.pdbx_model_details 'Even better guessing'
_struct.pdbx_model_type_details 'Guess'
+loop_
+_struct_conf.id
+_struct_conf.conf_type_id
+_struct_conf.beg_label_comp_id
+_struct_conf.beg_label_asym_id
+_struct_conf.beg_label_seq_id
+_struct_conf.end_label_comp_id
+_struct_conf.end_label_asym_id
+_struct_conf.end_label_seq_id
+_struct_conf.details
+HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 .
+HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 .
+STRN1 STRN_P PRO A 1 LEU A 5 .
+STRN2 STRN_P CYS B 295 PHE B 299 .
+STRN3 STRN_P CYS A 95 PHE A 299 .
+STRN4 STRN_P PRO B 201 LEU B 205 .
+TURN1 TURN_TY1P_P ILE A 15 GLN A 18 .
+TURN2 TURN_TY2_P GLY A 49 GLY A 52 .
+TURN3 TURN_TY1P_P ILE A 55 HIS A 69 .
+TURN4 TURN_TY1_P THR A 91 GLY A 94 .
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol