diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index b0467c62a2ce3a4a5c74d50e9bb84a148eab892e..9c4f0d5a5bd1d7ae612ed9ca086e8b474a6ec283 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -34,7 +34,8 @@ The following categories of a mmCIF file are considered by the parser:
:class:`MMCifInfoStructDetails`.
* ``struct_conf``: Stores secondary structure information (practically helices)
in the :class:`entity <ost.mol.EntityHandle>`
-* ``struct_sheet_range``
+* ``struct_sheet_range``: Stores secondary structure information for sheets in
+ the :class:`entity <ost.mol.EntityHandle>`
Info Classes
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index e1222db86c50d02de5fe78b78ce70c36deee6249..68f971177e315727ce7edc79100d245cd2ed35f7 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -277,6 +277,21 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
indices_[SC_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
indices_[SC_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
cat_available = true;
+ } else if (header.GetCategory() == "struct_sheet_range") {
+ category_ = STRUCT_SHEET_RANGE;
+ // mandatory items
+ this->TryStoreIdx(SSR_BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+ this->TryStoreIdx(SSR_BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+ this->TryStoreIdx(SSR_BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_ASYM_ID, "end_label_asym_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_COMP_ID, "end_label_comp_id", header);
+ this->TryStoreIdx(SSR_END_LABEL_SEQ_ID, "end_label_seq_id", header);
+ this->TryStoreIdx(SSR_SHEET_ID, "sheet_id", header);
+ this->TryStoreIdx(SSR_ID, "id", header);
+ // optional items
+ indices_[SSR_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+ indices_[SSR_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -1162,11 +1177,8 @@ 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_[SC_BEG_LABEL_SEQ_ID]],
- "struct_conf.beg_label_seq_id");
- e_res_num = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]],
- "struct_conf.end_label_seq_id");
+
+ // fetch chain name, first
if(auth_chain_id_) {
if (indices_[SC_BEG_AUTH_ASYM_ID] != -1) {
chain_name = columns[indices_[SC_BEG_AUTH_ASYM_ID]];
@@ -1181,6 +1193,11 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
if (restrict_chains_.size() == 0 ||
restrict_chains_.find(chain_name.str()) != String::npos) {
+ // fetch start and end
+ s_res_num = this->TryGetInt(columns[indices_[SC_BEG_LABEL_SEQ_ID]],
+ "struct_conf.beg_label_seq_id");
+ e_res_num = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]],
+ "struct_conf.end_label_seq_id");
MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
to_res_num(e_res_num, ' '),
chain_name.str()};
@@ -1195,6 +1212,41 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
}
}
+void MMCifParser::ParseStructSheetRange(const std::vector<StringRef>& columns)
+{
+ StringRef chain_name;
+ int s_res_num;
+ int e_res_num;
+
+ if(auth_chain_id_) {
+ if (indices_[SSR_BEG_AUTH_ASYM_ID] != -1) {
+ chain_name = columns[indices_[SSR_BEG_AUTH_ASYM_ID]];
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+"Chain name by author requested but 'struct_sheet_range.beg_auth_asym_id' is not set.",
+ this->GetCurrentLinenum()));
+ }
+ } else {
+ chain_name = columns[indices_[SSR_BEG_LABEL_ASYM_ID]];
+ }
+
+ // restrict_chains feature not unit tested, since its about to be changed in
+ // the future
+ if (restrict_chains_.size() == 0 ||
+ restrict_chains_.find(chain_name.str()) != String::npos) {
+
+ s_res_num = this->TryGetInt(columns[indices_[SSR_BEG_LABEL_SEQ_ID]],
+ "struct_sheet_range.beg_label_seq_id");
+ e_res_num = this->TryGetInt(columns[indices_[SSR_END_LABEL_SEQ_ID]],
+ "struct_sheet_range.end_label_seq_id");
+
+ MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
+ to_res_num(e_res_num, ' '),
+ chain_name.str()};
+ strand_list_.push_back(hse);
+ }
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -1247,6 +1299,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing struct_conf entry")
this->ParseStructConf(columns);
break;
+ case STRUCT_SHEET_RANGE:
+ LOG_TRACE("processing struct_sheet_range entry")
+ this->ParseStructSheetRange(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 6005831d807f4f73c46408e9471c4275788b7fde..3f6f974c26c6e6b68966597be5c1d1be7cc96de1 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -286,6 +286,11 @@ protected:
/// \param columns data row
void ParseStructConf(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif struct_sheet_range (beta sheets) information
+ ///
+ /// \param columns data row
+ void ParseStructSheetRange(const std::vector<StringRef>& columns);
+
/// \struct types of secondary structure
typedef enum {
MMCIF_HELIX,
@@ -441,6 +446,20 @@ private:
SC_ID, ///< Unique identifier
} StructConfItems;
+ /// \enum items of the struct_sheet_range category
+ typedef enum {
+ SSR_BEG_LABEL_ASYM_ID, ///< start, chain name (atom_site.label_asym_id)
+ SSR_BEG_LABEL_COMP_ID, ///< start, atom_site.label_comp_id
+ SSR_BEG_LABEL_SEQ_ID, ///< start, residue number (atom_site.label_seq_id)
+ SSR_END_LABEL_ASYM_ID, ///< end, chain name (atom_site.label_asym_id)
+ SSR_END_LABEL_COMP_ID, ///< end, atom_site.label_comp_id
+ SSR_END_LABEL_SEQ_ID, ///< end, residue number (atom_site.label_seq_id)
+ SSR_SHEET_ID, ///< unique identifier
+ SSR_ID, ///< link to struct_sheet.id
+ SSR_BEG_AUTH_ASYM_ID, ///< alternative start, (atom_site.auth_asym_id)
+ SSR_END_AUTH_ASYM_ID, ///< alternative end, (atom_site.auth_asym_id)
+ } StructSheetRangeItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 621a5856d436ea3188ac386818d761b145745fce..2c1fcfee333719a3a922059ad186c60b42066014 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -61,6 +61,7 @@ public:
using MMCifParser::ParsePdbxStructOperList;
using MMCifParser::ParseStruct;
using MMCifParser::ParseStructConf;
+ using MMCifParser::ParseStructSheetRange;
using MMCifParser::TryStoreIdx;
using MMCifParser::SetRestrictChains;
using MMCifParser::SetReadSeqRes;
@@ -940,40 +941,95 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_conf_tests)
BOOST_CHECK_THROW(tmmcif_p.DetermineSecStructType(type), IOException);
BOOST_MESSAGE(" done.");
+
BOOST_MESSAGE(" testing auth_chain_id switch...");
+ StarLoopDesc tmmcif_h;
+ {
+ std::vector<StringRef> columns;
+ tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("conf_type_id", 12));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("beg_auth_asym_id", 16));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("HELX_RH_AL_P", 12));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("ARG", 3));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("DHLX1", 5));
+ columns.push_back(StringRef("A", 1));
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("conf_type_id", 12));
+ tmmcif_h.Add(StringRef("end_label_asym_id", 17));
+ tmmcif_h.Add(StringRef("end_label_comp_id", 17));
+ tmmcif_h.Add(StringRef("end_label_seq_id", 16));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.pop_back();
+ tmmcif_p.SetAuthChainID(true);
+ BOOST_CHECK_THROW(tmmcif_p.ParseStructConf(columns), IOException);
+ }
+ tmmcif_p.SetAuthChainID(false);
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+BOOST_AUTO_TEST_CASE(mmcif_struct_sheet_range_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_sheet_range_tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ BOOST_MESSAGE(" testing auth_chain_id switch...");
StarLoopDesc tmmcif_h;
std::vector<StringRef> columns;
- tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.SetCategory(StringRef("struct_sheet_range", 18));
+ tmmcif_h.Add(StringRef("sheet_id", 8));
tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
- tmmcif_h.Add(StringRef("conf_type_id", 12));
tmmcif_h.Add(StringRef("end_label_asym_id", 17));
tmmcif_h.Add(StringRef("end_label_comp_id", 17));
tmmcif_h.Add(StringRef("end_label_seq_id", 16));
tmmcif_h.Add(StringRef("id", 2));
tmmcif_h.Add(StringRef("beg_auth_asym_id", 16));
tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("Sheet1", 6));
columns.push_back(StringRef("A", 1));
columns.push_back(StringRef("ARG", 3));
columns.push_back(StringRef("1", 1));
- columns.push_back(StringRef("HELX_RH_AL_P", 12));
columns.push_back(StringRef("A", 1));
columns.push_back(StringRef("ARG", 3));
columns.push_back(StringRef("2", 1));
- columns.push_back(StringRef("DHLX1", 5));
+ columns.push_back(StringRef("DSTRAND", 7));
columns.push_back(StringRef("A", 1));
tmmcif_p.SetAuthChainID(true);
- BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructSheetRange(columns));
tmmcif_p.SetAuthChainID(false);
- BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructConf(columns));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseStructSheetRange(columns));
tmmcif_h.Clear();
- tmmcif_h.SetCategory(StringRef("struct_conf", 11));
+ tmmcif_h.SetCategory(StringRef("struct_sheet_range", 11));
+ tmmcif_h.Add(StringRef("sheet_id", 8));
tmmcif_h.Add(StringRef("beg_label_asym_id", 17));
tmmcif_h.Add(StringRef("beg_label_comp_id", 17));
tmmcif_h.Add(StringRef("beg_label_seq_id", 16));
- tmmcif_h.Add(StringRef("conf_type_id", 12));
tmmcif_h.Add(StringRef("end_label_asym_id", 17));
tmmcif_h.Add(StringRef("end_label_comp_id", 17));
tmmcif_h.Add(StringRef("end_label_seq_id", 16));
@@ -981,11 +1037,12 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_conf_tests)
tmmcif_p.OnBeginLoop(tmmcif_h);
columns.pop_back();
tmmcif_p.SetAuthChainID(true);
- BOOST_CHECK_THROW(tmmcif_p.ParseStructConf(columns), IOException);
+ BOOST_CHECK_THROW(tmmcif_p.ParseStructSheetRange(columns), IOException);
tmmcif_p.SetAuthChainID(false);
-
BOOST_MESSAGE(" done.");
+
+
BOOST_MESSAGE(" done.");
}
@@ -1139,6 +1196,9 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
BOOST_CHECK_EQUAL(rl[0].GetSecStructure().IsHelical(), true);
BOOST_CHECK_EQUAL(rl[1].GetSecStructure().IsHelical(), true);
BOOST_CHECK_EQUAL(rl[2].GetSecStructure().IsExtended(), true);
+ ch = eh.FindChain("C");
+ rl = ch.GetResidueList();
+ BOOST_CHECK_EQUAL(rl[0].GetSecStructure().IsExtended(), true);
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 3268d114eea08cf4bb0072cf9bcecea410391222..1cd5d1c357fe5a84db67d7fbafdae1231a3ae937 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -109,6 +109,17 @@ HELX1 HELX_RH_AL_P VAL A 11 THR A 12 .
STRN1 STRN ILE A 13 ILE A 13 .
HELX1 HELX_RH_AL_P ILE Z 1 ILE Z 1 .
+loop_
+_struct_sheet_range.sheet_id
+_struct_sheet_range.id
+_struct_sheet_range.beg_label_comp_id
+_struct_sheet_range.beg_label_asym_id
+_struct_sheet_range.beg_label_seq_id
+_struct_sheet_range.end_label_comp_id
+_struct_sheet_range.end_label_asym_id
+_struct_sheet_range.end_label_seq_id
+sheet_1 strand_a APS C 1 APS C 1
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol
@@ -152,10 +163,10 @@ ATOM C CB ILE A 13 . 1 21.236 34.463 16.492 1.00 22.67 . 13 21 ? A
ATOM C CG1 ILE A 13 . 1 20.478 33.469 17.371 1.00 22.14 . 13 22 ? A
ATOM C CG2 ILE A 13 . 1 21.357 33.986 15.016 1.00 21.75 . 13 23 ? A
# - - - - data truncated for brevity - - - -
-HETATM C C1 APS C 14 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? A
-HETATM C C2 APS C 14 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? A
-HETATM O O3 APS C 14 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? A
-HETATM N N4 APS C 14 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? A
+HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? A
+HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? A
+HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? A
+HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? A
# - - - - data truncated for brevity - - - -
# chain to be ignored by 'restrict_chains' feature
ATOM N N ILE Z 1 . 1 23.664 33.855 16.884 1.00 22.08 . 1 17 ? Z