diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 0c15c3767167c9245acd645b4b7ceff2d1991640..91c35928c21c39ee486e91e3b4d7818cafa2eb00 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1023,6 +1023,138 @@ void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
info_.SetStructDetails(details);
}
+MMCifParser::MMCifSecStructElement MMCifParser::DetermineSecStructType(
+ const StringRef& type) const
+{
+ if (type == StringRef("HELX_P", 6)) {
+ return MMCIF_HELIX;
+ } else if (type == StringRef("HELX_OT_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OT_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_AL_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_GA_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OM_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_PI_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_27_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_3T_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_PP_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_P", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OT_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_AL_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_GA_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OM_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_PI_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_27_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_3T_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_PP_P", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_N", 6)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_OT_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_OT_N", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_A_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_B_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_RH_Z_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_N", 9)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_OT_N", 12)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_A_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_B_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("HELX_LH_Z_N", 11)) {
+ return MMCIF_HELIX;
+ }
+ else if (type == StringRef("TURN_P", 6)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_OT_P", 9)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY1_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY1P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY2_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY2P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY3_P", 10)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("TURN_TY3P_P", 11)) {
+ return MMCIF_TURN;
+ }
+ else if (type == StringRef("STRN", 4)) {
+ return MMCIF_STRAND;
+ }
+
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Unknown secondary structure class found: "+
+ type.str(),
+ this->GetCurrentLinenum()));
+}
+
void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
{
StringRef chain_name;
@@ -1038,7 +1170,7 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
chain_name = columns[indices_[BEG_AUTH_ASYM_ID]];
} else { // unit test
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "foo",
+"Chain name by author requested but 'struct_conf.beg_auth_asym_id' is not set.",
this->GetCurrentLinenum()));
}
} else { // unit test
@@ -1048,7 +1180,14 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
to_res_num(e_res_num, ' '),
chain_name.str(),
columns[indices_[CONF_TYPE_ID]].str()};
- secstruct_list_.push_back(hse);
+
+ MMCifSecStructElement type =
+ DetermineSecStructType(columns[indices_[CONF_TYPE_ID]]);
+ if (type == MMCIF_HELIX) { // unit test helix and strand reading
+ secstruct_list_.push_back(hse);
+ } else if (type == MMCIF_STRAND) {
+ secstruct_list_.push_back(hse);
+ }
}
void MMCifParser::OnDataRow(const StarLoopDesc& header,
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 5bb2aeffd3bf7dab04a3ebd7ac8485bbb0bd04d0..2863d4537feb79f080bc9f52f95963d4f5e22e7c 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -275,7 +275,21 @@ protected:
/// \param columns data row
void ParseStructConf(const std::vector<StringRef>& columns);
+ /// \struct types of secondary structure
+ typedef enum {
+ MMCIF_HELIX,
+ MMCIF_STRAND,
+ MMCIF_TURN
+ } MMCifSecStructElement;
+
+ /// \brief Check whether an element was classified sheet or helix
+ ///
+ /// \param type Type to be classified
+ MMCifSecStructElement DetermineSecStructType(const StringRef& type) const;
+
/// \brief Transform data from struct_conf entry into secondary structure
+ ///
+ /// \param ent Entity to assign secondary structure to
void AssignSecStructure(mol::EntityHandle ent);
private:
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 99876427785ea3d741f081394d0036a4256df38d..997dd89ccbf2656abd210fedb56686906ded3327 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -66,6 +66,11 @@ public:
using MMCifParser::ClearState;
using MMCifParser::ConvertSEQRES;
using MMCifParser::GetInfo;
+ using MMCifParser::DetermineSecStructType;
+ using MMCifParser::MMCifSecStructElement;
+ using MMCifParser::MMCIF_HELIX;
+ using MMCifParser::MMCIF_TURN;
+ using MMCifParser::MMCIF_STRAND;
};
void SetAtomSiteHeader(StarLoopDesc* mmcif_h)
@@ -798,6 +803,144 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_tests)
BOOST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_struct_conf_tests)
+{
+ BOOST_MESSAGE(" Running mmcif_struct_conf_tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ BOOST_MESSAGE(" testing type validation");
+ StringRef type = StringRef("HELX_P", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_OT_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OT_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_AL_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_GA_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OM_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_PI_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_27_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_3T_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_PP_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OT_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_AL_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_GA_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OM_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_PI_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_27_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_3T_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_PP_P", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_N", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_OT_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_OT_N", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_A_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_B_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_RH_Z_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_N", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_OT_N", 12);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_A_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_B_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("HELX_LH_Z_N", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_HELIX);
+ type = StringRef("TURN_P", 6);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_OT_P", 9);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY1_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY1P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY2_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY2P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY3_P", 10);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("TURN_TY3P_P", 11);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_TURN);
+ type = StringRef("STRN", 4);
+ BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
+ TestMMCifParserProtected::MMCIF_STRAND);
+ type = StringRef("Foo", 3);
+ BOOST_CHECK_THROW(tmmcif_p.DetermineSecStructType(type), IOException);
+
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
{
BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index fdc059e508ab95ddb82f9c6d7290bf84cf6b0fbb..b8e2473936cc72486c5e06856bf2093456e6caba 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -106,10 +106,10 @@ _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 .
+STRN1 STRN PRO A 1 LEU A 5 .
+STRN2 STRN CYS B 295 PHE B 299 .
+STRN3 STRN CYS A 95 PHE A 299 .
+STRN4 STRN 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 .