diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 9c4f0d5a5bd1d7ae612ed9ca086e8b474a6ec283..0d8f0e43e7bb450778e07bcee399a90e6a6aa0bd 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -17,7 +17,7 @@ Loading mmCIF Files
Categories Available
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The following categories of a mmCIF file are considered by the parser:
+The following categories of a mmCIF file are considered by the reader:
* ``atom_site``: Used to build the :class:`entity <ost.mol.EntityHandle>`
* ``entity``: Involved in setting ChainTypes
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 87e060687a8e590f87d5b198e90199f3cf1f7bf9..143fc2fe22545ec56667ba17602310b8626bce64 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -324,7 +324,7 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
try:
ent = mol.CreateEntity()
- reader = MMCifParser(filename, ent, prof)
+ reader = MMCifReader(filename, ent, prof)
reader.read_seqres = seqres
#if reader.HasNext():
reader.Parse()
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 9034c8c16fe7d8c785e5579665b9afcac1ed0a04..1262328bff906df84c2c588f69b12b097e09bbc3 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -30,21 +30,21 @@ using namespace ost::mol;
void export_mmcif_io()
{
- class_<MMCifParser, boost::noncopyable>("MMCifParser", init<const String&, EntityHandle&, const IOProfile&>())
- .def("Parse", &MMCifParser::Parse)
- .def("SetRestrictChains", &MMCifParser::SetRestrictChains)
- .def("SetReadCanonicalSeqRes", &MMCifParser::SetReadCanonicalSeqRes)
- .def("GetSeqRes", &MMCifParser::GetSeqRes)
- .def("GetInfo", make_function(&MMCifParser::GetInfo,
+ class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
+ .def("Parse", &MMCifReader::Parse)
+ .def("SetRestrictChains", &MMCifReader::SetRestrictChains)
+ .def("SetReadCanonicalSeqRes", &MMCifReader::SetReadCanonicalSeqRes)
+ .def("GetSeqRes", &MMCifReader::GetSeqRes)
+ .def("GetInfo", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
.add_property("restrict_chains",
- make_function(&MMCifParser::GetRestrictChains,
+ make_function(&MMCifReader::GetRestrictChains,
return_value_policy<copy_const_reference>()),
- &MMCifParser::SetRestrictChains)
- .add_property("seqres", &MMCifParser::GetSeqRes)
- .add_property("read_seqres", &MMCifParser::GetReadSeqRes,
- &MMCifParser::SetReadSeqRes)
- .add_property("info", make_function(&MMCifParser::GetInfo,
+ &MMCifReader::SetRestrictChains)
+ .add_property("seqres", &MMCifReader::GetSeqRes)
+ .add_property("read_seqres", &MMCifReader::GetReadSeqRes,
+ &MMCifReader::SetReadSeqRes)
+ .add_property("info", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
;
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.cc b/modules/io/src/mol/entity_io_mmcif_handler.cc
index 4d4d99777cb45970b113f9c337f428dfce7162ad..23e9ff3c52a1fd2652b1bbf7c1b7995eac487a11 100644
--- a/modules/io/src/mol/entity_io_mmcif_handler.cc
+++ b/modules/io/src/mol/entity_io_mmcif_handler.cc
@@ -52,7 +52,7 @@ void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
std::istream& stream)
{
- MMCifParser reader(stream,ent,
+ MMCifReader reader(stream,ent,
IOProfileRegistry::Instance().GetDefault());
reader.Parse();
}
@@ -66,7 +66,7 @@ void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
const boost::filesystem::path& loc)
{
std::string filename=loc.string();
- MMCifParser reader(filename, ent,
+ MMCifReader reader(filename, ent,
IOProfileRegistry::Instance().GetDefault());
reader.Parse();
}
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 68f971177e315727ce7edc79100d245cd2ed35f7..1e48f28d32585e3720cfec6ebb33faf3a94b34f2 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -30,21 +30,21 @@
namespace ost { namespace io {
-MMCifParser::MMCifParser(std::istream& stream, mol::EntityHandle& ent_handle,
+MMCifReader::MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
const IOProfile& profile):
StarParser(stream, true), profile_(profile), ent_handle_(ent_handle)
{
this->Init();
}
-MMCifParser::MMCifParser(const String& filename, mol::EntityHandle& ent_handle,
+MMCifReader::MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
const IOProfile& profile):
StarParser(filename, true), profile_(profile), ent_handle_(ent_handle)
{
this->Init();
}
-void MMCifParser::Init()
+void MMCifReader::Init()
{
warned_name_mismatch_ = false;
category_ = DONT_KNOW;
@@ -65,7 +65,7 @@ void MMCifParser::Init()
info_ = MMCifInfo();
}
-void MMCifParser::ClearState()
+void MMCifReader::ClearState()
{
curr_chain_ = mol::ChainHandle();
curr_residue_ = mol::ResidueHandle();
@@ -84,12 +84,12 @@ void MMCifParser::ClearState()
strand_list_.clear();
}
-void MMCifParser::SetRestrictChains(const String& restrict_chains)
+void MMCifReader::SetRestrictChains(const String& restrict_chains)
{
restrict_chains_ = restrict_chains;
}
-bool MMCifParser::IsValidPDBIdent(const StringRef& pdbid)
+bool MMCifReader::IsValidPDBIdent(const StringRef& pdbid)
{
if (pdbid.length() == PDBID_LEN && isdigit(pdbid[0])) {
return true;
@@ -97,7 +97,7 @@ bool MMCifParser::IsValidPDBIdent(const StringRef& pdbid)
return false;
}
-bool MMCifParser::OnBeginData(const StringRef& data_name)
+bool MMCifReader::OnBeginData(const StringRef& data_name)
{
LOG_DEBUG("MCIFFReader: " << profile_);
Profile profile_import("MMCifReader::OnBeginData");
@@ -115,7 +115,7 @@ bool MMCifParser::OnBeginData(const StringRef& data_name)
return true;
}
-bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
+bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
{
bool cat_available = false;
category_ = DONT_KNOW;
@@ -302,7 +302,7 @@ mol::ResNum to_res_num(int num, char ins_code)
return mol::ResNum(num, ins_code==' ' ? '\0' : ins_code);
}
-bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
+bool MMCifReader::ParseAtomIdent(const std::vector<StringRef>& columns,
String& chain_name,
StringRef& res_name,
mol::ResNum& resnum,
@@ -355,7 +355,7 @@ bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
return true;
}
-void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
+void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT); // potbl
char alt_loc=0;
@@ -560,7 +560,7 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
}
-void MMCifParser::ParseEntity(const std::vector<StringRef>& columns)
+void MMCifReader::ParseEntity(const std::vector<StringRef>& columns)
{
bool store = false; // is it worth storing this record?
MMCifEntityDesc desc;
@@ -587,7 +587,7 @@ void MMCifParser::ParseEntity(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::ParseEntityPoly(const std::vector<StringRef>& columns)
+void MMCifReader::ParseEntityPoly(const std::vector<StringRef>& columns)
{
// we assume that the entity cat. ALWAYS comes before the entity_poly cat.
// search entity
@@ -650,7 +650,7 @@ void MMCifParser::ParseEntityPoly(const std::vector<StringRef>& columns)
}
}
-String MMCifParser::ConvertSEQRES(const String& seqres,
+String MMCifReader::ConvertSEQRES(const String& seqres,
conop::CompoundLibPtr comp_lib)
{
String can_seqres;
@@ -695,7 +695,7 @@ String MMCifParser::ConvertSEQRES(const String& seqres,
return can_seqres;
}
-void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
+void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
{
// create citation object
MMCifInfoCitation cit = MMCifInfoCitation();
@@ -756,7 +756,7 @@ void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
info_.AddCitation(cit);
}
-void MMCifParser::ParseCitationAuthor(const std::vector<StringRef>& columns)
+void MMCifReader::ParseCitationAuthor(const std::vector<StringRef>& columns)
{
// get/ pack values
MMCifCitationAuthorMap::iterator atm_it;
@@ -806,12 +806,12 @@ void MMCifParser::ParseCitationAuthor(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::ParseExptl(const std::vector<StringRef>& columns)
+void MMCifReader::ParseExptl(const std::vector<StringRef>& columns)
{
info_.SetMethod(columns[indices_[METHOD]].str());
}
-void MMCifParser::ParseRefine(const std::vector<StringRef>& columns)
+void MMCifReader::ParseRefine(const std::vector<StringRef>& columns)
{
StringRef col=columns[indices_[LS_D_RES_HIGH]];
if (col.size()!=1 || (col[0]!='?' && col[0]!='.')) {
@@ -820,7 +820,7 @@ void MMCifParser::ParseRefine(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::ParsePdbxStructAssembly(const std::vector<StringRef>& columns)
+void MMCifReader::ParsePdbxStructAssembly(const std::vector<StringRef>& columns)
{
if (indices_[PSA_DETAILS] != -1) {
bu_origin_map_.insert(std::pair<String,
@@ -833,7 +833,7 @@ void MMCifParser::ParsePdbxStructAssembly(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::StoreExpression(const char* l, const char* s,
+void MMCifReader::StoreExpression(const char* l, const char* s,
bool& is_range, int lborder,
std::vector<String>& single_block)
{
@@ -855,7 +855,7 @@ void MMCifParser::StoreExpression(const char* l, const char* s,
}
}
-void MMCifParser::StoreRange(const char*& l, const char* s, bool& is_range,
+void MMCifReader::StoreRange(const char*& l, const char* s, bool& is_range,
int& lborder, std::vector<String>& single_block)
{
if (is_range) {
@@ -872,7 +872,7 @@ void MMCifParser::StoreRange(const char*& l, const char* s, bool& is_range,
l = s+1;
}
-std::vector<std::vector<String> > MMCifParser::UnPackOperExperession(StringRef expression)
+std::vector<std::vector<String> > MMCifReader::UnPackOperExperession(StringRef expression)
{
std::vector<std::vector<String> > unpacked;
std::vector<String> single_block;
@@ -929,7 +929,7 @@ std::vector<std::vector<String> > MMCifParser::UnPackOperExperession(StringRef e
return unpacked;
}
-void MMCifParser::ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns)
+void MMCifReader::ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns)
{
MMCifBioUAssembly assembly;
assembly.biounit = MMCifInfoBioUnit();
@@ -948,7 +948,7 @@ void MMCifParser::ParsePdbxStructAssemblyGen(const std::vector<StringRef>& colum
bu_assemblies_.push_back(assembly);
}
-void MMCifParser::ParsePdbxStructOperList(const std::vector<StringRef>& columns)
+void MMCifReader::ParsePdbxStructOperList(const std::vector<StringRef>& columns)
{
MMCifInfoTransOpPtr op(new MMCifInfoTransOp);
@@ -998,7 +998,7 @@ void MMCifParser::ParsePdbxStructOperList(const std::vector<StringRef>& columns)
info_.AddOperation(op);
}
-void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
+void MMCifReader::ParseStruct(const std::vector<StringRef>& columns)
{
MMCifInfoStructDetails details = MMCifInfoStructDetails();
@@ -1040,7 +1040,7 @@ void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
info_.SetStructDetails(details);
}
-MMCifParser::MMCifSecStructElement MMCifParser::DetermineSecStructType(
+MMCifReader::MMCifSecStructElement MMCifReader::DetermineSecStructType(
const StringRef& type) const
{
if (type == StringRef("HELX_P", 6)) {
@@ -1172,7 +1172,7 @@ MMCifParser::MMCifSecStructElement MMCifParser::DetermineSecStructType(
this->GetCurrentLinenum()));
}
-void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
+void MMCifReader::ParseStructConf(const std::vector<StringRef>& columns)
{
StringRef chain_name;
int s_res_num;
@@ -1212,7 +1212,7 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::ParseStructSheetRange(const std::vector<StringRef>& columns)
+void MMCifReader::ParseStructSheetRange(const std::vector<StringRef>& columns)
{
StringRef chain_name;
int s_res_num;
@@ -1247,7 +1247,7 @@ void MMCifParser::ParseStructSheetRange(const std::vector<StringRef>& columns)
}
}
-void MMCifParser::OnDataRow(const StarLoopDesc& header,
+void MMCifReader::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
switch(category_) {
@@ -1311,7 +1311,7 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
}
}
-void MMCifParser::AssignSecStructure(mol::EntityHandle ent)
+void MMCifReader::AssignSecStructure(mol::EntityHandle ent)
{
for (MMCifHSVector::const_iterator i=helix_list_.begin(), e=helix_list_.end();
i!=e; ++i) {
@@ -1354,7 +1354,7 @@ void MMCifParser::AssignSecStructure(mol::EntityHandle ent)
}
}
-void MMCifParser::OnEndData()
+void MMCifReader::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 3f6f974c26c6e6b68966597be5c1d1be7cc96de1..130da8ea93f23fbd1f801d021ad07f620e113fdf 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -16,8 +16,8 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#ifndef OST_MMCIF_PARSER_HH
-#define OST_MMCIF_PARSER_HH
+#ifndef OST_MMCIF_READER_HH
+#define OST_MMCIF_READER_HH
#include <map>
@@ -39,7 +39,7 @@ namespace ost { namespace io {
///
/// mmcif is an instance of the \link StarParser STAR format\endlink to store
/// entries of the PDB. The following data categories should be covered by this
-/// parser:
+/// reader:
///
/// \li atom_site
/// \li entity
@@ -54,21 +54,21 @@ namespace ost { namespace io {
/// \li struct
/// \li struct_conf
/// \li struct_sheet_range
-class DLLEXPORT_OST_IO MMCifParser : public StarParser {
+class DLLEXPORT_OST_IO MMCifReader : public StarParser {
public:
- /// \brief create a MMCifParser
+ /// \brief create a MMCifReader
///
/// \param stream input stream
- MMCifParser(std::istream& stream, mol::EntityHandle& ent_handle,
+ MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
const IOProfile& profile);
- /// \brief create a MMCifParser
+ /// \brief create a MMCifReader
///
/// \param filename input file
- MMCifParser(const String& filename, mol::EntityHandle& ent_handle,
+ MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
const IOProfile& profile);
- /// \brief Initialise the parser.
+ /// \brief Initialise the reader.
///
/// \param loc Location of the file
void Init();
@@ -76,7 +76,7 @@ public:
/// \brief Set up a fresh instance
void ClearState();
- /// \brief Set names of restricted chains for the parser.
+ /// \brief Set names of restricted chains for the reader.
///
/// \param restrict_chains chain name
void SetRestrictChains(const String& restrict_chains);
@@ -328,7 +328,7 @@ private:
AUTH_SEQ_ID, ///< residue no. by author
TYPE_SYMBOL, ///< chemical element
CARTN_X, ///< Coordinates ||IMPORTANT: This 3 entries have to stay
- CARTN_Y, ///< Coordinates ||together for the parser to work!
+ CARTN_Y, ///< Coordinates ||together for the reader to work!
CARTN_Z, ///< Coordinates ||
OCCUPANCY,
B_ISO_OR_EQUIV,
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 2c1fcfee333719a3a922059ad186c60b42066014..be7e35400e2ee43b8811cfb79a7731ef544aceec 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -31,50 +31,50 @@
using namespace ost;
using namespace ost::io;
-class TestMMCifParserProtected : MMCifParser {
+class TestMMCifReaderProtected : MMCifReader {
public:
- TestMMCifParserProtected(std::istream& stream, mol::EntityHandle& ent_handle):
- MMCifParser(stream, ent_handle, IOProfile())
+ TestMMCifReaderProtected(std::istream& stream, mol::EntityHandle& ent_handle):
+ MMCifReader(stream, ent_handle, IOProfile())
{ }
- TestMMCifParserProtected(std::istream& stream, mol::EntityHandle& ent_handle,
+ TestMMCifReaderProtected(std::istream& stream, mol::EntityHandle& ent_handle,
const IOProfile& profile):
- MMCifParser(stream, ent_handle, profile)
+ MMCifReader(stream, ent_handle, profile)
{ }
- TestMMCifParserProtected(const String& filename,
+ TestMMCifReaderProtected(const String& filename,
mol::EntityHandle& ent_handle):
- MMCifParser(filename, ent_handle, IOProfile())
+ MMCifReader(filename, ent_handle, IOProfile())
{ }
- using MMCifParser::OnBeginLoop;
- using MMCifParser::OnEndData;
- using MMCifParser::IsValidPDBIdent;
- using MMCifParser::ParseAtomIdent;
- using MMCifParser::ParseAndAddAtom;
- using MMCifParser::ParseEntity;
- using MMCifParser::ParseEntityPoly;
- using MMCifParser::ParseCitation;
- using MMCifParser::ParseRefine;
- using MMCifParser::ParsePdbxStructAssemblyGen;
- using MMCifParser::ParsePdbxStructAssembly;
- using MMCifParser::ParsePdbxStructOperList;
- using MMCifParser::ParseStruct;
- using MMCifParser::ParseStructConf;
- using MMCifParser::ParseStructSheetRange;
- using MMCifParser::TryStoreIdx;
- using MMCifParser::SetRestrictChains;
- using MMCifParser::SetReadSeqRes;
- using MMCifParser::SetReadCanonicalSeqRes;
- 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;
- using MMCifParser::SetAuthChainID;
+ using MMCifReader::OnBeginLoop;
+ using MMCifReader::OnEndData;
+ using MMCifReader::IsValidPDBIdent;
+ using MMCifReader::ParseAtomIdent;
+ using MMCifReader::ParseAndAddAtom;
+ using MMCifReader::ParseEntity;
+ using MMCifReader::ParseEntityPoly;
+ using MMCifReader::ParseCitation;
+ using MMCifReader::ParseRefine;
+ using MMCifReader::ParsePdbxStructAssemblyGen;
+ using MMCifReader::ParsePdbxStructAssembly;
+ using MMCifReader::ParsePdbxStructOperList;
+ using MMCifReader::ParseStruct;
+ using MMCifReader::ParseStructConf;
+ using MMCifReader::ParseStructSheetRange;
+ using MMCifReader::TryStoreIdx;
+ using MMCifReader::SetRestrictChains;
+ using MMCifReader::SetReadSeqRes;
+ using MMCifReader::SetReadCanonicalSeqRes;
+ using MMCifReader::ClearState;
+ using MMCifReader::ConvertSEQRES;
+ using MMCifReader::GetInfo;
+ using MMCifReader::DetermineSecStructType;
+ using MMCifReader::MMCifSecStructElement;
+ using MMCifReader::MMCIF_HELIX;
+ using MMCifReader::MMCIF_TURN;
+ using MMCifReader::MMCIF_STRAND;
+ using MMCifReader::SetAuthChainID;
};
void SetAtomSiteHeader(StarLoopDesc* mmcif_h)
@@ -104,7 +104,7 @@ BOOST_AUTO_TEST_CASE(mmcif_isvalidpdbident)
// on changing the tests for a PDB id in mmcif files, extend this unit test
BOOST_MESSAGE(" Running mmcif_isvalidpdbident tests...");
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh);
+ TestMMCifReaderProtected tmmcif_p(s, eh);
StringRef id = StringRef("1FOO", 4);
BOOST_MESSAGE(" Testing valid id ('"+ id.str() +"')...");
BOOST_CHECK(tmmcif_p.IsValidPDBIdent(id));
@@ -125,7 +125,7 @@ BOOST_AUTO_TEST_CASE(mmcif_trystoreidx)
BOOST_MESSAGE(" Running mmcif_trystoreidx tests...");
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh, IOProfile());
+ TestMMCifReaderProtected tmmcif_p(s, eh, IOProfile());
StarLoopDesc mmcif_h;
mmcif_h.SetCategory(StringRef("Foo", 3));
// negative
@@ -150,7 +150,7 @@ BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
conop::Conopology::Instance().SetDefaultBuilder("RBB");
mol::EntityHandle eh=mol::CreateEntity();
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
std::vector<StringRef> columns;
StarLoopDesc tmmcif_h;
BOOST_CHECK_EQUAL(tmmcif_p.ConvertSEQRES("A(MSE)Y", compound_lib), "AMY");
@@ -166,7 +166,7 @@ BOOST_AUTO_TEST_CASE(mmcif_onbeginloop)
// add more tests on new mandatory items
BOOST_MESSAGE(" Running mmcif_onbeginloop tests...");
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- MMCifParser mmcif_p(s, eh, IOProfile());
+ MMCifReader mmcif_p(s, eh, IOProfile());
StarLoopDesc mmcif_h;
BOOST_MESSAGE(" testing atom_site items...");
mmcif_h.SetCategory(StringRef("atom_site", 9));
@@ -228,7 +228,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
BOOST_MESSAGE(" true positive test for models...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/model_truepos.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/model_truepos.mmcif", eh, profile);
BOOST_CHECK_NO_THROW(mmcif_p.Parse());
BOOST_REQUIRE_EQUAL(eh.GetChainCount(), 2);
BOOST_REQUIRE_EQUAL(eh.GetResidueCount(), 2);
@@ -240,7 +240,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
BOOST_MESSAGE(" test absent atom_site.pdbx_PDB_model_num entry...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
BOOST_CHECK_NO_THROW(mmcif_p.Parse());
}
BOOST_MESSAGE(" done.");
@@ -248,13 +248,13 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
BOOST_MESSAGE(" testing more than one atom_site block...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/model_multi_atom_site.mmcif", eh,
+ MMCifReader mmcif_p("testfiles/mmcif/model_multi_atom_site.mmcif", eh,
profile);
BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
}
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/model_multi_atom_site_inverted.mmcif",
+ MMCifReader mmcif_p("testfiles/mmcif/model_multi_atom_site_inverted.mmcif",
eh, profile);
BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
}
@@ -265,7 +265,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
// build dummy header
mol::EntityHandle eh = mol::CreateEntity();
StarLoopDesc tmmcif_h;
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
SetAtomSiteHeader(&tmmcif_h);
tmmcif_p.OnBeginLoop(tmmcif_h);
tmmcif_h.Add(StringRef("pdbx_PDB_model_num", 18));
@@ -285,7 +285,7 @@ BOOST_AUTO_TEST_CASE(mmcif_changing_label_entity_id)
BOOST_MESSAGE(" true positive test...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
BOOST_CHECK_NO_THROW(mmcif_p.Parse());
}
BOOST_MESSAGE(" done.");
@@ -294,7 +294,7 @@ BOOST_AUTO_TEST_CASE(mmcif_changing_label_entity_id)
BOOST_MESSAGE(" true negative test...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/changing_label_entity_id.mmcif", eh,
+ MMCifReader mmcif_p("testfiles/mmcif/changing_label_entity_id.mmcif", eh,
profile);
BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
}
@@ -309,7 +309,7 @@ BOOST_AUTO_TEST_CASE(mmcif_unknown_entity_type)
mol::EntityHandle eh = mol::CreateEntity();
std::vector<StringRef> columns;
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
StarLoopDesc tmmcif_h;
// build dummy header
@@ -352,7 +352,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
BOOST_MESSAGE(" fetching chain type...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
@@ -369,7 +369,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
BOOST_MESSAGE(" check missing entity description...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/model_truepos.mmcif",
+ MMCifReader mmcif_p("testfiles/mmcif/model_truepos.mmcif",
eh,
profile);
mmcif_p.Parse();
@@ -384,7 +384,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
BOOST_MESSAGE(" fetch details...");
{
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
@@ -404,7 +404,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
StarLoopDesc tmmcif_h;
mol::EntityHandle eh = mol::CreateEntity();
- MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
mmcif_p.SetReadSeqRes(true);
mmcif_p.Parse();
@@ -417,7 +417,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
{
mol::EntityHandle eh = mol::CreateEntity();
std::vector<StringRef> columns;
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
tmmcif_h.SetCategory(StringRef("entity_poly", 11));
tmmcif_h.Add(StringRef("entity_id", 9));
@@ -429,7 +429,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" testing type recognition...");
{
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
std::vector<StringRef> columns;
// create corresponding entity entry
@@ -485,7 +485,7 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" testing pdbx_seq_one_letter_code reading...");
{
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
std::vector<StringRef> columns;
tmmcif_h.Clear();
@@ -519,7 +519,7 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" testing pdbx_seq_one_letter_code_can reading...");
{
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
std::vector<StringRef> columns;
tmmcif_h.Clear();
@@ -560,7 +560,7 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
BOOST_MESSAGE(" Running mmcif_citation_tests...");
//build dummy citation
mol::EntityHandle eh;
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
StarLoopDesc tmmcif_h;
std::vector<StringRef> columns;
@@ -600,7 +600,7 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_author_tests)
mol::EntityHandle eh = mol::CreateEntity();
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
- MMCifParser mmcif_p(s, eh, profile);
+ MMCifReader mmcif_p(s, eh, profile);
BOOST_CHECK_NO_THROW(mmcif_p.Parse());
std::vector<String> authors =
@@ -622,7 +622,7 @@ BOOST_AUTO_TEST_CASE(mmcif_refine_tests)
mol::EntityHandle eh = mol::CreateEntity();
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
- MMCifParser mmcif_p(s, eh, profile);
+ MMCifReader mmcif_p(s, eh, profile);
BOOST_CHECK_NO_THROW(mmcif_p.Parse());
BOOST_CHECK_CLOSE(mmcif_p.GetInfo().GetResolution(), 2.0f, 0.001f);
}
@@ -630,7 +630,7 @@ BOOST_AUTO_TEST_CASE(mmcif_refine_tests)
BOOST_MESSAGE(" capturing fishy data lines...");
{
mol::EntityHandle eh;
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
StarLoopDesc tmmcif_h;
std::vector<StringRef> columns;
@@ -655,7 +655,7 @@ BOOST_AUTO_TEST_CASE(mmcif_biounit_tests)
BOOST_MESSAGE(" Running mmcif_biounit_tests...");
//build dummy biounit
mol::EntityHandle eh = mol::CreateEntity();
- TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
StarLoopDesc tmmcif_h;
std::vector<StringRef> columns;
@@ -774,7 +774,7 @@ 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);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
StarLoopDesc tmmcif_h;
std::vector<StringRef> columns;
@@ -811,132 +811,132 @@ 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);
+ TestMMCifReaderProtected 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);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_OT_P", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_P", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_OT_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_AL_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_GA_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_OM_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_PI_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_27_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_3T_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_PP_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_P", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_OT_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_AL_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_GA_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_OM_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_PI_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_27_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_3T_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_PP_P", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_N", 6);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_OT_N", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_N", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_OT_N", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_A_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_B_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_RH_Z_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_N", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_OT_N", 12);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_A_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_B_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("HELX_LH_Z_N", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_HELIX);
+ TestMMCifReaderProtected::MMCIF_HELIX);
type = StringRef("TURN_P", 6);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_OT_P", 9);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY1_P", 10);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY1P_P", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY2_P", 10);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY2P_P", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY3_P", 10);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("TURN_TY3P_P", 11);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_TURN);
+ TestMMCifReaderProtected::MMCIF_TURN);
type = StringRef("STRN", 4);
BOOST_CHECK(tmmcif_p.DetermineSecStructType(type) ==
- TestMMCifParserProtected::MMCIF_STRAND);
+ TestMMCifReaderProtected::MMCIF_STRAND);
type = StringRef("Foo", 3);
BOOST_CHECK_THROW(tmmcif_p.DetermineSecStructType(type), IOException);
@@ -995,7 +995,7 @@ 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);
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
BOOST_MESSAGE(" testing auth_chain_id switch...");
StarLoopDesc tmmcif_h;
@@ -1055,7 +1055,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
StarLoopDesc tmmcif_h;
- TestMMCifParserProtected tmmcif_p(s, eh, profile);
+ TestMMCifReaderProtected tmmcif_p(s, eh, profile);
std::vector<StringRef> columns;
String chain_name;
StringRef res_name;
@@ -1148,7 +1148,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseandaddatom)
BOOST_MESSAGE(" Running mmcif_parseandaddatom tests...");
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh, IOProfile());
+ TestMMCifReaderProtected tmmcif_p(s, eh, IOProfile());
std::vector<StringRef> cols;
//BOOST_MESSAGE(" testing short atom_site entry");
@@ -1163,7 +1163,7 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
mol::EntityHandle eh = mol::CreateEntity();
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
- MMCifParser mmcif_p(s, eh, profile);
+ MMCifReader mmcif_p(s, eh, profile);
mmcif_p.SetRestrictChains("A O C");