diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index bddfecc1b72ac81cf466cd0cad885b2125899710..ca7b1410ae584a142231d31e406690e0a72a5f00 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -299,37 +299,37 @@ void export_mmcif_io()
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtrList >, true >())
;
class_<MMCifInfoStructRef, MMCifInfoStructRefPtr>("MMCifInfoStructRef", no_init)
- .add_property("id", make_function(&MMCifInfoStructRef::GetID,
- return_value_policy<copy_const_reference>()))
- .add_property("db_name", make_function(&MMCifInfoStructRef::GetDBName,
- return_value_policy<copy_const_reference>()))
- .add_property("db_id", make_function(&MMCifInfoStructRef::GetDBID,
- return_value_policy<copy_const_reference>()))
- .add_property("entity_id", make_function(&MMCifInfoStructRef::GetEntityID,
- return_value_policy<copy_const_reference>()))
- .add_property("db_access", make_function(&MMCifInfoStructRef::GetDBAccess,
- return_value_policy<copy_const_reference>()))
- .def("GetAlignedSeq", &MMCifInfoStructRef::GetAlignedSeq, arg("align_id"))
- .def("GetAlignedSeqs", &MMCifInfoStructRef::GetAlignedSeqs)
- .add_property("aligned_seqs", &MMCifInfoStructRef::GetAlignedSeqs)
+ .add_property("id", make_function(&MMCifInfoStructRef::GetID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_name", make_function(&MMCifInfoStructRef::GetDBName,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_id", make_function(&MMCifInfoStructRef::GetDBID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("entity_id", make_function(&MMCifInfoStructRef::GetEntityID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("db_access", make_function(&MMCifInfoStructRef::GetDBAccess,
+ return_value_policy<copy_const_reference>()))
+ .def("GetAlignedSeq", &MMCifInfoStructRef::GetAlignedSeq, arg("align_id"))
+ .def("GetAlignedSeqs", &MMCifInfoStructRef::GetAlignedSeqs)
+ .add_property("aligned_seqs", &MMCifInfoStructRef::GetAlignedSeqs)
;
class_<MMCifInfoStructRefSeq, MMCifInfoStructRefSeqPtr>("MMCifInfoStructRefSeq", no_init)
- .add_property("align_id", make_function(&MMCifInfoStructRefSeq::GetID,
- return_value_policy<copy_const_reference>()))
- .add_property("chain_name", make_function(&MMCifInfoStructRefSeq::GetChainName,
- return_value_policy<copy_const_reference>()))
- .add_property("seq_begin", &MMCifInfoStructRefSeq::GetSeqBegin)
- .add_property("seq_end", &MMCifInfoStructRefSeq::GetSeqEnd)
- .add_property("db_begin", &MMCifInfoStructRefSeq::GetDBBegin)
- .add_property("db_end", &MMCifInfoStructRefSeq::GetDBEnd)
- .add_property("difs", make_function(&MMCifInfoStructRefSeq::GetDifs,
- return_value_policy<copy_const_reference>()))
+ .add_property("align_id", make_function(&MMCifInfoStructRefSeq::GetID,
+ return_value_policy<copy_const_reference>()))
+ .add_property("chain_name", make_function(&MMCifInfoStructRefSeq::GetChainName,
+ return_value_policy<copy_const_reference>()))
+ .add_property("seq_begin", &MMCifInfoStructRefSeq::GetSeqBegin)
+ .add_property("seq_end", &MMCifInfoStructRefSeq::GetSeqEnd)
+ .add_property("db_begin", &MMCifInfoStructRefSeq::GetDBBegin)
+ .add_property("db_end", &MMCifInfoStructRefSeq::GetDBEnd)
+ .add_property("difs", make_function(&MMCifInfoStructRefSeq::GetDifs,
+ return_value_policy<copy_const_reference>()))
;
class_<MMCifInfoStructRefSeqDif,
- MMCifInfoStructRefSeqDifPtr>("MMCifInfoStructRefSeqDif", no_init)
- .add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
- return_value_policy<copy_const_reference>()))
- .add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
+ MMCifInfoStructRefSeqDifPtr>("MMCifInfoStructRefSeqDif", no_init)
+ .add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
+ return_value_policy<copy_const_reference>()))
+ .add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
.add_property("db_rnum", make_function(&MMCifInfoStructRefSeqDif::GetDBRNum,
return_value_policy<copy_const_reference>()))
;
@@ -379,13 +379,13 @@ void export_mmcif_io()
;
class_<MMCifInfoStructRefs>("MMCifInfoStructRefs", init<>())
- .def(vector_indexing_suite<MMCifInfoStructRefs, true>())
+ .def(vector_indexing_suite<MMCifInfoStructRefs, true>())
;
class_<MMCifInfoStructRefSeqs>("MMCifInfoStructRefSeqs", init<>())
- .def(vector_indexing_suite<MMCifInfoStructRefSeqs, true>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqs, true>())
;
class_<MMCifInfoStructRefSeqDifs>("MMCifInfoStructRefSeqDifs", init<>())
- .def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
;
class_<std::vector<MMCifInfoBioUnit> >("MMCifInfoBioUnitList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
@@ -561,7 +561,7 @@ void export_mmcif_io()
.add_property("struct_details", &MMCifInfo::GetStructDetails,
&MMCifInfo::SetStructDetails)
.add_property("struct_refs", make_function(&MMCifInfo::GetStructRefs,
- return_value_policy<copy_const_reference>()))
+ return_value_policy<copy_const_reference>()))
.add_property("obsolete", &MMCifInfo::GetObsoleteInfo,
&MMCifInfo::SetObsoleteInfo)
.add_property("revisions", &MMCifInfo::GetRevisions)
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index f2c0bf7545634744acde58f727d06b350e885335..77ae604029e8a0b71a00a3c0b48fec6972c5bf61 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -195,18 +195,18 @@ void MMCifInfoBioUnit::Merge(MMCifInfoBioUnit& from)
MMCifInfoStructRefSeqPtr
MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
- int seq_begin, int seq_end, int db_begin,
- int db_end)
+ int seq_begin, int seq_end, int db_begin,
+ int db_end)
{
- std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
- if (i!=seqs_.end()) {
- throw IOException("duplicate align_id for struct_ref '"+id_+"'");
- }
- MMCifInfoStructRefSeqPtr p(new MMCifInfoStructRefSeq(aid, chain_name,
- seq_begin, seq_end,
- db_begin, db_end));
- seqs_[aid]=p;
- return p;
+ std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
+ if (i!=seqs_.end()) {
+ throw IOException("duplicate align_id for struct_ref '"+id_+"'");
+ }
+ MMCifInfoStructRefSeqPtr p(new MMCifInfoStructRefSeq(aid, chain_name,
+ seq_begin, seq_end,
+ db_begin, db_end));
+ seqs_[aid]=p;
+ return p;
}
@@ -221,10 +221,10 @@ MMCifInfoStructRef::GetAlignedSeq(const String& aid) const
MMCifInfoStructRefSeqDifPtr
MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String& details)
{
- MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum,
- details));
- difs_.push_back(d);
- return d;
+ MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum,
+ details));
+ difs_.push_back(d);
+ return d;
}
void MMCifInfo::AddEntityBranchLink(String chain_name,
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 8cfb031cb9a7d3466cfd176ec66f576ad8c91b3f..73d3c25d2b69feafb098ed4f0d1dbd00add0657a 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -846,47 +846,47 @@ typedef std::vector<MMCifInfoStructRefSeqDifPtr> MMCifInfoStructRefSeqDifs;
class DLLEXPORT_OST_IO MMCifInfoStructRef {
public:
MMCifInfoStructRef(const String& id, const String& ent_id,
- const String& db_name,
- const String& db_ident, const String& db_access):
- id_(id), ent_id_(ent_id), db_name_(db_name), db_ident_(db_ident),
- db_access_(db_access)
- { }
+ const String& db_name,
+ const String& db_ident, const String& db_access):
+ id_(id), ent_id_(ent_id), db_name_(db_name), db_ident_(db_ident),
+ db_access_(db_access)
+ { }
const String& GetID() const { return id_; }
const String& GetDBName() const { return db_name_; }
const String& GetDBID() const { return db_ident_; }
const String& GetEntityID() const { return ent_id_; }
const String& GetDBAccess() const { return db_access_; }
- MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id,
- const String& chain_name, int seq_begin,
- int seq_end, int db_begin, int db_end);
+ MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id,
+ const String& chain_name, int seq_begin,
+ int seq_end, int db_begin, int db_end);
MMCifInfoStructRefSeqPtr GetAlignedSeq(const String& align_id) const;
MMCifInfoStructRefSeqs GetAlignedSeqs() const
- {
- MMCifInfoStructRefSeqs seqs;
- seqs.reserve(seqs_.size());
- for (std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator
- i=seqs_.begin(), e=seqs_.end(); i!=e; ++i) {
- seqs.push_back(i->second);
- }
- return seqs;
- }
+ {
+ MMCifInfoStructRefSeqs seqs;
+ seqs.reserve(seqs_.size());
+ for (std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator
+ i=seqs_.begin(), e=seqs_.end(); i!=e; ++i) {
+ seqs.push_back(i->second);
+ }
+ return seqs;
+ }
private:
- String id_;
- String ent_id_;
- String db_name_;
- String db_ident_;
- String db_access_;
- std::map<String, MMCifInfoStructRefSeqPtr> seqs_;
+ String id_;
+ String ent_id_;
+ String db_name_;
+ String db_ident_;
+ String db_access_;
+ std::map<String, MMCifInfoStructRefSeqPtr> seqs_;
};
class DLLEXPORT_OST_IO MMCifInfoStructRefSeq {
public:
- MMCifInfoStructRefSeq(const String& align_id, const String& chain_name,
- int seq_begin, int seq_end,
- int db_begin, int db_end):
- id_(align_id), chain_name_(chain_name),
- seq_begin_(seq_begin), seq_end_(seq_end), db_begin_(db_begin), db_end_(db_end)
- { }
+ MMCifInfoStructRefSeq(const String& align_id, const String& chain_name,
+ int seq_begin, int seq_end,
+ int db_begin, int db_end):
+ id_(align_id), chain_name_(chain_name),
+ seq_begin_(seq_begin), seq_end_(seq_end), db_begin_(db_begin), db_end_(db_end)
+ { }
const String& GetID() const { return id_; }
const String& GetChainName() const { return chain_name_; }
@@ -894,30 +894,30 @@ public:
int GetSeqEnd() const { return seq_end_; }
int GetDBBegin() const { return db_begin_; }
int GetDBEnd() const { return db_end_; }
- MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum,
+ MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum,
const String& details);
const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
private:
- String id_;
- String chain_name_;
- int seq_begin_;
- int seq_end_;
- int db_begin_;
- int db_end_;
- std::vector<MMCifInfoStructRefSeqDifPtr> difs_;
+ String id_;
+ String chain_name_;
+ int seq_begin_;
+ int seq_end_;
+ int db_begin_;
+ int db_end_;
+ std::vector<MMCifInfoStructRefSeqDifPtr> difs_;
};
class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
public:
- MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details):
- seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
- int GetSeqRNum() const { return seq_rnum_;}
- const String& GetDBRNum() const { return db_rnum_; }
- const String& GetDetails() const { return details_; }
+ MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details):
+ seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
+ int GetSeqRNum() const { return seq_rnum_;}
+ const String& GetDBRNum() const { return db_rnum_; }
+ const String& GetDetails() const { return details_; }
private:
- int seq_rnum_;
- String db_rnum_;
- String details_;
+ int seq_rnum_;
+ String db_rnum_;
+ String details_;
};
/// \brief Store information on branched structures (oligosaccharides)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 6f0293a2f0aa46e0e2a08380551012b770de9cd6..f4e2057b0b184fde25476d4ea0c840312fad7d09 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -33,7 +33,7 @@ namespace ost { namespace io {
bool is_undef(StringRef value)
{
- return value.size()==1 && (value[0]=='?' || value[0]=='.');
+ return value.size()==1 && (value[0]=='?' || value[0]=='.');
}
MMCifReader::MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
@@ -308,7 +308,7 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[SR_DB_ACCESS]=header.GetIndex("pdbx_db_accession");
cat_available = true;
} else if (header.GetCategory() == "struct_ref_seq") {
- category_ = STRUCT_REF_SEQ;
+ category_ = STRUCT_REF_SEQ;
this->TryStoreIdx(SRS_ALIGN_ID, "align_id", header);
this->TryStoreIdx(SRS_STRUCT_REF_ID, "ref_id", header);
this->TryStoreIdx(SRS_ENT_ALIGN_BEG, "seq_align_beg", header);
@@ -1632,17 +1632,17 @@ void MMCifReader::AssignSecStructure(mol::EntityHandle ent)
void MMCifReader::ParseStructRef(const std::vector<StringRef>& columns)
{
- String ent_id=columns[indices_[SR_ENTITY_ID]].str();
- String db_name=columns[indices_[SR_DB_NAME]].str();
- String db_code=columns[indices_[SR_DB_CODE]].str();
- String id=columns[indices_[SR_ID]].str();
- String db_access;
- if (indices_[SR_DB_ACCESS]!=-1) {
- db_access=columns[indices_[SR_DB_ACCESS]].str();
- }
- MMCifInfoStructRefPtr sr(new MMCifInfoStructRef(id, ent_id, db_name,
- db_code, db_access));
- struct_refs_.push_back(sr);
+ String ent_id=columns[indices_[SR_ENTITY_ID]].str();
+ String db_name=columns[indices_[SR_DB_NAME]].str();
+ String db_code=columns[indices_[SR_DB_CODE]].str();
+ String id=columns[indices_[SR_ID]].str();
+ String db_access;
+ if (indices_[SR_DB_ACCESS]!=-1) {
+ db_access=columns[indices_[SR_DB_ACCESS]].str();
+ }
+ MMCifInfoStructRefPtr sr(new MMCifInfoStructRef(id, ent_id, db_name,
+ db_code, db_access));
+ struct_refs_.push_back(sr);
}
void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
@@ -1651,43 +1651,43 @@ void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
String sr_id=columns[indices_[SRS_STRUCT_REF_ID]].str();
String chain_name;
if (indices_[SRS_PDBX_STRAND_ID]!=-1) {
- chain_name=columns[indices_[SRS_PDBX_STRAND_ID]].str();
+ chain_name=columns[indices_[SRS_PDBX_STRAND_ID]].str();
}
std::pair<bool,int> dbbeg=this->TryGetInt(columns[indices_[SRS_DB_ALIGN_BEG]],
- "_struct_ref_seq.db_align_beg",
- profile_.fault_tolerant);
+ "_struct_ref_seq.db_align_beg",
+ profile_.fault_tolerant);
std::pair<bool,int> dbend=this->TryGetInt(columns[indices_[SRS_DB_ALIGN_END]],
- "_struct_ref_seq.db_align_end",
- profile_.fault_tolerant);
+ "_struct_ref_seq.db_align_end",
+ profile_.fault_tolerant);
std::pair<bool,int> entbeg=this->TryGetInt(columns[indices_[SRS_ENT_ALIGN_BEG]],
- "_struct_ref_seq.seq_align_beg",
- profile_.fault_tolerant);
+ "_struct_ref_seq.seq_align_beg",
+ profile_.fault_tolerant);
std::pair<bool,int> entend=this->TryGetInt(columns[indices_[SRS_ENT_ALIGN_END]],
- "_struct_ref_seq.seq_align_END",
- profile_.fault_tolerant);
+ "_struct_ref_seq.seq_align_END",
+ profile_.fault_tolerant);
if (!(dbbeg.first && dbend.first && entbeg.first && entend.first)) {
- return;
+ return;
}
bool found=false;
for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(),
- e=struct_refs_.end(); i!=e; ++i) {
- if ((*i)->GetID()==sr_id) {
- (*i)->AddAlignedSeq(aln_id, chain_name, entbeg.second, entend.second,
- dbbeg.second, dbend.second);
- found=true;
- break;
- }
+ e=struct_refs_.end(); i!=e; ++i) {
+ if ((*i)->GetID()==sr_id) {
+ (*i)->AddAlignedSeq(aln_id, chain_name, entbeg.second, entend.second,
+ dbbeg.second, dbend.second);
+ found=true;
+ break;
+ }
}
if (!found) {
- if (profile_.fault_tolerant) {
- LOG_ERROR("struct_ref_seq.ref_id points to inexistent struct_ref '"
- << sr_id << "'");
- return;
- }
- std::stringstream ss;
- ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
- ss << sr_id << "'";
- throw IOException(ss.str());
+ if (profile_.fault_tolerant) {
+ LOG_ERROR("struct_ref_seq.ref_id points to inexistent struct_ref '"
+ << sr_id << "'");
+ return;
+ }
+ std::stringstream ss;
+ ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
+ ss << sr_id << "'";
+ throw IOException(ss.str());
}
}
@@ -1716,27 +1716,27 @@ void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
}
String details;
if (indices_[SRSD_DETAILS]!=-1) {
- details=columns[indices_[SRSD_DETAILS]].str();
+ details=columns[indices_[SRSD_DETAILS]].str();
}
bool found=false;
for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(),
- e=struct_refs_.end(); i!=e; ++i) {
- if (MMCifInfoStructRefSeqPtr s=(*i)->GetAlignedSeq(aln_id)) {
- s->AddDif(seq_rnum.second, db_rnum, details);
- found=true;
- break;
- }
+ e=struct_refs_.end(); i!=e; ++i) {
+ if (MMCifInfoStructRefSeqPtr s=(*i)->GetAlignedSeq(aln_id)) {
+ s->AddDif(seq_rnum.second, db_rnum, details);
+ found=true;
+ break;
+ }
}
if (!found) {
- if (profile_.fault_tolerant) {
- LOG_ERROR("struct_ref_seq_dif.align_id points to inexistent "
- "struct_ref_seq '" << aln_id << "'");
- return;
- }
- std::stringstream ss;
- ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
- ss << aln_id << "'";
- throw IOException(ss.str());
+ if (profile_.fault_tolerant) {
+ LOG_ERROR("struct_ref_seq_dif.align_id points to inexistent "
+ "struct_ref_seq '" << aln_id << "'");
+ return;
+ }
+ std::stringstream ss;
+ ss << "struct_ref_seq.ref_id points to inexistent struct_ref '";
+ ss << aln_id << "'";
+ throw IOException(ss.str());
}
}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index cc61e9ca3eac72cf3c30d984d13d697524568611..23cfc2f4bc50c66bc4312680e1fbddeb6d77e879 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -203,7 +203,7 @@ protected:
/// \param columns data row
void ParseCitation(const std::vector<StringRef>& columns);
- const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
+ const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
/// \brief Fetch mmCIF citation_author information
///
@@ -423,13 +423,13 @@ private:
// \enum items of the struct_ref category
typedef enum {
- SR_ENTITY_ID,
- SR_ID,
- SR_DB_CODE,
- SR_DB_NAME,
- SR_DB_ACCESS
- } StructRefItems;
-
+ SR_ENTITY_ID,
+ SR_ID,
+ SR_DB_CODE,
+ SR_DB_NAME,
+ SR_DB_ACCESS
+ } StructRefItems;
+
/// \enum items of the struct_ref_seq category
typedef enum {
SRS_ALIGN_ID,
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 4670b815a720cffb4bd61a0c38dd9313e5acc130..52d3a2c002fe7ba4dbcd3fda1b2dba9bbdf9a173 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1098,7 +1098,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
columns.push_back(StringRef("30.691", 6)); // Cartn_y
columns.push_back(StringRef("11.795", 6)); // Cartn_z
BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
- cif_chain_name, res_name,
+ cif_chain_name, res_name,
resnum, valid_res_num, atom_name,
alt_loc), true);
columns.pop_back();
@@ -1118,7 +1118,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
columns.push_back(StringRef("30.691", 6)); // Cartn_y
columns.push_back(StringRef("11.795", 6)); // Cartn_z
BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
- cif_chain_name, res_name,
+ cif_chain_name, res_name,
resnum, valid_res_num, atom_name,
alt_loc), false);
}