From b7f87fa4c44db5a8e19a435492313a912365f584 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 8 May 2012 14:32:56 +0200
Subject: [PATCH] added support for struct_ref, and friends
The mmCIF reader now also parses struct_ref_seq and
struct_ref_seq_dif. Includes unit tests and docs
---
modules/io/doc/mmcif.rst | 99 ++++++++++++-
modules/io/pymod/export_mmcif_io.cc | 43 +++++-
modules/io/src/mol/mmcif_info.cc | 36 +++++
modules/io/src/mol/mmcif_info.hh | 92 +++++++++++-
modules/io/src/mol/mmcif_reader.cc | 136 +++++++++++++++++-
modules/io/src/mol/mmcif_reader.hh | 41 +++++-
modules/io/tests/test_mmcif_reader.cc | 34 +++++
.../io/tests/testfiles/mmcif/struct_ref.cif | 47 ++++++
8 files changed, 522 insertions(+), 6 deletions(-)
create mode 100644 modules/io/tests/testfiles/mmcif/struct_ref.cif
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 078a66667..7e1c330a4 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -38,6 +38,9 @@ The following categories of a mmCIF file are considered by the reader:
the :class:`entity <ost.mol.EntityHandle>`
* ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded
entries, stored in :class:`MMCifInfoObsolete`.
+* ``struct_ref`` stored in :class:`MMCifInfoStructRef`
+* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeq`
+* ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefDif`
Info Classes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -93,6 +96,9 @@ of the annotation available.
Also available as :meth:`GetStructDetails`. May also be modified by
:meth:`SetStructDetails`.
+ .. attribute:: struct_refs
+
+ Lists all links to external databases in the mmCIF file.
.. method:: AddCitation(citation)
Add a citation to the citation list of an info object.
@@ -452,7 +458,7 @@ of the annotation available.
See :attr:`operations`
- .. method:: PDBize(asu, seqres=None, min_polymer_size=10)
+.. function:: PDBize(asu, seqres=None, min_polymer_size=10)
Returns the biological assembly (bio unit) for an entity. The new entity
created is well suited to be saved as a PDB file. Therefore the function
@@ -676,6 +682,95 @@ of the annotation available.
See :attr:`replace_pdb_id`
-.. LocalWords: autofunction ChainTypes exptl attr pdbx oper conf spr biounits
+.. class:: MMCifINfoStructRef
+
+ Holds the information of the struct_ref category. The category describes the
+ link of polymers in the mmCIF file to sequences stored in external databases
+ such as uniprot. The related categories ``struct_ref_seq`` and
+ ``struct_ref_seq_dif`` also list differences between the sequences of the
+ deposited structure and the sequences in the database. A promintent example of
+ such differences include point mutations and/or expression tags.
+
+ .. attribute:: db_name
+
+
+ Name of the external database, for example UNP for uniprot.
+
+ :type: :class:`str`
+
+
+ .. attribute:: db_id
+
+ Name of the reference sequence in the database pointed to by :attr:`db_name`.
+
+ :type: :class:`str`
+
+ .. attribute:: db_access
+
+ Alternative accession code for the sequence in the database pointed to by
+ :attr:`db_name`.
+
+ :type: :class:`str`
+
+ .. method:: GetAlignedSeq(name)
+
+ Returns the aligned sequence for the given name, None if the sequence does
+ not exist.
+
+ .. attribute:: aligned_seqs
+
+ List of aligned sequences (all entries of the struct_ref_seq category
+ mapping to this struct_ref).
+
+.. class:: MMCifInfoStructRefSeq
+
+ An aligned range of residues between a sequence in a reference database and the
+ deposited sequence.
+
+ .. attribute:: align_id
+
+ Uniquely identifies every struct_ref_seq item in the mmCIF file.
+ :type: :class:`str`
+
+ .. attribute:: seq_begin
+ seq_end
+ The starting point (1-based) and end point of the aligned range in the
+ deposited sequence, respectively.
+
+ :type: :class:`int`
+
+ .. attribute:: db_begin
+ db_end
+ The starting point (1-based) and end point of the aligned range in the
+ database sequence, respectively.
+
+ :type: :class:`int`
+
+ .. attribute:: difs
+
+ List of differences between the deposited sequence and the sequence in the
+ database.
+
+ .. attribute:: chain_name
+
+ Chain name of the polymer in the mmCIF file.
+
+.. class:: MMCifInfoStructRefSeqDif
+
+ A particular difference between the deposited sequence and the sequence in
+ the database.
+
+ .. attribute:: rnum
+
+ The residue number (1-based) of the residue in the deposited sequence
+
+ :type: :class:`int`
+
+ .. attribute:: details
+
+ A textual description of the difference, e.g. point mutation,
+ expressiontag, purification artifact.
+
+ :type: :class:`str`
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index b502aa515..908886257 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -138,7 +138,37 @@ void export_mmcif_io()
init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtrList >, true >())
;
-
+ class_<MMCifInfoStructRef, MMCifInfoStructRefPtr>("MMCifInfoStructRef", no_init)
+ .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>()))
+ ;
+ class_<MMCifInfoStructRefSeqDif,
+ MMCifInfoStructRefSeqDifPtr>("MMCifInfoStructRefSeqDif", no_init)
+ .add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails,
+ return_value_policy<copy_const_reference>()))
+ .add_property("rnum", &MMCifInfoStructRefSeqDif::GetRNum)
+ ;
class_<MMCifInfoBioUnit>("MMCifInfoBioUnit", init<>())
.def("SetDetails", &MMCifInfoBioUnit::SetDetails)
.def("GetDetails", &MMCifInfoBioUnit::GetDetails)
@@ -156,6 +186,15 @@ void export_mmcif_io()
return_value_policy<copy_const_reference>()))
;
+ class_<MMCifInfoStructRefs>("MMCifInfoStructRefs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefs, true>())
+ ;
+ class_<MMCifInfoStructRefSeqs>("MMCifInfoStructRefSeqs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqs, true>())
+ ;
+ class_<MMCifInfoStructRefSeqDifs>("MMCifInfoStructRefSeqDifs", init<>())
+ .def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
+ ;
typedef std::vector<MMCifInfoBioUnit> MMCifInfoBioUnitList;
class_<std::vector<MMCifInfoBioUnit> >("MMCifInfoBioUnitList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
@@ -246,6 +285,8 @@ void export_mmcif_io()
return_value_policy<copy_const_reference>()))
.add_property("struct_details", &MMCifInfo::GetStructDetails,
&MMCifInfo::SetStructDetails)
+ .add_property("struct_refs", make_function(&MMCifInfo::GetStructRefs,
+ return_value_policy<copy_const_reference>()))
.add_property("obsolete", &MMCifInfo::GetObsoleteInfo,
&MMCifInfo::SetObsoleteInfo)
;
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 1e4c89281..d99b0bd22 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -36,4 +36,40 @@ void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
throw IOException("No citation for identifier '" + id.str() + "' found.");
}
+
+
+MMCifInfoStructRefSeqPtr
+MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
+ 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;
+}
+
+
+MMCifInfoStructRefSeqPtr
+MMCifInfoStructRef::GetAlignedSeq(const String& aid) const
+{
+
+ std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
+ return i==seqs_.end() ? MMCifInfoStructRefSeqPtr() : i->second;
+}
+
+MMCifInfoStructRefSeqDifPtr
+MMCifInfoStructRefSeq::AddDif(int rnum, const String& details)
+{
+ MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(rnum, details));
+ difs_.push_back(d);
+ return d;
+}
+
+
}} //ns
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 469e52188..81d5b546a 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -20,6 +20,7 @@
#define OST_MMCIF_INFO_HH
#include <vector>
+#include <map>
#include <boost/shared_ptr.hpp>
#include <ost/geom/geom.hh>
#include <ost/string_ref.hh>
@@ -605,6 +606,92 @@ private:
String replaced_pdb_id_; ///< replaced entry
};
+class MMCifInfoStructRef;
+class MMCifInfoStructRefSeq;
+class MMCifInfoStructRefSeqDif;
+
+
+typedef boost::shared_ptr<MMCifInfoStructRef> MMCifInfoStructRefPtr;
+typedef boost::shared_ptr<MMCifInfoStructRefSeq> MMCifInfoStructRefSeqPtr;
+typedef boost::shared_ptr<MMCifInfoStructRefSeqDif> MMCifInfoStructRefSeqDifPtr;
+
+typedef std::vector<MMCifInfoStructRefPtr> MMCifInfoStructRefs;
+typedef std::vector<MMCifInfoStructRefSeqPtr> MMCifInfoStructRefSeqs;
+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& 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 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;
+ }
+private:
+ 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)
+ { }
+
+ const String& GetID() const { return id_; }
+ const String& GetChainName() const { return chain_name_; }
+ int GetSeqBegin() const { return seq_begin_; }
+ 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& 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_;
+};
+
+class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
+public:
+ MMCifInfoStructRefSeqDif(int rnum, const String& details):
+ rnum_(rnum), details_(details) {}
+ int GetRNum() const { return rnum_;}
+ const String& GetDetails() const { return details_; }
+private:
+ int rnum_;
+ String details_;
+};
+
/// \brief container class for additional information from MMCif files
///
/// \section mmcif annotation information
@@ -731,7 +818,8 @@ public:
{
return obsolete_;
}
-
+ const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
+ void SetStructRefs(const MMCifInfoStructRefs& sr) { struct_refs_=sr; }
//protected:
private:
@@ -743,8 +831,10 @@ private:
std::vector<MMCifInfoCitation> citations_; ///< list of citations
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
+ MMCifInfoStructRefs struct_refs_;
};
+
}} // ns
#endif
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 09fa8b6ef..f2b66ee35 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -300,7 +300,31 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
this->TryStoreIdx(PDB_ID, "pdb_id", header);
this->TryStoreIdx(REPLACE_PDB_ID, "replace_pdb_id", header);
cat_available = true;
- }
+ } else if (header.GetCategory() == "struct_ref") {
+ category_ = STRUCT_REF;
+ this->TryStoreIdx(SR_ENTITY_ID, "entity_id", header);
+ this->TryStoreIdx(SR_ID, "id", header);
+ this->TryStoreIdx(SR_DB_NAME, "db_name", header);
+ this->TryStoreIdx(SR_DB_CODE, "db_code", header);
+ indices_[SR_DB_ACCESS]=header.GetIndex("pdbx_db_accession");
+ cat_available = true;
+ } else if (header.GetCategory() == "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);
+ this->TryStoreIdx(SRS_ENT_ALIGN_END, "seq_align_end", header);
+ this->TryStoreIdx(SRS_DB_ALIGN_BEG, "db_align_beg", header);
+ this->TryStoreIdx(SRS_DB_ALIGN_END, "db_align_end", header);
+ indices_[SRS_PDBX_STRAND_ID]=header.GetIndex("pdbx_strand_id");
+ cat_available = true;
+ } else if (header.GetCategory()=="struct_ref_seq_dif") {
+ category_ = STRUCT_REF_SEQ_DIF;
+ this->TryStoreIdx(SRSD_ALIGN_ID, "align_id", header);
+ this->TryStoreIdx(SRSD_RNUM, "seq_num", header);
+ indices_[SRSD_DETAILS]=header.GetIndex("details");
+ cat_available = true;
+ }
category_counts_[category_]++;
return cat_available;
}
@@ -1328,6 +1352,18 @@ void MMCifReader::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing pdbx_database_PDB_obs_spr entry")
this->ParsePdbxDatabasePdbObsSpr(columns);
break;
+ case STRUCT_REF:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRef(columns);
+ break;
+ case STRUCT_REF_SEQ:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRefSeq(columns);
+ break;
+ case STRUCT_REF_SEQ_DIF:
+ LOG_TRACE("processing struct_ref entry");
+ this->ParseStructRefSeqDif(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1379,6 +1415,103 @@ 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);
+}
+
+void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
+{
+ String aln_id=columns[indices_[SRS_ALIGN_ID]].str();
+ 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();
+ }
+ std::pair<bool,int> dbbeg=this->TryGetInt(columns[indices_[SRS_DB_ALIGN_BEG]],
+ "_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);
+ std::pair<bool,int> entbeg=this->TryGetInt(columns[indices_[SRS_ENT_ALIGN_BEG]],
+ "_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);
+ if (!(dbbeg.first && dbend.first && entbeg.first && entend.first)) {
+ 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;
+ }
+ }
+ 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());
+ }
+}
+
+void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
+{
+ String aln_id=columns[indices_[SRSD_ALIGN_ID]].str();
+ std::pair<bool,int> rnum=this->TryGetInt(columns[indices_[SRSD_RNUM]],
+ "_struct_ref_seq_dif.seq_num",
+ profile_.fault_tolerant);
+ if (!rnum.first) {
+ return;
+ }
+ String details;
+ if (indices_[SRSD_DETAILS]!=-1) {
+ 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(rnum.second, 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());
+ }
+}
+
void MMCifReader::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -1427,6 +1560,7 @@ void MMCifReader::OnEndData()
std::vector<MMCifInfoTransOpPtr> operation_list;
std::map<String, String>::const_iterator buom_it;
std::vector<MMCifInfoTransOpPtr> operations = info_.GetOperations();
+ info_.SetStructRefs(struct_refs_);
std::vector<MMCifInfoTransOpPtr>::const_iterator buop_it;
for (bua_it = bu_assemblies_.begin();
bua_it != bu_assemblies_.end();
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index af12c813a..2a8f549ec 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -229,6 +229,7 @@ protected:
/// \param columns data row
void ParseCitation(const std::vector<StringRef>& columns);
+ const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
/// \brief convert the seqres data item to canonical form.
///
/// The seqres sequence lists non-standard residues in paranthesis. For
@@ -242,7 +243,15 @@ protected:
///
/// \param columns data row
void ParseCitationAuthor(const std::vector<StringRef>& columns);
-
+
+ /// \ brief parse a row in the struct_ref category
+ void ParseStructRef(const std::vector<StringRef>& columns);
+
+ /// \brief parse row in the struct_ref_seq category
+ void ParseStructRefSeq(const std::vector<StringRef>& columns);
+
+ /// \brief parse row in the struct_ref_seq_dif category
+ void ParseStructRefSeqDif(const std::vector<StringRef>& columns);
/// \brief Fetch mmCIF exptl information
///
/// \param columns data row
@@ -401,6 +410,32 @@ private:
METHOD_DETAILS ///< details about assembly computation
} PdbxStructAssemblyItems;
+ // \enum items of the struct_ref category
+ typedef enum {
+ 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,
+ SRS_STRUCT_REF_ID,
+ SRS_PDBX_STRAND_ID,
+ SRS_DB_ALIGN_BEG,
+ SRS_DB_ALIGN_END,
+ SRS_ENT_ALIGN_BEG,
+ SRS_ENT_ALIGN_END
+ } StructRefSeqItems;
+
+ /// \enum items of the struct_ref_seq_dif category
+ typedef enum {
+ SRSD_ALIGN_ID,
+ SRSD_RNUM,
+ SRSD_DETAILS
+ } StructRefSeqDifItems;
/// \enum items of the pdbx_struct_assembly_gen category
typedef enum {
ASSEMBLY_ID, ///< link to pdbx_struct_assembly.id
@@ -490,6 +525,9 @@ private:
STRUCT_CONF,
STRUCT_SHEET_RANGE,
PDBX_DATABASE_PDB_OBS_SPR,
+ STRUCT_REF,
+ STRUCT_REF_SEQ,
+ STRUCT_REF_SEQ_DIF,
DONT_KNOW
} MMCifCategory;
@@ -550,6 +588,7 @@ private:
std::map<String, String> bu_origin_map_; ///< pdbx_struct_assembly.details
MMCifHSVector helix_list_; ///< for storing struct_conf sec.struct. data
MMCifHSVector strand_list_; ///< for storing struct_conf sec.struct. data
+ MMCifInfoStructRefs struct_refs_;
};
}}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index e33f6ad6f..b2294ba90 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -614,6 +614,40 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_author_tests)
BOOST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_struct_ref)
+{
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/struct_ref.cif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ mmcif_p.Parse();
+ MMCifInfoStructRefs refs=mmcif_p.GetInfo().GetStructRefs();
+ BOOST_CHECK_EQUAL(refs.size(), 1);
+ MMCifInfoStructRefPtr sr1=refs[0];
+ BOOST_CHECK_EQUAL(sr1->GetDBName(), "UNP");
+ BOOST_CHECK_EQUAL(sr1->GetDBID(), "BLA2_BACCE");
+ BOOST_CHECK_EQUAL(sr1->GetDBAccess(), "P04190");
+ BOOST_CHECK_EQUAL(sr1->GetID(), "1");
+ MMCifInfoStructRefSeqs seqs=sr1->GetAlignedSeqs();
+ BOOST_CHECK_EQUAL(seqs.size(), 2);
+ BOOST_CHECK_EQUAL(seqs[0]->GetID(), "1");
+ BOOST_CHECK_EQUAL(seqs[0]->GetChainName(), "A");
+ BOOST_CHECK_EQUAL(seqs[0]->GetSeqBegin(), 1);
+ BOOST_CHECK_EQUAL(seqs[0]->GetSeqEnd(), 19);
+ BOOST_CHECK_EQUAL(seqs[0]->GetDBBegin(), 31);
+ BOOST_CHECK_EQUAL(seqs[0]->GetDBEnd(), 49);
+ BOOST_CHECK_EQUAL(seqs[1]->GetID(), "13");
+ BOOST_CHECK_EQUAL(seqs[1]->GetChainName(), "B");
+ BOOST_CHECK_EQUAL(seqs[1]->GetSeqBegin(), 1);
+ BOOST_CHECK_EQUAL(seqs[1]->GetSeqEnd(), 19);
+ BOOST_CHECK_EQUAL(seqs[1]->GetDBBegin(), 31);
+ BOOST_CHECK_EQUAL(seqs[1]->GetDBEnd(), 49);
+ MMCifInfoStructRefSeqDifs diffs=seqs[0]->GetDifs();
+ BOOST_CHECK_EQUAL(diffs.size(), 1);
+ BOOST_CHECK_EQUAL(diffs[0]->GetRNum(), 91);
+ BOOST_CHECK_EQUAL(diffs[0]->GetDetails(), "ENGINEERED MUTATION");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_refine_tests)
{
BOOST_MESSAGE(" Running mmcif_refine_tests...");
diff --git a/modules/io/tests/testfiles/mmcif/struct_ref.cif b/modules/io/tests/testfiles/mmcif/struct_ref.cif
new file mode 100644
index 000000000..1d87ec60b
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/struct_ref.cif
@@ -0,0 +1,47 @@
+data_2bfl
+# taken from 2bfl.cif
+_struct_ref.id 1
+_struct_ref.db_name UNP
+_struct_ref.db_code BLA2_BACCE
+_struct_ref.entity_id 1
+_struct_ref.pdbx_seq_one_letter_code ?
+_struct_ref.pdbx_align_begin ?
+_struct_ref.biol_id .
+_struct_ref.pdbx_db_accession P04190
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.pdbx_PDB_id_code
+_struct_ref_seq.pdbx_strand_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.pdbx_seq_align_beg_ins_code
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.pdbx_seq_align_end_ins_code
+_struct_ref_seq.pdbx_db_accession
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.pdbx_db_align_beg_ins_code
+_struct_ref_seq.db_align_end
+_struct_ref_seq.pdbx_db_align_end_ins_code
+_struct_ref_seq.pdbx_auth_seq_align_beg
+_struct_ref_seq.pdbx_auth_seq_align_end
+1 1 2BFL A 1 ? 19 ? P04190 31 ? 49 ? 27 45
+13 1 2BFL B 1 ? 19 ? P04190 31 ? 49 ? 27 45
+#
+loop_
+_struct_ref_seq_dif.align_id
+_struct_ref_seq_dif.pdbx_pdb_id_code
+_struct_ref_seq_dif.mon_id
+_struct_ref_seq_dif.pdbx_pdb_strand_id
+_struct_ref_seq_dif.seq_num
+_struct_ref_seq_dif.pdbx_pdb_ins_code
+_struct_ref_seq_dif.pdbx_seq_db_name
+_struct_ref_seq_dif.pdbx_seq_db_accession_code
+_struct_ref_seq_dif.db_mon_id
+_struct_ref_seq_dif.pdbx_seq_db_seq_num
+_struct_ref_seq_dif.details
+_struct_ref_seq_dif.pdbx_auth_seq_num
+_struct_ref_seq_dif.pdbx_ordinal
+1 2BFL CYS A 91 ? UNP P04190 ARG 121 'ENGINEERED MUTATION' 121 1
+13 2BFL CYS B 91 ? UNP P04190 ARG 121 'ENGINEERED MUTATION' 121 2
+
--
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