diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 340d16c985e46752351ed7b877e10d5d041796f2..c744d54eed3679a115853d5343f291835fe95398 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -397,6 +397,14 @@ of the annotation available.
Establish all bonds stored for branched entities.
+ .. method:: GetEntityDesc(entity_id)
+
+ Get info of type :class:`MMCifEntityDesc` for specified *entity_id*.
+ The entity id for a chain can be fetched with :func:`GetMMCifEntityIdTr`.
+
+ :param entity_id: ID of entity
+ :type entity_id: :class:`str`
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
@@ -1349,6 +1357,62 @@ of the annotation available.
See :attr:`bond_order`
+.. class:: MMCifEntityDesc
+
+ Data collected for certain mmCIF entity
+
+ .. attribute:: type
+
+ The ost chain type which can be assigned to :class:`ost.mol.ChainHandle`
+
+ :type: :class:`ost.mol.ChainType`
+
+ .. attribute:: entity_type
+
+ value of _entity.type token
+
+ :class:`str`
+
+ .. attribute:: entity_poly_type
+
+ value of _entity_poly.type token - empty string if entity is not of type
+ "polymer"
+
+ :class:`str`
+
+ .. attribute:: branched_type
+
+ value of _pdbx_entity_branch.type token - empty string if entity is not of
+ type "branched"
+
+ :type: :class:`str`
+
+ .. attribute:: details
+
+ value of _entity.pdbx_description token
+
+ :class:`str`
+
+ .. attribute:: seqres
+
+ SEQRES with gentle preprocessing - empty string if entity is not of type
+ "polymer". By default, the :class:`ost.io.MMCifReader` reads the value of the
+ _entity_poly.pdbx_seq_one_letter_code token. Copies all letters but
+ searches a :class:`ost.conop.CompoundLib` for compound names in brackets.
+ *seqres* gets an 'X' if no compound is found or the respective compound has
+ one letter code '?'. Uses the one letter code of the found compound
+ otherwise. So it's basically a canonical SEQRES with exactly one character
+ per residue.
+
+ :type: :class:`str`
+
+ .. attribute:: mon_ids
+
+ Monomer ids of all residues in a polymer - empty if entity is not of
+ type "polymer". Read from _entity_poly_seq category.
+
+ :type: :class:`ost.base.StringList`
+
Writing mmCIF files
--------------------------------------------------------------------------------
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 411750b9194a884052a542ba891550ff042c152a..200e4255696c3bb5c3084e94a3460d3651deaa15 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -485,6 +485,16 @@ void export_mmcif_io()
.def(self_ns::str(self))
;
+ class_<MMCifEntityDesc>("MMCifEntityDesc", init<>())
+ .add_property("type", &MMCifEntityDesc::type)
+ .add_property("entity_type", &MMCifEntityDesc::entity_type)
+ .add_property("entity_poly_type", &MMCifEntityDesc::entity_poly_type)
+ .add_property("branched_type", &MMCifEntityDesc::branched_type)
+ .add_property("details", &MMCifEntityDesc::details)
+ .add_property("seqres", &MMCifEntityDesc::seqres)
+ .add_property("mon_ids", &MMCifEntityDesc::mon_ids)
+ ;
+
class_<MMCifInfo>("MMCifInfo", init<>())
.def("AddCitation", &MMCifInfo::AddCitation)
.def("GetCitations", make_function(&MMCifInfo::GetCitations,
@@ -525,6 +535,8 @@ void export_mmcif_io()
.def("ConnectBranchLinks", &MMCifInfo::ConnectBranchLinks)
.def("GetEntityBranchChainNames", &WrapGetNames)
.def("GetEntityBranchChains", &MMCifInfo::GetEntityBranchChains)
+ .def("SetEntityDesc", &MMCifInfo::SetEntityDesc)
+ .def("GetEntityDesc", &MMCifInfo::GetEntityDesc, return_value_policy<copy_const_reference>())
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index ef44d4813fef36f2c709888b2acaef4d007342ee..96f256ca91fc80811eb8380d67a611d43ce3e116 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -293,6 +293,23 @@ void MMCifInfo::ConnectBranchLinks()
}
}
+const MMCifEntityDesc& MMCifInfo::GetEntityDesc(const String& entity_id) const {
+ MMCifEntityDescMap::const_iterator it = entity_desc_.find(entity_id);
+ if(it == entity_desc_.end()) {
+ throw IOException("No EntityDesc for entity id \""+entity_id+"\"");
+ }
+ return it->second;
+}
+
+void MMCifInfo::SetEntityDesc(const String& entity_id,
+ const MMCifEntityDesc& entity_desc)
+{
+ if(entity_desc_.find(entity_id) != entity_desc_.end()) {
+ throw IOException("EntityDesc for entity_id \""+entity_id+"\" already set");
+ }
+ entity_desc_[entity_id] = entity_desc;
+}
+
std::ostream& operator<<(std::ostream& os, const MMCifInfoEntityBranchLink& eb)
{
os << "<MMCifInfoEntityBranchLink atom1:" << eb.GetAtom1() << " atom2:"
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 389d7d1cd433eaf646634426c33f8bb10b5729a4..5114b4d9e1526d382e765d39b05d69171c7d64cc 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -959,6 +959,20 @@ private:
};
typedef std::map<String, std::vector<MMCifInfoEntityBranchLink> > MMCifInfoEntityBranchLinkMap;
+
+/// \struct keeping track of entity information
+typedef struct {
+ mol::ChainType type; ///< characterise entity
+ String entity_type; ///< value of _entity.type
+ String entity_poly_type; ///< value of _entity_poly.type
+ String branched_type; ///< value of _pdbx_entity_branch.type
+ String details; ///< description of this entity
+ String seqres; ///< chain of monomers
+ std::vector<String> mon_ids; ///< list of full monomer names
+} MMCifEntityDesc;
+typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
+
+
/// \brief container class for additional information from MMCif files
///
/// \section mmcif annotation information
@@ -1201,6 +1215,11 @@ public:
///
void ConnectBranchLinks();
+ const MMCifEntityDesc& GetEntityDesc(const String& entity_id) const;
+
+ void SetEntityDesc(const String& entity_id,
+ const MMCifEntityDesc& entity_desc);
+
//protected:
private:
@@ -1216,6 +1235,7 @@ private:
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
MMCifInfoStructRefs struct_refs_;
+ MMCifEntityDescMap entity_desc_;
std::map<String, String> cif_2_pdb_chain_id_;
std::map<String, String> pdb_2_cif_chain_id_;
std::map<String, String> cif_2_entity_id_;
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index b6c2167cb5bc78b902be3bcce04a7601775cb5a3..9ad17290f263753625b45c7f26e485a03fe05b0d 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -92,6 +92,7 @@ void MMCifReader::ClearState()
revision_types_.clear();
database_PDB_rev_added_ = false;
entity_branch_link_map_.clear();
+ entity_poly_seq_map_.clear();
}
void MMCifReader::SetRestrictChains(const String& restrict_chains)
@@ -389,6 +390,13 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[BL_ATOM_STEREO_CONFIG_2] = header.GetIndex("atom_stereo_config_2");
indices_[BL_VALUE_ORDER] = header.GetIndex("value_order");
cat_available = true;
+ } else if(header.GetCategory() == "entity_poly_seq") {
+ category_ = ENTITY_POLY_SEQ;
+ // mandatory
+ this->TryStoreIdx(EPS_ENTITY_ID, "entity_id", header);
+ this->TryStoreIdx(EPS_MON_ID, "mon_id", header);
+ this->TryStoreIdx(EPS_NUM, "num", header);
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -710,15 +718,19 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
columns[indices_[GROUP_PDB]][0]=='H');
}
-MMCifReader::MMCifEntityDescMap::iterator MMCifReader::GetEntityDescMapIterator(
+MMCifEntityDescMap::iterator MMCifReader::GetEntityDescMapIterator(
const String& entity_id)
{
MMCifEntityDescMap::iterator edm_it = entity_desc_map_.find(entity_id);
// if the entity ID is not already stored, insert it with empty values
if (edm_it == entity_desc_map_.end()) {
MMCifEntityDesc desc = {.type=mol::CHAINTYPE_N_CHAINTYPES,
+ .entity_type = "",
+ .entity_poly_type = "",
+ .branched_type = "",
.details="",
- .seqres=""};
+ .seqres="",
+ .mon_ids=std::vector<String>()};
edm_it = entity_desc_map_.insert(entity_desc_map_.begin(),
MMCifEntityDescMap::value_type(entity_id,
desc));
@@ -738,6 +750,8 @@ void MMCifReader::ParseEntity(const std::vector<StringRef>& columns)
if (edm_it->second.type == mol::CHAINTYPE_N_CHAINTYPES) {
edm_it->second.type = mol::ChainTypeFromString(columns[indices_[E_TYPE]]);
}
+ // but set entity_type anyways
+ edm_it->second.entity_type = columns[indices_[E_TYPE]].str();
} else {
// don't deal with entities without type
entity_desc_map_.erase(edm_it);
@@ -758,6 +772,7 @@ void MMCifReader::ParseEntityPoly(const std::vector<StringRef>& columns)
// store type
if (indices_[EP_TYPE] != -1) {
edm_it->second.type = mol::ChainTypeFromString(columns[indices_[EP_TYPE]]);
+ edm_it->second.entity_poly_type = columns[indices_[EP_TYPE]].str();
}
// store seqres
@@ -1633,6 +1648,10 @@ void MMCifReader::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing pdbx_entity_branch_link entry");
this->ParsePdbxEntityBranchLink(columns);
break;
+ case ENTITY_POLY_SEQ:
+ LOG_TRACE("processing entity_poly_seq entry");
+ this->ParseEntityPolySeq(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1780,6 +1799,7 @@ void MMCifReader::ParsePdbxEntityBranch(const std::vector<StringRef>& columns)
// store type
if (indices_[BR_ENTITY_TYPE] != -1) {
edm_it->second.type = mol::ChainTypeFromString(columns[indices_[EP_TYPE]]);
+ edm_it->second.branched_type = columns[indices_[EP_TYPE]].str();
}
}
@@ -1833,6 +1853,45 @@ void MMCifReader::ParsePdbxEntityBranchLink(const std::vector<StringRef>& column
blm_it->second.push_back(link_pair);
}
+void MMCifReader::ParseEntityPolySeq(const std::vector<StringRef>& columns)
+{
+ std::pair<bool, int> tmp = columns[indices_[EPS_NUM]].to_int();
+ if(!tmp.first) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Could not cast "
+ "_entity_poly_seq.num to integer: "
+ + columns[indices_[EPS_NUM]].str(),
+ this->GetCurrentLinenum()));
+ }
+ int num = tmp.second;
+
+ if(num < 1) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "_entity_poly_seq.num are "
+ "expected to be ints >= 1. Got:"
+ + columns[indices_[EPS_NUM]].str(),
+ this->GetCurrentLinenum()));
+ }
+
+ // [] inserts new value if not present in container
+ std::map<int, String>& entity_map =
+ entity_poly_seq_map_[columns[indices_[EPS_ENTITY_ID]].str()];
+
+ if(entity_map.find(num) != entity_map.end()) {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "_entity_poly_seq.num must be "
+ "unique in same "
+ "_entity_poly_seq.entity_id. "
+ "entity_id: " +
+ columns[indices_[EPS_ENTITY_ID]].str() +
+ ", num: " +
+ columns[indices_[EPS_ENTITY_ID]].str(),
+ this->GetCurrentLinenum()));
+ }
+
+ entity_map[num] = columns[indices_[EPS_MON_ID]].str();
+}
+
void MMCifReader::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -1972,6 +2031,21 @@ void MMCifReader::OnEndData()
}
}
+ // conclude EntityDesc (add entity_poly_seq if present) and add to MMCifInfo
+ for(auto entity_it: entity_desc_map_) {
+ if(entity_poly_seq_map_.find(entity_it.first) != entity_poly_seq_map_.end()) {
+ int max_num = 1;
+ for(auto seqres_it: entity_poly_seq_map_[entity_it.first]) {
+ max_num = std::max(max_num, seqres_it.first);
+ }
+ entity_it.second.mon_ids.assign(max_num, "?");
+ for(auto seqres_it: entity_poly_seq_map_[entity_it.first]) {
+ entity_it.second.mon_ids[seqres_it.first-1] = seqres_it.second;
+ }
+ }
+ info_.SetEntityDesc(entity_it.first, entity_it.second);
+ }
+
LOG_INFO("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index f2f2d2dbd78069a778c6cd3ccab9d49abb7b0cb1..43f6cc220a8db607af23f8884edf20a35e407b71 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -338,6 +338,11 @@ protected:
/// \param columns data row
void ParsePdbxEntityBranchLink(const std::vector<StringRef>& columns);
+ /// \brief Fetch mmCIF entity_poly_seq information
+ ///
+ /// \param columns data row
+ void ParseEntityPolySeq(const std::vector<StringRef>& columns);
+
/// \struct types of secondary structure
typedef enum {
MMCIF_HELIX,
@@ -595,6 +600,13 @@ private:
BL_VALUE_ORDER /// < bond order
} EntityBranchLinkItems;
+ /// \enum items of the entity_poly_seq category
+ typedef enum {
+ EPS_ENTITY_ID,
+ EPS_MON_ID,
+ EPS_NUM
+ } EntityPolySeqItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -620,17 +632,10 @@ private:
PDBX_DATABASE_STATUS,
PDBX_ENTITY_BRANCH,
PDBX_ENTITY_BRANCH_LINK,
+ ENTITY_POLY_SEQ,
DONT_KNOW
} MMCifCategory;
- /// \struct keeping track of entity information
- typedef struct {
- mol::ChainType type; ///< characterise entity
- String details; ///< description of this entity
- String seqres; ///< chain of monomers
- } MMCifEntityDesc;
- typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
-
/// \brief Get an iterator for MMCifEntityDescMap by finding an element or
/// inserting a new one into the map.
/// \param entity_id ID of the entity to talk to
@@ -729,6 +734,8 @@ private:
bool database_PDB_rev_added_;
// for entity_branch connections
MMCifPdbxEntityBranchLinkMap entity_branch_link_map_;
+ // for storing entity_poly_seq
+ std::map<String, std::map<int, String> > entity_poly_seq_map_;
};
/// \brief Translate mmCIF info on bond type (e.g.