diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 25c58ff9ced52ae52170239f132ccdc57c946674..dfa32874dec3b28ed93e6625b23534a7e4919ce7 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -195,4 +195,48 @@ MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String&
return d;
}
+void MMCifInfo::AddEntityBranchLink(String chain_name,
+ mol::AtomHandle atom1,
+ mol::AtomHandle atom2)
+{
+ // check if element already exists
+ MMCifInfoEntityBranchMap::iterator blm_it = entity_branches_.find(chain_name);
+ if (blm_it == entity_branches_.end()) {
+ // `find` points to the end of the map so chain_name was not found
+ std::pair<MMCifInfoEntityBranchMap::iterator, bool> rit =
+ entity_branches_.insert(MMCifInfoEntityBranchMap::value_type(chain_name,
+ std::vector<MMCifInfoEntityBranch>()));
+ // let blm_it point to the new element so we can add to the vector
+ blm_it = rit.first;
+ }
+ // add new branch element
+ blm_it->second.push_back(MMCifInfoEntityBranch(atom1, atom2));
+}
+
+const std::vector<MMCifInfoEntityBranch> MMCifInfo::GetEntityBranchLinks() const
+{
+ std::vector<MMCifInfoEntityBranch> all_links;
+ MMCifInfoEntityBranchMap::const_iterator blm_it;
+ for (blm_it = entity_branches_.begin();
+ blm_it != entity_branches_.end(); ++blm_it) {
+ std::copy(blm_it->second.begin(), blm_it->second.end(),
+ std::back_inserter(all_links));
+ }
+ return all_links;
+}
+
+void MMCifInfo::ConnectBranchLinks(mol::XCSEditor editor)
+{
+ MMCifInfoEntityBranchMap::iterator blm_it;
+ for (blm_it = entity_branches_.begin();
+ blm_it != entity_branches_.end(); ++blm_it) {
+ for (std::vector<MMCifInfoEntityBranch>::iterator blv_it =
+ blm_it->second.begin();
+ blv_it != blm_it->second.end();
+ ++blv_it) {
+ editor.Connect(blv_it->GetAtom1(), blv_it->GetAtom2());
+ }
+ }
+}
+
}} //ns
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index c152229ef838e7ce1d0abb4d39688112d3662def..dde4589923fc55d1b6197a4f7f83b4f5ee92af49 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -26,6 +26,7 @@
#include <ost/geom/geom.hh>
#include <ost/string_ref.hh>
#include <ost/io/module_config.hh>
+#include <ost/mol/mol.hh>
namespace ost { namespace io {
@@ -918,6 +919,21 @@ private:
String details_;
};
+/// \brief Store information on brnached structures (oligosaccharides)
+///
+class DLLEXPORT_OST_IO MMCifInfoEntityBranch {
+public:
+ MMCifInfoEntityBranch(mol::AtomHandle atom1, mol::AtomHandle atom2):
+ atom1_(atom1), atom2_(atom2) {}
+ mol::AtomHandle GetAtom1() const { return atom1_;}
+ mol::AtomHandle GetAtom2() const { return atom2_; }
+
+private:
+ mol::AtomHandle atom1_;
+ mol::AtomHandle atom2_;
+};
+typedef std::map<String, std::vector<MMCifInfoEntityBranch> > MMCifInfoEntityBranchMap;
+
/// \brief container class for additional information from MMCif files
///
/// \section mmcif annotation information
@@ -1126,6 +1142,26 @@ public:
{
return revisions_;
}
+
+ /// \brief Add bond information for a branched entity
+ ///
+ /// \param chain_name chain the bond belongs to
+ /// \param atom1 first atom of the bond
+ /// \param atom2 second atom of the bond
+ void AddEntityBranchLink(String chain_name,
+ mol::AtomHandle atom1,
+ mol::AtomHandle atom2);
+
+ /// \brief Get all links for all branched entities
+ ///
+ const std::vector<MMCifInfoEntityBranch> GetEntityBranchLinks() const;
+ //GetEntityBranchChains
+ //GetEntityBranchByChain
+
+ /// \brief Connect all atoms listed as links for branched entities.
+ ///
+ void ConnectBranchLinks(mol::XCSEditor editor);
+
//protected:
private:
@@ -1140,10 +1176,11 @@ private:
std::vector<MMCifInfoCitation> citations_; ///< list of citations
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
- MMCifInfoStructRefs struct_refs_;
+ MMCifInfoStructRefs struct_refs_;
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_;
+ std::map<String, std::vector<MMCifInfoEntityBranch> > entity_branches_;
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 1b7f9a00382ad94035d2883a7bab0e921fe8c77e..8eeb71924f49d0a30a03325ca9b493513f129cf0 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -90,6 +90,7 @@ void MMCifReader::ClearState()
revisions_.clear();
revision_types_.clear();
database_PDB_rev_added_ = false;
+ entity_branch_link_map_.clear();
}
void MMCifReader::SetRestrictChains(const String& restrict_chains)
@@ -368,6 +369,23 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
this->TryStoreIdx(BR_ENTITY_ID, "entity_id", header);
this->TryStoreIdx(BR_ENTITY_TYPE, "type", header);
cat_available = true;
+ } else if (header.GetCategory() == "pdbx_entity_branch_link") {
+ category_ = PDBX_ENTITY_BRANCH_LINK;
+ // mandatory
+ this->TryStoreIdx(BL_ENTITY_ID, "entity_id", header);
+ this->TryStoreIdx(BL_ATOM_ID_1, "atom_id_1", header);
+ this->TryStoreIdx(BL_ATOM_ID_2, "atom_id_2", header);
+ this->TryStoreIdx(BL_COMP_ID_1, "comp_id_1", header);
+ this->TryStoreIdx(BL_COMP_ID_2, "comp_id_2", header);
+ this->TryStoreIdx(BL_ENTITY_BRANCH_LIST_NUM_1, "entity_branch_list_num_1",
+ header);
+ this->TryStoreIdx(BL_ENTITY_BRANCH_LIST_NUM_2, "entity_branch_list_num_2",
+ header);
+ // optional items
+ indices_[BL_ATOM_STEREO_CONFIG_1] = header.GetIndex("atom_stereo_config_1");
+ indices_[BL_ATOM_STEREO_CONFIG_2] = header.GetIndex("atom_stereo_config_2");
+ indices_[BL_VALUE_ORDER] = header.GetIndex("value_order");
+ cat_available = true;
}
category_counts_[category_]++;
return cat_available;
@@ -1551,6 +1569,10 @@ void MMCifReader::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing pdbx_entity_branch entry");
this->ParsePdbxEntityBranch(columns);
break;
+ case PDBX_ENTITY_BRANCH_LINK:
+ LOG_TRACE("processing pdbx_entity_branch_link entry");
+ this->ParsePdbxEntityBranchLink(columns);
+ break;
default:
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1711,6 +1733,52 @@ void MMCifReader::ParsePdbxEntityBranch(const std::vector<StringRef>& columns)
}
}
+void MMCifReader::ParsePdbxEntityBranchLink(const std::vector<StringRef>& columns)
+{
+ MMCifPdbxEntityBranchLink link_pair;
+
+ String entity_id(columns[indices_[BL_ENTITY_ID]].str());
+
+ // list of entities -> pairs of info for link
+ link_pair.res_num_1 =
+ this->TryGetInt(columns[indices_[BL_ENTITY_BRANCH_LIST_NUM_1]],
+ "pdbx_entity_branch_link.entity_branch_list_num_1");
+ link_pair.cmp_1 = columns[indices_[BL_COMP_ID_1]].str();
+ link_pair.atm_nm_1 = columns[indices_[BL_ATOM_ID_1]].str();
+ link_pair.res_num_2 =
+ this->TryGetInt(columns[indices_[BL_ENTITY_BRANCH_LIST_NUM_2]],
+ "pdbx_entity_branch_link.entity_branch_list_num_2");
+ link_pair.cmp_2 = columns[indices_[BL_COMP_ID_2]].str();
+ link_pair.atm_nm_2 = columns[indices_[BL_ATOM_ID_2]].str();
+
+ /*if (indices_[BL_ATOM_STEREO_CONFIG_1] != -1) {
+ char A = *columns[indices_[BL_ATOM_STEREO_CONFIG_1]].begin();
+ }*/
+ // check stereo values to be N S R
+ /*if (indices_[BL_ATOM_STEREO_CONFIG_2] != -1) {
+ }*/
+ // check value order to be ... git grep bond_order
+ /*if (indices_[BL_VALUE_ORDER] != -1) {
+ }*/
+
+ std::pair<MMCifPdbxEntityBranchLinkMap::iterator, bool> rit;
+
+ // check if element already exists
+ MMCifPdbxEntityBranchLinkMap::iterator blm_it =
+ entity_branch_link_map_.find(entity_id);
+
+ // if the entity was not seen before, create it in the map
+ if (blm_it == entity_branch_link_map_.end()) {
+ rit = entity_branch_link_map_.insert(
+ MMCifPdbxEntityBranchLinkMap::value_type(entity_id,
+ std::vector<MMCifPdbxEntityBranchLink>()));
+ blm_it = rit.first;
+ }
+
+ // add the link pair
+ blm_it->second.push_back(link_pair);
+}
+
void MMCifReader::OnEndData()
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -1718,10 +1786,12 @@ void MMCifReader::OnEndData()
// process chain types
std::vector<std::pair<mol::ChainHandle, String> >::const_iterator css;
MMCifEntityDescMap::const_iterator edm_it;
+ MMCifPdbxEntityBranchLinkMap::const_iterator blm_it;
+ std::vector<MMCifPdbxEntityBranchLink>::const_iterator bl_it;
String pdb_auth_chain_name;
for (css = chain_id_pairs_.begin(); css != chain_id_pairs_.end(); ++css) {
+ // chain description
edm_it = entity_desc_map_.find(css->second);
-
if (edm_it != entity_desc_map_.end()) {
editor.SetChainType(css->first, edm_it->second.type);
editor.SetChainDescription(css->first, edm_it->second.details);
@@ -1745,6 +1815,21 @@ void MMCifReader::OnEndData()
LOG_WARNING("No entity description found for atom_site.label_entity_id '"
<< css->second << "'");
}
+ // find
+ blm_it = entity_branch_link_map_.find(css->second);
+ // store linker pair
+ if (blm_it != entity_branch_link_map_.end()) {
+ for (bl_it = blm_it->second.begin(); bl_it != blm_it->second.end();
+ ++bl_it) {
+ mol::ResidueHandle res1 = css->first.FindResidue(to_res_num(
+ bl_it->res_num_1, ' '));
+ mol::ResidueHandle res2 = css->first.FindResidue(to_res_num(
+ bl_it->res_num_2, ' '));
+ info_.AddEntityBranchLink(css->first.GetName(),
+ res1.FindAtom(bl_it->atm_nm_1),
+ res2.FindAtom(bl_it->atm_nm_2));
+ }
+ }
}
// process citations (couple with authors
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 5e1e2204a9da08e6bdfbdd920f5fd1d8af7ccbc9..8d975600c4737a8e36e55277ec8e04c148817098 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -57,6 +57,7 @@ namespace ost { namespace io {
/// \li pdbx_database_PDB_obs_spr
/// \li database_PDB_rev
/// \li pdbx_entity_branch
+/// \li pdbx_entity_branch_link
class DLLEXPORT_OST_IO MMCifReader : public StarParser {
public:
/// \brief create a MMCifReader
@@ -332,6 +333,11 @@ protected:
/// \param columns data row
void ParsePdbxEntityBranch(const std::vector<StringRef>& columns);
+ /// \brief Fetch mmCIF pdbx_entity_branch_link information
+ ///
+ /// \param columns data row
+ void ParsePdbxEntityBranchLink(const std::vector<StringRef>& columns);
+
/// \struct types of secondary structure
typedef enum {
MMCIF_HELIX,
@@ -573,6 +579,20 @@ private:
BR_ENTITY_TYPE ///< type of branched molecular entity
} EntityBranchItems;
+ /// \enum items of the pdbx_entity_branch_link category
+ typedef enum {
+ BL_ENTITY_ID, /// < pointer to entity.id
+ BL_ATOM_ID_1, /// < atom identifier (element + number)
+ BL_ATOM_ID_2, /// < atom identifier (element + number)
+ BL_COMP_ID_1, /// < tlc of component
+ BL_COMP_ID_2, /// < tlc of component
+ BL_ENTITY_BRANCH_LIST_NUM_1, /// < res. no. (pdbx_entity_branch_list.num)
+ BL_ENTITY_BRANCH_LIST_NUM_2, /// < res. no. (pdbx_entity_branch_list.num)
+ BL_ATOM_STEREO_CONFIG_1, /// < chiral configuration (R/ S)
+ BL_ATOM_STEREO_CONFIG_2, /// < chiral configuration (R/ S)
+ BL_VALUE_ORDER /// < bond order
+ } EntityBranchLinkItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
@@ -597,6 +617,7 @@ private:
PDBX_AUDIT_REVISION_DETAILS,
PDBX_DATABASE_STATUS,
PDBX_ENTITY_BRANCH,
+ PDBX_ENTITY_BRANCH_LINK,
DONT_KNOW
} MMCifCategory;
@@ -651,6 +672,18 @@ private:
int minor; ///< minor version
};
+ /// \struct to keep entity_branch linker pairs while parsing
+ typedef struct {
+ int res_num_1; ///< index of the linked residue relative to its chain
+ String cmp_1; ///< tlc of residue (sugar)
+ String atm_nm_1; ///< (IUPAC) name of the linking atom
+ int res_num_2; ///< index of the linked residue relative to its chain
+ String cmp_2; ///< tlc of residue (sugar)
+ String atm_nm_2; ///< index of the linked residue relative to its chain
+ } MMCifPdbxEntityBranchLink;
+ typedef std::map<String, std::vector<MMCifPdbxEntityBranchLink> >
+ MMCifPdbxEntityBranchLinkMap;
+
// members
MMCifCategory category_;
int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
@@ -686,6 +719,8 @@ private:
std::vector<MMCifRevisionDesc> revisions_;
std::map<int, String> revision_types_;
bool database_PDB_rev_added_;
+ // for entity_branch connections
+ MMCifPdbxEntityBranchLinkMap entity_branch_link_map_;
};
}}
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index efb35d54ff84a5772b7193ba0a0c2382880585c2..25fccecea2f033714d51253ae3cfbed453173b69 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -22,6 +22,7 @@
#include <ost/io/io_exception.hh>
#include <ost/io/mol/mmcif_info.hh>
+#include <ost/mol/mol.hh>
using namespace ost;
using namespace ost::io;
@@ -278,6 +279,27 @@ BOOST_AUTO_TEST_CASE(mmcif_info_revisions)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_info_branch)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_info_branch tests...");
+
+ // create a dummy entity to start an editor...
+ mol::EntityHandle eh = mol::CreateEntity();
+ mol::XCSEditor editor = eh.EditXCS();
+ mol::ChainHandle ch = editor.InsertChain("A");
+ mol::ResidueHandle res1 = editor.AppendResidue(ch, "NAG");
+ mol::ResidueHandle res2 = editor.AppendResidue(ch, "NAG");
+ // create AtomHandles for testing
+ mol::AtomHandle atom1 = editor.InsertAtom(res2, "C1",geom::Vec3());
+ mol::AtomHandle atom2 = editor.InsertAtom(res1, "O4",geom::Vec3());
+
+ MMCifInfoEntityBranch branch1(atom1, atom2);
+ BOOST_CHECK(branch1.GetAtom1().GetQualifiedName() == "A.NAG2.C1");
+ BOOST_CHECK(branch1.GetAtom2().GetQualifiedName() == "A.NAG1.O4");
+
+ BOOST_TEST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_CASE(mmcif_info)
{
BOOST_TEST_MESSAGE(" Running mmcif_info tests...");
@@ -311,6 +333,37 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
BOOST_CHECK(info.GetRevisions().GetSize() == 0);
+ // simple check that we can add branch links
+ mol::EntityHandle eh = mol::CreateEntity();
+ mol::XCSEditor editor = eh.EditXCS();
+ mol::ChainHandle ch1 = editor.InsertChain("A");
+ mol::ResidueHandle res11 = editor.AppendResidue(ch1, "NAG");
+ mol::ResidueHandle res12 = editor.AppendResidue(ch1, "NAG");
+ // create AtomHandles for testing
+ mol::AtomHandle atom11 = editor.InsertAtom(res12, "C1",geom::Vec3());
+ mol::AtomHandle atom12 = editor.InsertAtom(res11, "O4",geom::Vec3());
+ mol::ChainHandle ch2 = editor.InsertChain("B");
+ mol::ResidueHandle res21 = editor.AppendResidue(ch2, "BMA");
+ mol::ResidueHandle res22 = editor.AppendResidue(ch2, "MAN");
+ // create AtomHandles for testing
+ mol::AtomHandle atom21 = editor.InsertAtom(res22, "C1",geom::Vec3());
+ mol::AtomHandle atom22 = editor.InsertAtom(res21, "O3",geom::Vec3());
+ info.AddEntityBranchLink(ch1.GetName(), atom11, atom12);
+ info.AddEntityBranchLink(ch2.GetName(), atom21, atom22);
+ std::vector<MMCifInfoEntityBranch> blinks = info.GetEntityBranchLinks();
+
+ BOOST_CHECK(blinks.size() == 2);
+ BOOST_CHECK(blinks[0].GetAtom1().GetQualifiedName() == "A.NAG2.C1");
+ BOOST_CHECK(blinks[0].GetAtom2().GetQualifiedName() == "A.NAG1.O4");
+ BOOST_CHECK(blinks[1].GetAtom1().GetQualifiedName() == "B.MAN2.C1");
+ BOOST_CHECK(blinks[1].GetAtom2().GetQualifiedName() == "B.BMA1.O3");
+
+ // check that branch links get bonds
+ info.ConnectBranchLinks(editor);
+
+ BOOST_CHECK(atom11.GetBondPartners()[0] == atom12);
+ BOOST_CHECK(atom22.GetBondPartners()[0] == atom21);
+
BOOST_TEST_MESSAGE(" done.");
}