SCHWED-4849: Allow to get branched entity information for a specific chain

modules/io/doc/mmcif.rst

@@ -52,7 +52,8 @@ The following categories of a mmCIF file are considered by the reader:
   (mmCIF dictionary version >= 5) used to fill :class:`MMCifInfoRevisions`
 * ``pdbx_entity_branch`` and ``pdbx_entity_branch_link`` used for
   :class:`MMCifInfoEntityBranchLink`, a list of links is available by
-  :meth:`~MMCifInfo.GetEntityBranchLinks`
+  :meth:`~MMCifInfo.GetEntityBranchLinks` and
+  :meth:`~MMCifInfo.GetEntityBranchByChain`
 
 Notes:
 
@@ -313,6 +314,18 @@ of the annotation available.
     information is available by the stored
     :class:`AtomHandles <ost.mol.AtomHandle>` of each entry.
 
+    :returns: :class:`list` of :class:`MMCifInfoEntityBranchLink`
+
+  .. method:: GetEntityBranchByChain(chain_name)
+
+    Get bond information for chains with branched entities. Returns all
+    :class:`MMCifInfoEntityBranchLink` objects in one list if chain is a
+    branched entity, an empty list otherwise.
+
+    :param chain_name: Chain name to check for branch links
+    :type chain_name: :class:`str`
+    :returns: :class:`list` of :class:`MMCifInfoEntityBranchLink`
+
   .. method:: AddEntityBranchLink(chain_name, atom1, atom2, bond_order)
 
     Add bond information for a branched entity.
@@ -327,7 +340,19 @@ of the annotation available.
     :type bond_order: :class:`int`
     :returns: Nothing
 
-  .. method:: ConnectBranchLinks()
+  .. method:: GetEntityBranchChainNames
+
+    Get a list of chain names which contain branched entities.
+
+    :returns: :class:`list` of :class:`str`
+
+  .. method:: GetEntityBranchChains
+
+    Get a list of chains which contain branched entities.
+
+    :returns: :class:`list` of :class:`~ost.mol.ChainHandle`
+
+  .. method:: ConnectBranchLinks
 
     Establish all bonds stored for branched entities.
 
@@ -1246,18 +1271,6 @@ of the annotation available.
     :type editor: :class:`~ost.mol.XCSEditor`
     :returns: Nothing
 
-  .. method:: GetEntityBranchChainNames
-
-    Get a list of chain names which contain branched entities.
-
-    :returns: :class:`list` of :class:`str`
-
-  .. method:: GetEntityBranchChains
-
-    Get a list of chains which contain branched entities.
-
-    :returns: :class:`list` of :class:`~ost.mol.ChainHandle`
-
   .. method:: GetAtom1
 
     See :attr:`atom1`
@@ -1286,7 +1299,7 @@ of the annotation available.
 ..  LocalWords:  SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
 ..  LocalWords:  biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
 ..  LocalWords:  auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
-..  LocalWords:  GetRevisions AddRevision SetRevisionsDateOriginal GetSize
+..  LocalWords:  GetRevisions AddRevision SetRevisionsDateOriginal GetSize str
 ..  LocalWords:  GetNum num GetStatus GetLastDate GetFirstRelease storable
 ..  LocalWords:  cas isbn pubmed asu seqres conop casp COMPND OBSLTE LoadMMCIF
 ..  LocalWords:  SetChainList MMCifInfoTransOp ChainTypes MMCifInfoStructRef
@@ -1295,3 +1308,4 @@ of the annotation available.
 ..  LocalWords:  chainintervalls GetChainIntervalList GetMethodDetails GetAtom
 ..  LocalWords:  GetOperationsIntervalList SetMethodDetails oligosaccharides
 ..  LocalWords:  SetAtom GetBondOrder SetBondOrder MMCifInfoEntityBranchLink
+..  LocalWords:  GetEntityBranchByChain param

modules/io/pymod/export_mmcif_io.cc

@@ -413,6 +413,7 @@ void export_mmcif_io()
     .def("GetRevisions", &MMCifInfo::GetRevisions)
     .def("AddEntityBranchLink", &MMCifInfo::AddEntityBranchLink)
     .def("GetEntityBranchLinks", &MMCifInfo::GetEntityBranchLinks)
+    .def("GetEntityBranchByChain", &MMCifInfo::GetEntityBranchByChain)
     .def("ConnectBranchLinks", &MMCifInfo::ConnectBranchLinks)
     .def("GetEntityBranchChainNames", &WrapGetNames)
     .def("GetEntityBranchChains", &MMCifInfo::GetEntityBranchChains)

modules/io/src/mol/mmcif_info.cc

@@ -227,6 +227,18 @@ const std::vector<MMCifInfoEntityBranchLink> MMCifInfo::GetEntityBranchLinks() c
   return all_links;
 }
 
+const std::vector<MMCifInfoEntityBranchLink> MMCifInfo::GetEntityBranchByChain(
+                                                 const String& chain_name) const
+{
+  // search the requested chain
+  MMCifInfoEntityBranchLinkMap::const_iterator blm_it =
+                                               entity_branches_.find(chain_name);
+  if (blm_it != entity_branches_.end()) {
+    return blm_it->second;
+  }
+  return std::vector<MMCifInfoEntityBranchLink>();
+}
+
 const std::vector<String> MMCifInfo::GetEntityBranchChainNames() const
 {
   std::vector<String> chain_names;

modules/io/src/mol/mmcif_info.hh

@@ -1181,15 +1181,19 @@ public:
   ///
   const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchLinks() const;
 
+  /// \brief Check if a chain is a branched entity and return it
+  ///
+  /// \param chain_name Name of the chain to check
+  const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchByChain(
+                                                const String& chain_name) const;
+
   /// \brief Get the names of all chains of branched entities.
   ///
   const std::vector<String> GetEntityBranchChainNames() const;
 
   /// \brief Get the all chains of branched entities.
   ///
-const mol::ChainHandleList GetEntityBranchChains() const;
-
-  //GetEntityBranchByChain
+  const mol::ChainHandleList GetEntityBranchChains() const;
 
   /// \brief Connect all atoms listed as links for branched entities.
   ///

modules/io/src/mol/mmcif_reader.hh

@@ -631,7 +631,8 @@ private:
 
   /// \brief Get an iterator for MMCifEntityDescMap by finding an element or
   ///        inserting a new one into the map.
-  MMCifEntityDescMap::iterator GetEntityDescMapIterator(const String&);
+  /// \param entity_id ID of the entity to talk to
+  MMCifEntityDescMap::iterator GetEntityDescMapIterator(const String& entity_id);
 
   /// \struct assembly information
   typedef struct {

modules/io/tests/test_io_mmcif.py

@@ -306,6 +306,12 @@ class TestMMCifInfo(unittest.TestCase):
     self.assertEqual(chains[0].name, 'A')
     self.assertEqual(chains[1].name, 'B')
 
+    blinks = info.GetEntityBranchByChain('B')
+    self.assertEqual(len(blinks), 1)
+    self.assertEqual(blinks[0].atom1.qualified_name, "B.NAG2.C1")
+    blinks = info.GetEntityBranchByChain('C')
+    self.assertEqual(len(blinks), 0)
+
 if __name__== '__main__':
   from ost import testutils
   testutils.RunTests()

modules/io/tests/test_mmcif_info.cc

@@ -377,6 +377,13 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
   BOOST_CHECK(chains[0].GetName() == "A");
   BOOST_CHECK(chains[1].GetName() == "B");
 
+  // check retrieval of links by chain name
+  std::vector<MMCifInfoEntityBranchLink> cblinks =
+    info.GetEntityBranchByChain("A");
+  BOOST_CHECK(cblinks.size() == 1);
+  cblinks = info.GetEntityBranchByChain("C");
+  BOOST_CHECK(cblinks.size() == 0);
+
   BOOST_TEST_MESSAGE("  done.");
 }