From 4626551395b91ed6d581b90663e4284b1022c8b4 Mon Sep 17 00:00:00 2001
From: B13nch3n <stefan.bienert@me.com>
Date: Wed, 22 Jul 2020 09:45:21 +0200
Subject: [PATCH] SCHWED-4849: Allow to get branched entity information for a
specific chain
---
modules/io/doc/mmcif.rst | 44 +++++++++++++++++++----------
modules/io/pymod/export_mmcif_io.cc | 1 +
modules/io/src/mol/mmcif_info.cc | 12 ++++++++
modules/io/src/mol/mmcif_info.hh | 10 +++++--
modules/io/src/mol/mmcif_reader.hh | 3 +-
modules/io/tests/test_io_mmcif.py | 6 ++++
modules/io/tests/test_mmcif_info.cc | 7 +++++
7 files changed, 64 insertions(+), 19 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 2a9bccd2e..510cd7d45 100644
--- a/modules/io/doc/mmcif.rst
+++ b/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
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index ea953160f..11223672c 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/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)
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 62ea686e6..ce93b6778 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/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;
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index bebccefa0..b97949105 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/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.
///
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 03ceb32c9..c6e2e32fd 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/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 {
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 0da0a4c2e..20162281d 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/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()
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index a2b78b054..5370d2ce1 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/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.");
}
--
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