diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index fb0e2ebe10a1c1e9f36a54168e3fa5ab9cfecb5b..aa7b290a563cefa37aa4fdea444203856293a94b 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -334,17 +334,21 @@ void export_mmcif_io()
;
class_<MMCifInfoEntityBranch>("MMCifInfoEntityBranch", init<mol::AtomHandle,
- mol::AtomHandle>())
+ mol::AtomHandle, unsigned char>())
.def("GetAtom1", &MMCifInfoEntityBranch::GetAtom1)
.def("GetAtom2", &MMCifInfoEntityBranch::GetAtom2)
+ .def("GetBondOrder", &MMCifInfoEntityBranch::GetBondOrder)
.def("ConnectBranchLink", &MMCifInfoEntityBranch::ConnectBranchLink)
.def("SetAtom1", &MMCifInfoEntityBranch::SetAtom1)
.def("SetAtom2", &MMCifInfoEntityBranch::SetAtom2)
+ .def("SetBondOrder", &MMCifInfoEntityBranch::SetBondOrder)
.def(self_ns::str(self))
.add_property("atom1", &MMCifInfoEntityBranch::GetAtom1,
&MMCifInfoEntityBranch::SetAtom1)
.add_property("atom2", &MMCifInfoEntityBranch::GetAtom2,
&MMCifInfoEntityBranch::SetAtom2)
+ .add_property("bond_order", &MMCifInfoEntityBranch::GetBondOrder,
+ &MMCifInfoEntityBranch::SetBondOrder)
;
class_<MMCifInfoEntityBranchMap>("MMCifInfoEntityBranchMap", init<>())
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index c797a14f8ede547fef96a1f427beb8d6c71fc63a..43dca70f8eab97b2954550883d56386f2191e382 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -197,7 +197,8 @@ MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String&
void MMCifInfo::AddEntityBranchLink(String chain_name,
mol::AtomHandle atom1,
- mol::AtomHandle atom2)
+ mol::AtomHandle atom2,
+ unsigned char bond_order)
{
// check if element already exists
MMCifInfoEntityBranchMap::iterator blm_it = entity_branches_.find(chain_name);
@@ -210,7 +211,7 @@ void MMCifInfo::AddEntityBranchLink(String chain_name,
blm_it = rit.first;
}
// add new branch element
- blm_it->second.push_back(MMCifInfoEntityBranch(atom1, atom2));
+ blm_it->second.push_back(MMCifInfoEntityBranch(atom1, atom2, bond_order));
}
const std::vector<MMCifInfoEntityBranch> MMCifInfo::GetEntityBranchLinks() const
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 4e5e62a9df730981b7760b6247501b08ab428d4f..db32cd504f87940951a490e1c3188486fb3f7c49 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -923,14 +923,18 @@ private:
///
class DLLEXPORT_OST_IO MMCifInfoEntityBranch {
public:
- MMCifInfoEntityBranch(mol::AtomHandle atom1, mol::AtomHandle atom2):
- atom1_(atom1), atom2_(atom2) {}
+ MMCifInfoEntityBranch(mol::AtomHandle atom1,
+ mol::AtomHandle atom2,
+ unsigned char bond_order):
+atom1_(atom1), atom2_(atom2), bond_order_(bond_order) {}
mol::AtomHandle GetAtom1() const { return atom1_;}
mol::AtomHandle GetAtom2() const { return atom2_; }
+ unsigned char GetBondOrder() const { return bond_order_; }
void SetAtom1(mol::AtomHandle atom) { atom1_ = atom; }
void SetAtom2(mol::AtomHandle atom) { atom2_ = atom; }
+ void SetBondOrder(unsigned char bond_order) { bond_order_ = bond_order; }
void ConnectBranchLink(mol::XCSEditor editor) {
- editor.Connect(atom1_, atom2_);
+ editor.Connect(atom1_, atom2_, bond_order_);
}
bool operator==(const MMCifInfoEntityBranch& eb) const {
@@ -950,6 +954,7 @@ public:
private:
mol::AtomHandle atom1_;
mol::AtomHandle atom2_;
+ unsigned char bond_order_;
};
typedef std::map<String, std::vector<MMCifInfoEntityBranch> > MMCifInfoEntityBranchMap;
@@ -1169,7 +1174,8 @@ public:
/// \param atom2 second atom of the bond
void AddEntityBranchLink(String chain_name,
mol::AtomHandle atom1,
- mol::AtomHandle atom2);
+ mol::AtomHandle atom2,
+ unsigned char bond_order);
/// \brief Get all links for all branched entities
///
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 8eeb71924f49d0a30a03325ca9b493513f129cf0..1eb1220708e8538aeb81dcc1f647e98795f62523 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1757,9 +1757,13 @@ void MMCifReader::ParsePdbxEntityBranchLink(const std::vector<StringRef>& column
// 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) {
- }*/
+ // check value order
+ if (indices_[BL_VALUE_ORDER] != -1) {
+ link_pair.bond_order = MMCifValueOrderToOSTBondOrder(
+ columns[indices_[BL_VALUE_ORDER]]);
+ } else {
+ link_pair.bond_order = 1;
+ }
std::pair<MMCifPdbxEntityBranchLinkMap::iterator, bool> rit;
@@ -1827,7 +1831,8 @@ void MMCifReader::OnEndData()
bl_it->res_num_2, ' '));
info_.AddEntityBranchLink(css->first.GetName(),
res1.FindAtom(bl_it->atm_nm_1),
- res2.FindAtom(bl_it->atm_nm_2));
+ res2.FindAtom(bl_it->atm_nm_2),
+ bl_it->bond_order);
}
}
}
@@ -1924,4 +1929,64 @@ void MMCifReader::OnEndData()
<< strand_list_.size() << " strands");
}
+unsigned char MMCifValueOrderToOSTBondOrder(const StringRef value_order)
+{
+ if (value_order == StringRef("sing", 4)) {
+ return 1;
+ }
+ if (value_order == StringRef("doub", 4)) {
+ return 2;
+ }
+ if (value_order == StringRef("trip", 4)) {
+ return 3;
+ }
+ LOG_WARNING("Non-covered bond order found: '" << value_order << "'");
+ if (value_order == StringRef("arom", 4)) {
+ return 4;
+ }
+ if (value_order == StringRef("delo", 4)) {
+ return 5;
+ }
+ if (value_order == StringRef("pi", 2)) {
+ return 6;
+ }
+ if (value_order == StringRef("poly", 4)) {
+ return 7;
+ }
+ if (value_order == StringRef("quad", 4)) {
+ return 8;
+ }
+ return 1;
+}
+
+String OSTBondOrderToMMCifValueOrder(const unsigned char bond_order)
+{
+ if (bond_order == 1) {
+ return String("sing");
+ }
+ if (bond_order == 2) {
+ return String("doub");
+ }
+ if (bond_order == 3) {
+ return String("trip");
+ }
+ if (bond_order == 4) {
+ return String("arom");
+ }
+ if (bond_order == 5) {
+ return String("delo");
+ }
+ if (bond_order == 6) {
+ return String("pi");
+ }
+ if (bond_order == 7) {
+ return String("poly");
+ }
+ if (bond_order == 8) {
+ return String("quad");
+ }
+ LOG_WARNING("Unknow bond order found: '" << (int)bond_order << "'");
+ return String("");
+}
+
}}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 8d975600c4737a8e36e55277ec8e04c148817098..a9339c6acc6d423ff49b03d22efd8eb778dbb290 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -680,6 +680,7 @@ private:
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
+ unsigned char bond_order; ///< ID of value_order as OST bond_order
} MMCifPdbxEntityBranchLink;
typedef std::map<String, std::vector<MMCifPdbxEntityBranchLink> >
MMCifPdbxEntityBranchLinkMap;
@@ -723,6 +724,18 @@ private:
MMCifPdbxEntityBranchLinkMap entity_branch_link_map_;
};
+/// \brief Translate mmCIF info on bond type (e.g.
+/// pdbx_entity_branch_link.value_order) to OST bond_order
+///
+/// \param value_order abbreviation detemrining the bond order
+DLLEXPORT_OST_IO unsigned char MMCifValueOrderToOSTBondOrder(
+ const StringRef value_order);
+
+/// \brief Translate an OST bond_order to mmCIF value_order
+///
+/// \param bond_order OST bond order
+DLLEXPORT_OST_IO String OSTBondOrderToMMCifValueOrder(
+ const unsigned char bond_order);
}}
#endif
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 8f850f55eef11d668729513c8ecdd9fc1b5ee6dd..8e909c349449776b44018dff29bb43607909430c 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -272,8 +272,9 @@ class TestMMCifInfo(unittest.TestCase):
res2 = editor.AppendResidue(ch, "MAN");
atom1 = editor.InsertAtom(res2, "C1", geom.Vec3());
atom2 = editor.InsertAtom(res1, "O3", geom.Vec3());
- branch = io.MMCifInfoEntityBranch(atom1, atom2)
+ branch = io.MMCifInfoEntityBranch(atom1, atom2, 1)
self.assertEqual(branch.atom1.qualified_name, "A.MAN2.C1")
+ self.assertEqual(branch.bond_order, 1)
branch.ConnectBranchLink(editor)
self.assertEqual(atom2.GetBondPartners()[0].qualified_name, "A.MAN2.C1")
@@ -285,14 +286,16 @@ class TestMMCifInfo(unittest.TestCase):
atom3 = editor.InsertAtom(res2, "C1", geom.Vec3());
atom4 = editor.InsertAtom(res1, "O4", geom.Vec3());
info = io.MMCifInfo()
- info.AddEntityBranchLink("A", atom1, atom2)
- info.AddEntityBranchLink(ch.name, atom3, atom4)
+ info.AddEntityBranchLink("A", atom1, atom2, 1)
+ info.AddEntityBranchLink(ch.name, atom3, atom4, 1)
blinks = info.GetEntityBranchLinks()
self.assertEqual(blinks[0].GetAtom1().qualified_name, "A.MAN2.C1")
self.assertEqual(blinks[0].atom2.qualified_name, "A.BMA1.O3")
+ self.assertEqual(blinks[0].GetBondOrder(), 1)
self.assertEqual(blinks[1].atom1.qualified_name, "B.NAG2.C1")
self.assertEqual(blinks[1].GetAtom2().qualified_name, "B.NAG1.O4")
+ self.assertEqual(blinks[1].GetBondOrder(), 1)
info.ConnectBranchLinks()
self.assertEqual(atom4.GetBondPartners()[0].qualified_name, "B.NAG2.C1")
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 6265eba1db4486dffef8ac04eeea2030d6af4f9d..2c4a760e3e41df03a2ddd32ff8d90b88ddf8be4d 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -293,10 +293,11 @@ BOOST_AUTO_TEST_CASE(mmcif_info_branch)
mol::AtomHandle atom1 = editor.InsertAtom(res2, "C1",geom::Vec3());
mol::AtomHandle atom2 = editor.InsertAtom(res1, "O4",geom::Vec3());
- MMCifInfoEntityBranch branch1(atom1, atom2);
+ MMCifInfoEntityBranch branch1(atom1, atom2, 1);
BOOST_CHECK(branch1.GetAtom1().GetQualifiedName() == "A.NAG2.C1");
BOOST_CHECK(branch1.GetAtom2().GetQualifiedName() == "A.NAG1.O4");
-
+ BOOST_CHECK(branch1.GetBondOrder() == 1);
+
BOOST_TEST_MESSAGE(" done.");
}
@@ -348,15 +349,17 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
// 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);
+ info.AddEntityBranchLink(ch1.GetName(), atom11, atom12, 1);
+ info.AddEntityBranchLink(ch2.GetName(), atom21, atom22, 1);
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[0].GetBondOrder() == 1);
BOOST_CHECK(blinks[1].GetAtom1().GetQualifiedName() == "B.MAN2.C1");
BOOST_CHECK(blinks[1].GetAtom2().GetQualifiedName() == "B.BMA1.O3");
+ BOOST_CHECK(blinks[1].GetBondOrder() == 1);
// check that branch links get bonds
info.ConnectBranchLinks();