diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 0572ce2b9f34d6dd332b131273cd7460cfb80cca..33aa310fee90640e8ee9f3fdcf560ca58c04223d 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -3,14 +3,14 @@ mmCIF File Format
.. currentmodule:: ost.io
-The mmCIF file format is an alternate container for structural entities, also
-provided by the PDB. Here we describe how to load those files and how to deal
-with information provided above the common PDB format (:class:`MMCifInfo`,
+The mmCIF file format is a container for structural entities provided by the
+PDB. Here we describe how to load those files and how to deal with information
+provided above the legacy PDB format (:class:`MMCifInfo`,
:class:`MMCifInfoCitation`, :class:`MMCifInfoTransOp`,
:class:`MMCifInfoBioUnit`, :class:`MMCifInfoStructDetails`,
:class:`MMCifInfoObsolete`, :class:`MMCifInfoStructRef`,
:class:`MMCifInfoStructRefSeq`, :class:`MMCifInfoStructRefSeqDif`,
-:class:`MMCifInfoRevisions`).
+:class:`MMCifInfoRevisions`, :class:`MMCifInfoEntityBranchLink`).
Loading mmCIF Files
@@ -50,6 +50,9 @@ The following categories of a mmCIF file are considered by the reader:
:class:`MMCifInfoRevisions`
* ``pdbx_audit_revision_history`` and ``pdbx_audit_revision_details``
(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`
Notes:
@@ -303,6 +306,31 @@ of the annotation available.
See :attr:`obsolete`
+ .. method:: GetEntityBranchLinks()
+
+ Get bond information for branched entities. Returns all
+ :class:`MMCifInfoEntityBranchLink` objects in one list. Chain and residue
+ information is available by the stored
+ :class:`AtomHandles <ost.mol.AtomHandle>` of each entry.
+
+ .. method:: AddEntityBranchLink(chain_name, atom1, atom2, bond_order)
+
+ Add bond information for a branched entity.
+
+ :param chain_name: Chain the bond belongs to
+ :type chain_name: :class:`str`
+ :param atom1: First atom of the bond
+ :type atom1: :class:`~ost.mol.AtomHandle`
+ :param atom2: Second atom of the bond
+ :type atom2: :class:`~ost.mol.AtomHandle`
+ :param bond_order: bond order (e.g. 1=single, 2=double, 3=triple)
+ :type bond_order: :class:`int`
+ :returns: Nothing
+
+ .. method:: ConnectBranchLinks()
+
+ Establish all bonds stored for branched entities.
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 8f5836c6edc63be2c592389e26d2526b4c993b6a..cf8063d011627d477fd7401d004d7b6664a621f7 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -277,9 +277,9 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
def LoadMMCIF(filename, fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, seqres=False, info=False):
"""
- Load MMCIF file from disk and return one or more entities. Several options
- allow to customize the exact behaviour of the MMCIF import. For more
- information on these options, see :doc:`profile`.
+ Load a mmCIF file and return one or more entities. Several options allow to
+ customize the exact behaviour of the mmCIF import. For more information on
+ these options, see :doc:`profile`.
Residues are flagged as ligand if they are mentioned in a HET record.
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index aa7b290a563cefa37aa4fdea444203856293a94b..b8dae1b0509e0e13fc081f52d3456555bf350324 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -333,31 +333,33 @@ void export_mmcif_io()
.add_property("first_release", &MMCifInfoRevisions::GetFirstRelease)
;
- class_<MMCifInfoEntityBranch>("MMCifInfoEntityBranch", init<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)
+ class_<MMCifInfoEntityBranchLink>("MMCifInfoEntityBranchLink",
+ init<mol::AtomHandle,
+ mol::AtomHandle, unsigned char>())
+ .def("GetAtom1", &MMCifInfoEntityBranchLink::GetAtom1)
+ .def("GetAtom2", &MMCifInfoEntityBranchLink::GetAtom2)
+ .def("GetBondOrder", &MMCifInfoEntityBranchLink::GetBondOrder)
+ .def("ConnectBranchLink", &MMCifInfoEntityBranchLink::ConnectBranchLink)
+ .def("SetAtom1", &MMCifInfoEntityBranchLink::SetAtom1)
+ .def("SetAtom2", &MMCifInfoEntityBranchLink::SetAtom2)
+ .def("SetBondOrder", &MMCifInfoEntityBranchLink::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)
+ .add_property("atom1", &MMCifInfoEntityBranchLink::GetAtom1,
+ &MMCifInfoEntityBranchLink::SetAtom1)
+ .add_property("atom2", &MMCifInfoEntityBranchLink::GetAtom2,
+ &MMCifInfoEntityBranchLink::SetAtom2)
+ .add_property("bond_order", &MMCifInfoEntityBranchLink::GetBondOrder,
+ &MMCifInfoEntityBranchLink::SetBondOrder)
;
- class_<MMCifInfoEntityBranchMap>("MMCifInfoEntityBranchMap", init<>())
- .def(map_indexing_suite<MMCifInfoEntityBranchMap>())
+ class_<MMCifInfoEntityBranchLinkMap>("MMCifInfoEntityBranchLinkMap", init<>())
+ .def(map_indexing_suite<MMCifInfoEntityBranchLinkMap>())
;
- class_<std::vector<MMCifInfoEntityBranch> >("MMCifInfoEntityBranchList",
- init<>())
- .def(vector_indexing_suite<std::vector<MMCifInfoEntityBranch> >())
+ class_<std::vector<MMCifInfoEntityBranchLink> >(
+ "MMCifInfoEntityBranchLinkList",
+ init<>())
+ .def(vector_indexing_suite<std::vector<MMCifInfoEntityBranchLink> >())
.def(self_ns::str(self))
;
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 43dca70f8eab97b2954550883d56386f2191e382..5db86d1cc86144d3cdeadb221b62ed2b241bebe4 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -201,23 +201,24 @@ void MMCifInfo::AddEntityBranchLink(String chain_name,
unsigned char bond_order)
{
// check if element already exists
- MMCifInfoEntityBranchMap::iterator blm_it = entity_branches_.find(chain_name);
+ MMCifInfoEntityBranchLinkMap::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>()));
+ std::pair<MMCifInfoEntityBranchLinkMap::iterator, bool> rit =
+ entity_branches_.insert(MMCifInfoEntityBranchLinkMap::value_type(chain_name,
+ std::vector<MMCifInfoEntityBranchLink>()));
// 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, bond_order));
+ blm_it->second.push_back(MMCifInfoEntityBranchLink(atom1, atom2, bond_order));
}
-const std::vector<MMCifInfoEntityBranch> MMCifInfo::GetEntityBranchLinks() const
+const std::vector<MMCifInfoEntityBranchLink> MMCifInfo::GetEntityBranchLinks() const
{
- std::vector<MMCifInfoEntityBranch> all_links;
- MMCifInfoEntityBranchMap::const_iterator blm_it;
+ std::vector<MMCifInfoEntityBranchLink> all_links;
+ MMCifInfoEntityBranchLinkMap::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(),
@@ -228,12 +229,13 @@ const std::vector<MMCifInfoEntityBranch> MMCifInfo::GetEntityBranchLinks() const
void MMCifInfo::ConnectBranchLinks()
{
- MMCifInfoEntityBranchMap::iterator blm_it;
+ MMCifInfoEntityBranchLinkMap::iterator blm_it;
for (blm_it = entity_branches_.begin();
blm_it != entity_branches_.end(); ++blm_it) {
// We assume that one chain only comes from one entity, so we go with one
// editor per chain
- std::vector<MMCifInfoEntityBranch>::iterator blv_it = blm_it->second.begin();
+ std::vector<MMCifInfoEntityBranchLink>::iterator blv_it =
+ blm_it->second.begin();
if (blv_it != blm_it->second.end()) {
mol::XCSEditor editor = blv_it->GetAtom1().GetEntity().EditXCS();
for (; blv_it != blm_it->second.end(); ++blv_it) {
@@ -243,18 +245,18 @@ void MMCifInfo::ConnectBranchLinks()
}
}
-std::ostream& operator<<(std::ostream& os, const MMCifInfoEntityBranch& eb)
+std::ostream& operator<<(std::ostream& os, const MMCifInfoEntityBranchLink& eb)
{
- os << "<MMCifInfoEntityBranch atom1:" << eb.GetAtom1() << " atom2:"
+ os << "<MMCifInfoEntityBranchLink atom1:" << eb.GetAtom1() << " atom2:"
<< eb.GetAtom2() << ">";
return os;
}
std::ostream& operator<<(std::ostream& os,
- const std::vector<MMCifInfoEntityBranch>& eb_list)
+ const std::vector<MMCifInfoEntityBranchLink>& eb_list)
{
- os << "<MMCifInfoEntityBranchList";
- std::vector<MMCifInfoEntityBranch>::const_iterator bl_it;
+ os << "<MMCifInfoEntityBranchLinkList";
+ std::vector<MMCifInfoEntityBranchLink>::const_iterator bl_it;
for (bl_it = eb_list.begin(); bl_it != eb_list.end(); ++bl_it) {
os << " <atom1:" << bl_it->GetAtom1() << " atom2:"
<< bl_it->GetAtom2() << ">";
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index db32cd504f87940951a490e1c3188486fb3f7c49..15237188546fe36add5a81a786d8ac72c96e9ed0 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -921,11 +921,11 @@ private:
/// \brief Store information on brnached structures (oligosaccharides)
///
-class DLLEXPORT_OST_IO MMCifInfoEntityBranch {
+class DLLEXPORT_OST_IO MMCifInfoEntityBranchLink {
public:
- MMCifInfoEntityBranch(mol::AtomHandle atom1,
- mol::AtomHandle atom2,
- unsigned char bond_order):
+ MMCifInfoEntityBranchLink(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_; }
@@ -937,7 +937,7 @@ atom1_(atom1), atom2_(atom2), bond_order_(bond_order) {}
editor.Connect(atom1_, atom2_, bond_order_);
}
- bool operator==(const MMCifInfoEntityBranch& eb) const {
+ bool operator==(const MMCifInfoEntityBranchLink& eb) const {
if (this->atom1_ != eb.atom1_) {
return false;
}
@@ -947,7 +947,7 @@ atom1_(atom1), atom2_(atom2), bond_order_(bond_order) {}
return true;
}
- bool operator!=(const MMCifInfoEntityBranch& eb) const {
+ bool operator!=(const MMCifInfoEntityBranchLink& eb) const {
return !this->operator == (eb);
}
@@ -956,7 +956,7 @@ private:
mol::AtomHandle atom2_;
unsigned char bond_order_;
};
-typedef std::map<String, std::vector<MMCifInfoEntityBranch> > MMCifInfoEntityBranchMap;
+typedef std::map<String, std::vector<MMCifInfoEntityBranchLink> > MMCifInfoEntityBranchLinkMap;
/// \brief container class for additional information from MMCif files
///
@@ -1179,7 +1179,7 @@ public:
/// \brief Get all links for all branched entities
///
- const std::vector<MMCifInfoEntityBranch> GetEntityBranchLinks() const;
+ const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchLinks() const;
//GetEntityBranchChains
//GetEntityBranchByChain
@@ -1205,14 +1205,14 @@ private:
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_;
+ std::map<String, std::vector<MMCifInfoEntityBranchLink> > entity_branches_;
};
DLLEXPORT_OST_IO std::ostream& operator<<(std::ostream& os,
- const MMCifInfoEntityBranch& eb);
+ const MMCifInfoEntityBranchLink& eb);
DLLEXPORT_OST_IO std::ostream& operator<<(std::ostream& os,
- const std::vector<MMCifInfoEntityBranch>& eb_list);
+ const std::vector<MMCifInfoEntityBranchLink>& eb_list);
}} // ns
#endif
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 8e909c349449776b44018dff29bb43607909430c..d0f902ac48aa8b2ad744a8c189c8a96009703acd 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -264,7 +264,7 @@ class TestMMCifInfo(unittest.TestCase):
self.assertEqual(len(crambin_pdb.atoms), 327)
def test_mmcifinfo_entitybranch(self):
- # test MMCifInfoEntityBranch
+ # test MMCifInfoEntityBranchLink
eh = mol.CreateEntity()
editor = eh.EditXCS();
ch = editor.InsertChain("A");
@@ -272,7 +272,7 @@ 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, 1)
+ branch = io.MMCifInfoEntityBranchLink(atom1, atom2, 1)
self.assertEqual(branch.atom1.qualified_name, "A.MAN2.C1")
self.assertEqual(branch.bond_order, 1)
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 2c4a760e3e41df03a2ddd32ff8d90b88ddf8be4d..0ab74afb94bb1c3056bdf1042a9b2c1b36f5b67c 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -293,7 +293,7 @@ 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, 1);
+ MMCifInfoEntityBranchLink 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);
@@ -351,7 +351,7 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
mol::AtomHandle atom22 = editor.InsertAtom(res21, "O3",geom::Vec3());
info.AddEntityBranchLink(ch1.GetName(), atom11, atom12, 1);
info.AddEntityBranchLink(ch2.GetName(), atom21, atom22, 1);
- std::vector<MMCifInfoEntityBranch> blinks = info.GetEntityBranchLinks();
+ std::vector<MMCifInfoEntityBranchLink> blinks = info.GetEntityBranchLinks();
BOOST_CHECK(blinks.size() == 2);
BOOST_CHECK(blinks[0].GetAtom1().GetQualifiedName() == "A.NAG2.C1");