diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 4151f7269f101d4cc37d7d97d5bafff65945cc65..af007259420189de595538d71a69c4e3aea0bde0 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,8 @@
+Changes in Release 1.2.2
+
+ * Fixed loop indentation in the PDBize function for bio units, leading to
+ exponential running time/ memory consumption. This problem only affected a
+ fraction of PDB entries.
Changes in Release 1.2.1
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2b5f474ea2248f547e2211ed3a1532b94c0343f6..5e2de9e91baf2f3d894cc86338d9a50e4b0a98ad 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
project(OpenStructure CXX C)
set (OST_VERSION_MAJOR 1)
set (OST_VERSION_MINOR 2)
-set (OST_VERSION_PATCH 1)
+set (OST_VERSION_PATCH 2)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST)
diff --git a/deployment/linux/ldd-rec.pl b/deployment/linux/ldd-rec.pl
index e770bb6c07398416c2b4062365bd2530c6cd40b0..52e8455cfa101782b2bc9d8afef7e5ba712f4b73 100644
--- a/deployment/linux/ldd-rec.pl
+++ b/deployment/linux/ldd-rec.pl
@@ -16,7 +16,7 @@ push @check_queue, @ARGV;
while (@check_queue) {
my $to_check = pop @check_queue;
- if (exists $checked_libs{$to_check}) {
+ if (exists $checked_libs{$to_check} or $to_check =~ /ld-linux.so.2/) {
next;
} else {
$checked_libs{$to_check} = 1;
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 8b73a3391ec8a0a8ac5f4e41357b17738320d1d2..653088ad1a41dd9da22958bc28b8cc67f663bdfe 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -86,6 +86,8 @@ void export_Scene()
.def("GetAutoAutoslab",&Scene::GetAutoAutoslab)
.def("AutoslabMax",&Scene::AutoslabMax)
.def("Remove", remove1)
+ .def("Register", &Scene::Register)
+ .def("Unregister", &Scene::Unregister)
.def("Remove", remove2)
.add_property("viewport", &Scene::GetViewport)
.def("RequestRedraw", &Scene::RequestRedraw)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 855ed0ea208cfd8cd77ef537edd736144f6260ff..38934cc7943df2c6d1cec5f40dd43c34485368e6 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -160,6 +160,42 @@ of the annotation available.
.. method:: GetStructDetails()
+ .. method:: AddMMCifPDBChainTr(cif_chain_id, pdb_chain_id)
+
+ Set up a translation for a certain mmCIF chain name to the traditional PDB
+ chain name.
+
+ :param cif_chain_id: atom_site.label_asym_id
+ :type cif_chain_id: :class:`str`
+ :param pdb_chain_id: atom_site.auth_asym_id
+ :type pdb_chain_id: :class:`str`
+
+ .. method:: GetMMCifPDBChainTr(cif_chain_id)
+
+ Get the translation of a certain mmCIF chain name to the traditional PDB
+ chain name.
+
+ :param cif_chain_id: atom_site.label_asym_id
+ :type cif_chain_id: :class:`str`
+ :returns: atom_site.auth_asym_id as :class:`str`
+
+ .. method:: AddPDBCMMCifhainTr(pdb_chain_id, cif_chain_id)
+
+ Set up a translation for a certain PDB chain name to the mmCIF chain name.
+
+ :param pdb_chain_id: atom_site.label_asym_id
+ :type pdb_chain_id: :class:`str`
+ :param cif_chain_id: atom_site.auth_asym_id
+ :type cif_chain_id: :class:`str`
+
+ .. method:: GetPDBMMCifChainTr(pdb_chain_id)
+
+ Get the translation of a certain PDB chain name to the mmCIF chain name.
+
+ :param pdb_chain_id: atom_site.auth_asym_id
+ :type pdb_chain_id: :class:`str`
+ :returns: atom_site.label_asym_id as :class:`str`
+
.. class:: MMCifInfoCitation
This stores citation information from an input file.
@@ -746,6 +782,7 @@ of the annotation available.
.. attribute:: align_id
Uniquely identifies every struct_ref_seq item in the mmCIF file.
+
:type: :class:`str`
.. attribute:: seq_begin
@@ -793,4 +830,5 @@ of the annotation available.
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
-.. LocalWords: biounits biounit uniprot UNP seqs
+.. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
+.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 0d6d0e142147cfc499b279610081f5a0fba28610..71ea2ec6c2dcf829de2f6d6b90fa05450b4b844d 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -387,19 +387,19 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
tr = geom.Mat4()
tr = trans * rot
trans_matrices.append(tr)
- for op_n in range(1, len(operations)):
- tmp_ops = list()
- for o in operations[op_n]:
- rot = geom.Mat4()
- rot.PasteRotation(o.rotation)
- trans = geom.Mat4()
- trans.PasteTranslation(o.translation)
- tr = geom.Mat4()
- tr = trans * rot
- for t_o in trans_matrices:
- tp = t_o * tr
- tmp_ops.append(tp)
- trans_matrices = tmp_ops
+ for op_n in range(1, len(operations)):
+ tmp_ops = list()
+ for o in operations[op_n]:
+ rot = geom.Mat4()
+ rot.PasteRotation(o.rotation)
+ trans = geom.Mat4()
+ trans.PasteTranslation(o.translation)
+ tr = geom.Mat4()
+ tr = trans * rot
+ for t_o in trans_matrices:
+ tp = t_o * tr
+ tmp_ops.append(tp)
+ trans_matrices = tmp_ops
# select chains into a view as basis for each transformation
assu = asu.Select('cname=' + ','.join(biounit.GetChainList()))
# use each transformation on the view, store as entity and transform, PDBize
@@ -425,6 +425,9 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
edi.SetChainDescription(new_chain, chain.description)
edi.SetChainType(new_chain, chain.type)
new_chain.SetStringProp('original_name', chain.name)
+ if chain.HasProp("pdb_auth_chain_name"):
+ new_chain.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
for res in chain.residues:
new_res = edi.AppendResidue(new_chain, res.name, res.number)
_CopyAtoms(res, new_res, edi, tr)
@@ -455,6 +458,10 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
mol.ResNum(last_rnum+1, ins_code))
new_res.SetStringProp('description', chain.description)
new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp("original_name", chain.name)
+ if chain.HasProp("pdb_auth_chain_name"):
+ new_res.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
ins_code = chr(ord(ins_code)+1)
_CopyAtoms(res, new_res, edi, tr)
conop.ConnectAll(pdb_bu)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 6654393be01fefaefa346b9f86bcdef5f63e9c7e..18ec3713b0eaabad5121727e1389fa87001782df 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -280,6 +280,10 @@ void export_mmcif_io()
.def("GetStructDetails", &MMCifInfo::GetStructDetails)
.def("SetObsoleteInfo", &MMCifInfo::SetObsoleteInfo)
.def("GetObsoleteInfo", &MMCifInfo::GetObsoleteInfo)
+.def("AddMMCifPDBChainTr", &MMCifInfo::AddMMCifPDBChainTr)
+ .def("GetMMCifPDBChainTr", &MMCifInfo::GetMMCifPDBChainTr)
+ .def("AddPDBMMCifChainTr", &MMCifInfo::AddPDBMMCifChainTr)
+ .def("GetPDBMMCifChainTr", &MMCifInfo::GetPDBMMCifChainTr)
.add_property("citations", make_function(&MMCifInfo::GetCitations,
return_value_policy<copy_const_reference>()))
.add_property("biounits", make_function(&MMCifInfo::GetBioUnits,
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index c8565a2e809ff1f84b182b9f73e4cacd1866c509..29f0db7463188068b3584a49457126d7ec1601d0 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -22,6 +22,42 @@
namespace ost { namespace io {
+void MMCifInfo::AddMMCifPDBChainTr(String cif, String pdb)
+{
+ std::map<String, String>::iterator tr_it = cif_2_pdb_chain_id_.find(cif);
+ if (tr_it != cif_2_pdb_chain_id_.end()) {
+ throw IOException("mmCIF chain id '"+ cif +"' is already mapped to '"+
+ tr_it->second+"'.");
+ }
+ cif_2_pdb_chain_id_.insert(std::pair<String, String>(cif, pdb));
+}
+
+String MMCifInfo::GetMMCifPDBChainTr(String cif) const
+{
+ std::map<String, String>::const_iterator tr_it =
+ cif_2_pdb_chain_id_.find(cif);
+ if (tr_it == cif_2_pdb_chain_id_.end()) { return ""; }
+ return tr_it->second;
+}
+
+void MMCifInfo::AddPDBMMCifChainTr(String pdb, String cif)
+{
+ std::map<String, String>::iterator tr_it = pdb_2_cif_chain_id_.find(pdb);
+ if (tr_it != pdb_2_cif_chain_id_.end()) {
+ throw IOException("PDB chain id '"+ pdb +"' is already mapped to '"+
+ tr_it->second+"'.");
+ }
+ pdb_2_cif_chain_id_.insert(std::pair<String, String>(pdb, cif));
+}
+
+String MMCifInfo::GetPDBMMCifChainTr(String pdb) const
+{
+ std::map<String, String>::const_iterator tr_it =
+ pdb_2_cif_chain_id_.find(pdb);
+ if (tr_it == pdb_2_cif_chain_id_.end()) { return ""; }
+ return tr_it->second;
+}
+
void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
{
// find citation
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index b240e5a1c86eedaddd76de2ba71bbe009b590f3d..3eebf54b2369947c9d007e616c4d33c2f968750c 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -22,6 +22,7 @@
#include <vector>
#include <map>
#include <boost/shared_ptr.hpp>
+#include <ost/seq/sequence_list.hh>
#include <ost/geom/geom.hh>
#include <ost/string_ref.hh>
#include <ost/io/module_config.hh>
@@ -771,6 +772,30 @@ public:
/// \return experiment resolution
Real GetResolution() const { return resolution_; }
+ /// \brief Add a new mmCIF/ PDB chain name tuple.
+ ///
+ /// \param cif chain name as used by the mmCIF file (label_asym_id)
+ /// \param pdb chain name as used in the PDB file (auth_asym_id)
+ void AddMMCifPDBChainTr(String cif, String pdb);
+
+ /// \brief Get a PDB chain name for a CIF chain name
+ ///
+ /// \param cif chain name as used by the mmCIF file (label_asym_id)
+ /// \return chain name as used in the PDB file (auth_asym_id)
+ String GetMMCifPDBChainTr(String cif) const;
+
+ /// \brief Add a new PDB/ mmCIF chain name tuple.
+ ///
+ /// \param pdb chain name as used by the PDB file (auth_asym_id)
+ /// \param cif chain name as used in the mmCIF file (label_asym_id)
+ void AddPDBMMCifChainTr(String pdb, String cif);
+
+ /// \brief Get a CIF chain name for a PDB chain name
+ ///
+ /// \param pdb chain name as used by the mmCIF file (auth_asym_id)
+ /// \return chain name as used in the PDB file (label_asym_id)
+ String GetPDBMMCifChainTr(String pdb) const;
+
/// \brief Add a biounit
///
/// \param bu biounit to be added
@@ -848,6 +873,8 @@ private:
std::vector<MMCifInfoBioUnit> biounits_; ///< list of biounits
std::vector<MMCifInfoTransOpPtr> transops_;
MMCifInfoStructRefs struct_refs_;
+ std::map<String, String> cif_2_pdb_chain_id_;
+ std::map<String, String> pdb_2_cif_chain_id_;
};
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 2bcdee810c013971aec9f1c9f631320bbfe719b6..762939ca817800366ee487ffadef9da493f5103a 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1539,6 +1539,7 @@ void MMCifReader::OnEndData()
// process chain types
std::vector<std::pair<mol::ChainHandle, String> >::const_iterator css;
MMCifEntityDescMap::const_iterator edm_it;
+ String pdb_auth_chain_name;
for (css = chain_id_pairs_.begin(); css != chain_id_pairs_.end(); ++css) {
edm_it = entity_desc_map_.find(css->second);
@@ -1548,6 +1549,9 @@ void MMCifReader::OnEndData()
if (edm_it->second.seqres.length() > 0) {
seqres_.AddSequence(seq::CreateSequence(css->first.GetName(),
edm_it->second.seqres));
+ pdb_auth_chain_name = css->first.GetStringProp("pdb_auth_chain_name");
+ info_.AddMMCifPDBChainTr(css->first.GetName(), pdb_auth_chain_name);
+ info_.AddPDBMMCifChainTr(pdb_auth_chain_name, css->first.GetName());
} else if (edm_it->second.type!=mol::CHAINTYPE_WATER) {
// mark everything that doesn't have SEQRES as ligand and isn't of type
// water as ligand
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 3d26747976b618212b05d0416012ecc2b78f5fc5..65e4fdaecb42ec54fb50d3c579f24ba8b7ae8adb 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -202,7 +202,17 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
#else
BOOST_CHECK_CLOSE(info.GetResolution(), 1.9f, 0.001f);
#endif
-
+
+ info.AddMMCifPDBChainTr("A", "B");
+ BOOST_CHECK_THROW(info.AddMMCifPDBChainTr("A", "B"), IOException);
+ BOOST_CHECK("B" == info.GetMMCifPDBChainTr("A"));
+ BOOST_CHECK("" == info.GetMMCifPDBChainTr("C"));
+
+ info.AddPDBMMCifChainTr("A", "B");
+ BOOST_CHECK_THROW(info.AddPDBMMCifChainTr("A", "B"), IOException);
+ BOOST_CHECK("B" == info.GetPDBMMCifChainTr("A"));
+ BOOST_CHECK("" == info.GetPDBMMCifChainTr("C"));
+
BOOST_MESSAGE(" done.");
}
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index ce890cf9d3be305019cbc431726433df8a06beee..68b2fbb5769c6e735ec7e30cb7311f002f9b3346 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -168,10 +168,10 @@ ATOM C CB ILE A 13 . 1 21.236 34.463 16.492 1.00 22.67 . 13 21 ? A
ATOM C CG1 ILE A 13 . 1 20.478 33.469 17.371 1.00 22.14 . 13 22 ? A
ATOM C CG2 ILE A 13 . 1 21.357 33.986 15.016 1.00 21.75 . 13 23 ? A
# - - - - data truncated for brevity - - - -
-HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? A
-HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? A
-HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? A
-HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? A
+HETATM C C1 APS C 1 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 ? C
+HETATM C C2 APS C 1 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 ? C
+HETATM O O3 APS C 1 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 ? C
+HETATM N N4 APS C 1 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 ? C
# - - - - data truncated for brevity - - - -
# chain to be ignored by 'restrict_chains' feature
ATOM N N ILE Z 1 . 1 23.664 33.855 16.884 1.00 22.08 . 1 17 ? Z
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 2142989048973aaec76da73470c078e69e212c16..3a320ce22843667079c1f03ffa80586dfeadb5ae 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -109,8 +109,8 @@ int main (int argc, char **argv)
{
// sets some default values for parameters
String version = "1.2";
- Real bond_tolerance = 15.0;
- Real angle_tolerance = 15.0;
+ Real bond_tolerance = 12.0;
+ Real angle_tolerance = 12.0;
Real radius=15.0;
int sequence_separation = 0;