diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index b88f983bef4c94aeaae19b6c777bd9c3b9cc41a6..8af2ab6cc20f088401c9e80038d8bc98e31f8561 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -1142,7 +1142,8 @@ class Table(object):
def PlotHistogram(self, col, x_range=None, num_bins=10, normed=False,
histtype='stepfilled', align='mid', x_title=None,
- y_title=None, title=None, clear=True, save=False):
+ y_title=None, title=None, clear=True, save=False,
+ color=None, y_range=None):
"""
Create a histogram of the data in col for the range *x_range*, split into
*num_bins* bins and plot it using Matplotlib.
@@ -1153,9 +1154,16 @@ class Table(object):
:param x_range: start and end value for first dimension (e.g. [start_x, end_x])
:type x_range: :class:`list` of length two
+ :param y_range: start and end value for second dimension (e.g. [start_y, end_y])
+ :type y_range: :class:`list` of length two
+
:param num_bins: number of bins in range
:type num_bins: :class:`int`
+ :param color: Color to be used for the histogram. If not set, color will be
+ determined by matplotlib
+ :type color: :class:`str`
+
:param normed: normalize histogram
:type normed: :class:`bool`
@@ -1202,7 +1210,9 @@ class Table(object):
if len(self.rows)==0:
return None
-
+ kwargs={}
+ if color:
+ kwargs['color']=color
idx = self.GetColIndex(col)
data = []
for r in self.rows:
@@ -1213,21 +1223,23 @@ class Table(object):
plt.clf()
n, bins, patches = plt.hist(data, bins=num_bins, range=x_range,
- normed=normed, histtype=histtype, align=align)
+ normed=normed, histtype=histtype, align=align,
+ **kwargs)
- if x_title:
+ if x_title!=None:
nice_x=x_title
else:
nice_x=MakeTitle(col)
plt.xlabel(nice_x, size='x-large')
-
- if y_title:
+ if y_range:
+ plt.ylim(y_range)
+ if y_title!=None:
nice_y=y_title
else:
nice_y="bin count"
plt.ylabel(nice_y, size='x-large')
- if title:
+ if title!=None:
nice_title=title
else:
nice_title="Histogram of %s"%nice_x
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index dbf9ce5bbc39da3573fb4482258c349d3ab6b5e9..18728c2cf3feee60f5727efffd5a61c098f4151b 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -107,6 +107,8 @@ void export_Scene()
.def("Autoslab", autoslab3) // DEPRECATED
.def("AutoslabMax",&Scene::AutoslabMax) // DEPRECATED
.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/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index 122745ba46772dc3fd9679db6d6ac4f4fbd528fe..4ac7f7cfe75a5fe6a0e843a4389e64e02e8228ed 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -85,6 +85,7 @@ set(OST_GUI_PYMOD_MODULES
init_splash.py
traj.py
helpwidget.py
+ table.py
)
set(OST_GUI_PYMOD_DNG_MODULES
diff --git a/modules/gui/pymod/init_spacenav.py b/modules/gui/pymod/init_spacenav.py
index 847ec5d4b983057a715c85882924daabb87cc6cb..c05a59a2dbee5d372870ec12db1090bb485c5e46 100644
--- a/modules/gui/pymod/init_spacenav.py
+++ b/modules/gui/pymod/init_spacenav.py
@@ -23,7 +23,9 @@ class SpacenavControl(QtCore.QObject):
if r==0.0:
return 0.0
rr=r/abs(r)*max(0.0,abs(r)-0.9)
- return rr/abs(rr)*(math.pow(1.01,abs(rr))-1.0)*40.0/self.speed if abs(rr)>0.0 else 0.0
+ if abs(rr)>0:
+ return rr/abs(rr)*(math.pow(1.01,abs(rr))-1.0)*40.0/self.speed
+ return 0.0
if(self.trans):
tf.ApplyXAxisTranslation(d(tx))
tf.ApplyYAxisTranslation(d(ty))
diff --git a/modules/gui/pymod/table.py b/modules/gui/pymod/table.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd65e9ff69ad2a9f496894c3e30b58ad5f18e52e
--- /dev/null
+++ b/modules/gui/pymod/table.py
@@ -0,0 +1,49 @@
+from PyQt4.QtGui import *
+from PyQt4.QtCore import *
+
+
+__all__=('Table', )
+
+class TableModel(QAbstractTableModel):
+ def __init__(self, table, parent=None):
+ QAbstractTableModel.__init__(self, parent)
+ self.table=table
+
+ def rowCount(self, index):
+ return len(self.table.rows)
+
+ def headerData(self, section, orientation, role):
+ if role!=Qt.DisplayRole or orientation!=Qt.Horizontal:
+ return QVariant()
+ return self.table.col_names[section]
+
+ def columnCount(self, index):
+ return len(self.table.col_names)
+
+ def sort(self, column, order):
+ o='+'
+ if order!=Qt.AscendingOrder:
+ o='-'
+ self.table.Sort(by=self.table.col_names[column], order=o)
+ self.reset()
+
+ def data(self, index, role):
+ if not index.isValid() or role!=Qt.DisplayRole:
+ return QVariant()
+ row=self.table.rows[index.row()]
+ return QVariant(row[index.column()])
+
+class Table(QTableView):
+ def __init__(self, table):
+ QTableView.__init__(self)
+ self._model=TableModel(table)
+ self.setFrameShape(QFrame.NoFrame)
+ self.setAttribute(Qt.WA_MacSmallSize)
+ self.setShowGrid(False)
+ #self.horizontalHeader().setStretchLastSection(True)
+ self.setContextMenuPolicy(Qt.CustomContextMenu)
+ self.setSelectionBehavior(QAbstractItemView.SelectRows)
+ self.setSizePolicy(QSizePolicy.MinimumExpanding,
+ QSizePolicy.MinimumExpanding)
+ self.setSortingEnabled(True)
+ self.setModel(self._model)
\ No newline at end of file
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index e1891ae2c6e8f9148b363747eac05784e4be605c..8b0fd88d3456405632b9068fb98fed33359e5aea 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -332,6 +332,13 @@ void PythonShellWidget::setup_state_machine_()
single_line->addTransition(clear_all_tr_sl);
connect(clear_all_tr_sl,SIGNAL(triggered()),this,SLOT(handle_clear_all_()));
+ single_line->addTransition(new KeyEventTransition(Qt::Key_Left,
+ DNG_ARROW_MODIFIERS,
+ single_line,
+ true,
+ new EditPositionGuard(this,EditPositionGuard::EQUAL,
+ EditPositionGuard::ANCHOREQUAL |EditPositionGuard::ANCHORBIGGER)));
+
//multi line inactive transitions
multi_line_inactive->addTransition(new KeyEventTransition(Qt::Key_Return,
Qt::NoModifier,
@@ -878,6 +885,7 @@ void PythonShellWidget::insertFromMimeData(const QMimeData * source)
if(lines.size()>0){
set_block_type_(block_edit_start_,document()->lastBlock(),BLOCKTYPE_BLOCKEDIT);
}
+ setFocus();
}
GutterBlockList PythonShellWidget::GetGutterBlocks(const QRect& rect)
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.cc b/modules/gui/src/sequence_viewer/sequence_viewer.cc
index 024355c1b5325b87f60b67b462c55a4abef73b75..a34e917b6c20e86e2ba752c08d3b5e2ced3a2c29 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.cc
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.cc
@@ -96,6 +96,7 @@ SequenceViewer::SequenceViewer(bool stand_alone, bool observe_scene,
layout->setSpacing(0);
this->setLayout(layout);
+ toolbar_ = new QToolBar(this);
this->InitActions();
@@ -120,7 +121,6 @@ SequenceViewer::SequenceViewer(bool stand_alone, bool observe_scene,
void SequenceViewer::InitMenuBar()
{
- toolbar_ = new QToolBar(this);
toolbar_->setToolButtonStyle(Qt::ToolButtonIconOnly);
toolbar_->setIconSize(QSize(16,16));
toolbar_->addActions(action_list_);
@@ -164,7 +164,7 @@ void SequenceViewer::InitActions()
icon_path.cd("gui");
icon_path.cd("icons");
- QAction* find_action = new QAction(this);
+ QAction* find_action = new QAction(toolbar_);
find_action->setText("Find Dialog");
find_action->setShortcut(QKeySequence(tr("Ctrl+F")));
find_action->setCheckable(true);
@@ -173,8 +173,8 @@ void SequenceViewer::InitActions()
action_list_.append(find_action);
connect(find_action, SIGNAL(triggered(bool)), this, SLOT(FindInSequence()));
- display_mode_actions_ = new QActionGroup(this);
- QAction* menu_action = new QAction(this);
+ display_mode_actions_ = new QActionGroup(toolbar_);
+ QAction* menu_action = new QAction(toolbar_);
menu_action->setText("Menubar");
menu_action->setShortcut(QKeySequence(tr("Ctrl+M")));
menu_action->setToolTip("Display Options (Ctrl+M)");
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 758862eeb797c966b2336edd499ba00a930b065a..da1bed9d710d3ec33a4c7dfc16cbc02f6812348e 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -179,6 +179,23 @@ of the annotation available.
: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.
@@ -813,4 +830,4 @@ 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 AddMMCifPDBChainTr cif asym
-.. LocalWords: auth GetMMCifPDBChainTr
+.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index f94c257e647a6499992dea5172169a029ddd8d85..f2527066afca1d2d715c97dcc1413276eafa7a6b 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -282,6 +282,8 @@ void export_mmcif_io()
.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 140676fe6c409c03e2da8a427c2a502da2a936c3..29f0db7463188068b3584a49457126d7ec1601d0 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -40,6 +40,24 @@ String MMCifInfo::GetMMCifPDBChainTr(String cif) const
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 68aa79befa08c11015178075d7daceea3d86c051..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>
@@ -783,6 +784,18 @@ public:
/// \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
@@ -861,6 +874,7 @@ private:
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 6f35d4a2f206286578d20339fff710a1d0d1a2eb..762939ca817800366ee487ffadef9da493f5103a 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -500,8 +500,6 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
// store entity id
chain_id_pairs_.push_back(std::pair<mol::ChainHandle,String>(curr_chain_,
columns[indices_[LABEL_ENTITY_ID]].str()));
- // store mmCIF - PDB chain name mapping
- info_.AddMMCifPDBChainTr(cif_chain_name, auth_chain_name);
}
assert(curr_chain_.IsValid());
} else if (chain_id_pairs_.back().second != // unit test
@@ -1541,6 +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);
@@ -1550,6 +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 d5a1ac1a465edbbe121d173b4167244adf804b27..65e4fdaecb42ec54fb50d3c579f24ba8b7ae8adb 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -208,6 +208,11 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
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