diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 8891b9639dcdac2c2c38132c8028cd0836951e91..70fff8b1708376fa63fce83575973a6f86c0de3c 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,16 @@
+Changes In Release 1.3.2
+--------------------------------------------------------------------------------
+
+ * Fixed atom ordering in the GetFrameFromEntity() function in the
+ structure_analysis.py module.
+ * Fix atom indices generated by CoordGroup::Filter()
+ * small tweaks to lDDT output
+ * small tweaks to molck
+ * Repaired bio unit parsing from mmCIF file/ PDBizing bio units, before
+ chains with different transformations were ignored
+ * use new remote loader written in Python to work around crash on Mountain
+ Lion
+
Changes In Release 1.3.1
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f4ce4d675a556308f5b1031c3f4446050d9a15eb..93d9c7d5884931ad3c4ae72135a7a39f551ac5dc 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 3)
-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/create_bundle_centos5.py b/deployment/linux/create_bundle_centos5.py
index dd141cba74437a0c150775e275459c83a14abb7e..36aa8a6877c2a702fcc6919ff4eab102c88465f8 100644
--- a/deployment/linux/create_bundle_centos5.py
+++ b/deployment/linux/create_bundle_centos5.py
@@ -12,7 +12,7 @@ import PyQt4
qt4_plugins_location='/usr/lib/qt47/plugins'
qt4_qmake_location='/usr/lib/qt47/bin/qmake'
ssl_crypto_location='/lib/'
-chemlib_dictionary_location='/home/bundler/ost/ChemLib/1.2.2/compounds.chemlib'
+chemlib_dictionary_location='/home/bundler/compounds.chemlib'
list_of_excluded_libraries=[
'ld-linux',
'libexpat',
@@ -75,9 +75,10 @@ directory_name='openstructure-linux-'+archstring+'-'+additional_label
print 'Hardcoding package python binary path in openstructure executables'
subprocess.call('rm -f scripts/ost_config.in.pre* scripts/ost_config.in.backup',shell=True,cwd='../../')
subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.prepreprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.prepreprepre > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#unset PYTHONPATH/ unset PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
print 'Compiling Openstructure'
subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DQT_QMAKE_EXECUTABLE='+qt4_qmake_location+' -DPREFIX='+directory_name+' -DCOMPOUND_LIB='+chemlib_dictionary_location+' -DENABLE_IMG=ON -DUSE_RPATH=ON -DENABLE_GUI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
@@ -128,7 +129,7 @@ for entry in filtered_dep_list:
print 'Copy python executable into package directory structure'
subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+'/* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../')
subprocess.call('cp -pRL '+sip_module_location+'/sip* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('cp -pRL '+qt4_module_location+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
diff --git a/deployment/linux/create_bundle_centos6.py b/deployment/linux/create_bundle_centos6.py
index 48fc8596dfc9b1ec88be7470721f153ffd824ebd..cfb2669676fbcad27513e86a35dff63d7b7ef34e 100644
--- a/deployment/linux/create_bundle_centos6.py
+++ b/deployment/linux/create_bundle_centos6.py
@@ -12,7 +12,7 @@ import PyQt4
qt4_plugins_location='/usr/lib/qt4/plugins'
qt4_qmake_location='/usr/lib/qt4/bin/qmake'
ssl_crypto_location='/usr/lib/'
-chemlib_dictionary_location='/home/bundler/ost/ChemLib/1.2.2/compounds.chemlib'
+chemlib_dictionary_location='/home/bundler/compounds.chemlib'
list_of_excluded_libraries=[
'ld-linux',
'libexpat',
@@ -75,9 +75,10 @@ directory_name='openstructure-linux-'+archstring+'-'+additional_label
print 'Hardcoding package python binary path in openstructure executables'
subprocess.call('rm -f scripts/ost_config.in.pre* scripts/ost_config.in.backup',shell=True,cwd='../../')
subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.prepreprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.prepreprepre > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#unset PYTHONPATH/ unset PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
print 'Compiling Openstructure'
subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DQT_QMAKE_EXECUTABLE='+qt4_qmake_location+' -DPREFIX='+directory_name+' -DCOMPOUND_LIB='+chemlib_dictionary_location+' -DENABLE_IMG=ON -DUSE_RPATH=ON -DENABLE_GUI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
@@ -128,7 +129,7 @@ for entry in filtered_dep_list:
print 'Copy python executable into package directory structure'
subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+'/* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../')
subprocess.call('cp -pRL '+sip_module_location+'/sip* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('cp -pRL '+qt4_module_location+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
diff --git a/deployment/linux/create_bundle_lucid.py b/deployment/linux/create_bundle_lucid.py
index aec419bd5d17043c6a273044ad14e20abacec3f7..17e6b1a443b829b9ff967224402dbaf794c59692 100644
--- a/deployment/linux/create_bundle_lucid.py
+++ b/deployment/linux/create_bundle_lucid.py
@@ -68,9 +68,10 @@ directory_name='openstructure-linux-'+archstring+'-'+additional_label
print 'Hardcoding package python binary path in openstructure executables'
subprocess.call('rm -f scripts/ost_config.in.pre* scripts/ost_config.in.backup',shell=True,cwd='../../')
subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.prepreprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.prepreprepre > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#unset PYTHONPATH/ unset PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
print 'Compiling Openstructure'
subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DCOMPOUND_LIB='+chemlib_dictionary_location+' -DENABLE_IMG=ON -DUSE_RPATH=ON -DENABLE_GUI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
@@ -121,7 +122,7 @@ for entry in filtered_dep_list:
print 'Copy python executable into package directory structure'
subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+'/* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../')
subprocess.call('cp -pRL '+sip_module_location+'/sip* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('cp -pRL '+qt4_module_location+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
diff --git a/deployment/linux/create_bundle_precise.py b/deployment/linux/create_bundle_precise.py
index 9ffeff82463112f79e857ecc8f7bf202deef91da..1bde046d6b089a9bdd9b4fa3d4aaee43d8a7328a 100644
--- a/deployment/linux/create_bundle_precise.py
+++ b/deployment/linux/create_bundle_precise.py
@@ -68,9 +68,10 @@ directory_name='openstructure-linux-'+archstring+'-'+additional_label
print 'Hardcoding package python binary path in openstructure executables'
subprocess.call('rm -f scripts/ost_config.in.pre* scripts/ost_config.in.backup',shell=True,cwd='../../')
subprocess.call('mv scripts/ost_config.in scripts/ost_config.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/python/g" scripts/ost_config.in.backup > scripts/ost_config.in.prepreprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost_config.in.prepreprepre > scripts/ost_config.in.preprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost_config.in.preprepre > scripts/ost_config.in.prepre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#unset PYTHONPATH/ unset PYTHONPATH/g" scripts/ost_config.in.prepre > scripts/ost_config.in.pre',shell=True,cwd='../../')
subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/ost_config.in.pre > scripts/ost_config.in',shell=True,cwd='../../')
print 'Compiling Openstructure'
subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DCOMPOUND_LIB='+chemlib_dictionary_location+' -DUSE_RPATH=ON -DENABLE_IMG=ON -DENABLE_GUI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
@@ -121,7 +122,7 @@ for entry in filtered_dep_list:
print 'Copy python executable into package directory structure'
subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
print 'Copy python libraries into package directory structure'
-subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
+subprocess.call('cp -pRL '+system_python_libs+'/* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_executable+'/dist-packages',shell=True,cwd='../../')
subprocess.call('cp -pRL '+sip_module_location+'/sip* '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
subprocess.call('cp -pRL '+qt4_module_location+' '+directory_name+'/'+libdir+'/'+system_python_executable+'/',shell=True,cwd='../../')
diff --git a/modules/gfx/pymod/gradients.xml b/modules/gfx/pymod/gradients.xml
index bd79d60947eefc96fcf343f930990cca004d4b9d..999345e3032a89940a0ca3e69c0a22b906f1267d 100644
--- a/modules/gfx/pymod/gradients.xml
+++ b/modules/gfx/pymod/gradients.xml
@@ -75,5 +75,18 @@
0.0 0.901960784314 0.0 0.392156862745 1
1.0 0.352941176471 0.176470588235 0.529411764706 1
</Gradient>
+<Gradient Name="RED_TO_GREEN">5
+0.00 0.886275 0.0745098 0.0509804 1
+0.25 1 0.505882 0 1
+0.50 0.988235 1 0 1
+0.75 0.67451 1 0 1
+1.00 0.176471 1 0 1
+</Gradient>
+<Gradient Name="BLUE_TO_GREEN">3
+0.00 0.0313726 0.286275 0.501961 1
+0.50 0.567727 0.988205 1 1
+1.00 0.176471 1 0 1
+</Gradient>
+
</Gradients>
</EMDataInfo>
diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index 4ac7f7cfe75a5fe6a0e843a4389e64e02e8228ed..d4515a2f31ebe7541eb05c4981d3aa8f02b016a6 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -6,7 +6,6 @@ set(OST_GUI_PYMOD_SOURCES
export_tool.cc
export_py_shell.cc
export_gosty.cc
- export_remote_site_loader.cc
export_scene_win.cc
export_sequence_viewer.cc
export_perspective.cc
@@ -37,6 +36,7 @@ init_inspector.py
inspector_widget.py
map_level_widget.py
preset.py
+remote.py
preset_editor_list_model.py
preset_editor_widget.py
preset_info_handler.py
@@ -54,11 +54,6 @@ trace_widget.py
tube_widget.py
uniform_color_widget.py
visibility_op.py
-file_loader.py
-loader_info_handler.py
-loader_list_model.py
-loader_manager_widget.py
-immutable_loader_info_handler.py
line_trace_widget.py
wireframe_widget.py
query_editor.py
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index d46af73d8e1a93678a576698e06bdd69b552b84c..b8a68e539c9e2fca127ca82c797409564c049b2d 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -22,6 +22,8 @@ from ost.gui.init_context_menu import _InitContextMenu
from ost.gui.init_splash import _InitSplash
from ost.gui.dng import termuse
from ost.gui.dng import superpositiondialog
+from ost.gui.scene.remote import RemoteLoader
+
import ost.gui.dng.menu
from PyQt4.QtGui import *
def _my_exit(code):
@@ -55,7 +57,6 @@ def _InitPanels(app):
panels = app.perspective.panels
panels.AddWidgetToPool('ost.gui.FileBrowser', -1)
panels.AddWidgetToPool('ost.gui.PythonShell', 1)
- panels.AddWidgetToPool('ost.gui.RemoteLoader', -1)
panels.AddWidgetToPool('ost.gui.SceneWin', 1)
panels.AddWidgetToPool('ost.gui.SequenceViewer', 1)
panels.AddWidgetToPool('ost.gui.MessageWidget', 1)
@@ -63,8 +64,6 @@ def _InitPanels(app):
panels.AddWidget(gui.PanelPosition.LEFT_PANEL, app.scene_win)
panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL,
'ost.gui.FileBrowser', False)
- panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL,
- 'ost.gui.RemoteLoader', False)
panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.seq_viewer)
panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.py_shell)
panels.AddWidget(gui.PanelPosition.RIGHT_PANEL, app.message_widget)
diff --git a/modules/gui/pymod/dng/menu.py b/modules/gui/pymod/dng/menu.py
index 75d2ae2ba34ba30328cf57a6fef4656bcf4fbba0..800c3f80525048c26a14c3454dd8d8f3950a9313 100644
--- a/modules/gui/pymod/dng/menu.py
+++ b/modules/gui/pymod/dng/menu.py
@@ -2,7 +2,6 @@ from PyQt4.QtCore import *
from PyQt4.QtGui import *
from ost import *
from ost import gui
-from ost.gui.scene.loader_manager_widget import LoaderManagerWidget
from ost.gui.init_splash import _InitSplash
from ost.gui.dng import termuse
from ost.gui.dng import superpositiondialog
@@ -204,7 +203,6 @@ class WindowMenu(QMenu):
def __init__(self, parent=None):
QMenu.__init__(self, parent)
self.setTitle('Window')
- self.loader_manager=LoaderManagerWidget()
gosty=gui.GostyApp.Instance()
QObject.connect(self, SIGNAL('aboutToShow()'), self._AboutToShow)
inspector_visible=gosty.GetWidget('InspectorDialog').isVisible()
diff --git a/modules/gui/pymod/export_file_loader.cc b/modules/gui/pymod/export_file_loader.cc
index ab978f09a21c6b42224bbdec59371b55ca713dd7..b39d6dadd8383cbe9b42c31d085528ace7dc6aca 100644
--- a/modules/gui/pymod/export_file_loader.cc
+++ b/modules/gui/pymod/export_file_loader.cc
@@ -24,7 +24,6 @@ using namespace boost::python;
#include <QString>
#include <ost/gui/file_loader.hh>
-#include <ost/gui/loader_manager.hh>
using namespace ost;
using namespace ost::gui;
@@ -41,48 +40,13 @@ void load_object_b(const QString& file_name, const QString& selection)
FileLoader::LoadObject(file_name, selection);
}
-void load_from_site_a(const QString& id)
-{
- FileLoader::LoadFrom(id);
-}
-
-void load_from_site_b(const QString& id, const QString& site)
-{
- FileLoader::LoadFrom(id,site);
-}
-
-void load_from_site_c(const QString& id, const QString& site, const QString& selection)
-{
- FileLoader::LoadFrom(id,site,selection);
-}
-
-void add_remote_site_loader(LoaderManager* loader_manager, const QString& site, RemoteSiteLoader* site_loader){
- loader_manager->AddRemoteSiteLoader(site,site_loader);
-}
-
}
void export_FileLoader()
{
- class_<LoaderManager, LoaderManagerPtr, boost::noncopyable>("LoaderManager", no_init)
- .def("GetSiteLoaderIdents", &LoaderManager::GetSiteLoaderIdents)
- .def("AddRemoteSiteLoader", &add_remote_site_loader)
- .def("RemoveRemoteSiteLoader", &LoaderManager::RemoveRemoteSiteLoader)
- .def("SetDefaultRemoteSiteIdent", &LoaderManager::SetDefaultRemoteSiteIdent)
- .def("GetDefaultRemoteSiteIdent", &LoaderManager::GetDefaultRemoteSiteIdent)
- ;
-
class_<FileLoader, boost::noncopyable>("FileLoader", no_init)
.def("LoadObject", &load_object_a)
.def("LoadObject", &load_object_b)
.staticmethod("LoadObject")
- .def("LoadFrom", &load_from_site_a)
- .def("LoadFrom", &load_from_site_b)
- .def("LoadFrom", &load_from_site_c)
- .staticmethod("LoadFrom")
- .def("GetSiteLoaderIdents", &FileLoader::GetSiteLoaderIdents)
- .staticmethod("GetSiteLoaderIdents")
- .def("GetLoaderManager", &FileLoader::GetLoaderManager)
- .staticmethod("GetLoaderManager")
;
}
diff --git a/modules/gui/pymod/export_remote_site_loader.cc b/modules/gui/pymod/export_remote_site_loader.cc
deleted file mode 100644
index 80ad570496f295d32cd7ed4cf1aa8ee668731dd9..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/export_remote_site_loader.cc
+++ /dev/null
@@ -1,76 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#include <boost/python.hpp>
-#include <string>
-
-
-#include <ost/gui/remote_site_loader.hh>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-
-#include "sip_handler.hh"
-
-using namespace ost;
-using namespace ost::gui;
-using namespace boost::python;
-
-struct WrappedRemoteSiteLoader : public RemoteSiteLoader
-{
- WrappedRemoteSiteLoader(PyObject *p):
- RemoteSiteLoader(), self(p)
- { }
-
- virtual void LoadById(const QString& id, const QString& selection=QString()){
- return call_method<void, std::string>(self, "LoadById", id.toStdString(), selection.toStdString());
- }
-
- virtual QString GetRemoteSiteName(){
- return call_method<QString>(self, "GetRemoteSiteName");
- }
-
- virtual bool IsImg() const{
- return call_method<bool>(self, "IsImg");
- }
-
- virtual QNetworkReply* ById(const QString& id, const QString& selection=QString()){
- object obj = call_method<object, std::string, std::string>(self, "ById", id.toStdString(), selection.toStdString());
- QNetworkReply* network_reply= get_cpp_qobject<QNetworkReply>(obj);
- if(network_reply){
- return network_reply;
- }
- return NULL;
- }
-
- private:
- PyObject* self;
-};
-
-void export_RemoteSiteLoader()
-{
- class_<RemoteSiteLoader, WrappedRemoteSiteLoader, boost::noncopyable>("RemoteSiteLoader")
- .def("LoadById",&WrappedRemoteSiteLoader::LoadById)
- .def("GetRemoteSiteName", &WrappedRemoteSiteLoader::GetRemoteSiteName)
- .def("IsImg", &WrappedRemoteSiteLoader::IsImg)
- ;
-
-}
-
-
-
diff --git a/modules/gui/pymod/init_menubar.py b/modules/gui/pymod/init_menubar.py
index cc8dd3b618b34679ea766ff6648a6ea06bb1f9d6..761e483bb3493284a4078904dd24113a5011ddc2 100644
--- a/modules/gui/pymod/init_menubar.py
+++ b/modules/gui/pymod/init_menubar.py
@@ -25,8 +25,6 @@ import ost
from PyQt4 import QtCore, QtGui
from ost.gui import FileLoader
-from ost.gui.scene.file_loader import GenericLoader
-from ost.gui.scene.loader_manager_widget import LoaderManagerWidget
from ost.gui.init_splash import _InitSplash
from ost.gui.dng import termuse
class InitMenuBar(QtCore.QObject):
@@ -74,15 +72,6 @@ class InitMenuBar(QtCore.QObject):
self.connect(reset, QtCore.SIGNAL('triggered()'), self.ResetView)
window.addAction(reset)
- #Options
- #Add file loader to menu
- loader_manager = QtGui.QAction('File &Loader', self)
- loader_manager.setStatusTip('Loader Manager')
- self.connect(loader_manager, QtCore.SIGNAL('triggered()'), self.LoaderManager)
- options.addAction(loader_manager)
-
- self.loader_manager = LoaderManagerWidget()
-
def Exit(self):
reply = QtGui.QMessageBox()
reply.addButton(QtGui.QMessageBox.Yes)
@@ -93,9 +82,6 @@ class InitMenuBar(QtCore.QObject):
if(QtCore.QFileInfo(filename).isFile()):
FileLoader.LoadObject(str(filename))
- def LoaderManager(self):
- self.loader_manager.exec_()
-
def OpenDocs(self):
QtGui.QDesktopServices.openUrl(QtCore.QUrl("http://www.openstructure.org/docs/"))
diff --git a/modules/gui/pymod/scene/file_loader.py b/modules/gui/pymod/scene/file_loader.py
index ba7efb375eb525f1bfd0fa58ebd1eab9665b3750..a0acf4140669bee32e6c4e34c6ec44ea2c1888a5 100644
--- a/modules/gui/pymod/scene/file_loader.py
+++ b/modules/gui/pymod/scene/file_loader.py
@@ -26,7 +26,7 @@ import re
from PyQt4 import QtCore, QtGui, QtNetwork
from ost.gui import FileLoader
-
+"""
class BaseRemoteLoader(gui.RemoteSiteLoader):
def __init__(self):
gui.RemoteSiteLoader.__init__(self)
@@ -195,3 +195,4 @@ class GenericLoader(BaseRemoteLoader):
default = bool(int(group.GetAttribute(GenericLoader.DEFAULT_ATTRIBUTE_NAME)))
return GenericLoader(name, url, up_case, file_type, tmp_url, img, default)
+"""
diff --git a/modules/gui/pymod/scene/loader_info_handler.py b/modules/gui/pymod/scene/loader_info_handler.py
deleted file mode 100644
index 079620eccab9957c669d66c3996e9d1442be30b6..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/scene/loader_info_handler.py
+++ /dev/null
@@ -1,60 +0,0 @@
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-#------------------------------------------------------------------------------
-# -*- coding: utf-8 -*-
-
-from ost import gui
-from ost import gfx
-from ost import info
-from PyQt4 import QtCore, QtGui
-from immutable_loader_info_handler import ImmutableLoaderInfoHandler
-
-#Generic Loader Info Handler
-class LoaderInfoHandler(ImmutableLoaderInfoHandler):
-
- def __init__(self, file_name):
- ImmutableLoaderInfoHandler.__init__(self, file_name)
-
- def StoreLoader(self,name, loader):
- group = self.loaders_.CreateGroup(ImmutableLoaderInfoHandler.LOADER_GROUP_NAME)
- group.SetAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME, str(name))
- loader.ToInfo(group)
- self.handle_.Export(self.file_name_)
-
- def RemoveLoader(self, name):
- group_list = self.loaders_.GetGroups(ImmutableLoaderInfoHandler.LOADER_GROUP_NAME)
- group_to_del = None
- for group in group_list:
- if group.HasAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME):
- groupname = group.GetAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME)
- if name == groupname:
- group_to_del = group
- break
-
- if group_to_del != None:
- self.loaders_.Remove(group_to_del)
- self.handle_.Export(self.file_name_)
-
- def RenameLoader(self, old, new):
- group_list = self.loaders_.GetGroups(ImmutableLoaderInfoHandler.LOADER_GROUP_NAME)
- for group in group_list:
- if group.HasAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME):
- groupname = group.GetAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME)
- if old == groupname:
- group.SetAttribute(ImmutableLoaderInfoHandler.NAME_ATTRIBUTE_NAME, new)
- self.handle_.Export(self.file_name_)
\ No newline at end of file
diff --git a/modules/gui/pymod/scene/loader_list_model.py b/modules/gui/pymod/scene/loader_list_model.py
deleted file mode 100644
index c033df0388f7f6f36e1290c371318d4b4c91a6a4..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/scene/loader_list_model.py
+++ /dev/null
@@ -1,156 +0,0 @@
-from ost import gui
-from ost import gfx
-import os
-import ost
-from PyQt4 import QtCore, QtGui
-from immutable_loader_info_handler import ImmutableLoaderInfoHandler
-from loader_info_handler import LoaderInfoHandler
-from ost.gui import LoaderManager
-
-class LoaderListModel(QtCore.QAbstractListModel):
-
- IMMUTABLE_LOADERS_PATH = os.path.join(ost.GetSharedDataPath(),"scene",
- "loaders.xml")
- MUTABLE_LOADERS_PATH = "user_loaders.xml"
-
- def __init__(self, parent=None, *args):
- QtCore.QAbstractListModel.__init__(self, parent, *args)
-
- self.data_ = list()
-
- #Info Handler
- self.immutable_infoh_ = ImmutableLoaderInfoHandler(LoaderListModel.IMMUTABLE_LOADERS_PATH)
- self.infoh_ = LoaderInfoHandler(LoaderListModel.MUTABLE_LOADERS_PATH)
- self.LoadLoaderFromInfo()
-
- self.loader_manager_ = gui.FileLoader.GetLoaderManager()
-
- def AddItem(self, name, loader, row, editable, save):
- if self.NameIsValid(name):
- self.insertRow(row, QtCore.QModelIndex())
- self.data_[row] = [name, loader, editable]
- model_index = self.createIndex(row,0)
- index = self.index(row)
- end_index = self.createIndex(self.rowCount(),0)
- if save:
- self.AddLoaderToInfo(name, loader)
- self.emit(QtCore.SIGNAL("dataChanged"),model_index, end_index)
- gui.FileLoader.GetLoaderManager().AddRemoteSiteLoader(name, loader)
- if(loader.IsDefault()):
- gui.FileLoader.GetLoaderManager().SetDefaultRemoteSiteIdent(name)
- return True
- return False
-
- def IsEditable(self, row):
- return self.data_[row][2]
-
- def RemoveItem(self, row):
- if self.IsEditable(row):
- name = self.data_[row][0]
- self.removeRow(row, QtCore.QModelIndex())
- model_index = self.createIndex(row,0)
- self.infoh_.RemoveLoader(name)
- self.emit(QtCore.SIGNAL("dataChanged"),model_index, model_index)
- self.loader_manager_.RemoveRemoteSiteLoader(name)
- return True
- return False
-
- def AddLoaderToInfo(self, name, loader):
- self.infoh_.StoreLoader(name, loader)
-
- def RemoveLoaderFromInfo(self, name):
- self.infoh_.RemoveLoader(name)
-
- def SetItem(self, model_index, loader):
- row = model_index.row()
- name = self.data_[row][0]
- self.data_[row][1] = loader
- model_index = self.createIndex(row,0)
- index = self.index(row)
- end_index = self.createIndex(self.rowCount(),0)
- self.RemoveLoaderFromInfo(self.data_[row][0])
- self.AddLoaderToInfo(self.data_[row][0], loader)
- self.emit(QtCore.SIGNAL("dataChanged"),model_index, end_index)
- self.loader_manager_.RemoveRemoteSiteLoader(name)
- self.loader_manager_.AddRemoteSiteLoader(name, loader)
- return True
-
- def LoadLoaderFromInfo(self):
- if self.immutable_infoh_:
- loaders = self.immutable_infoh_.GetLoaders()
- for k, v in loaders.iteritems():
- self.AddItem(k, v, self.GetLastRow(), False, False)
-
- loaders = self.infoh_.GetLoaders()
- for k, v in loaders.iteritems():
- self.AddItem(k, v, self.GetLastRow(), True, False)
-
- def GetLoader(self, model_index):
- if model_index.isValid():
- return self.data_[model_index.row()][1]
-
- def GetLastRow(self):
- return self.rowCount()
-
- #Helper
- def NameIsValid(self, string):
- if len(string)==0:
- return False
- for values in self.data_:
- if string == values[0]:
- return False
- return True
-
- #Overwritten Methods
- def rowCount(self, parent=QtCore.QModelIndex()):
- return len(self.data_)
-
- def data(self, index, role):
- if index.isValid() and index.row()< self.rowCount():
- data = self.data_[index.row()]
- if role == QtCore.Qt.DisplayRole:
- return QtCore.QVariant(data[0])
- return QtCore.QVariant()
-
- def setData(self, index, value, role):
- if index.isValid():
- row = index.row()
- if not self.data_[row]:
- self.data_[row] = list()
- if role == QtCore.Qt.EditRole and self.NameIsValid(value.toString()):
- old_name = str(self.data_[row][0])
- new_name = value.toString()
- self.data_[row][0] = new_name
- self.infoh_.RenameLoader(old_name,str(new_name))
- self.emit(QtCore.SIGNAL("dataChanged"),index, index)
- self.loader_manager_.RemoveRemoteSiteLoader(old_name)
- self.loader_manager_.AddRemoteSiteLoader(str(new_name), self.data_[row][1])
- return True
- elif role == QtCore.Qt.DisplayRole:
- self.data_[row][0] = value.toString()
- return False
-
- def flags(self, index):
- if index.isValid():
- flags = QtCore.QAbstractItemModel.flags(self,index)
- if self.IsEditable(index.row()):
- return flags | QtCore.Qt.ItemIsEditable
- else:
- return flags
- return QtCore.Qt.ItemIsEnabled
-
- def insertRow(self, position, index):
- self.beginInsertRows(index, position, position)
- self.data_.insert(position,list())
- self.endInsertRows()
- return True
-
- def removeRow(self, position, index):
- self.beginRemoveRows(index, position, position)
- del self.data_[position]
- self.endRemoveRows()
- return True
-
-
-
-
diff --git a/modules/gui/pymod/scene/loader_manager_widget.py b/modules/gui/pymod/scene/loader_manager_widget.py
deleted file mode 100644
index d1fd7795d0d30f517c783d87498878766811488e..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/scene/loader_manager_widget.py
+++ /dev/null
@@ -1,199 +0,0 @@
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-#------------------------------------------------------------------------------
-# -*- coding: utf-8 -*-
-
-import os
-import ost
-from ost import gui
-from ost import gfx
-from datetime import datetime
-from PyQt4 import QtCore, QtGui
-
-from loader_list_model import LoaderListModel
-from file_loader import GenericLoader
-
-#Gradient Preset Widget
-class LoaderManagerWidget(QtGui.QDialog):
- ICONS_DIR = os.path.join(ost.GetSharedDataPath(), "gui", "icons/")
- def __init__(self, parent=None):
- QtGui.QDialog.__init__(self, parent)
-
- #Title
- self.text_ = "Loader Manager"
-
- #Create Ui elements
- self.list_view_ = QtGui.QListView()
-
- #Create Model
- self.list_model_ = LoaderListModel(self)
- self.list_view_.setModel(self.list_model_)
- self.list_view_.setEditTriggers(QtGui.QAbstractItemView.NoEditTriggers)
-
- loader_label = QtGui.QLabel(self.text_)
- font = loader_label.font()
- font.setBold(True)
-
- self.add_action = QtGui.QAction("+",self)
- self.add_action.setIcon(QtGui.QIcon(LoaderManagerWidget.ICONS_DIR+"add_icon.png"))
-
- QtCore.QObject.connect(self.add_action, QtCore.SIGNAL("triggered()"), self.Add)
-
- self.add_button_ = QtGui.QToolButton(self)
- self.add_button_.setIconSize(QtCore.QSize(20,20))
- self.add_button_.setDefaultAction(self.add_action)
-
- grid = QtGui.QGridLayout()
- grid.setContentsMargins(0,5,0,0)
- grid.addWidget(loader_label, 0, 0, 1, 1)
- qhbox = QtGui.QHBoxLayout()
- grid.addWidget(self.list_view_,1,0,3,3)
- grid.addWidget(self.add_button_,4,0,1,1)
- self.setLayout(grid)
-
- self.list_view_.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
- QtCore.QObject.connect(self.list_view_, QtCore.SIGNAL("customContextMenuRequested(const QPoint)"), self.contextMenuEvent)
- self.CreateContextMenu()
-
- QtCore.QObject.connect(self.list_view_, QtCore.SIGNAL("doubleClicked(const QModelIndex)"), self.Edit)
-
- def CreateContextMenu(self):
- self.contextMenu_ = QtGui.QMenu("Context menu", self)
- self.remove_ = QtGui.QAction("Remove", self.list_view_)
- self.rename_ = QtGui.QAction("Rename", self.list_view_)
- self.edit_ = QtGui.QAction("Edit", self.list_view_)
- self.contextMenu_.addAction(self.remove_)
- self.contextMenu_.addAction(self.rename_)
- self.contextMenu_.addAction(self.edit_)
- #Connect Signals with Slots
- QtCore.QObject.connect(self.remove_, QtCore.SIGNAL("triggered()"), self.Remove)
- QtCore.QObject.connect(self.rename_, QtCore.SIGNAL("triggered()"), self.Rename)
- QtCore.QObject.connect(self.edit_, QtCore.SIGNAL("triggered()"), self.Edit)
-
- def contextMenuEvent(self, pos):
- #ContextMenu
- index = self.list_view_.indexAt(pos)
- if index.isValid():
- if self.list_model_.IsEditable(index.row()):
- self.contextMenu_.popup(QtGui.QCursor.pos())
-
- def Add(self):
- row = self.list_model_.GetLastRow()
- edit_widget = LoaderEditWidget()
-
- if edit_widget.exec_() and self.list_model_.AddItem(datetime.now().isoformat(' '), edit_widget.GetLoader(), row, True, True):
- index = self.list_model_.index(row)
- self.list_view_.setCurrentIndex(index)
- self.Rename()
-
- def Edit(self):
- current_index = self.list_view_.currentIndex()
- loader = self.list_model_.GetLoader(current_index)
- edit_widget = LoaderEditWidget()
- edit_widget.SetLoader(loader)
- if edit_widget.exec_():
- self.list_model_.SetItem(current_index, edit_widget.GetLoader())
-
-
- def Remove(self):
- if(self.list_view_.currentIndex().isValid()):
- ret = QtGui.QMessageBox.warning(self, "Delete File Loader",
- "Delete File Loader?",
- QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
- if ret == QtGui.QMessageBox.Yes:
- self.list_model_.RemoveItem(self.list_view_.currentIndex().row())
-
- def Rename(self):
- if(self.list_view_.currentIndex().isValid()):
- self.list_view_.edit(self.list_view_.currentIndex())
-
- def GetText(self):
- return self.text_
-
-
-
-
-class LoaderEditWidget(QtGui.QDialog):
- def __init__(self, parent=None):
- QtGui.QDialog.__init__(self, parent)
- name_ext_label = QtGui.QLabel("Name Extension")
- self.name_ext_edit_ = QtGui.QLineEdit()
-
- url_label = QtGui.QLabel("Url")
- self.url_edit_ = QtGui.QLineEdit()
- self.add_id_button_ = QtGui.QToolButton(self)
- self.add_id_button_.setDefaultAction(QtGui.QAction("ID",self))
-
- file_ext_label = QtGui.QLabel("File Type")
- self.file_ext_auto_ = QtGui.QCheckBox("Auto")
- self.file_ext_edit_ = QtGui.QLineEdit()
-
- self.hbox_ = QtGui.QHBoxLayout()
- self.ok_button_ = QtGui.QPushButton("OK")
- self.cancel_button_ = QtGui.QPushButton("Cancel")
- self.hbox_.addWidget(self.ok_button_)
- self.hbox_.addStretch()
- self.hbox_.addWidget(self.cancel_button_)
-
- grid = QtGui.QGridLayout()
- grid.setContentsMargins(0,5,0,0)
- grid.addWidget(name_ext_label, 0, 0, 1, 1)
- grid.addWidget(self.name_ext_edit_, 0, 1, 1, 4)
- grid.addWidget(url_label, 1, 0, 1, 1)
- grid.addWidget(self.url_edit_, 1, 1, 1, 3)
- grid.addWidget(self.add_id_button_, 1, 4, 1, 1)
- grid.addWidget(file_ext_label, 2, 0, 1, 1)
- grid.addWidget(self.file_ext_auto_, 2, 1, 1, 1)
- grid.addWidget(self.file_ext_edit_, 2, 2, 1, 3)
- grid.addLayout(self.hbox_,3,0,1,2)
- grid.setRowStretch(2, 1)
- self.setLayout(grid)
-
- QtCore.QObject.connect(self.add_id_button_, QtCore.SIGNAL("clicked()"), self.AppendId)
- QtCore.QObject.connect(self.file_ext_auto_, QtCore.SIGNAL("stateChanged(int)"), self.CbStateChanged)
- QtCore.QObject.connect(self.ok_button_, QtCore.SIGNAL("clicked()"), self.Ok)
- QtCore.QObject.connect(self.cancel_button_, QtCore.SIGNAL("clicked()"), self.Cancel)
-
- def GetLoader(self):
- name_ext = str(self.name_ext_edit_.text())
- url = str(self.url_edit_.text())
- file_ext = None
- if not self.file_ext_auto_.isChecked():
- file_ext = str(self.file_ext_edit_.text())
-
- return GenericLoader(name_ext, url, False, file_ext)
-
- def SetLoader(self, loader):
- self.name_ext_edit_.setText(loader.name_)
- self.url_edit_.setText(loader.url_)
- if loader.file_type_ is not None:
- self.file_ext_edit_.setText(loader.file_type_)
- self.file_ext_auto_.setChecked(False)
- else:
- self.file_ext_auto_.setChecked(True)
- def AppendId(self):
- self.url_edit_.setText(self.url_edit_.text()+"${ID}")
-
- def CbStateChanged(self, state):
- self.file_ext_edit_.setEnabled(not self.file_ext_auto_.isChecked())
-
- def Ok(self):
- self.accept()
-
- def Cancel(self):
- self.reject()
diff --git a/modules/gui/pymod/scene/remote.py b/modules/gui/pymod/scene/remote.py
new file mode 100644
index 0000000000000000000000000000000000000000..46a7553b41a1c6b12ae43f6f6d99aead520ea0bd
--- /dev/null
+++ b/modules/gui/pymod/scene/remote.py
@@ -0,0 +1,78 @@
+from PyQt4.QtCore import *
+from PyQt4.QtGui import *
+import threading
+from ost import LogError
+from ost import gui, gfx
+from ost.io.remote import RemoteLoad, REMOTE_REPOSITORIES
+import re
+
+class RemoteLoader(QWidget):
+ def __init__(self):
+ QWidget.__init__(self)
+ self._line = QLineEdit(self)
+ self._load = QToolButton(self)
+ self._load.setAttribute(Qt.WA_MacSmallSize)
+ QObject.connect(self._line, SIGNAL('returnPressed()'),
+ self._DoLoad)
+ QObject.connect(self._load, SIGNAL('clicked()'),
+ self._DoLoad)
+ hbox = QHBoxLayout(self)
+ hbox.addWidget(self._line,1)
+ hbox.addWidget(self._load,0)
+ self.setLayout(hbox)
+ hbox.setMargin(3)
+ hbox.setSpacing(3)
+ self._menu = self._RemoteMenu()
+ self._load.setMenu(self._menu)
+ self._current_repo = 'pdb'
+ self._UpdateLoadButton(self._current_repo)
+ self.setFixedHeight(self._load.height())
+ self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
+
+ def _RemoteMenu(self):
+ menu = QMenu()
+ action_group = QActionGroup(menu)
+ for k,v in REMOTE_REPOSITORIES.iteritems():
+ action = menu.addAction(v.name)
+ action.setCheckable(True)
+ if k == 'pdb':
+ action.setChecked(True)
+ action.setData(QVariant(k))
+ action_group.addAction(action)
+ QObject.connect(menu, SIGNAL('triggered(QAction*)'),
+ self._ToggleRepo)
+ return menu
+ def _UpdateLoadButton(self, current):
+ name = REMOTE_REPOSITORIES[current].name
+ self._load.setText('load from %s ' % name)
+
+ def _ToggleRepo(self, action):
+ self._current_repo = str(action.data().toString())
+ self._UpdateLoadButton(self._current_repo)
+
+
+ def _DoLoad(self):
+ split_ids = []
+ for p in str(self._line.text()).split(','):
+ for k in p.split():
+ if len(k.strip()):
+ split_ids.append(k.strip())
+ self._line.setText('')
+ for split_id in split_ids:
+ try:
+ ent = RemoteLoad(split_id, from_repo=self._current_repo)
+ except Exception, e:
+ LogError(str(e))
+ continue
+ g = gfx.Entity(split_id, ent)
+ try:
+ gfx.Scene().Add(g)
+ except Exception, e:
+ LogError(str(e))
+
+remote_loader=RemoteLoader()
+remote_loader_for_panel=gui.Widget(remote_loader)
+remote_loader_for_panel.qobject.setSizePolicy(QSizePolicy.Expanding,
+ QSizePolicy.Fixed)
+panels=gui.GostyApp.Instance().perspective.panels
+panels.AddWidgetToPool("Remote Loader",remote_loader_for_panel)
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index 81b6ff7889a3c5d91d2c42cf558fdd1a0a1f7cbd..a4474a6f861e427982f701581f852c2ea14c63bf 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -38,7 +38,6 @@ void export_SipHandler();
void export_SceneSelection();
void export_MainArea();
void export_MenuBar();
-void export_RemoteSiteLoader();
void export_FileLoader();
void export_FileViewer();
void export_Widget();
@@ -118,7 +117,6 @@ BOOST_PYTHON_MODULE(_ost_gui)
export_SceneWin();
export_SceneSelection();
export_SequenceViewer();
- export_RemoteSiteLoader();
export_FileLoader();
export_FileViewer();
export_Widget();
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index b4d9ee6e433268164006b2c8806b1ebaf905e168..83819bc0b7d7c3e151ebe797d90c4b1e08a87998 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -166,7 +166,6 @@ set(OST_GUI_HEADERS
file_browser.hh
file_type_dialog.hh
file_viewer.hh
-remote_loader.hh
gl_canvas.hh
gl_win.hh
scene_menu.hh
@@ -176,7 +175,6 @@ module_config.hh
main.hh
main_area.hh
perspective.hh
-remote_site_loader.hh
scene_selection.hh
main_window.hh
dock_widget.hh
@@ -188,7 +186,6 @@ widget_pool.hh
widget_registry.hh
widget_state_saver.hh
file_loader.hh
-loader_manager.hh
)
set(OST_GUI_SOURCES
@@ -198,7 +195,6 @@ widget_registry.cc
file_browser.cc
file_type_dialog.cc
file_viewer.cc
-remote_loader.cc
main.cc
gl_canvas.cc
dock_widget.cc
@@ -208,7 +204,6 @@ scene_menu.cc
widget.cc
admin.cc
widget_pool.cc
-remote_site_loader.cc
messages/message_widget.cc
messages/message_box_widget.cc
messages/log_reader.cc
@@ -237,7 +232,6 @@ widget_state_saver.cc
scene_selection.cc
widget_geom_handler.cc
file_loader.cc
-loader_manager.cc
panels/button_bar.cc
panels/drop_box.cc
panels/panel_bar.cc
@@ -305,7 +299,6 @@ set(HEADERS_TO_BE_MOCCED
file_browser.hh
file_type_dialog.hh
file_viewer.hh
-remote_loader.hh
gl_canvas.hh
gl_win.hh
scene_menu.hh
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index d31c2f0b891ddd592ce55033ee0cbb298d2f7d8a..bc69ba7b852e035afa0c9417b46f2c4217d39f03 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -59,7 +59,6 @@
#include <QMenuBar>
namespace ost { namespace gui {
-LoaderManagerPtr FileLoader::loader_manager_ = LoaderManagerPtr();
#if OST_IMG_ENABLED
QList<img::ImageHandle> FileLoader::loaded_images_;
@@ -161,36 +160,6 @@ gfx::GfxObjP FileLoader::NoHandlerFound(const QString& filename)
return gfx::GfxObjP();
}
-void FileLoader::LoadFrom(const QString& id, const QString& site, const QString& selection)
-{
- if(!loader_manager_)
- loader_manager_ = LoaderManagerPtr(new LoaderManager());
- RemoteSiteLoader* remote_site = loader_manager_->GetRemoteSiteLoader(site);
- if(remote_site){
- remote_site->LoadById(id,selection);
- }
- else{
- remote_site = loader_manager_->GetCurrentSiteLoader();
- if(remote_site){
- remote_site->LoadById(id,selection);
- }
- }
-}
-
-LoaderManagerPtr FileLoader::GetLoaderManager()
-{
- if(!loader_manager_)
- loader_manager_ = LoaderManagerPtr(new LoaderManager());
- return loader_manager_;
-}
-
-std::vector<String> FileLoader::GetSiteLoaderIdents()
-{
- if(!loader_manager_)
- loader_manager_ = LoaderManagerPtr(new LoaderManager());
- return loader_manager_->GetSiteLoaderIdents();
-}
-
void FileLoader::HandleError(const Error& e, ErrorType type, const QString& filename, gfx::GfxObjP obj)
{
if(type==GFX_ADD || type==GFX_MULTIPLE_ADD){
diff --git a/modules/gui/src/file_loader.hh b/modules/gui/src/file_loader.hh
index 32a4ba18e9b685ce8086d47edef10cc1c22e4e04..23419b613eb851fb9aeeec56ce8c9efe91701050 100644
--- a/modules/gui/src/file_loader.hh
+++ b/modules/gui/src/file_loader.hh
@@ -24,8 +24,6 @@
#include <ost/gfx/gfx_object.hh>
#include <ost/gui/module_config.hh>
-#include <ost/gui/remote_site_loader.hh>
-#include <ost/gui/loader_manager.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/entity_io_handler.hh>
@@ -64,7 +62,6 @@ private:
static gfx::GfxObjP NoHandlerFound(const QString& filename);
virtual ~FileLoader();
- static LoaderManagerPtr loader_manager_;
#if OST_IMG_ENABLED
static QList<img::ImageHandle> loaded_images_;
@@ -72,9 +69,7 @@ private:
public:
static void LoadObject(const QString& filename, const QString& selection=QString());
- static void LoadFrom(const QString& id, const QString& site=QString(), const QString& selection=QString());
static std::vector<String> GetSiteLoaderIdents();
- static LoaderManagerPtr GetLoaderManager();
};
} }
diff --git a/modules/gui/src/loader_manager.cc b/modules/gui/src/loader_manager.cc
deleted file mode 100644
index bfe2853dc926669bdf33ddbee80bb360925c46f0..0000000000000000000000000000000000000000
--- a/modules/gui/src/loader_manager.cc
+++ /dev/null
@@ -1,112 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <ost/gui/gosty_app.hh>
-#include "loader_manager.hh"
-
-#include <ost/gui/perspective.hh>
-#include <QDir>
-#include <QAction>
-#include <QMenu>
-#include <QFileInfo>
-#include <QMessageBox>
-#include <QMenuBar>
-
-
-namespace ost { namespace gui {
-
-LoaderManager::LoaderManager():
- site_loaders_(),
- site_actions_(new QActionGroup(GostyApp::Instance()->GetPerspective()->GetMenuBar())),
- default_site_()
-
-{
- site_actions_->setExclusive(true);
-}
-
-void LoaderManager::AddRemoteSiteLoader(const QString& ident, RemoteSiteLoader* site_loader)
-{
- site_loaders_.insert(ident,site_loader);
-
- QAction* action = new QAction(ident,site_actions_);
- action->setCheckable(true);
- site_actions_->addAction(action);
- if(site_actions_->checkedAction()==NULL){
- action->setChecked(true);
- }
-}
-
-void LoaderManager::RemoveRemoteSiteLoader(const QString& ident)
-{
- site_loaders_.remove(ident);
-
- QList<QAction*> actions = site_actions_->actions();
- QAction* action = NULL;
- for (int i=0; i<actions.size(); i++){
- if(actions[i]->text()==ident){
- action = actions[i];
- break;
- }
- }
- if(action){
- site_actions_->removeAction(action);
- }
-}
-
-
-RemoteSiteLoader* LoaderManager::GetRemoteSiteLoader(const QString& ident)
-{
- if(site_loaders_.contains(ident)){
- return site_loaders_[ident];
- }
- return NULL;
-}
-
-RemoteSiteLoader* LoaderManager::GetCurrentSiteLoader()
-{
- if(site_actions_->checkedAction()!=NULL)
- return site_loaders_[site_actions_->checkedAction()->text()];
- return NULL;
-}
-
-std::vector<String> LoaderManager::GetSiteLoaderIdents()
-{
- QList<QString> keys = site_loaders_.keys();
- std::vector<String> sites;
- for(int i=0;i<keys.size();i++){
- sites.push_back(keys.at(i).toStdString());
- }
- return sites;
-}
-
-RemoteSiteLoader* LoaderManager::GetDefaultRemoteSiteLoader()
-{
- return GetRemoteSiteLoader(GetDefaultRemoteSiteIdent());
-}
-
-QString LoaderManager::GetDefaultRemoteSiteIdent(){
- return default_site_;
-}
-
-void LoaderManager::SetDefaultRemoteSiteIdent(const QString& ident){
- default_site_ = ident;
-}
-
-LoaderManager::~LoaderManager(){}
-
-} }
diff --git a/modules/gui/src/loader_manager.hh b/modules/gui/src/loader_manager.hh
deleted file mode 100644
index f969b289c45282d13e5f8541f31f0f96e66157e2..0000000000000000000000000000000000000000
--- a/modules/gui/src/loader_manager.hh
+++ /dev/null
@@ -1,59 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_GUI_LOADER_MANAGER_HH
-#define OST_GUI_LOADER_MANAGER_HH
-#include <vector>
-
-#include <boost/shared_ptr.hpp>
-
-#include <QString>
-#include <QMap>
-
-#include <ost/gui/remote_site_loader.hh>
-
-namespace ost { namespace gui {
-
-class DLLEXPORT_OST_GUI LoaderManager {
-
-public:
- LoaderManager();
- virtual ~LoaderManager();
- std::vector<String> GetSiteLoaderIdents();
- void AddRemoteSiteLoader(const QString& ident, RemoteSiteLoader* site_loader);
- void RemoveRemoteSiteLoader(const QString& ident);
- RemoteSiteLoader* GetRemoteSiteLoader(const QString& ident);
- RemoteSiteLoader* GetCurrentSiteLoader();
- RemoteSiteLoader* GetDefaultRemoteSiteLoader();
- QString GetDefaultRemoteSiteIdent();
- void SetDefaultRemoteSiteIdent(const QString& ident);
- QMenu* GetSiteMenu();
-
-private:
- QMap<QString,RemoteSiteLoader*> site_loaders_;
- QActionGroup* site_actions_;
- QString default_site_;
-
-
-};
-
-typedef boost::shared_ptr<LoaderManager> LoaderManagerPtr;
-
-} }
-
-#endif /* OST_GUI_LOADER_MANAGER_HH */
diff --git a/modules/gui/src/remote_loader.cc b/modules/gui/src/remote_loader.cc
deleted file mode 100644
index a75a0b4a12dbbfe02f0c8af5b766ec3cb2cd7545..0000000000000000000000000000000000000000
--- a/modules/gui/src/remote_loader.cc
+++ /dev/null
@@ -1,208 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <vector>
-
-#include <ost/platform.hh>
-
-#include <ost/gui/file_loader.hh>
-#include <ost/gui/loader_manager.hh>
-
-#include "widget_registry.hh"
-#include "remote_loader.hh"
-
-#include <QString>
-#include <QSettings>
-#include <QNetworkReply>
-#include <QHBoxLayout>
-#include <QDir>
-namespace ost { namespace gui {
-
-RemoteLoader::RemoteLoader(QWidget* parent):
- Widget(NULL, parent)
-{
- img_support_=OST_IMG_ENABLED;
- line_edit_ = new QLineEdit(this);
- button_ = new QToolButton(this);
- button_->setAttribute(Qt::WA_MacSmallSize);
- progress_bar_ = new QProgressBar(this);
- progress_bar_->setAttribute(Qt::WA_MacSmallSize);
- progress_bar_->setVisible(false);
- progress_bar_->setRange(0,0);
-
- QHBoxLayout* l=new QHBoxLayout(this);
- l->addWidget(line_edit_);
- l->addWidget(button_);
- l->addWidget(progress_bar_);
- l->setMargin(3);
- l->setSpacing(2);
-
- connect(button_, SIGNAL(clicked()), this,
- SLOT(Clicked()));
-
- QDir icon_path(GetSharedDataPath().c_str());
- icon_path.cd("gui");
- icon_path.cd("icons");
- site_loader_menu_ = new QMenu(this);
- site_actions_ = new QActionGroup(site_loader_menu_);
-
- site_loader_menu_ = new QMenu(this);
- site_actions_ = new QActionGroup(site_loader_menu_);
-
- QAction* select_url_action = new QAction(this);
- select_url_action->setText("URL");
- select_url_action->setToolTip("Select remote URL");
- select_url_action->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+
- QString("site_icon.png")));
- action_list_.append(select_url_action);
- connect(select_url_action, SIGNAL(triggered(bool)), this, SLOT(UrlClick()));
- this->BuildMenu();
- this->RenameButton();
- this->setFixedHeight(button_->height());
- this->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
-}
-
-void RemoteLoader::UrlClick()
-{
- this->BuildMenu();
- site_loader_menu_->exec(QCursor::pos());
-}
-
-void RemoteLoader::BuildMenu(String active_loader)
-{
- if(!active_loader.empty()){
- selected_site_loader_ = active_loader;
- }
- else if(site_actions_->checkedAction()!=NULL){
- selected_site_loader_=site_actions_->checkedAction()->text().toStdString();
- }
- site_loader_menu_->clear();
- QList<QAction*> actions = site_actions_->actions();
- for(int i=0;i<actions.size();i++){
- site_actions_->removeAction(actions[i]);
- }
- std::vector<String> site_loaders = FileLoader::GetSiteLoaderIdents();
- for(unsigned int i=0; i<site_loaders.size(); i++){
- QString loader_ident(site_loaders[i].c_str());
- RemoteSiteLoader* loader = FileLoader::GetLoaderManager()->GetRemoteSiteLoader(loader_ident);
- if(loader && ((loader->IsImg() && img_support_) || !loader->IsImg())){
- QAction* action = new QAction(loader_ident,site_loader_menu_);
- connect(action, SIGNAL(triggered()), this, SLOT(RenameButton()));
- action->setCheckable(true);
- site_actions_->addAction(action);
- if((site_actions_->checkedAction()==NULL && loader_ident == FileLoader::GetLoaderManager()->GetDefaultRemoteSiteIdent()) ||selected_site_loader_==loader_ident.toStdString() ){
- action->setChecked(true);
- }
- site_loader_menu_->addAction(action);
- }
- }
-}
-
-ActionList RemoteLoader::GetActions()
-{
- return action_list_;
-}
-
-bool RemoteLoader::Save(const QString& prefix)
-{
- this->BuildMenu();
- QSettings settings;
- settings.beginGroup(prefix);
- settings.setValue("loader", site_actions_->checkedAction()->text());
- settings.endGroup();
- return true;
-}
-
-bool RemoteLoader::Restore(const QString& prefix)
-{
- QSettings settings;
- settings.beginGroup(prefix);
- if (settings.contains("loader")) {
- this->BuildMenu(settings.value("loader").toString().toStdString());
- }
- else{
- this->BuildMenu();
- }
- this->RenameButton();
- return true;
-}
-
-void RemoteLoader::Clicked()
-{
- this->BuildMenu();
- if(!line_edit_->text().isEmpty() && site_actions_->checkedAction()){
- RemoteSiteLoader* loader = FileLoader::GetLoaderManager()->GetRemoteSiteLoader(site_actions_->checkedAction()->text());
-
- QString text = line_edit_->text().simplified();
- QString id = text;
- QString selection = "";
- int pos = text.indexOf('[');
- if(pos >= 0){
- id = text.left(pos);
- selection = text.right(text.size()-(pos+1));
- pos = selection.lastIndexOf(']');
- if(pos>=0){
- selection = selection.left(pos);
- }
- }
- QNetworkReply* network_reply = loader->ById(id,selection);
- if(network_reply){
- progress_bar_->reset();
- connect(network_reply, SIGNAL(downloadProgress(qint64,qint64)), this, SLOT(UpdateProgress(qint64,qint64)));
- connect(network_reply, SIGNAL(finished()), this, SLOT(DownloadFinished()));
- this->ShowProgressBar(true);
- }
- line_edit_->setText("");
- line_edit_->setFocus();
- }
-}
-
-void RemoteLoader::keyPressEvent(QKeyEvent* event){
- if (event->key() == Qt::Key_Return || event->key() == Qt::Key_Enter) {
- this->Clicked();
- }
-}
-
-void RemoteLoader::ShowProgressBar(bool visibility){
- button_->setVisible(!visibility);
- line_edit_->setVisible(!visibility);
- progress_bar_->setVisible(visibility);
-}
-
-void RemoteLoader::UpdateProgress(qint64 read, qint64 total){
- progress_bar_->setMaximum(total);
- progress_bar_->setValue(read);
-
-}
-
-void RemoteLoader::DownloadFinished(){
- this->ShowProgressBar(false);
-}
-
-
-void RemoteLoader::RenameButton(){
- if(site_actions_->checkedAction()){
- QString text = "Load (" + site_actions_->checkedAction()->text() + ")";
- button_->setText(text);
- }
-}
-
-OST_REGISTER_WIDGET_WITH_DEFAULT_FACTORY(ost::gui, RemoteLoader, "Remote Loader");
-
-}}
-
diff --git a/modules/img/alg/src/discrete_shrink.cc b/modules/img/alg/src/discrete_shrink.cc
index d24979b3f5b632d6376342bbb8db0b84e128a004..ba01ae54635d9c4bab555b1772f38f5c43b1129b 100644
--- a/modules/img/alg/src/discrete_shrink.cc
+++ b/modules/img/alg/src/discrete_shrink.cc
@@ -49,6 +49,7 @@ void do_shrink(const ImageStateImpl<T,D>& isi, T& dest, const Extent& inner_ext)
T sum(0);
Real count=0.0;
for(ExtentIterator bit(inner_ext);!bit.AtEnd();++bit) {
+ LOG_VERBOSE("inner extent point:" << Point(bit)<<","<<isi.GetExtent().Contains(Point(bit)));
sum+=isi.Value(bit);
count+=1.0;
}
@@ -61,18 +62,27 @@ void do_shrink(const ImageStateImpl<T,D>& isi, T& dest, const Extent& inner_ext)
template <typename T, class D>
ImageStateBasePtr DiscreteShrinkFnc::VisitState(const ImageStateImpl<T,D>& isi) const
{
- Size size(isi.GetExtent().GetSize());
- Point start(isi.GetExtent().GetStart());
+ Size size(isi.GetLogicalExtent().GetSize());
+ Point start(isi.GetLogicalExtent().GetStart());
Size newsize;
div_t dt;
- dt = div(static_cast<int>(size[0]),bs_[0]); newsize[0] = dt.quot + ((dt.rem>0) ? 1 : 0);
- dt = div(static_cast<int>(size[1]),bs_[1]); newsize[1] = dt.quot + ((dt.rem>0) ? 1 : 0);
- dt = div(static_cast<int>(size[2]),bs_[2]); newsize[2] = dt.quot + ((dt.rem>0) ? 1 : 0);
-
+ dt = div(static_cast<int>(size[0]),bs_[0]);
+ newsize[0] = dt.quot + ((dt.rem>0) ? 1 : 0);
+ dt = div(static_cast<int>(size[1]),bs_[1]);
+ newsize[1] = dt.quot + ((dt.rem>0) ? 1 : 0);
+ dt = div(static_cast<int>(size[2]),bs_[2]);
+ newsize[2] = dt.quot + ((dt.rem>0) ? 1 : 0);
Extent new_ext(newsize);
+ Point newstart;
- LOG_DEBUG("extent of shrunken image" << isi.GetExtent() << " " << new_ext);
+ dt = div(start[0],bs_[0]); newstart[0] = dt.quot;
+ dt = div(start[1],bs_[1]); newstart[1] = dt.quot;
+ dt = div(start[2],bs_[2]); newstart[2] = dt.quot;
+
+ new_ext.Shift(newstart);
+
+ LOG_DEBUG("extent of shrunken image" << isi.GetExtent() << " " << new_ext<< new_ext.GetEnd());
geom::Vec3 ao = isi.GetAbsoluteOrigin();
@@ -80,26 +90,18 @@ ImageStateBasePtr DiscreteShrinkFnc::VisitState(const ImageStateImpl<T,D>& isi)
new_ps.SetExtent(new_ext);
typename ImageStateImpl<T,D>::SharedPtrType ni(new ImageStateImpl<T,D>(new_ext,new_ps));
+ ni->SetAbsoluteOrigin(ao);
+ ni->GetSampling().SetPixelSampling(CompMultiply(ni->GetSampling().GetPixelSampling(),Vec3(bs_[0],bs_[1],bs_[2])));
- for(ExtentIterator it(new_ext); !it.AtEnd(); ++it) {
+ for(ExtentIterator it(ni->GetExtent(),ni->GetDomain()); !it.AtEnd(); ++it) {
Point t(it[0]*bs_[0],
it[1]*bs_[1],
it[2]*bs_[2]);
-
- Extent inner_ext = Overlap(Extent(t+start,bs_),isi.GetExtent());
-
+ Extent inner_ext = Overlap(Extent(t,bs_),isi.GetExtent());
do_shrink(isi,ni->Value(it),inner_ext);
}
- Point newstart;
-
- dt = div(start[0],bs_[0]); newstart[0] = dt.quot;
- dt = div(start[1],bs_[1]); newstart[1] = dt.quot;
- dt = div(start[2],bs_[2]); newstart[2] = dt.quot;
- ni->SetAbsoluteOrigin(ao);
- ni->SetSpatialOrigin(newstart);
- ni->GetSampling().SetPixelSampling(CompMultiply(ni->GetSampling().GetPixelSampling(),Vec3(bs_[0],bs_[1],bs_[2])));
return ni;
}
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index a887323546f8b9687ec9c6e0bde909903261d2d7..df9a948bd44cb5b17c9e3174d97c6cc64fb83e01 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -130,7 +130,14 @@ of the annotation available.
.. method:: AddBioUnit(biounit)
- Add a bio unit to the bio unit list of an info object.
+ Add a bio unit to the bio unit list of an info object. If the
+ :attr:`id <MMCifInfoBioUnit.id>` of ``biounit`` already exists in the set
+ of assemblies, both will be merged. This means that
+ :attr:`chain <MMCifInfoBioUnit.chains>` and
+ :attr:`operations <MMCifInfoBioUnit.operations>` lists will be concatenated
+ and the interval lists
+ (:attr:`operationsintervalls <MMCifInfoBioUnit.operationsintervalls>`,
+ :attr:`chainintervalls <MMCifInfoBioUnit.chainintervalls>`) will be updated.
:param biounit: Bio unit to be added.
:type biounit: :class:`MMCifInfoBioUnit`
@@ -499,7 +506,17 @@ of the annotation available.
Chains involved in this bio unit. If not provided, resembles an empty list.
Also available as :meth:`GetChainList`. May also be modified by
- :meth:`AddChain`.
+ :meth:`AddChain` or :meth:`SetChainList`.
+
+ .. attribute:: chainintervalls
+
+ List of intervals on the chain list. Needed if there a several sets of
+ chains and transformations to create the bio unit. Comes as a list of
+ tuples. First component is the start, second is the right border of the
+ interval.
+
+ Also available as :meth:`GetChainIntervalList`. Is automatically modified by
+ :meth:`AddChain`, :meth:`SetChainList` and :meth:`MMCifInfo.AddBioUnit`.
.. attribute:: operations
@@ -509,6 +526,16 @@ of the annotation available.
Also available as :meth:`GetOperations`. May be modified by
:meth:`AddOperations`
+ .. attribute:: operationsintervalls
+
+ List of intervals on the operations list. Needed if there a several sets of
+ chains and transformations to create the bio unit. Comes as a list of
+ tuples. First component is the start, second is the right border of the
+ interval.
+
+ Also available as :meth:`GetOperationsIntervalList`. Is automatically
+ modified by :meth:`AddOperations` and :meth:`MMCifInfo.AddBioUnit`.
+
.. method:: GetID()
See :attr:`id`
@@ -529,9 +556,22 @@ of the annotation available.
See :attr:`chains`
+ .. method:: SetChainList(chains)
+
+ See :attr:`chains`, also resets :attr:`chainintervalls` to contain only one
+ interval enclosing the whole chain list.
+
+ :param chains: List of chain names.
+ :type chains: :class:`~ost.StringList`
+
.. method:: AddChain(chain name)
- See :attr:`chains`
+ See :attr:`chains`, also extends the right border of the last entry in
+ :attr:`chainintervalls`.
+
+ .. method:: GetChainIntervalList()
+
+ See :attr:`chainintervalls`
.. method:: GetOperations()
@@ -539,7 +579,12 @@ of the annotation available.
.. method:: AddOperations(list of operations)
- See :attr:`operations`
+ See :attr:`operations`, also extends the right border of the last entry in
+ :attr:`operationsintervalls`.
+
+ .. method:: GetOperationsIntervalList()
+
+ See :attr:`operationsintervalls`
.. function:: PDBize(asu, seqres=None, min_polymer_size=10, transformation=False)
@@ -567,7 +612,7 @@ of the annotation available.
:param asu: Asymmetric unit to work on. Should be created from a mmCIF
file.
- :type asu: :class:`~ost.mol.EntityHandle>`
+ :type asu: :class:`~ost.mol.EntityHandle`
:param seqres: If set to a valid sequence list, the length of the seqres
records will be used to determine if a certain chain has the minimally
required length.
@@ -948,3 +993,8 @@ of the annotation available.
.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
.. LocalWords: GetRevisions AddRevision SetRevisionsDateOriginal GetSize
.. LocalWords: GetNum num GetStatus GetLastDate GetFirstRelease storable
+.. LocalWords: SetChainList MMCifInfoTransOp ChainTypes MMCifInfoStructRef
+.. LocalWords: MMCifInfoRevisions bool difs MMCifInfoStructRefSeqDif rnum
+.. LocalWords: SetDateOriginal GetDateOriginal yyyy operationsintervalls
+.. LocalWords: chainintervalls GetChainIntervalList
+.. LocalWords: GetOperationsIntervalList
diff --git a/modules/io/pymod/CMakeLists.txt b/modules/io/pymod/CMakeLists.txt
index 007569fff38887504ed15d21231b2b5d4464b346..6763a0189c4d779f8d2777576ba576d886201af4 100644
--- a/modules/io/pymod/CMakeLists.txt
+++ b/modules/io/pymod/CMakeLists.txt
@@ -10,7 +10,7 @@ endif()
set(OST_IO_PYMOD_MODULES
__init__.py
- hhsearch.py
+ remote.py
repository.py
)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index e9e597d726f5d921fb6938f12a13a221610b16b8..7cf8437f7c60b8efb080ae5790e79e70542bf30e 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -58,30 +58,6 @@ def _override(val1, val2):
else:
return val1
-def __GetModelFromPDB(model_id, output_dir, file_pattern='pdb%s.ent.gz'):
- file_name = file_pattern % model_id
- file_path = os.path.join(output_dir,file_name)
- try:
- server="ftp.wwpdb.org"
- ftp=ftplib.FTP(server,"anonymous","user@")
- ftp.cwd("pub/pdb/data/structures/all/pdb")
- ftp_retrfile=open(file_path,"wb")
- ftp.retrbinary("RETR "+file_name,ftp_retrfile.write)
- ftp_retrfile.close()
- except:
- conn=httplib.HTTPConnection('www.pdb.org')
- conn.request('GET', '/pdb/files/%s.pdb.gz' % model_id )
- response=conn.getresponse()
- if response.status==200:
- data=response.read()
- f=open(os.path.join(output_dir, file_pattern % model_id), 'w+')
- f.write(data)
- f.close()
- else:
- conn.close()
- return False
- return os.path.getsize(file_path) > 0
-
def LoadPDB(filename, restrict_chains="", no_hetatms=None,
fault_tolerant=None, load_multi=False, quack_mode=None,
join_spread_atom_records=None, calpha_only=None,
@@ -154,12 +130,11 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
join_spread_atom_records)
+ tmp_file = None # avoid getting out of scope
if remote:
- output_dir = tempfile.gettempdir()
- if __GetModelFromPDB(filename, output_dir):
- filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
- else:
- raise IOError('Can not load PDB %s from www.pdb.org'%filename)
+ from ost.io.remote import RemoteGet
+ tmp_file =RemoteGet(filename)
+ filename = tmp_file.name
conop_inst=conop.Conopology.Instance()
builder=conop_inst.GetBuilder("DEFAULT")
@@ -380,105 +355,110 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
return atom_pos_wrong
chain_names='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz'
+ cur_chain_name = 0
+ water_chain = mol.ChainHandle()
+ ligand_chain = mol.ChainHandle()
+ a_pos_wrong = False
+ pdb_bu = mol.CreateEntity()
+ edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
+ chains = biounit.GetChainList()
+ c_intvls = biounit.GetChainIntervalList()
+ o_intvls = biounit.GetOperationsIntervalList()
# create list of operations
# for cartesian products, operations are stored in a list, multiplied with
# the next list of operations and re-stored... until all lists of operations
# are multiplied in an all-against-all manner.
operations = biounit.GetOperations()
- trans_matrices = list()
- if len(operations) > 0:
- for op in operations[0]:
- rot = geom.Mat4()
- rot.PasteRotation(op.rotation)
- trans = geom.Mat4()
- trans.PasteTranslation(op.translation)
- 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]:
+ for i in range(0,len(c_intvls)):
+ trans_matrices = list()
+ l_operations = operations[o_intvls[i][0]:o_intvls[i][1]]
+ if len(l_operations) > 0:
+ for op in l_operations[0]:
rot = geom.Mat4()
- rot.PasteRotation(o.rotation)
+ rot.PasteRotation(op.rotation)
trans = geom.Mat4()
- trans.PasteTranslation(o.translation)
+ trans.PasteTranslation(op.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
- # the result while adding everything to one large entity
- pdb_bu = mol.CreateEntity()
- edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
- cur_chain_name = 0
- water_chain = mol.ChainHandle()
- ligand_chain = mol.ChainHandle()
- a_pos_wrong = False
- for tr in trans_matrices:
- # do a PDBize, add each new entity to the end product
- for chain in assu.chains:
- residue_count = len(chain.residues)
- if seqres:
- seqres_chain = seqres.FindSequence(chain.name)
- if seqres_chain.IsValid():
- residue_count = len(seqres_chain)
- if chain.is_polymer and residue_count >= min_polymer_size:
- if len(chain_names) == cur_chain_name:
- raise RuntimeError('Running out of chain names')
- new_chain = edi.InsertChain(chain_names[cur_chain_name])
- cur_chain_name += 1
- 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)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
- elif chain.type == mol.CHAINTYPE_WATER:
- if not water_chain.IsValid():
- # water gets '-' as name
- water_chain = edi.InsertChain('-')
- edi.SetChainDescription(water_chain, chain.description)
- edi.SetChainType(water_chain, chain.type)
- for res in chain.residues:
- new_res = edi.AppendResidue(water_chain, res.name)
- new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
- new_res.SetStringProp('description', chain.description)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
- else:
- if not ligand_chain.IsValid():
- # all ligands, put in one chain, are named '_'
- ligand_chain = edi.InsertChain('_')
- last_rnum = 0
- else:
- last_rnum = ligand_chain.residues[-1].number.num
- residues=chain.residues
- ins_code='\0'
- if len(residues)>1:
- ins_code='A'
- for res in chain.residues:
- new_res = edi.AppendResidue(ligand_chain, res.name,
- 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)
+ trans_matrices.append(tr)
+ for op_n in range(1, len(l_operations)):
+ tmp_ops = list()
+ for o in l_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(chains[c_intvls[i][0]:c_intvls[i][1]]))
+ # use each transformation on the view, store as entity and transform, PDBize
+ # the result while adding everything to one large entity
+ for tr in trans_matrices:
+ # do a PDBize, add each new entity to the end product
+ for chain in assu.chains:
+ residue_count = len(chain.residues)
+ if seqres:
+ seqres_chain = seqres.FindSequence(chain.name)
+ if seqres_chain.IsValid():
+ residue_count = len(seqres_chain)
+ if chain.is_polymer and residue_count >= min_polymer_size:
+ if len(chain_names) == cur_chain_name:
+ raise RuntimeError('Running out of chain names')
+ new_chain = edi.InsertChain(chain_names[cur_chain_name])
+ cur_chain_name += 1
+ 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_res.SetStringProp("pdb_auth_chain_name",
- chain.GetStringProp("pdb_auth_chain_name"))
- ins_code = chr(ord(ins_code)+1)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
+ 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)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
+ elif chain.type == mol.CHAINTYPE_WATER:
+ if not water_chain.IsValid():
+ # water gets '-' as name
+ water_chain = edi.InsertChain('-')
+ edi.SetChainDescription(water_chain, chain.description)
+ edi.SetChainType(water_chain, chain.type)
+ for res in chain.residues:
+ new_res = edi.AppendResidue(water_chain, res.name)
+ new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp('description', chain.description)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
+ else:
+ if not ligand_chain.IsValid():
+ # all ligands, put in one chain, are named '_'
+ ligand_chain = edi.InsertChain('_')
+ last_rnum = 0
+ else:
+ last_rnum = ligand_chain.residues[-1].number.num
+ residues=chain.residues
+ ins_code='\0'
+ if len(residues)>1:
+ ins_code='A'
+ for res in chain.residues:
+ new_res = edi.AppendResidue(ligand_chain, res.name,
+ 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)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
move_to_origin = None
if a_pos_wrong:
start = pdb_bu.bounds.min
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 78cd7e124f08460009e4f5b98432080e8422ae95..9a21bdb1af003bdaa33406e7f7e98754f8a606ea 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -21,6 +21,7 @@
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace boost::python;
+#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/io/mol/io_profile.hh>
#include <ost/io/mol/mmcif_reader.hh>
#include <ost/io/mol/mmcif_info.hh>
@@ -172,23 +173,44 @@ void export_mmcif_io()
.add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum)
.add_property("db_rnum", &MMCifInfoStructRefSeqDif::GetDBRNum)
;
+
+ typedef std::pair<int, int> IntPair;
+ to_python_converter<IntPair, PairToTupleConverter<int, int> >();
+ typedef std::vector<IntPair> VectorIntPair;
+ class_<VectorIntPair>("VectorIntPair", init<>())
+ .def(vector_indexing_suite<VectorIntPair, true>())
+ ;
+
class_<MMCifInfoBioUnit>("MMCifInfoBioUnit", init<>())
.def("SetDetails", &MMCifInfoBioUnit::SetDetails)
.def("GetDetails", &MMCifInfoBioUnit::GetDetails)
.def("AddChain", &MMCifInfoBioUnit::AddChain)
+ .def("SetChainList", &MMCifInfoBioUnit::SetChainList)
.def("GetChainList", make_function(&MMCifInfoBioUnit::GetChainList,
return_value_policy<copy_const_reference>()))
+ .def("GetChainIntervalList",
+ make_function(&MMCifInfoBioUnit::GetChainIntervalList,
+ return_value_policy<copy_const_reference>()))
.def("AddOperations", &MMCifInfoBioUnit::AddOperations)
.def("GetOperations", make_function(&MMCifInfoBioUnit::GetOperations,
return_value_policy<copy_const_reference>()))
+ .def("GetOperationsIntervalList",
+ make_function(&MMCifInfoBioUnit::GetOperationsIntervalList,
+ return_value_policy<copy_const_reference>()))
.def("SetID", &MMCifInfoBioUnit::SetID)
.def("GetID", &MMCifInfoBioUnit::GetID)
.add_property("details", &MMCifInfoBioUnit::GetDetails,
&MMCifInfoBioUnit::SetDetails)
.add_property("chains", make_function(&MMCifInfoBioUnit::GetChainList,
return_value_policy<copy_const_reference>()))
+ .add_property("chainintervalls", make_function(
+ &MMCifInfoBioUnit::GetChainIntervalList,
+ return_value_policy<copy_const_reference>()))
.add_property("operations", make_function(&MMCifInfoBioUnit::GetOperations,
return_value_policy<copy_const_reference>()))
+ .add_property("operationsintervalls", make_function(
+ &MMCifInfoBioUnit::GetOperationsIntervalList,
+ return_value_policy<copy_const_reference>()))
.add_property("id", &MMCifInfoBioUnit::GetID, &MMCifInfoBioUnit::SetID)
;
diff --git a/modules/io/pymod/remote.py b/modules/io/pymod/remote.py
new file mode 100644
index 0000000000000000000000000000000000000000..102cf680711ffafaeb98aab2c5f6a0aff082044d
--- /dev/null
+++ b/modules/io/pymod/remote.py
@@ -0,0 +1,93 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2011 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+#------------------------------------------------------------------------------
+
+import urllib2
+import tempfile
+
+from ost.io import LoadPDB, LoadMMCIF
+
+class RemoteRepository:
+ """
+ A remote repository represents a structural database accessible through the
+ internet, e.g. the PDB or SWISS-MODEL template library.
+ """
+ def __init__(self, name, url_pattern, type, id_transform='upper'):
+ self.name = name
+ self.url_pattern = url_pattern
+ self.type = type
+ if type not in ('cif', 'pdb'):
+ raise ValueError('only cif and pdb types are supported')
+ self.id_transform = id_transform
+
+ def URLForID(self, id):
+ if self.id_transform == 'upper':
+ id = id.upper()
+ if self.id_transform == 'lower':
+ id = id.lower()
+ return self.url_pattern.replace('$ID', id)
+
+ def Get(self, id):
+ remote_url = self.URLForID(id)
+ tmp_file_suffix = '.%s' % self.type
+ if remote_url.endswith('.gz'):
+ tmp_file_suffix+='.gz'
+
+ try:
+ connection = urllib2.urlopen(remote_url)
+ status = connection.getcode()
+ except urllib2.HTTPError, e:
+ status = e.code
+ msg = 'Could not load %s from %s (status code %d)'
+ if status!=200:
+ raise IOError(msg % (id , self.name ,status))
+ tmp_file = tempfile.NamedTemporaryFile(suffix=tmp_file_suffix)
+ contents = ''.join(connection)
+ tmp_file.write(contents)
+ tmp_file.flush()
+ return tmp_file
+
+ def Load(self, id):
+ tmp_file = self.Get(id)
+ if self.type == 'pdb':
+ return LoadPDB(tmp_file.name)
+ if self.type == 'cif':
+ return LoadMMCIF(tmp_file.name)
+
+REMOTE_REPOSITORIES = {
+ 'pdb' : RemoteRepository('pdb.org (PDB)', 'http://www.pdb.org/pdb/files/$ID.ent.gz',
+ type='pdb', id_transform='upper'),
+ 'smtl' : RemoteRepository('SMTL', 'http://beta.swissmodel.expasy.org/templates/$ID.pdb',
+ type='pdb', id_transform='lower'),
+ 'cif' : RemoteRepository('pdb.org (mmCIF)', 'http://www.pdb.org/pdb/files/$ID.cif.gz',
+ type='cif', id_transform='lower'),
+ 'pdb_redo' : RemoteRepository('pdbredo', 'http://www.cmbi.ru.nl/pdb_redo/$ID/$ID_besttls.pdb',
+ type='pdb'),
+}
+
+def RemoteGet(id, from_repo='pdb'):
+ remote_repo = REMOTE_REPOSITORIES.get(from_repo, None)
+ if not remote_repo:
+ raise ValueError('%s is not a valid repository' % from_repo)
+ return remote_repo.Get(id)
+
+def RemoteLoad(id ,from_repo='pdb'):
+ remote_repo = REMOTE_REPOSITORIES.get(from_repo, None)
+ if not remote_repo:
+ raise ValueError('%s is not a valid repository' % from_repo)
+ return remote_repo.Load(id)
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 29f0db7463188068b3584a49457126d7ec1601d0..e7f391894cab4e8ace515de79fa14f6e047fd683 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -72,7 +72,75 @@ void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
throw IOException("No citation for identifier '" + id.str() + "' found.");
}
+void MMCifInfo::AddBioUnit(MMCifInfoBioUnit bu)
+{
+ std::vector<MMCifInfoBioUnit>::iterator bu_it;
+ for (bu_it = biounits_.begin(); bu_it != biounits_.end(); ++bu_it) {
+ if (bu_it->GetID() == bu.GetID()) {
+ break;
+ }
+ }
+ if (bu_it != biounits_.end()) {
+ bu_it->Merge(bu);
+ return;
+ }
+ biounits_.push_back(bu);
+}
+void MMCifInfoBioUnit::AddChain(String chain)
+{
+ chains_.push_back(chain);
+
+ if (tr_chains_.size()) {
+ tr_chains_.back().second = chains_.size();
+ }
+ else {
+ std::pair<int, int> tr_interval = std::pair<int, int>(0, 1);
+ tr_chains_.push_back(tr_interval);
+ }
+}
+
+void MMCifInfoBioUnit::SetChainList(std::vector<String> chains)
+{
+ chains_ = chains;
+
+ if (tr_chains_.size()) {
+ tr_chains_.clear();
+ }
+ std::pair<int, int> tr_interval = std::pair<int, int>(0, chains_.size());
+ tr_chains_.push_back(tr_interval);
+}
+
+void MMCifInfoBioUnit::AddOperations(std::vector<MMCifInfoTransOpPtr> operations)
+{
+ operations_.push_back(operations);
+
+ if (tr_operations_.size()) {
+ tr_operations_.back().second = operations_.size();
+ }
+ else {
+ std::pair<int, int> tr_interval = std::pair<int, int>(0, 1);
+ tr_operations_.push_back(tr_interval);
+ }
+}
+
+void MMCifInfoBioUnit::Merge(MMCifInfoBioUnit& from)
+{
+ // merge chains
+ int old_size = chains_.size();
+ chains_.insert(chains_.end(), from.chains_.begin(), from.chains_.end());
+ std::pair<int, int> tr_interval = std::pair<int, int>(old_size,
+ chains_.size());
+ tr_chains_.push_back(tr_interval);
+ // merge operations
+ old_size = operations_.size();
+ operations_.insert(operations_.end(),
+ from.operations_.begin(),
+ from.operations_.end());
+ tr_interval.first = old_size;
+ tr_interval.second = operations_.size();
+ tr_operations_.push_back(tr_interval);
+}
MMCifInfoStructRefSeqPtr
MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
@@ -108,5 +176,4 @@ MMCifInfoStructRefSeq::AddDif(int seq_rnum, int db_rnum, const String& details)
return d;
}
-
}} //ns
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index f567af0520381f6b726be63046235e2dd0b9a87a..52a44aedc1baf2dcea4255f4a4980eeaec03570f 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -241,6 +241,11 @@ public:
/// \brief Create a biounit.
MMCifInfoBioUnit(): id_(""), details_("") {};
+ /// \brief Merge chains & operations, set intervals
+ ///
+ /// \param from biounit to read data from
+ void Merge(MMCifInfoBioUnit& from);
+
/// \brief Set id
///
/// \param id id
@@ -262,19 +267,39 @@ public:
/// \brief Add a chain name
///
/// \param chain chain name
- void AddChain(String chain) { chains_.push_back(chain); }
+ void AddChain(String chain);
+
+ /// \brief Set a vector of chain names
+ ///
+ /// \param chains chain name
+ void SetChainList(std::vector<String> chains);
+
/// \brief Get vector of chain names
///
/// \return chains
const std::vector<String>& GetChainList() const { return chains_; }
+ /// \brief Get the list of intervals of chains
+ ///
+ /// \return pair-intervals
+ const std::vector<std::pair<int, int> >& GetChainIntervalList()
+ {
+ return tr_chains_;
+ }
+
/// \brief Add a set of operations
///
/// \param operations vector of operations to be added
- void AddOperations(std::vector<MMCifInfoTransOpPtr> operations)
+ void AddOperations(std::vector<MMCifInfoTransOpPtr> operations);
+
+ /// \brief Get the list of intervals of operations
+ ///
+ /// \return pair-intervals
+ const std::vector<std::pair<int, int> >& GetOperationsIntervalList()
{
- operations_.push_back(operations);
+ return tr_operations_;
}
+
/// \brief Get the list of operations
///
/// \return vector of vectors of iterators.
@@ -293,6 +318,12 @@ public:
if (this->chains_ != bu.chains_) {
return false;
}
+ if (this->tr_chains_ != bu.tr_chains_) {
+ return false;
+ }
+ if (this->tr_operations_ != bu.tr_operations_) {
+ return false;
+ }
if (this->operations_.size() == bu.operations_.size()) {
std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator th_ops_it;
std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator bu_ops_it;
@@ -329,8 +360,10 @@ public:
private:
String id_; ///< pdbx_struct_assembly.id
String details_; ///< pdbx_struct_assembly.details
- std::vector<String> chains_; ///< chains involved in this assembly
+ std::vector<String> chains_; ///< all chains of this this assembly
+ std::vector<std::pair<int, int> > tr_chains_; //< chains of a transformation
std::vector<std::vector<MMCifInfoTransOpPtr> > operations_;
+ std::vector<std::pair<int, int> > tr_operations_; //< ops. of a transformation
};
class DLLEXPORT_OST_IO MMCifInfoCitation {
@@ -888,10 +921,7 @@ public:
/// \brief Add a biounit
///
/// \param bu biounit to be added
- void AddBioUnit(MMCifInfoBioUnit bu) // unit test
- {
- biounits_.push_back(bu);
- }
+ void AddBioUnit(MMCifInfoBioUnit bu);
/// \brief Get the list of biounits stored in an info object.
///
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 33e71d4e3daeced0ddf26484cdfb4c0dfe9bbccf..91d46cb9b86646add1832a8ea972b6c316a3cba7 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -981,14 +981,13 @@ std::vector<std::vector<String> > MMCifReader::UnPackOperExperession(StringRef e
void MMCifReader::ParsePdbxStructAssemblyGen(const std::vector<StringRef>& columns)
{
MMCifBioUAssembly assembly;
- assembly.biounit = MMCifInfoBioUnit();
- assembly.biounit.SetID(columns[indices_[ASSEMBLY_ID]].str());
+ assembly.biounit_id = columns[indices_[ASSEMBLY_ID]].str();
std::vector<StringRef> tmp_chains=columns[indices_[ASYM_ID_LIST]].split(',');
std::vector<StringRef>::const_iterator tc_it;
for (tc_it = tmp_chains.begin(); tc_it != tmp_chains.end(); ++tc_it) {
- assembly.biounit.AddChain(tc_it->str());
+ assembly.chains.push_back(tc_it->str());
}
assembly.operations =
@@ -1620,19 +1619,22 @@ void MMCifReader::OnEndData()
std::vector<MMCifInfoTransOpPtr> operations = info_.GetOperations();
info_.SetStructRefs(struct_refs_);
std::vector<MMCifInfoTransOpPtr>::const_iterator buop_it;
+ MMCifInfoBioUnit biounit;
for (bua_it = bu_assemblies_.begin();
bua_it != bu_assemblies_.end();
++bua_it) {
+ biounit = MMCifInfoBioUnit();
// pair with pdbx_struct_assembly entry
- buom_it = bu_origin_map_.find(bua_it->biounit.GetID());
+ buom_it = bu_origin_map_.find(bua_it->biounit_id);
if (buom_it == bu_origin_map_.end()) {
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"No pdbx_struct_assembly.id '"+
- bua_it->biounit.GetID() +
+ bua_it->biounit_id +
"' found as requested by pdbx_struct_assembly_gen."));
}
- bua_it->biounit.SetDetails(buom_it->second);
- bua_it->biounit.SetID(buom_it->first);
+ biounit.SetDetails(buom_it->second);
+ biounit.SetID(buom_it->first);
+ biounit.SetChainList(bua_it->chains);
// pair with pdbx_struct_oper_list
for (aol_it = bua_it->operations.begin();
@@ -1657,9 +1659,9 @@ void MMCifReader::OnEndData()
"' found as requested by pdbx_struct_assembly_gen."));
}
}
- bua_it->biounit.AddOperations(operation_list);
+ biounit.AddOperations(operation_list);
}
- info_.AddBioUnit(bua_it->biounit);
+ info_.AddBioUnit(biounit);
}
bu_assemblies_.clear();
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index b8f6daed068fd5c96293d4d8e6442d24a74b3e0b..d91cf340355be48f58664a4ada5e02966365e931 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -559,9 +559,11 @@ private:
/// \struct assembly information
typedef struct {
- MMCifInfoBioUnit biounit;
+ String biounit_id; ///< identifier for the bu
+ std::vector<String> chains; ///< chains affected by
+ /// this operations
std::vector<std::vector<String> > operations; ///< list of links to
- /// MMCifBioUOperation
+ /// MMCifBioUOperation
} MMCifBioUAssembly;
typedef std::vector<MMCifBioUAssembly> MMCifBioUAssemblyVector;
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index ba3eb6b63e008060e267f3fd8cb97ed838ac5b33..be7594314f103c127f2c6297066daf45f24e7d21 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -69,14 +69,38 @@ class TestMMCifInfo(unittest.TestCase):
b.SetDetails('Details')
self.assertEquals(b.GetDetails(), 'Details')
b.AddChain('A')
+ b.AddChain('B')
cl = b.GetChainList()
+ il = b.GetChainIntervalList()
self.assertEquals(cl[0], 'A')
+ self.assertEquals(il[0][0], 0)
+ self.assertEquals(il[0][1], 2)
+ s = ost.StringList()
+ s.append('B')
+ s.append('C')
+ s.append('D')
+ b.SetChainList(s)
+ cl = b.GetChainList()
+ il = b.GetChainIntervalList()
+ self.assertEquals(il[0][0], 0)
+ self.assertEquals(il[0][1], 3)
+ self.assertEquals(cl[0], 'B')
+ self.assertEquals(cl[1], 'C')
+ self.assertEquals(cl[2], 'D')
i = io.MMCifInfo()
i.AddBioUnit(b)
+ i.AddBioUnit(b)
+ b.SetID("2")
+ i.AddBioUnit(b)
bl = i.GetBioUnits()
- self.assertEquals(len(bl), 1)
+ il = bl[0].GetChainIntervalList()
+ self.assertEquals(il[0][0], 0)
+ self.assertEquals(il[0][1], 3)
+ self.assertEquals(il[1][0], 3)
+ self.assertEquals(il[1][1], 6)
+ self.assertEquals(len(bl), 2)
def test_mmcifinfo_transoperation(self):
@@ -102,6 +126,10 @@ class TestMMCifInfo(unittest.TestCase):
b.AddOperations(ol)
oll = b.GetOperations()
self.assertEquals(oll[0][0].GetID(), '1')
+ tr_ol = b.GetOperationsIntervalList()
+ self.assertEquals(len(tr_ol), 1)
+ self.assertEquals(tr_ol[0][0], 0)
+ self.assertEquals(tr_ol[0][1], 1)
def test_mmcifinfo_biounit_pdbize(self):
ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
@@ -170,7 +198,7 @@ class TestMMCifInfo(unittest.TestCase):
seqres=True,
info=True)
pdb_ent, t = info.GetBioUnits()[0].PDBize(ent, transformation=True)
- self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[0], -915.759, 3)
+ self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[0], -915.8, 1)
self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[1], -952.345, 2)
self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.75, 2)
self.assertEquals(geom.Equal(t,
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 3f3e21baf4b8a9e3f10b8f65380338668015bfd3..71dc2ddf40d7433c60629497288cf6e989528a5d 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -109,10 +109,23 @@ BOOST_AUTO_TEST_CASE(mmcif_info_biounit)
MMCifInfoBioUnit bu = MMCifInfoBioUnit();
bu.SetDetails("author_defined_assembly");
+ bu.SetID("1");
+ bu.AddChain("B");
bu.AddChain("A");
BOOST_CHECK(bu.GetDetails() == "author_defined_assembly");
BOOST_CHECK(bu.GetChainList().back() == "A");
+ std::vector<std::pair<int, int> > tr = bu.GetChainIntervalList();
+ BOOST_CHECK(tr[0].first == 0);
+ BOOST_CHECK(tr[0].second == 2);
+
+ std::vector<String> chains;
+ chains.push_back("B");
+ bu.SetChainList(chains);
+ BOOST_CHECK(bu.GetChainList().back() == "B");
+ tr = bu.GetChainIntervalList();
+ BOOST_CHECK(tr[0].first == 0);
+ BOOST_CHECK(tr[0].second == 1);
MMCifInfo info = MMCifInfo();
info.AddBioUnit(bu);
@@ -120,6 +133,18 @@ BOOST_AUTO_TEST_CASE(mmcif_info_biounit)
BOOST_CHECK(biounits.size() == 1);
BOOST_CHECK(biounits.back() == bu);
+ info.AddBioUnit(bu);
+ bu.SetID("2");
+ info.AddBioUnit(bu);
+ biounits = info.GetBioUnits();
+ BOOST_CHECK(biounits.size() == 2);
+ tr = biounits.front().GetChainIntervalList();
+ BOOST_CHECK(tr.size() == 2);
+ BOOST_CHECK(tr[0].first == 0);
+ BOOST_CHECK(tr[0].second == 1);
+ BOOST_CHECK(tr[1].first == 1);
+ BOOST_CHECK(tr[1].second == 2);
+
BOOST_MESSAGE(" done.");
}
@@ -148,6 +173,10 @@ BOOST_AUTO_TEST_CASE(mmcif_info_transoperation)
MMCifInfoBioUnit bu = MMCifInfoBioUnit();
bu.AddOperations(ops);
BOOST_CHECK((*(bu.GetOperations().begin()->begin())) == op);
+ std::vector<std::pair<int, int> > tr = bu.GetOperationsIntervalList();
+ BOOST_CHECK(tr.size() == 1);
+ BOOST_CHECK(tr.back().first == 0);
+ BOOST_CHECK(tr.back().second == 1);
BOOST_MESSAGE(" done.");
}
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 66b14294022870a6dfe967ce407994388ef6679d..5a3e5e7c9ac93646263e05e18b45e198bcb734b3 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -276,7 +276,7 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:param clash_distance: minimum clashing distance (in Angstroms)
:param tolerance: tolerance threshold (in Angstroms)
- .. method GetClashingDistance()
+ .. method:: GetClashingDistance()
Recovers a reference distance and a tolerance threshold from the list
@@ -285,6 +285,15 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: a tuple containing the minimum clashing distance and the tolerance threshold
+ .. method:: GetAdjustedClashingDistance()
+
+ Recovers a reference distance from the list, already adjusted by the tolerance threshold
+
+ :param ele1: string containing the first element's name
+ :param ele2: string containing the second element's name
+
+ :returns: the adjusted minimum clashing distance
+
.. method:: GetMaxAdjustedDistance()
Returns the longest clashing distance in the list, after adjustment with tolerance threshold
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 126d0196f2d6ff25148a6724df5dd63a1e764d6a..b8c09d51d67b99b606ddc9c99af55afe37823dd4 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -6,11 +6,11 @@ import ost.mol.alg.structure_analysis
import ost.mol.alg.helix_kinks
# Fills a list of reference clashing distances from a file (requires a path to the file)
-def FillClashingDistancesFromFile(filename,default_clashing_distance,default_tolerance):
+def FillClashingDistancesFromFile(filename):
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
- return FillClashingDistances(lines,default_clashing_distance,default_tolerance)
+ return FillClashingDistances(lines)
# Fills a list of bond stereo-chemical statistics from a file (requires a path to the file)
def FillBondStereoChemicalParamsFromFile(filename):
@@ -33,7 +33,7 @@ def DefaultClashingDistances():
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
- return FillClashingDistances(lines,1.5,0.0)
+ return FillClashingDistances(lines)
# Returns the default list of bond stereo-chemical statistics (from the default OpenStructure parameter file)
def DefaultBondStereoChemicalParams():
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
index 7cbd0dd4b32bb7e6f4093ed23bbbb52a700fc320..1ad301618bc64e8d1673e2c95b1e9d1dd3a208ef 100644
--- a/modules/mol/alg/pymod/structure_analysis.py
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -13,7 +13,7 @@ def GetFrameFromEntity(eh):
Input:
eh : EntityHandle
"""
- return ost.mol.CreateCoordFrame(eh.GetAtomPosList())
+ return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
def GetDistanceBetwCenterOfMass(sele1,sele2):
"""
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 08ad6631efe89ce483e9cc653c2baec321db6927..b775b6396338c2ee45357bcfd56d259e6704b002 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -24,6 +24,7 @@
#include <ost/mol/alg/superpose_frames.hh>
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/mol/alg/consistency_checks.hh>
+#include <ost/export_helper/pair_to_tuple_conv.hh>
using namespace boost::python;
using namespace ost;
@@ -60,7 +61,7 @@ ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const St
return ost::mol::alg::FillStereoChemicalParams(header,stereo_chemical_props_file_vector);
}
-ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance)
+ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file)
{
int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
std::vector<String> stereo_chemical_props_file_vector(stereo_chemical_props_file_length);
@@ -103,6 +104,9 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
export_entity_to_density();
#endif
+ to_python_converter<std::pair<Real,Real>,
+ PairToTupleConverter<Real, Real> >();
+
def("LocalDistDiffTest", lddt_a, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_c, (arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_b, (arg("ref_index")=0, arg("mdl_index")=1));
@@ -124,6 +128,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::ClashingDistances> ("ClashingDistances",init<>())
.def("SetClashingDistance",&mol::alg::ClashingDistances::SetClashingDistance)
.def("GetClashingDistance",&mol::alg::ClashingDistances::GetClashingDistance)
+ .def("GetAdjustedClashingDistance",&mol::alg::ClashingDistances::GetAdjustedClashingDistance)
.def("GetMaxAdjustedDistance",&mol::alg::ClashingDistances::GetMaxAdjustedDistance)
.def("IsEmpty",&mol::alg::ClashingDistances::IsEmpty)
@@ -162,7 +167,8 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
- def("ResidueNamesMatch",&mol::alg::ResidueNamesMatch);
+ def("ResidueNamesMatch",&mol::alg::ResidueNamesMatch,
+ (arg("probe"), arg("reference"), arg("log_as_error")=false));
}
diff --git a/modules/mol/alg/src/consistency_checks.cc b/modules/mol/alg/src/consistency_checks.cc
index 371f3c37b6b8fbc921ecd3a82fa647251992b216..bdc0ab646f8fb4bb42762034fa6c618b54a8ca98 100644
--- a/modules/mol/alg/src/consistency_checks.cc
+++ b/modules/mol/alg/src/consistency_checks.cc
@@ -24,19 +24,8 @@
namespace ost { namespace mol { namespace alg {
-/// \brief Checks that residue types with the same ResNum in the two structures match
-///
-/// Requires a reference structure and a probe structure. The function checks that all the
-/// residues in the reference structure that appear in the probe structure (i.e., that have the
-/// same ResNum) are of the same residue type. Chains are paired by index, not by chain name
-/// (i.e., the first chain of the reference will be compared with the first chain of the probe,
-/// the second with the second, etc.)
-
-
-
-
-
-bool ResidueNamesMatch (const mol::EntityView& probe, const mol::EntityView& reference)
+bool ResidueNamesMatch(const EntityView& probe, const EntityView& reference,
+ bool log_as_error)
{
bool return_value = true;
ChainViewList ref_chains = reference.GetChainList();
@@ -51,8 +40,12 @@ bool ResidueNamesMatch (const mol::EntityView& probe, const mol::EntityView& ref
if (probe_residue.IsValid()) {
if (probe_residue.GetName()!=rri->GetName()) {
return_value = false;
- LOG_VERBOSE("Name mismatch for residue " << probe_residue.GetNumber() << " in chain " << rci);
- LOG_VERBOSE("In reference: " << rri->GetName() << ", in compared structure: " << probe_residue.GetName());
+ if (log_as_error) {
+ LOG_ERROR("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+ } else {
+ LOG_WARNING("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+ }
+
}
}
}
diff --git a/modules/mol/alg/src/consistency_checks.hh b/modules/mol/alg/src/consistency_checks.hh
index 77cffda1ce3639c37111cc0b7d8fa120015e9958..34eb4568b82f54cdfba2e5b2423d176d322d9a2f 100644
--- a/modules/mol/alg/src/consistency_checks.hh
+++ b/modules/mol/alg/src/consistency_checks.hh
@@ -31,8 +31,9 @@ namespace ost { namespace mol { namespace alg {
/// same ResNum) are of the same residue type. Chains are comapred by order, not by chain name
/// (i.e.: the first chain of the reference will be compared with the first chain of the probe
/// structure, etc.)
-
-bool DLLEXPORT_OST_MOL_ALG ResidueNamesMatch (const mol::EntityView& probe, const mol::EntityView& reference);
+bool DLLEXPORT_OST_MOL_ALG ResidueNamesMatch(const EntityView& probe,
+ const EntityView& reference,
+ bool log_as_error=false);
}}}
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 27ffb844853f7d68821d3356ec6895ef4389b4f1..b7a22ba13b0e30852669e132cf77a089d0874428 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -19,6 +19,7 @@
#include <ost/log.hh>
#include <ost/mol/mol.hh>
#include <sstream>
+#include <iomanip>
#include <math.h>
#include "filter_clashes.hh"
#include <ost/units.hh>
@@ -107,6 +108,12 @@ std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,c
return find_ci->second;
}
+Real ClashingDistances::GetAdjustedClashingDistance(const String& ele1,const String& ele2) const
+{
+ std::pair <Real,Real> clash_dist = GetClashingDistance(ele1,ele2);
+ return clash_dist.first-clash_dist.second;
+}
+
void ClashingDistances::PrintAllDistances() const
{
for (std::map <String,std::pair<float,float> >::const_iterator index = min_distance_.begin();index != min_distance_.end();++index) {
@@ -460,6 +467,7 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
if (remove_bb) {
LOG_INFO("ACTION: removing whole residue " << res);
+ res.SetBoolProp("stereo_chemical_violation_backbone",true);
continue;
}
if (remove_sc) {
@@ -472,15 +480,16 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
filtered.AddAtom(atom);
}
}
+ res.SetBoolProp("stereo_chemical_violation_sidechain",true);
continue;
}
filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
}
Real avg_zscore_bonds = running_sum_zscore_bonds/static_cast<float>(bond_count);
Real avg_zscore_angles = running_sum_zscore_angles/static_cast<float>(angle_count);
- LOG_SCRIPT("Average Z-Score for bond lengths: " << avg_zscore_bonds);
- LOG_SCRIPT("Bonds outside of tolerance range: " << bad_bond_count << " out of " << bond_count);
- LOG_SCRIPT("Bond\tAvg Length\tAvg zscore\tNum Bonds")
+ std::cout << "Average Z-Score for bond lengths: " << std::fixed << std::setprecision(5) << avg_zscore_bonds << std::endl;
+ std::cout << "Bonds outside of tolerance range: " << bad_bond_count << " out of " << bond_count << std::endl;
+ std::cout << "Bond\tAvg Length\tAvg zscore\tNum Bonds" << std::endl;
for (std::map<String,Real>::const_iterator bls_it=bond_length_sum.begin();bls_it!=bond_length_sum.end();++bls_it) {
String key = (*bls_it).first;
@@ -489,10 +498,11 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
Real sum_bond_zscore=bond_zscore_sum[key];
Real avg_length=sum_bond_length/static_cast<Real>(counter);
Real avg_zscore=sum_bond_zscore/static_cast<Real>(counter);
- LOG_SCRIPT(key << "\t" << avg_length << "\t" << avg_zscore << "\t" << counter);
+ std::cout << key << "\t" << std::fixed << std::setprecision(5) << std::left << std::setw(10) << avg_length << "\t" << std::left << std::setw(10) << avg_zscore << "\t" << counter << std::endl;
}
- LOG_SCRIPT("Average Z-Score angle widths: " << avg_zscore_angles);
- LOG_SCRIPT("Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count);
+ std::cout << "Average Z-Score angle widths: " << std::fixed << std::setprecision(5) << avg_zscore_angles << std::endl;
+ std::cout << "Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count << std::endl;
+ filtered.AddAllInclusiveBonds();
return filtered;
}
@@ -575,6 +585,7 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
if (remove_bb) {
LOG_VERBOSE("ACTION: removing whole residue " << res);
+ res.SetBoolProp("steric_clash",true);
continue;
}
if (remove_sc) {
@@ -587,6 +598,7 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
filtered.AddAtom(atom);
}
}
+ res.SetBoolProp("steric_clash",true);
continue;
}
filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
@@ -595,8 +607,9 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
if (bad_distance_count!=0) {
average_offset = average_offset_sum / static_cast<Real>(bad_distance_count);
}
- LOG_SCRIPT(bad_distance_count << " non-bonded short-range distances shorter than tolerance distance");
- LOG_SCRIPT("Distances shorter than tolerance are on average shorter by: " << average_offset);
+ std::cout << bad_distance_count << " non-bonded short-range distances shorter than tolerance distance" << std::endl;
+ std::cout << "Distances shorter than tolerance are on average shorter by: " << std::fixed << std::setprecision(5) << average_offset << std::endl;
+ filtered.AddAllInclusiveBonds();
return filtered;
}
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index f9d7473b6ce1eb0d5044c6f46a4bebadc86bff83..e294cd4895ad9790a3b001a73873f8b7b4812cc8 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -40,6 +40,9 @@ public:
/// \brief Recovers a reference distance and a tolerance threshold (respectively) from the list
std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
+ /// \brief Recovers a reference distance already adjusted by the tolerance threshold from the list
+ Real GetAdjustedClashingDistance(const String& ele1,const String& ele2) const;
+
/// \brief Recovers the longest distance in the list, corrected by tolerance
Real GetMaxAdjustedDistance() const;
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index a7615007b548256067a4c2c093c7f248fc1b7012..ebf1a6e89f26f6144d4af58bd0efeea27d2f7e99 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -83,7 +83,6 @@ void usage()
std::cerr << " -v <level> verbosity level (0=results only,1=problems reported, 2=full report)" << std::endl;
std::cerr << " -b <value> tolerance in stddevs for bonds" << std::endl;
std::cerr << " -a <value> tolerance in stddevs for angles" << std::endl;
- std::cerr << " -m <value> clashing distance for unknwon atom types" << std::endl;
std::cerr << " -r <value> distance inclusion radius" << std::endl;
std::cerr << " -i <value> sequence separation" << std::endl;
std::cerr << " -e print version" << std::endl;
@@ -97,7 +96,11 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
int second=0;
int first=0;
if (v.GetResidueList().size()==0) {
- return std::make_pair<int,int>(0,1);
+ if (glob_dist_list.size()==0) {
+ return std::make_pair<int,int>(0,-1);
+ } else {
+ return std::make_pair<int,int>(0,glob_dist_list.size());
+ }
}
ChainView vchain=v.GetChainList()[0];
for (GlobalRDMap::const_iterator i=glob_dist_list.begin();i!=glob_dist_list.end();++i)
@@ -111,6 +114,17 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
return std::make_pair<int,int>(first,second);
}
+bool is_resnum_in_globalrdmap(const ResNum& resnum, const GlobalRDMap& glob_dist_list)
+{
+ for (GlobalRDMap::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
+ ResNum rn = i->first;
+ if (rn==resnum) {
+ return true;
+ }
+ }
+ return false;
+}
+
int main (int argc, char **argv)
{
// sets some default values for parameters
@@ -241,8 +255,9 @@ int main (int argc, char **argv)
if (!ref) {
exit(-1);
}
- ref_list.push_back(ref.CreateFullView());
- glob_dist_list = CreateDistanceList(ref.CreateFullView(),radius);
+ EntityView refview=ref.GetChainList()[0].Select("peptide=true");
+ ref_list.push_back(refview);
+ glob_dist_list = CreateDistanceList(refview,radius);
} else {
std::cout << "Multi-reference mode: On" << std::endl;
for (std::vector<StringRef>::const_iterator ref_file_split_sr_it = ref_file_split_sr.begin();
@@ -258,6 +273,7 @@ int main (int argc, char **argv)
exit(-1);
}
}
+ EntityView refview=ref.GetChainList()[0].Select("peptide=true");
ref_list.push_back(ref.CreateFullView());
}
glob_dist_list = CreateDistanceListFromMultipleReferences (ref_list,cutoffs,sequence_separation,radius);
@@ -272,6 +288,7 @@ int main (int argc, char **argv)
std::cout << "Stereo-chemical and steric clash checks: Off " << std::endl;
}
std::cout << "Inclusion Radius: " << radius << std::endl;
+
std::cout << "Sequence separation: " << sequence_separation << std::endl;
if (structural_checks) {
std::cout << "Parameter filename: " << parameter_filename << std::endl;
@@ -284,6 +301,12 @@ int main (int argc, char **argv)
}
LOG_INFO("LDDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
+ // error if the reference structure is empty
+ if (glob_dist_list.size()==0) {
+ std::cout << "ERROR: No valid distance to check in the reference structure(s). Please check that the first chain of the reference structure(s) contains a peptide." << std::endl;
+ exit(-1);
+ }
+
// cycles through the models to evaluate
for (size_t i=0; i<files.size(); ++i) {
EntityHandle model=load(files[i], profile);
@@ -293,17 +316,17 @@ int main (int argc, char **argv)
}
continue;
}
- EntityView v=model.CreateFullView();
-
+ EntityView v=model.GetChainList()[0].Select("peptide=true");
+ EntityView outv=model.GetChainList()[0].Select("peptide=true");
for (std::vector<EntityView>::const_iterator ref_list_it = ref_list.begin();
ref_list_it != ref_list.end(); ++ref_list_it) {
- bool cons_check = ResidueNamesMatch(v,*ref_list_it);
+ bool cons_check = ResidueNamesMatch(v,*ref_list_it,consistency_checks);
if (cons_check==false) {
if (consistency_checks==true) {
- LOG_ERROR("Residue names in model: " << files[i] << " are inconsistent with one or more references");
+ LOG_ERROR("Residue names in model: " << files[i] << " and in reference structure(s) are inconsistent.");
exit(-1);
} else {
- LOG_WARNING("Residue names in model: " << files[i] << " are inconsistent with one or more references");
+ LOG_WARNING("Residue names in model: " << files[i] << " and in reference structure(s) are inconsistent.");
}
}
}
@@ -313,7 +336,11 @@ int main (int argc, char **argv)
String filestring=BFPathToString(pathstring);
std::cout << "File: " << files[i] << std::endl;
std::pair<int,int> cov = compute_coverage(v,glob_dist_list);
- std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+ if (cov.second == -1) {
+ std::cout << "Coverage: 0 (0 out of 0 residues)" << std::endl;
+ } else {
+ std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+ }
if (structural_checks) {
// reads in parameter files
@@ -355,8 +382,6 @@ int main (int argc, char **argv)
std::cout << e.what() << std::endl;
exit(-1);
}
- cov = compute_coverage(v,glob_dist_list);
- std::cout << "Coverage after stereo-chemical checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
try {
v=alg::FilterClashes(v,nonbonded_table);
} catch (std::exception& e) {
@@ -364,8 +389,6 @@ int main (int argc, char **argv)
std::cout << e.what() << std::endl;
exit(-1);
}
- cov = compute_coverage(v,glob_dist_list);
- std::cout << "Coverage after clashing checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
}
if (cov.first==0) {
std::cout << "Global LDDT score: 0.0" << std::endl;
@@ -381,20 +404,67 @@ int main (int argc, char **argv)
<< " checked, over " << cutoffs.size() << " thresholds)" << std::endl;
// prints the residue-by-residue statistics
- std::cout << "Local LDDT Score:" << std::endl;
- std::cout << "Chain\tResName\tResNum\tScore\t(Conserved/Total, over " << cutoffs.size() << " thresholds)" << std::endl;
- for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
- ResidueView ritv = *rit;
- Real lddt_local = 0;
- int conserved_dist = 0;
- int total_dist = 0;
- if (ritv.HasProp(label)) {
+ if (structural_checks) {
+ std::cout << "Local LDDT Scores:" << std::endl;
+ std::cout << "(A 'Yes' in the 'Quality Problems' column stands for problems" << std::endl;
+ std::cout << "in the side-chain of a residue, while a 'Yes+' for problems" << std::endl;
+ std::cout << "in the backbone)" << std::endl;
+ } else {
+ std::cout << "Local LDDT Scores:" << std::endl;
+ }
+ if (structural_checks) {
+ std::cout << "Chain\tResName\tResNum\tAsses.\tQ.Prob.\tScore\t(Conserved/Total, over " << cutoffs.size() << " thresholds)" << std::endl;
+ } else {
+ std::cout << "Chain\tResName\tResNum\tAsses.\tScore\t(Conserved/Total, over " << cutoffs.size() << " thresholds)" << std::endl;
+ }
+ for (ResidueViewIter rit=outv.ResiduesBegin();rit!=outv.ResiduesEnd();++rit){
+ ResidueView ritv=*rit;
+ ResNum rnum = ritv.GetNumber();
+ bool assessed = false;
+ String assessed_string="No";
+ bool quality_problems = false;
+ String quality_problems_string="No";
+ Real lddt_local = -1;
+ String lddt_local_string="-";
+ int conserved_dist = -1;
+ int total_dist = -1;
+ String dist_string = "-";
+ if (is_resnum_in_globalrdmap(rnum,glob_dist_list)) {
+ assessed = true;
+ assessed_string="Yes";
+ }
+ if (ritv.HasProp("stereo_chemical_violation_sidechain") || ritv.HasProp("steric_clash_sidechain")) {
+ quality_problems = true;
+ quality_problems_string="Yes";
+ }
+ if (ritv.HasProp("stereo_chemical_violation_backbone") || ritv.HasProp("steric_clash_backbone")) {
+ quality_problems = true;
+ quality_problems_string="Yes+";
+ }
+
+ if (assessed==true) {
+ if (ritv.HasProp(label)) {
lddt_local=ritv.GetFloatProp(label);
+ std::stringstream stkeylddt;
+ stkeylddt << std::fixed << std::setprecision(4) << lddt_local;
+ lddt_local_string=stkeylddt.str();
conserved_dist=ritv.GetIntProp(label+"_conserved");
- total_dist=ritv.GetIntProp(label+"_total");
+ total_dist=ritv.GetIntProp(label+"_total");
+ std::stringstream stkeydist;
+ stkeydist << "("<< conserved_dist << "/" << total_dist << ")";
+ dist_string=stkeydist.str();
+ } else {
+ lddt_local = 0;
+ lddt_local_string="0.0000";
+ conserved_dist = 0;
+ total_dist = 0;
+ dist_string="(0/0)";
+ }
}
- if (lddt_local!=0) {
- std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << std::setprecision(4) << lddt_local << "\t" << "("<< conserved_dist << "/" << total_dist << ")" <<std::endl;
+ if (structural_checks) {
+ std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << assessed_string << '\t' << quality_problems_string << '\t' << lddt_local_string << "\t" << dist_string << std::endl;
+ } else {
+ std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << assessed_string << '\t' << lddt_local_string << "\t" << dist_string << std::endl;
}
}
std::cout << std::endl;
diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index 5f7ab1154ad0c785cca591fd5ee47c5b01ee700c..fcad815704b856e8a86363e66c30f5cf18dfdb9b 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -52,6 +52,7 @@ void export_Bond()
.def("GetBondOrder",&BondHandle::GetBondOrder)
.def("SetBondOrder",&BondHandle::SetBondOrder)
.def("IsValid", &BondHandle::IsValid)
+ .def("GetHashCode", &BondHandle::GetHashCode)
.def(self == self)
.def(self != self)
.def(self_ns::str(self))
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index bb55d9bd68234616da9d4bf69d646adccf559d71..280024f0a8f513bedd30a83790239446525b9563 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -155,7 +155,7 @@ void export_Entity()
.def("GetMass", &EntityHandle::GetMass)
.def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
- .def("GetAtomPosList", &EntityHandle::GetAtomPosList)
+ .def("GetAtomPosList", &EntityHandle::GetAtomPosList, arg("ordered_by_index")=false)
.def("GetGeometricCenter", geom_center<EntityHandle>)
.add_property("geometric_center", geom_center<EntityHandle>)
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index c818fbc1cec5ee0c0fa1be6fbb51eb59750133f0..a24ca3abb276770cebf67b00524e1ad4c401b970 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -240,5 +240,12 @@ unsigned long AtomBase::GetIndex() const
return Impl()->GetIndex();
}
+void AtomBase::SetIndex(const unsigned long index)
+{
+ this->CheckValidity();
+ return impl_->SetIndex(index);
+}
+
+
}} // ns
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 13795311560e4c81d46063156c75aa6459359131..4ddc13f2f46cea4c19c0e0372bb313b936d51386 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -141,6 +141,7 @@ public:
void SetRadius(Real radius);
+ void SetIndex (const unsigned long index);
const geom::Mat3& GetAnisou() const;
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 5af231a559b8e07db90f6ec34d539aa238ed63ea..d02eecc2751e49fc66ac64579a102ce632615265 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -239,8 +239,12 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first,
indices.push_back(i->GetIndex());
}
new_ent=CreateEntityFromView(selected, false);
+ //we have to correct the atom indices in the new entity
+ AtomHandleList new_atoms=new_ent.GetAtomList();
+ for (int i=0,e=atoms.size();i!=e;++i){
+ new_atoms[i].SetIndex(i);
+ }
}
-
CoordGroupHandle filtered_cg=CreateCoordGroup(new_ent.GetAtomList());
std::vector<geom::Vec3> vecs(indices.size());
if (last==-1) last=this->GetFrameCount();
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index e34e11d2e233ab4a60da62e20c3e085c4ece1f58..7bf3ed349d82cc621198d17be211f4a3b39b3b1a 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -402,16 +402,23 @@ AtomHandleList EntityHandle::GetAtomList() const
return atoms;
}
-geom::Vec3List EntityHandle::GetAtomPosList() const {
+bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
+{
+ return a1.GetIndex()<a2.GetIndex();
+}
+
+geom::Vec3List EntityHandle::GetAtomPosList(bool ordered_by_index) const {
this->CheckValidity();
geom::Vec3List atom_pos_list;
atom_pos_list.reserve(this->GetAtomCount());
AtomHandleList atom_list=this->GetAtomList();
+ if (ordered_by_index){
+ std::sort(atom_list.begin(),atom_list.end(),less_index);
+ }
for (AtomHandleList::const_iterator a=atom_list.begin(), e=atom_list.end(); a!=e; ++a) {
atom_pos_list.push_back(a->GetPos());
}
return atom_pos_list;
- //return Impl()->GetAtomPosList();
}
EntityHandle EntityHandle::GetHandle() const
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index fe2a439135306d6f2a7c080ed91f1e15604faea0..c2888c9e2efbf790090164c253757dfb24b9553b 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -289,7 +289,7 @@ public:
AtomHandleList GetAtomList() const;
/// \brief get complete list of atom positions
- geom::Vec3List GetAtomPosList() const;
+ geom::Vec3List GetAtomPosList(bool ordered_by_index = false) const;
/// \brief Get editor for external coordinate system to manipulate atom
/// positions
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index f756d7cd30c29db720aeba659643c18bb872e4c9..531d5a8ad5eb3a579a4ba608d2bc27159ff95d52 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -32,6 +32,9 @@ export DYLD_LIBRARY_PATH="$DNG_LIBDIR:${DYLD_LIBRARY_PATH}"
export LD_LIBRARY_PATH="$DNG_LIBDIR:${LD_LIBRARY_PATH}"
# set QT_PLUGIN_PATH for bundle (commented except in linux bundles)
#export QT_PLUGIN_PATH="$BIN_DIR/plugins"
+# unset PYTHONPATH for bundle (commented except in linux bundles)
+#unset PYTHONPATH
+
# retrieve absolute path to python executable
pyexec="@PYTHON_BINARY@"
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 6b896ac68313eb65e8ed10c75040f6bdd2bfa3c2..94e5a97f5120b9522a3d8678518c44fbe84f4cb7 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -289,6 +289,7 @@ int main(int argc, char *argv[])
}
std::cerr << " --> removed " << hremoved << " hydrogen atoms" << std::endl;
}
+
if (rm_oxt_atoms) {
std::cerr << "removing OXT atoms" << std::endl;
int oremoved=0;
@@ -302,19 +303,6 @@ int main(int argc, char *argv[])
std::cerr << " --> removed " << oremoved << " OXT atoms" << std::endl;
}
- if (rm_non_std) {
- std::cerr << "removing OXT atoms" << std::endl;
- int oremoved=0;
- AtomHandleList atoms=ent.GetAtomList();
- for (AtomHandleList::const_iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
- if (i->GetName()=="OXT") {
- edi.DeleteAtom(*i);
- oremoved++;
- }
- }
- std::cerr << " --> removed " << oremoved << " OXT atoms" << std::endl;
- }
-
checker.CheckForCompleteness();
checker.CheckForUnknownAtoms();
checker.CheckForNonStandard();
@@ -339,6 +327,7 @@ int main(int argc, char *argv[])
}
std::cerr << std::endl;
}
+
if (assign_elem) {
ChainHandleList chains=ent.GetChainList();
for (ChainHandleList::const_iterator c=chains.begin();c!=chains.end();++c) {