From 73239df52b1074314b0ccb5135085d690719aa51 Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 25 Mar 2010 12:22:01 +0000
Subject: [PATCH] -updating bundling script for windows -adding GetAtomList to
chainhandles and enabling .atoms property -fixing already defined getprop in
windows in entitity_view
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1886 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
deployment/win/create_archive.bat | 33 ++++++++++++++-----------
modules/gfx/src/impl/entity_renderer.hh | 4 +++
modules/mol/base/pymod/export_chain.cc | 2 ++
modules/mol/base/src/chain_handle.cc | 8 ++++++
modules/mol/base/src/chain_handle.hh | 13 ++++++++--
modules/mol/base/src/entity_view.cc | 2 ++
6 files changed, 45 insertions(+), 17 deletions(-)
diff --git a/deployment/win/create_archive.bat b/deployment/win/create_archive.bat
index 98f7aeb44..06902f502 100644
--- a/deployment/win/create_archive.bat
+++ b/deployment/win/create_archive.bat
@@ -2,20 +2,23 @@
REM create a zip archive for deployment on windows
REM no regisrty entries
REM no PATHs will be changed except in the DNG session
-if exist openstructure rmdir /S /Q openstructure
-if exist OpenStructure_WIN32.zip del OpenStructure_WIN32.zip
-REM dir /S openstructure
-mkdir openstructure\share\openstructure\examples
-mkdir openstructure\lib\site-packages
-mkdir openstructure\bin
-xcopy /E /I ..\..\examples openstructure\share\openstructure\examples
-xcopy /E /I ..\..\stage\share openstructure\share\
+set inst_dir=openstructure1.0.0a1_1885
+set archive_name=OpenStructureWin32
+if exist "%inst_dir%" rmdir /S /Q "%inst_dir%"
+if exist %archive_name%.zip del %archive_name%.zip*.*
+REM dir /S %inst_dir%
+mkdir "%inst_dir%\share\openstructure\examples"
+mkdir "%inst_dir%\lib\site-packages"
+mkdir "%inst_dir%\bin"
+xcopy /E /I ..\..\examples "%inst_dir%\share\openstructure\examples"
+xcopy /E /I ..\..\stage\share "%inst_dir%\share\"
+REM xcopy /E /I ..\..\website\html "%inst_dir%\share\doc"
+copy d:\programs\bin\python.exe "%inst_dir%\bin"
-xcopy /E /I d:\programs\bin openstructure\bin
-REM copy d:\programs\lib\boost*iostreams*.* d:\programs\lib\boost*unit_test_frame*.* d:\programs\lib\boost*python*.* d:\programs\lib\boost*math*.* d:\programs\lib\boost*system*.* d:\programs\lib\boost*program_options*.* d:\programs\lib\boost*regex*.* d:\programs\lib\_*.* d:\programs\lib\*.py d:\programs\lib\*png*13*.* d:\programs\lib\*zlib*.* d:\programs\lib\*tif*.* d:\programs\lib\py*.* d:\programs\lib\*select*.* d:\programs\lib\*unicode*.* openstructure\lib
-
-xcopy /E /I /EXCLUDE:excludes d:\programs\lib openstructure\lib
-xcopy /E /I ..\..\stage\lib openstructure\lib
-xcopy /E /I ..\..\stage\bin openstructure\bin
+xcopy /E /I /EXCLUDE:excludes d:\programs\lib "%inst_dir%\lib"
+xcopy /E /I ..\..\stage\lib "%inst_dir%\lib"
+xcopy /E /I /EXCLUDE:excludes ..\..\stage\bin "%inst_dir%\bin"
set PATH="c:\Program Files (x86)"\7-Zip\;%PATH%
-7z a -r -tzip OpenStructure_WIN32.zip openstructure > log
\ No newline at end of file
+REM 7z a -r -t7z %archive_name% "%inst_dir%" > log
+REM if exist %archive_name%.7z copy /b 7zS.sfx + config.txt + %archive_name%.7z %archive_name%.exe
+7z a -r -tzip %archive_name% "%inst_dir%" > log
diff --git a/modules/gfx/src/impl/entity_renderer.hh b/modules/gfx/src/impl/entity_renderer.hh
index fe0d54138..3a262d073 100644
--- a/modules/gfx/src/impl/entity_renderer.hh
+++ b/modules/gfx/src/impl/entity_renderer.hh
@@ -23,6 +23,10 @@
Author: Stefan Scheuber, Marco Biasini
*/
+
+#if defined(GetProp)
+#undef GetProp
+#endif
#include <vector>
#include <ost/mol/query_view_wrapper.hh>
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index dba3791fd..71896935b 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -53,6 +53,8 @@ void export_Chain()
;
generic_prop_def<ChainBase>(chain_base);
class_<ChainHandle, bases<ChainBase> >("ChainHandle", init<>())
+ .def("GetAtomList", &ChainHandle::GetAtomList)
+ .add_property("atoms", &ChainHandle::GetAtomList)
.def("GetResidueList", &ChainHandle::GetResidueList)
.add_property("residues", &ChainHandle::GetResidueList)
.add_property("entity", &ChainHandle::GetEntity)
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 3306f2421..156eca176 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -92,6 +92,14 @@ AtomHandle ChainHandle::FindAtom(const ResNum& num,
}
+AtomHandleList ChainHandle::GetAtomList() const
+{
+ this->CheckValidity();
+ AtomHandleList atoms;
+ std::copy(AtomsBegin(), AtomsEnd(), std::back_inserter(atoms));
+ return atoms;
+}
+
ResidueHandleList ChainHandle::GetResidueList() const
{
ResidueHandleList reslist;
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index f2796309b..0faa7ee8f 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -115,12 +115,21 @@ public:
///
/// \sa EntityHandle::GetResidueCount()
int GetResidueCount() const;
-
+
+ /// \brief Retrieve atoms of this chain as a list
+ ///
+ /// The atoms are ordered by atom number in ascending order. If you only
+ /// want to determine the number of atoms, use the dedicated
+ /// \c ChainHandle::GetAtomCount
+
+
+ AtomHandleList GetAtomList() const;
+
/// \brief Get residues of this chain as a list
///
/// The residues are ordered by residue number in ascending order. If you only
/// want to determine the number of residues, use the dedicated
- /// \c ResidueHandle::GetResidueCount
+ /// \c ChainHandle::GetResidueCount
ResidueHandleList GetResidueList() const;
/// \brief Get iterator pointing to begin of residues
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index 16cbc6cc2..00e9585ce 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -582,6 +582,7 @@ EntityView EntityView::Copy() const
ChainView EntityView::AddChain(const ChainView& chain_view,
ViewAddFlags flags)
{
+ this->CheckValidity();
ChainView cv;
if (flags & ViewAddFlag::CHECK_DUPLICATES &&
(cv=this->FindChain(chain_view.GetHandle()))) {
@@ -623,6 +624,7 @@ AtomViewList EntityView::FindWithin(const geom::Vec3& center, Real radius) const
// could use some heuristic here to decide whether it is useful
// to use the FindWithin method of the handle or do a full search of
// all atoms included in the view.
+ this->CheckValidity();
AtomHandleList ahl=this->GetHandle().FindWithin(center, radius);
AtomViewList avl;
for (AtomHandleList::iterator i=ahl.begin(), e=ahl.end(); i!=e; ++i) {
--
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