summaryrefslogtreecommitdiff
path: root/science
diff options
context:
space:
mode:
authorYuri Victorovich <yuri@FreeBSD.org>2018-07-09 04:41:17 +0000
committerYuri Victorovich <yuri@FreeBSD.org>2018-07-09 04:41:17 +0000
commitbf0d9c64e9c61fef24c242f805b0a1c124348ff1 (patch)
treeda7535451d2dda68cae14b818de91b14c4969e0d /science
parentsecurity/highwayhash: Update g20170512 -> g20180626 (diff)
New port: science/openstructure: Molecular modelling and visualization environment
Notes
Notes: svn path=/head/; revision=474223
Diffstat (limited to 'science')
-rw-r--r--science/Makefile1
-rw-r--r--science/openstructure/Makefile36
-rw-r--r--science/openstructure/distinfo3
-rw-r--r--science/openstructure/files/patch-cmake__support_CopyDependencies.cmake15
-rw-r--r--science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake18
-rw-r--r--science/openstructure/files/patch-cmake__support_FindPython.cmake10
-rw-r--r--science/openstructure/files/patch-cmake__support_OST.cmake20
-rw-r--r--science/openstructure/files/patch-modules_config_base.hh29
-rw-r--r--science/openstructure/files/patch-modules_db_src_sqlite3.c11
-rw-r--r--science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh11
-rw-r--r--science/openstructure/files/patch-modules_gui_src_CMakeLists.txt13
-rw-r--r--science/openstructure/files/patch-modules_gui_src_gosty.cc11
-rw-r--r--science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc11
-rw-r--r--science/openstructure/pkg-descr17
-rw-r--r--science/openstructure/pkg-plist963
15 files changed, 1169 insertions, 0 deletions
diff --git a/science/Makefile b/science/Makefile
index 5ec46488dad8..64fd4af78798 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -131,6 +131,7 @@
SUBDIR += nifticlib
SUBDIR += openbabel
SUBDIR += openkim
+ SUBDIR += openstructure
SUBDIR += p5-Algorithm-SVMLight
SUBDIR += p5-Chemistry-3DBuilder
SUBDIR += p5-Chemistry-Bond-Find
diff --git a/science/openstructure/Makefile b/science/openstructure/Makefile
new file mode 100644
index 000000000000..d5dbd451482e
--- /dev/null
+++ b/science/openstructure/Makefile
@@ -0,0 +1,36 @@
+# $FreeBSD$
+
+PORTNAME= openstructure
+DISTVERSION= 1.7.1
+CATEGORIES= science
+
+MAINTAINER= yuri@FreeBSD.org
+COMMENT= Molecular modelling and visualization environment
+
+LICENSE= LGPL3
+LICENSE_FILE= ${WRKSRC}/LICENSE.txt
+
+BUILD_DEPENDS= fftw3>0:math/fftw3
+LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \
+ libfftw3f.so:math/fftw3-float \
+ libpng16.so:graphics/png \
+ libtiff.so:graphics/tiff \
+ ${PY_BOOST}
+RUN_DEPENDS= ${PYNUMPY}
+
+USES= cmake:outsource eigen:3 python pyqt:4 qt:4 shebangfix
+SHEBANG_FILES= scripts/dng.in scripts/ost.in scripts/ost_config.in
+USE_GITHUB= yes
+GH_ACCOUNT= yurivict
+USE_QT= corelib gui network opengl xml qmake_build moc_build rcc_build uic_build
+USE_PYQT= core gui
+USE_GL= gl glu
+USE_LDCONFIG= yes
+
+BINARY_ALIAS= python=${PYTHON_CMD}
+CMAKE_ARGS= -DPYTHON_INCLUDE_PATH=${PYTHON_INCLUDEDIR} \
+ -DPYTHON_LIBRARIES=${PYTHON_LIBDIR} \
+ -DFREEBSD_BOOST_PYTHON_COMPONENT=python${PYTHON_VER:S/.//} \
+ -DFREEBSD_PYTHON_LIBRARY=python${PYTHON_VER}
+
+.include <bsd.port.mk>
diff --git a/science/openstructure/distinfo b/science/openstructure/distinfo
new file mode 100644
index 000000000000..190a2e6395a8
--- /dev/null
+++ b/science/openstructure/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1531090646
+SHA256 (yurivict-openstructure-1.7.1_GH0.tar.gz) = 9a76974ee379f9d2cc37726f58c7660a47ae74482b29f08da97033a74ca98551
+SIZE (yurivict-openstructure-1.7.1_GH0.tar.gz) = 59270686
diff --git a/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake b/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake
new file mode 100644
index 000000000000..fe47164623db
--- /dev/null
+++ b/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake
@@ -0,0 +1,15 @@
+--- cmake_support/CopyDependencies.cmake.orig 2018-07-09 02:47:08 UTC
++++ cmake_support/CopyDependencies.cmake
+@@ -996,10 +996,10 @@ function(copy_python include_path versio
+ endforeach()
+ else()
+ file(COPY ${python_root_dir}/${LIB_DIR}/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version} PATTERN "*.pyc" EXCLUDE)
+- if("${LIB_DIR}" MATCHES "lib64")
++ if("${LIB_DIR}" MATCHES "lib")
+ # for 64 bit systems we have to copy the python dir within lib in addition as norarch site packages might get installed there
+ file(COPY ${python_root_dir}/lib/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/python${version} PATTERN "*.pyc" EXCLUDE)
+- endif("${LIB_DIR}" MATCHES "lib64")
++ endif("${LIB_DIR}" MATCHES "lib")
+ endif()
+ file(GLOB py_config_files "${include_path}/pyconfig*.h")
+ file(COPY ${py_config_files} DESTINATION ${CMAKE_INSTALL_PREFIX}/include/python${version})
diff --git a/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake b/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake
new file mode 100644
index 000000000000..c18db5597504
--- /dev/null
+++ b/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake
@@ -0,0 +1,18 @@
+--- cmake_support/FindOPENSTRUCTURE.cmake.orig 2018-07-09 03:09:01 UTC
++++ cmake_support/FindOPENSTRUCTURE.cmake
+@@ -27,7 +27,7 @@ macro(find_OPENSTRUCTURE OPENSTRUCTURE_R
+ NAMES ost_${LIB}
+ HINTS "${PYTHON_ROOT}"
+ PATH ${OPENSTRUCTURE_ROOT}
+- PATH_SUFFIXES lib lib64
++ PATH_SUFFIXES lib
+ NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+ )
+ if (NOT FOUND_LIB)
+@@ -84,4 +84,4 @@ else (OPENSTRUCTURE_FOUND)
+ if (OPENSTRUCTURE_FIND_REQUIRED)
+ message(FATAL_ERROR "Could not find OpenStructure")
+ endif ()
+-endif ()
+\ No newline at end of file
++endif ()
diff --git a/science/openstructure/files/patch-cmake__support_FindPython.cmake b/science/openstructure/files/patch-cmake__support_FindPython.cmake
new file mode 100644
index 000000000000..c9f792a29fa5
--- /dev/null
+++ b/science/openstructure/files/patch-cmake__support_FindPython.cmake
@@ -0,0 +1,10 @@
+--- cmake_support/FindPython.cmake.orig 2018-07-08 23:04:29 UTC
++++ cmake_support/FindPython.cmake
+@@ -75,7 +75,6 @@ macro(_find_python_bin PYTHON_ROOT VERSI
+ NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}" python.exe
+ HINTS "${PYTHON_ROOT}"
+ PATH_SUFFIXES bin
+- NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
+ )
+ else()
+ find_program(PYTHON_BINARY
diff --git a/science/openstructure/files/patch-cmake__support_OST.cmake b/science/openstructure/files/patch-cmake__support_OST.cmake
new file mode 100644
index 000000000000..e88bd1c466d6
--- /dev/null
+++ b/science/openstructure/files/patch-cmake__support_OST.cmake
@@ -0,0 +1,20 @@
+--- cmake_support/OST.cmake.orig 2018-02-27 14:29:54 UTC
++++ cmake_support/OST.cmake
+@@ -834,7 +834,7 @@ macro(setup_stage)
+ check_architecture()
+ endif()
+ set (ARCH ${CMAKE_NATIVE_ARCH})
+- if ("${ARCH}" MATCHES "64" AND NOT _UBUNTU_LAYOUT)
++ if ("${ARCH}" MATCHES "64" AND NOT _UBUNTU_LAYOUT AND NOT ${CMAKE_SYSTEM_NAME} MATCHES "FreeBSD")
+ set(LIB_DIR lib64 )
+ set(LIB_STAGE_PATH "${STAGE_DIR}/lib64" )
+ else()
+@@ -902,7 +902,7 @@ set(_BOOST_MIN_VERSION 1.31)
+
+ macro(setup_boost)
+ set (Boost_NO_BOOST_CMAKE TRUE)
+- find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS python REQUIRED)
++ find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${FREEBSD_BOOST_PYTHON_COMPONENT} REQUIRED)
+ set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
+ set(Boost_LIBRARIES)
+ find_package(Boost ${_BOOST_MIN_VERSION}
diff --git a/science/openstructure/files/patch-modules_config_base.hh b/science/openstructure/files/patch-modules_config_base.hh
new file mode 100644
index 000000000000..5d29060e4768
--- /dev/null
+++ b/science/openstructure/files/patch-modules_config_base.hh
@@ -0,0 +1,29 @@
+--- modules/config/base.hh.orig 2018-07-09 01:41:40 UTC
++++ modules/config/base.hh
+@@ -56,22 +56,26 @@ typedef unsigned short Word;
+ #ifndef round_function
+ #define round_function
+ #ifndef round
++#if !defined(__FreeBSD__)
+ inline Real round( Real d )
+ {
+ return floor(d+Real(0.5));
+ }
+ #endif
+ #endif
++#endif
+
+ #ifndef rint_function
+ #define rint_function
+ #ifndef rint
++#if !defined(__FreeBSD__)
+ inline Real rint(Real d)
+ {
+ return floor(d+Real(0.5));
+ }
+ #endif
+ #endif
++#endif
+
+ #if _MSC_VER
+ #pragma warning(disable:4251)
diff --git a/science/openstructure/files/patch-modules_db_src_sqlite3.c b/science/openstructure/files/patch-modules_db_src_sqlite3.c
new file mode 100644
index 000000000000..fe5e4584cc47
--- /dev/null
+++ b/science/openstructure/files/patch-modules_db_src_sqlite3.c
@@ -0,0 +1,11 @@
+--- modules/db/src/sqlite3.c.orig 2018-07-09 00:05:56 UTC
++++ modules/db/src/sqlite3.c
+@@ -15341,7 +15341,7 @@ SQLITE_PRIVATE void sqlite3MemSetDefault
+ ** SQLITE_WITHOUT_ZONEMALLOC symbol is defined.
+ */
+ #include <sys/sysctl.h>
+-#include <malloc/malloc.h>
++#include <stdlib.h>
+ #include <libkern/OSAtomic.h>
+ static malloc_zone_t* _sqliteZone_;
+ #define SQLITE_MALLOC(x) malloc_zone_malloc(_sqliteZone_, (x))
diff --git a/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh b/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh
new file mode 100644
index 000000000000..a9594f64ea1f
--- /dev/null
+++ b/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh
@@ -0,0 +1,11 @@
+--- modules/gfx/src/offscreen_buffer.hh.orig 2018-07-09 00:19:53 UTC
++++ modules/gfx/src/offscreen_buffer.hh
+@@ -58,7 +58,7 @@ public:
+ bool IsValid();
+ */
+
+-#if defined(__linux__)
++#if defined(__linux__) || defined(__FreeBSD__)
+ #if OST_MESA_SUPPORT_ENABLED
+ #include "impl/mesa_offscreen_buffer.hh"
+ #else
diff --git a/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt b/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt
new file mode 100644
index 000000000000..880c10bb0449
--- /dev/null
+++ b/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt
@@ -0,0 +1,13 @@
+--- modules/gui/src/CMakeLists.txt.orig 2018-02-27 14:29:54 UTC
++++ modules/gui/src/CMakeLists.txt
+@@ -472,8 +472,9 @@ qt4_wrap_cpp(OST_GOSTY_MOC "gosty.hh"
+ OPTIONS -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED
+ -DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
+
+-set(LINK LINK ${BOOST_PROGRAM_OPTIONS_LIBRARIES})
++set(LINK LINK ${BOOST_PROGRAM_OPTIONS_LIBRARIES} ${FREEBSD_PYTHON_LIBRARY})
+
++link_directories(${CMAKE_INSTALL_PREFIX}/lib)
+ executable_libexec(NAME gosty SOURCES gosty.cc ${OST_GOSTY_MOC} ${OST_QT_RESOURCE}
+ DEPENDS_ON ost_gui ${LINK})
+
diff --git a/science/openstructure/files/patch-modules_gui_src_gosty.cc b/science/openstructure/files/patch-modules_gui_src_gosty.cc
new file mode 100644
index 000000000000..de8716c2c00d
--- /dev/null
+++ b/science/openstructure/files/patch-modules_gui_src_gosty.cc
@@ -0,0 +1,11 @@
+--- modules/gui/src/gosty.cc.orig 2018-07-09 03:10:04 UTC
++++ modules/gui/src/gosty.cc
+@@ -111,7 +111,7 @@ String setup_python_search_path(const St
+ #ifdef _MSC_VER
+ String loc=root+"\\lib\\"+site_pkgs.str()+"\\site-packages";
+ #else
+-# if (defined(__ppc64__) || defined(__x86_64__)) && !defined(__APPLE__) && !OST_UBUNTU_LAYOUT
++# if (defined(__ppc64__) || defined(__x86_64__)) && !defined(__APPLE__) && !OST_UBUNTU_LAYOUT && !defined(__FreeBSD__)
+ String loc=root+"/lib64/"+site_pkgs.str()+"/site-packages";
+ # else
+ String loc=root+"/lib/"+site_pkgs.str()+"/site-packages";
diff --git a/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc b/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc
new file mode 100644
index 000000000000..33fc51e38bdb
--- /dev/null
+++ b/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc
@@ -0,0 +1,11 @@
+--- modules/img/base/src/raster_image/raster_image.cc.orig 2018-07-09 00:06:35 UTC
++++ modules/img/base/src/raster_image/raster_image.cc
+@@ -25,7 +25,7 @@
+ */
+
+ #ifndef __APPLE__
+-#include <malloc.h>
++#include <stdlib.h>
+ #endif
+ #include <cmath>
+ #include <iostream>
diff --git a/science/openstructure/pkg-descr b/science/openstructure/pkg-descr
new file mode 100644
index 000000000000..045b43d30f65
--- /dev/null
+++ b/science/openstructure/pkg-descr
@@ -0,0 +1,17 @@
+This project aims to provide an open-source, modular, flexible, molecular
+modelling and visualization environment.
+
+Molecular structures are a central aspect of OpenStructure and a rich
+understanding of macromolecular structure datasets with access to atoms,
+residues, chains, bonds and torsions is offered.
+
+Features:
+* Intuitive representation of structural subsets, so-called EntityViews, that
+ can be created with a dedicated query language or constructed manually for
+ more complex cases.
+* Real-time rendering of molecular structures
+* Interactive Analysis of Trajectories
+* Support for common file formats such as PDB, mmCIF, SDF, PQR
+* Read more about molecular structures in OpenStructure
+
+WWW: https://openstructure.org/
diff --git a/science/openstructure/pkg-plist b/science/openstructure/pkg-plist
new file mode 100644
index 000000000000..927af2276c07
--- /dev/null
+++ b/science/openstructure/pkg-plist
@@ -0,0 +1,963 @@
+bin/chemdict_tool
+bin/dng
+bin/lddt
+bin/molck
+bin/ost
+include/ost/base.hh
+include/ost/boost_filesystem_helper.hh
+include/ost/config.hh
+include/ost/conop/amino_acids.hh
+include/ost/conop/compound.hh
+include/ost/conop/compound_lib.hh
+include/ost/conop/compound_lib_base.hh
+include/ost/conop/conop.hh
+include/ost/conop/diag.hh
+include/ost/conop/heuristic.hh
+include/ost/conop/minimal_compound_lib.hh
+include/ost/conop/model_check.hh
+include/ost/conop/module_config.hh
+include/ost/conop/nonstandard.hh
+include/ost/conop/processor.hh
+include/ost/conop/ring_finder.hh
+include/ost/conop/rule_based.hh
+include/ost/db/module_config.hh
+include/ost/db/sqlite3.h
+include/ost/db/sqlite_conv.hh
+include/ost/db/sqlite_wrap.hh
+include/ost/dllexport.hh
+include/ost/dyn_cast.hh
+include/ost/export_helper/generic_property_def.hh
+include/ost/export_helper/pair_to_tuple_conv.hh
+include/ost/export_helper/vec_to_list_conv.hh
+include/ost/fixed_string.hh
+include/ost/generic_property.hh
+include/ost/geom/aligned_cuboid.hh
+include/ost/geom/circular_iterator.hh
+include/ost/geom/composite.hh
+include/ost/geom/composite2.hh
+include/ost/geom/composite2_op.hh
+include/ost/geom/composite3.hh
+include/ost/geom/composite3_op.hh
+include/ost/geom/composite_op.hh
+include/ost/geom/constants.hh
+include/ost/geom/def.hh
+include/ost/geom/exc.hh
+include/ost/geom/export_helper/vector.hh
+include/ost/geom/geom.hh
+include/ost/geom/mat.hh
+include/ost/geom/mat2.hh
+include/ost/geom/mat3.hh
+include/ost/geom/mat4.hh
+include/ost/geom/module_config.hh
+include/ost/geom/point_cloud.hh
+include/ost/geom/quat.hh
+include/ost/geom/transform.hh
+include/ost/geom/vec.hh
+include/ost/geom/vec2.hh
+include/ost/geom/vec3.hh
+include/ost/geom/vec4.hh
+include/ost/geom/vec_mat_predicates.hh
+include/ost/geom/vecmat2_op.hh
+include/ost/geom/vecmat3_op.hh
+include/ost/geom/vecmat4_op.hh
+include/ost/geom/vecmat_op.hh
+include/ost/gfx/bitmap_io.hh
+include/ost/gfx/collada_exporter.hh
+include/ost/gfx/color.hh
+include/ost/gfx/color_ops/basic_gradient_color_op.hh
+include/ost/gfx/color_ops/by_chain_color_op.hh
+include/ost/gfx/color_ops/by_element_color_op.hh
+include/ost/gfx/color_ops/color_op.hh
+include/ost/gfx/color_ops/entity_view_color_op.hh
+include/ost/gfx/color_ops/gradient_color_op.hh
+include/ost/gfx/color_ops/gradient_level_color_op.hh
+include/ost/gfx/color_ops/map_handle_color_op.hh
+include/ost/gfx/color_ops/uniform_color_op.hh
+include/ost/gfx/entity.hh
+include/ost/gfx/entity_fw.hh
+include/ost/gfx/exporter.hh
+include/ost/gfx/exporter_fw.hh
+include/ost/gfx/gfx.hh
+include/ost/gfx/gfx_fw.hh
+include/ost/gfx/gfx_node.hh
+include/ost/gfx/gfx_node_fw.hh
+include/ost/gfx/gfx_node_visitor.hh
+include/ost/gfx/gfx_object.hh
+include/ost/gfx/gfx_object_base.hh
+include/ost/gfx/gfx_object_fw.hh
+include/ost/gfx/gfx_prim.hh
+include/ost/gfx/gfx_test_object.hh
+include/ost/gfx/gl_helper.hh
+include/ost/gfx/gl_include.hh
+include/ost/gfx/glext_include.hh
+include/ost/gfx/glwin_base.hh
+include/ost/gfx/gost_exporter.hh
+include/ost/gfx/gradient.hh
+include/ost/gfx/gradient_manager.hh
+include/ost/gfx/impl/backbone_trace.hh
+include/ost/gfx/impl/cartoon_renderer.hh
+include/ost/gfx/impl/connect_renderer_base.hh
+include/ost/gfx/impl/cpk_renderer.hh
+include/ost/gfx/impl/custom_renderer.hh
+include/ost/gfx/impl/debug_renderer.hh
+include/ost/gfx/impl/entity_detail.hh
+include/ost/gfx/impl/entity_renderer.hh
+include/ost/gfx/impl/entity_renderer_fw.hh
+include/ost/gfx/impl/fast_spheres.hh
+include/ost/gfx/impl/glx_offscreen_buffer.hh
+include/ost/gfx/impl/line_trace_renderer.hh
+include/ost/gfx/impl/map_iso_gen.hh
+include/ost/gfx/impl/map_iso_gen_s.hh
+include/ost/gfx/impl/map_iso_spec.hh
+include/ost/gfx/impl/map_octree.hh
+include/ost/gfx/impl/mapped_property.hh
+include/ost/gfx/impl/octree_isocont.hh
+include/ost/gfx/impl/simple_renderer.hh
+include/ost/gfx/impl/sline_renderer.hh
+include/ost/gfx/impl/tabulated_trig.hh
+include/ost/gfx/impl/trace_renderer.hh
+include/ost/gfx/impl/trace_renderer_base.hh
+include/ost/gfx/input.hh
+include/ost/gfx/map_handle_color_op.hh
+include/ost/gfx/map_iso.hh
+include/ost/gfx/map_iso_prop.hh
+include/ost/gfx/map_slab.hh
+include/ost/gfx/material.hh
+include/ost/gfx/module_config.hh
+include/ost/gfx/offscreen_buffer.hh
+include/ost/gfx/povray.hh
+include/ost/gfx/povray_fw.hh
+include/ost/gfx/prim_list.hh
+include/ost/gfx/primitives.hh
+include/ost/gfx/render_mode.hh
+include/ost/gfx/render_options/cartoon_render_options.hh
+include/ost/gfx/render_options/cpk_render_options.hh
+include/ost/gfx/render_options/custom_render_options.hh
+include/ost/gfx/render_options/line_render_options.hh
+include/ost/gfx/render_options/line_trace_render_options.hh
+include/ost/gfx/render_options/render_options.hh
+include/ost/gfx/render_options/simple_render_options.hh
+include/ost/gfx/render_options/sline_render_options.hh
+include/ost/gfx/render_options/trace_render_options.hh
+include/ost/gfx/render_pass.hh
+include/ost/gfx/scene.hh
+include/ost/gfx/scene_observer.hh
+include/ost/gfx/selection.hh
+include/ost/gfx/surface.hh
+include/ost/gfx/symmetry_node.hh
+include/ost/gfx/texture.hh
+include/ost/gfx/vertex_array.hh
+include/ost/gfx/vertex_array_helper.hh
+include/ost/gui/admin.hh
+include/ost/gui/data_viewer/argand.hh
+include/ost/gui/data_viewer/data_viewer.hh
+include/ost/gui/data_viewer/data_viewer_panel.hh
+include/ost/gui/data_viewer/data_viewer_panel_base.hh
+include/ost/gui/data_viewer/draw_overlay.hh
+include/ost/gui/data_viewer/drawing_functions.hh
+include/ost/gui/data_viewer/fft_panel.hh
+include/ost/gui/data_viewer/img2qt.hh
+include/ost/gui/data_viewer/info_panel.hh
+include/ost/gui/data_viewer/mask_overlay.hh
+include/ost/gui/data_viewer/null_overlay.hh
+include/ost/gui/data_viewer/overlay.hh
+include/ost/gui/data_viewer/overlay_base.hh
+include/ost/gui/data_viewer/overlay_base_fw.hh
+include/ost/gui/data_viewer/overlay_manager.hh
+include/ost/gui/data_viewer/overlay_manager_fw.hh
+include/ost/gui/data_viewer/overlay_manager_gui.hh
+include/ost/gui/data_viewer/overlay_manager_observer.hh
+include/ost/gui/data_viewer/pointlist_overlay.hh
+include/ost/gui/data_viewer/pointlist_overlay_base.hh
+include/ost/gui/data_viewer/strategies.hh
+include/ost/gui/data_viewer/strategies_fw.hh
+include/ost/gui/data_viewer/viewer_normalizer.hh
+include/ost/gui/dock_widget.hh
+include/ost/gui/file_browser.hh
+include/ost/gui/file_loader.hh
+include/ost/gui/file_type_dialog.hh
+include/ost/gui/file_viewer.hh
+include/ost/gui/gl_canvas.hh
+include/ost/gui/gl_win.hh
+include/ost/gui/gosty_app.hh
+include/ost/gui/main.hh
+include/ost/gui/main_area.hh
+include/ost/gui/main_window.hh
+include/ost/gui/messages/log_reader.hh
+include/ost/gui/messages/message_box_widget.hh
+include/ost/gui/messages/message_widget.hh
+include/ost/gui/module_config.hh
+include/ost/gui/panels/bottom_bar.hh
+include/ost/gui/panels/button_bar.hh
+include/ost/gui/panels/button_box.hh
+include/ost/gui/panels/drop_box.hh
+include/ost/gui/panels/event_button.hh
+include/ost/gui/panels/panel_bar.hh
+include/ost/gui/panels/panel_bar_widget_holder.hh
+include/ost/gui/panels/panel_manager.hh
+include/ost/gui/panels/panel_widget_container.hh
+include/ost/gui/panels/side_bar.hh
+include/ost/gui/panels/splitter_panel_bar.hh
+include/ost/gui/panels/tabbed_panel_bar.hh
+include/ost/gui/perspective.hh
+include/ost/gui/python_shell/completer_base.hh
+include/ost/gui/python_shell/dir_model.hh
+include/ost/gui/python_shell/gutter.hh
+include/ost/gui/python_shell/main_thread_runner.hh
+include/ost/gui/python_shell/output_redirector.hh
+include/ost/gui/python_shell/path_completer.hh
+include/ost/gui/python_shell/python_completer.hh
+include/ost/gui/python_shell/python_context_parser.hh
+include/ost/gui/python_shell/python_interpreter.hh
+include/ost/gui/python_shell/python_interpreter_worker.hh
+include/ost/gui/python_shell/python_shell.hh
+include/ost/gui/python_shell/python_shell_fw.hh
+include/ost/gui/python_shell/python_shell_text_document_layout.hh
+include/ost/gui/python_shell/python_shell_widget.hh
+include/ost/gui/python_shell/python_syntax_highlighter.hh
+include/ost/gui/python_shell/python_tokenizer.hh
+include/ost/gui/python_shell/shell_history.hh
+include/ost/gui/python_shell/state.hh
+include/ost/gui/python_shell/state_machine.hh
+include/ost/gui/python_shell/text_logger.hh
+include/ost/gui/python_shell/transition.hh
+include/ost/gui/python_shell/transition_guard.hh
+include/ost/gui/scene_menu.hh
+include/ost/gui/scene_selection.hh
+include/ost/gui/scene_win/context_menu.hh
+include/ost/gui/scene_win/current_selection_node.hh
+include/ost/gui/scene_win/custom_part_node.hh
+include/ost/gui/scene_win/entity_node.hh
+include/ost/gui/scene_win/entity_part_node.hh
+include/ost/gui/scene_win/gfx_scene_node.hh
+include/ost/gui/scene_win/label_node.hh
+include/ost/gui/scene_win/render_mode_node.hh
+include/ost/gui/scene_win/render_modes_node.hh
+include/ost/gui/scene_win/root_node.hh
+include/ost/gui/scene_win/scene_node.hh
+include/ost/gui/scene_win/scene_win.hh
+include/ost/gui/scene_win/scene_win_model.hh
+include/ost/gui/sequence_viewer/align_properties_painter.hh
+include/ost/gui/sequence_viewer/alignment_view_object.hh
+include/ost/gui/sequence_viewer/background_painter.hh
+include/ost/gui/sequence_viewer/base_row.hh
+include/ost/gui/sequence_viewer/base_view_object.hh
+include/ost/gui/sequence_viewer/conservation_painter.hh
+include/ost/gui/sequence_viewer/painter.hh
+include/ost/gui/sequence_viewer/secstr_row.hh
+include/ost/gui/sequence_viewer/seq_secstr_painter.hh
+include/ost/gui/sequence_viewer/seq_selection_painter.hh
+include/ost/gui/sequence_viewer/seq_text_painter.hh
+include/ost/gui/sequence_viewer/sequence_delegate.hh
+include/ost/gui/sequence_viewer/sequence_model.hh
+include/ost/gui/sequence_viewer/sequence_row.hh
+include/ost/gui/sequence_viewer/sequence_search_bar.hh
+include/ost/gui/sequence_viewer/sequence_table_view.hh
+include/ost/gui/sequence_viewer/sequence_view_object.hh
+include/ost/gui/sequence_viewer/sequence_viewer.hh
+include/ost/gui/sequence_viewer/tick_painter.hh
+include/ost/gui/sequence_viewer/title_row.hh
+include/ost/gui/thin_splitter.hh
+include/ost/gui/tools/manipulator.hh
+include/ost/gui/tools/map_tool.hh
+include/ost/gui/tools/measure_tool.hh
+include/ost/gui/tools/mouse_event.hh
+include/ost/gui/tools/selection_tool.hh
+include/ost/gui/tools/tool.hh
+include/ost/gui/tools/tool_bar.hh
+include/ost/gui/tools/tool_manager.hh
+include/ost/gui/tools/tool_option.hh
+include/ost/gui/tools/tool_option_group.hh
+include/ost/gui/tools/tool_options.hh
+include/ost/gui/tools/tool_options_widget.hh
+include/ost/gui/tools/tool_options_win.hh
+include/ost/gui/widget.hh
+include/ost/gui/widget_geom_handler.hh
+include/ost/gui/widget_pool.hh
+include/ost/gui/widget_registry.hh
+include/ost/gui/widget_state_saver.hh
+include/ost/img/alg/alg_mirror.hh
+include/ost/img/alg/alg_shift.hh
+include/ost/img/alg/alg_transform.hh
+include/ost/img/alg/anisotropic.hh
+include/ost/img/alg/auto_correlate.hh
+include/ost/img/alg/clear.hh
+include/ost/img/alg/clip_min_max.hh
+include/ost/img/alg/conjugate.hh
+include/ost/img/alg/convolute.hh
+include/ost/img/alg/correlate.hh
+include/ost/img/alg/cross_correlate.hh
+include/ost/img/alg/density_slice.hh
+include/ost/img/alg/dft.hh
+include/ost/img/alg/discrete_shrink.hh
+include/ost/img/alg/fft.hh
+include/ost/img/alg/fftw_helper.hh
+include/ost/img/alg/fill.hh
+include/ost/img/alg/filter.hh
+include/ost/img/alg/fourier_filters.hh
+include/ost/img/alg/fractional_shift.hh
+include/ost/img/alg/gaussian.hh
+include/ost/img/alg/gaussian_gradient_magnitude.hh
+include/ost/img/alg/gaussian_laplacian.hh
+include/ost/img/alg/highest_peak_search_3d.hh
+include/ost/img/alg/histogram.hh
+include/ost/img/alg/line_average.hh
+include/ost/img/alg/line_iterator.hh
+include/ost/img/alg/local_sigma_threshold.hh
+include/ost/img/alg/mask_image.hh
+include/ost/img/alg/module_config.hh
+include/ost/img/alg/negate.hh
+include/ost/img/alg/norm.hh
+include/ost/img/alg/norm_linear.hh
+include/ost/img/alg/norm_log.hh
+include/ost/img/alg/norm_od.hh
+include/ost/img/alg/normalizer.hh
+include/ost/img/alg/normalizer_factory.hh
+include/ost/img/alg/polar.hh
+include/ost/img/alg/power_spectrum.hh
+include/ost/img/alg/randomize.hh
+include/ost/img/alg/rscrosscorr.hh
+include/ost/img/alg/smooth_mask_image.hh
+include/ost/img/alg/stat.hh
+include/ost/img/alg/stat_accumulator.hh
+include/ost/img/alg/stat_min_max.hh
+include/ost/img/alg/threshold.hh
+include/ost/img/alg/transcendentals.hh
+include/ost/img/alg/transform.hh
+include/ost/img/alg/transform_fw.hh
+include/ost/img/alg/transformation_base.hh
+include/ost/img/alg/transformations.hh
+include/ost/img/algorithm.hh
+include/ost/img/circle_mask.hh
+include/ost/img/composite_mask.hh
+include/ost/img/data.hh
+include/ost/img/data_algorithm.hh
+include/ost/img/data_observer.hh
+include/ost/img/data_types.hh
+include/ost/img/debug.hh
+include/ost/img/dllexport.hh
+include/ost/img/extent.hh
+include/ost/img/extent_iterator.hh
+include/ost/img/extent_mask.hh
+include/ost/img/image.hh
+include/ost/img/image_factory.hh
+include/ost/img/image_fw.hh
+include/ost/img/image_handle.hh
+include/ost/img/image_handle_fw.hh
+include/ost/img/image_impl.hh
+include/ost/img/image_list.hh
+include/ost/img/image_state.hh
+include/ost/img/image_state/binop.hh
+include/ost/img/image_state/dispatch.hh
+include/ost/img/image_state/image_state.hh
+include/ost/img/image_state/image_state_algorithm.hh
+include/ost/img/image_state/image_state_base.hh
+include/ost/img/image_state/image_state_base_fw.hh
+include/ost/img/image_state/image_state_def.hh
+include/ost/img/image_state/image_state_factory.hh
+include/ost/img/image_state/image_state_frequency_domain.hh
+include/ost/img/image_state/image_state_fw.hh
+include/ost/img/image_state/image_state_half_frequency_domain.hh
+include/ost/img/image_state/image_state_impl.hh
+include/ost/img/image_state/image_state_spatial_domain.hh
+include/ost/img/image_state/image_state_visitor.hh
+include/ost/img/image_state/image_state_visitor_fw.hh
+include/ost/img/image_state/index.hh
+include/ost/img/image_state/type_fw.hh
+include/ost/img/image_state/value_holder.hh
+include/ost/img/image_state_fw.hh
+include/ost/img/inverted_mask.hh
+include/ost/img/map.hh
+include/ost/img/mask.hh
+include/ost/img/mask_base.hh
+include/ost/img/mask_base_fw.hh
+include/ost/img/mask_info_convert.hh
+include/ost/img/mask_op.hh
+include/ost/img/mask_visitor.hh
+include/ost/img/module_config.hh
+include/ost/img/normalizer_fw.hh
+include/ost/img/normalizer_impl.hh
+include/ost/img/null_data.hh
+include/ost/img/observable.hh
+include/ost/img/paste_impl.hh
+include/ost/img/peak.hh
+include/ost/img/phase.hh
+include/ost/img/physical_units.hh
+include/ost/img/pixel_sampling.hh
+include/ost/img/point.hh
+include/ost/img/point_list.hh
+include/ost/img/polygon_mask.hh
+include/ost/img/progress.hh
+include/ost/img/raster_image/raster_image.hh
+include/ost/img/size.hh
+include/ost/img/spherical_mask.hh
+include/ost/img/util.cc
+include/ost/img/util.hh
+include/ost/img/value_util.hh
+include/ost/img/vecmat.hh
+include/ost/info/geom_info_conversion.hh
+include/ost/info/info.hh
+include/ost/info/info_error.hh
+include/ost/info/info_fw.hh
+include/ost/info/info_group.hh
+include/ost/info/info_handle.hh
+include/ost/info/info_impl.hh
+include/ost/info/info_impl_fw.hh
+include/ost/info/info_item.hh
+include/ost/info/info_path.hh
+include/ost/info/info_set.hh
+include/ost/info/info_verbose_visitor.hh
+include/ost/info/info_visitor.hh
+include/ost/info/item_type.hh
+include/ost/info/item_type_cast.hh
+include/ost/info/module_config.hh
+include/ost/integrity_error.hh
+include/ost/invalid_handle.hh
+include/ost/io/binary_data_sink.hh
+include/ost/io/binary_data_source.hh
+include/ost/io/chemdict_parser.hh
+include/ost/io/clustal_io_handler.hh
+include/ost/io/container_serialization.hh
+include/ost/io/convert.hh
+include/ost/io/convert_vax_data.h
+include/ost/io/converting_streams.hh
+include/ost/io/dcd_io.hh
+include/ost/io/entity_io_crd_handler.hh
+include/ost/io/entity_io_handler.hh
+include/ost/io/entity_io_mae_handler.hh
+include/ost/io/entity_io_mmcif_handler.hh
+include/ost/io/entity_io_pdb_handler.hh
+include/ost/io/entity_io_pqr_handler.hh
+include/ost/io/entity_io_sdf_handler.hh
+include/ost/io/fasta_io_handler.hh
+include/ost/io/formatted_line.hh
+include/ost/io/hhm_io_handler.hh
+include/ost/io/image_format.hh
+include/ost/io/image_format_conversion.cc
+include/ost/io/img/convert_vax_data.h
+include/ost/io/img/image_format.hh
+include/ost/io/img/image_format_conversion.cc
+include/ost/io/img/jpk_util.hh
+include/ost/io/img/load_map.hh
+include/ost/io/img/map_io_dat_handler.hh
+include/ost/io/img/map_io_df3_handler.hh
+include/ost/io/img/map_io_dm3_handler.hh
+include/ost/io/img/map_io_dx_handler.hh
+include/ost/io/img/map_io_handler.hh
+include/ost/io/img/map_io_ipl_handler.hh
+include/ost/io/img/map_io_jpk_handler.hh
+include/ost/io/img/map_io_mrc_handler.hh
+include/ost/io/img/map_io_nanoscope_handler.hh
+include/ost/io/img/map_io_png_handler.hh
+include/ost/io/img/map_io_situs_handler.hh
+include/ost/io/img/map_io_spi_handler.hh
+include/ost/io/img/map_io_tiff_handler.hh
+include/ost/io/img/tiff_util.hh
+include/ost/io/io_exception.hh
+include/ost/io/io_manager.hh
+include/ost/io/io_profile.hh
+include/ost/io/io_utils.hh
+include/ost/io/jpk_util.hh
+include/ost/io/load.hh
+include/ost/io/load_entity.hh
+include/ost/io/load_map.hh
+include/ost/io/load_surface.hh
+include/ost/io/map_io_dat_handler.hh
+include/ost/io/map_io_df3_handler.hh
+include/ost/io/map_io_dm3_handler.hh
+include/ost/io/map_io_dx_handler.hh
+include/ost/io/map_io_handler.hh
+include/ost/io/map_io_ipl_handler.hh
+include/ost/io/map_io_jpk_handler.hh
+include/ost/io/map_io_mrc_handler.hh
+include/ost/io/map_io_nanoscope_handler.hh
+include/ost/io/map_io_png_handler.hh
+include/ost/io/map_io_situs_handler.hh
+include/ost/io/map_io_spi_handler.hh
+include/ost/io/map_io_tiff_handler.hh
+include/ost/io/mmcif_info.hh
+include/ost/io/mmcif_reader.hh
+include/ost/io/module_config.hh
+include/ost/io/mol/chemdict_parser.hh
+include/ost/io/mol/dcd_io.hh
+include/ost/io/mol/entity_io_crd_handler.hh
+include/ost/io/mol/entity_io_handler.hh
+include/ost/io/mol/entity_io_mae_handler.hh
+include/ost/io/mol/entity_io_mmcif_handler.hh
+include/ost/io/mol/entity_io_pdb_handler.hh
+include/ost/io/mol/entity_io_pqr_handler.hh
+include/ost/io/mol/entity_io_sdf_handler.hh
+include/ost/io/mol/io_profile.hh
+include/ost/io/mol/load_entity.hh
+include/ost/io/mol/load_surface.hh
+include/ost/io/mol/mmcif_info.hh
+include/ost/io/mol/mmcif_reader.hh
+include/ost/io/mol/pdb_reader.hh
+include/ost/io/mol/pdb_str.hh
+include/ost/io/mol/pdb_writer.hh
+include/ost/io/mol/save_entity.hh
+include/ost/io/mol/sdf_reader.hh
+include/ost/io/mol/sdf_writer.hh
+include/ost/io/mol/star_parser.hh
+include/ost/io/mol/surface_io_handler.hh
+include/ost/io/mol/surface_io_msms_handler.hh
+include/ost/io/pdb_reader.hh
+include/ost/io/pdb_str.hh
+include/ost/io/pdb_writer.hh
+include/ost/io/pir_io_handler.hh
+include/ost/io/profile_io_handler.hh
+include/ost/io/promod_io_handler.hh
+include/ost/io/pssm_io_handler.hh
+include/ost/io/save.hh
+include/ost/io/save_entity.hh
+include/ost/io/sdf_reader.hh
+include/ost/io/sdf_writer.hh
+include/ost/io/seq/clustal_io_handler.hh
+include/ost/io/seq/fasta_io_handler.hh
+include/ost/io/seq/hhm_io_handler.hh
+include/ost/io/seq/load.hh
+include/ost/io/seq/pir_io_handler.hh
+include/ost/io/seq/profile_io_handler.hh
+include/ost/io/seq/promod_io_handler.hh
+include/ost/io/seq/pssm_io_handler.hh
+include/ost/io/seq/save.hh
+include/ost/io/seq/sequence_io_handler.hh
+include/ost/io/sequence_io_handler.hh
+include/ost/io/star_parser.hh
+include/ost/io/surface_io_handler.hh
+include/ost/io/surface_io_msms_handler.hh
+include/ost/io/swap_util.hh
+include/ost/io/tiff_util.hh
+include/ost/log.hh
+include/ost/log_sink.hh
+include/ost/message.hh
+include/ost/module_config.hh
+include/ost/mol/alg/accessibility.hh
+include/ost/mol/alg/adjacency_bitmap.hh
+include/ost/mol/alg/clash_score.hh
+include/ost/mol/alg/consistency_checks.hh
+include/ost/mol/alg/construct_cbeta.hh
+include/ost/mol/alg/contact_overlap.hh
+include/ost/mol/alg/distance_rmsd_test.hh
+include/ost/mol/alg/distance_test_common.hh
+include/ost/mol/alg/domain_find.hh
+include/ost/mol/alg/entity_to_density.hh
+include/ost/mol/alg/filter_clashes.hh
+include/ost/mol/alg/local_dist_diff_test.hh
+include/ost/mol/alg/module_config.hh
+include/ost/mol/alg/pdbize.hh
+include/ost/mol/alg/sec_struct.hh
+include/ost/mol/alg/sec_structure_segments.hh
+include/ost/mol/alg/similarity_matrix.hh
+include/ost/mol/alg/structure_analysis.hh
+include/ost/mol/alg/superpose_frames.hh
+include/ost/mol/alg/svd_superpose.hh
+include/ost/mol/alg/trajectory_analysis.hh
+include/ost/mol/atom_base.hh
+include/ost/mol/atom_handle.hh
+include/ost/mol/atom_view.hh
+include/ost/mol/bond_handle.hh
+include/ost/mol/bond_table.hh
+include/ost/mol/bounding_box.hh
+include/ost/mol/builder.hh
+include/ost/mol/chain_base.hh
+include/ost/mol/chain_handle.hh
+include/ost/mol/chain_type.hh
+include/ost/mol/chain_view.hh
+include/ost/mol/chem_class.hh
+include/ost/mol/chem_type.hh
+include/ost/mol/coord_frame.hh
+include/ost/mol/coord_group.hh
+include/ost/mol/coord_source.hh
+include/ost/mol/editor_base.hh
+include/ost/mol/editor_type_fw.hh
+include/ost/mol/entity_base.hh
+include/ost/mol/entity_handle.hh
+include/ost/mol/entity_observer.hh
+include/ost/mol/entity_observer_fw.hh
+include/ost/mol/entity_property_mapper.hh
+include/ost/mol/entity_view.hh
+include/ost/mol/entity_visitor.hh
+include/ost/mol/entity_visitor_fw.hh
+include/ost/mol/handle_type_fw.hh
+include/ost/mol/ics_editor.hh
+include/ost/mol/impl/atom_group.hh
+include/ost/mol/impl/atom_impl.hh
+include/ost/mol/impl/atom_impl_fw.hh
+include/ost/mol/impl/atom_prop.hh
+include/ost/mol/impl/chain_impl.hh
+include/ost/mol/impl/chain_impl_fw.hh
+include/ost/mol/impl/connector_impl.hh
+include/ost/mol/impl/connector_impl_fw.hh
+include/ost/mol/impl/dihedral.hh
+include/ost/mol/impl/entity_impl.hh
+include/ost/mol/impl/entity_impl_fw.hh
+include/ost/mol/impl/fragment_impl.hh
+include/ost/mol/impl/fragment_impl_fw.hh
+include/ost/mol/impl/pointer_iterator.hh
+include/ost/mol/impl/query_ast.hh
+include/ost/mol/impl/query_ast_fw.hh
+include/ost/mol/impl/query_impl.hh
+include/ost/mol/impl/query_impl_fw.hh
+include/ost/mol/impl/residue_impl.hh
+include/ost/mol/impl/residue_impl_fw.hh
+include/ost/mol/impl/surface_impl.hh
+include/ost/mol/impl/surface_impl_fw.hh
+include/ost/mol/impl/torsion_impl.hh
+include/ost/mol/impl/torsion_impl_fw.hh
+include/ost/mol/in_mem_coord_source.hh
+include/ost/mol/module_config.hh
+include/ost/mol/mol.hh
+include/ost/mol/not_connected_error.hh
+include/ost/mol/property_id.hh
+include/ost/mol/query.hh
+include/ost/mol/query_error.hh
+include/ost/mol/query_state.hh
+include/ost/mol/query_view_wrapper.hh
+include/ost/mol/residue_base.hh
+include/ost/mol/residue_handle.hh
+include/ost/mol/residue_prop.hh
+include/ost/mol/residue_view.hh
+include/ost/mol/sec_structure.hh
+include/ost/mol/spatial_organizer.hh
+include/ost/mol/surface.hh
+include/ost/mol/surface_builder.hh
+include/ost/mol/surface_handle.hh
+include/ost/mol/surface_prop.hh
+include/ost/mol/torsion_handle.hh
+include/ost/mol/transfer_connectivity.hh
+include/ost/mol/transform.hh
+include/ost/mol/view_op.hh
+include/ost/mol/view_type_fw.hh
+include/ost/mol/xcs_editor.hh
+include/ost/platform.hh
+include/ost/pod_vector.hh
+include/ost/profile.hh
+include/ost/ptr_observer.hh
+include/ost/range.hh
+include/ost/seq/alg/alignment_opts.hh
+include/ost/seq/alg/clip_alignment.hh
+include/ost/seq/alg/conservation.hh
+include/ost/seq/alg/contact_prediction_score.hh
+include/ost/seq/alg/contact_weight_matrix.hh
+include/ost/seq/alg/default_contact_weight_matrix.hh
+include/ost/seq/alg/default_pair_subst_weight_matrix.hh
+include/ost/seq/alg/distance_map.hh
+include/ost/seq/alg/entropy.hh
+include/ost/seq/alg/global_align.hh
+include/ost/seq/alg/ins_del.hh
+include/ost/seq/alg/local_align.hh
+include/ost/seq/alg/merge_pairwise_alignments.hh
+include/ost/seq/alg/module_config.hh
+include/ost/seq/alg/pair_subst_weight_matrix.hh
+include/ost/seq/alg/semiglobal_align.hh
+include/ost/seq/alg/sequence_identity.hh
+include/ost/seq/alg/sequence_similarity.hh
+include/ost/seq/alg/subst_weight_matrix.hh
+include/ost/seq/alg/variance_map.hh
+include/ost/seq/aligned_column.hh
+include/ost/seq/aligned_column_iterator.hh
+include/ost/seq/aligned_region.hh
+include/ost/seq/alignment_handle.hh
+include/ost/seq/impl/sequence_impl.hh
+include/ost/seq/impl/sequence_impl_fw.hh
+include/ost/seq/impl/sequence_list_impl.hh
+include/ost/seq/impl/sequence_list_impl_fw.hh
+include/ost/seq/impl/sequence_list_iterator.hh
+include/ost/seq/invalid_sequence.hh
+include/ost/seq/module_config.hh
+include/ost/seq/profile_handle.hh
+include/ost/seq/sequence_handle.hh
+include/ost/seq/sequence_list.hh
+include/ost/seq/sequence_op.hh
+include/ost/seq/views_from_sequences.hh
+include/ost/stdint.hh
+include/ost/stdint_msc.hh
+include/ost/string_ref.hh
+include/ost/test_utils/compare_files.hh
+include/ost/tri_matrix.hh
+include/ost/units.hh
+include/ost/version.hh
+lib/libost_base.so
+lib/libost_base.so.1.7
+lib/libost_base.so.1.7.1
+lib/libost_conop.so
+lib/libost_conop.so.1.7
+lib/libost_conop.so.1.7.1
+lib/libost_db.so
+lib/libost_db.so.1.7
+lib/libost_db.so.1.7.1
+lib/libost_geom.so
+lib/libost_geom.so.1.7
+lib/libost_geom.so.1.7.1
+lib/libost_gfx.so
+lib/libost_gfx.so.1.7
+lib/libost_gfx.so.1.7.1
+lib/libost_gui.so
+lib/libost_gui.so.1.7
+lib/libost_gui.so.1.7.1
+lib/libost_img.so
+lib/libost_img.so.1.7
+lib/libost_img.so.1.7.1
+lib/libost_img_alg.so
+lib/libost_img_alg.so.1.7
+lib/libost_img_alg.so.1.7.1
+lib/libost_info.so
+lib/libost_info.so.1.7
+lib/libost_info.so.1.7.1
+lib/libost_io.so
+lib/libost_io.so.1.7
+lib/libost_io.so.1.7.1
+lib/libost_mol.so
+lib/libost_mol.so.1.7
+lib/libost_mol.so.1.7.1
+lib/libost_mol_alg.so
+lib/libost_mol_alg.so.1.7
+lib/libost_mol_alg.so.1.7.1
+lib/libost_seq.so
+lib/libost_seq.so.1.7
+lib/libost_seq.so.1.7.1
+lib/libost_seq_alg.so
+lib/libost_seq_alg.so.1.7
+lib/libost_seq_alg.so.1.7.1
+%%PYTHON_SITELIBDIR%%/ost/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/_ost_base.so
+%%PYTHON_SITELIBDIR%%/ost/bindings/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/align_3dcomb.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/align_3dcomb.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/blast.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/blast.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/cadscore.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/cadscore.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/clustalw.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/clustalw.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/dssp.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/dssp.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/hbplus.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/hbplus.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/hhblits.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/hhblits.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/ialign.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/ialign.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/kclust.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/kclust.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/lga.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/lga.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/msms.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/msms.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/naccess.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/naccess.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/tmtools.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/tmtools.pyc
+%%PYTHON_SITELIBDIR%%/ost/bindings/utils.py
+%%PYTHON_SITELIBDIR%%/ost/bindings/utils.pyc
+%%PYTHON_SITELIBDIR%%/ost/conop/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/conop/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/conop/_ost_conop.so
+%%PYTHON_SITELIBDIR%%/ost/conop/cleanup.py
+%%PYTHON_SITELIBDIR%%/ost/conop/cleanup.pyc
+%%PYTHON_SITELIBDIR%%/ost/db/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/db/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/dng_startup.py
+%%PYTHON_SITELIBDIR%%/ost/geom/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/geom/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/geom/_ost_geom.so
+%%PYTHON_SITELIBDIR%%/ost/gfx/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/gfx/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/gfx/_ost_gfx.so
+%%PYTHON_SITELIBDIR%%/ost/gfx/py_gfx_obj.py
+%%PYTHON_SITELIBDIR%%/ost/gfx/py_gfx_obj.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/gui/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/_ost_gui.so
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/init.py
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/init.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/menu.py
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/menu.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/superpositiondialog.py
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/superpositiondialog.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/termuse.py
+%%PYTHON_SITELIBDIR%%/ost/gui/dng/termuse.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/gosty_startup.py
+%%PYTHON_SITELIBDIR%%/ost/gui/gosty_startup.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/helpwidget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/helpwidget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/init_context_menu.py
+%%PYTHON_SITELIBDIR%%/ost/gui/init_context_menu.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/init_menubar.py
+%%PYTHON_SITELIBDIR%%/ost/gui/init_menubar.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/init_spacenav.py
+%%PYTHON_SITELIBDIR%%/ost/gui/init_spacenav.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/init_splash.py
+%%PYTHON_SITELIBDIR%%/ost/gui/init_splash.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/color_options_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/color_options_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/color_select_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/color_select_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/combo_options_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/combo_options_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/cpk_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/cpk_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/custom_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/custom_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_editor_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_editor_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_info_handler.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_info_handler.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_list_model.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_list_model.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_preset_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/gradient_preset_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/hsc_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/hsc_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/immutable_gradient_info_handler.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/immutable_gradient_info_handler.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/immutable_preset_info_handler.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/immutable_preset_info_handler.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/init_inspector.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/init_inspector.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/inspector_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/inspector_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/line_trace_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/line_trace_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/map_level_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/map_level_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_editor_list_model.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_editor_list_model.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_editor_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_editor_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_info_handler.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_info_handler.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_list_model.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_list_model.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/preset_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/query_editor.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/query_editor.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/remote.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/remote.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_mode_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_mode_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_op.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_op.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_options_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/render_options_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/scene_observer_impl.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/scene_observer_impl.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/scene_selection_helper.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/scene_selection_helper.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/simple_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/simple_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/sline_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/sline_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/toolbar_options_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/toolbar_options_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/trace_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/trace_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/tube_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/tube_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/uniform_color_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/uniform_color_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/visibility_op.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/visibility_op.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/wireframe_widget.py
+%%PYTHON_SITELIBDIR%%/ost/gui/scene/wireframe_widget.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/table.py
+%%PYTHON_SITELIBDIR%%/ost/gui/table.pyc
+%%PYTHON_SITELIBDIR%%/ost/gui/trajectory_viewer.py
+%%PYTHON_SITELIBDIR%%/ost/gui/trajectory_viewer.pyc
+%%PYTHON_SITELIBDIR%%/ost/img/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/img/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/img/_ost_img.so
+%%PYTHON_SITELIBDIR%%/ost/img/alg/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/img/alg/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/img/alg/_ost_img_alg.so
+%%PYTHON_SITELIBDIR%%/ost/info/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/info/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/info/_ost_info.so
+%%PYTHON_SITELIBDIR%%/ost/io/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/io/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/io/_ost_io.so
+%%PYTHON_SITELIBDIR%%/ost/io/remote.py
+%%PYTHON_SITELIBDIR%%/ost/io/remote.pyc
+%%PYTHON_SITELIBDIR%%/ost/io/repository.py
+%%PYTHON_SITELIBDIR%%/ost/io/repository.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/mol/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/_ost_mol.so
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/_ost_mol_alg.so
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/hbond.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/hbond.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/helix_kinks.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/helix_kinks.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/qsscoring.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/qsscoring.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/structure_analysis.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/structure_analysis.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/superpose.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/superpose.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/trajectory_analysis.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/trajectory_analysis.pyc
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/views.py
+%%PYTHON_SITELIBDIR%%/ost/mol/alg/views.pyc
+%%PYTHON_SITELIBDIR%%/ost/ost_startup.py
+%%PYTHON_SITELIBDIR%%/ost/seq/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/seq/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/seq/_ost_seq.so
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/__init__.py
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/__init__.pyc
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/_ost_seq_alg.so
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/mat.py
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/mat.pyc
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/renumber.py
+%%PYTHON_SITELIBDIR%%/ost/seq/alg/renumber.pyc
+%%PYTHON_SITELIBDIR%%/ost/settings.py
+%%PYTHON_SITELIBDIR%%/ost/settings.pyc
+%%PYTHON_SITELIBDIR%%/ost/stutil.py
+%%PYTHON_SITELIBDIR%%/ost/stutil.pyc
+%%PYTHON_SITELIBDIR%%/ost/table.py
+%%PYTHON_SITELIBDIR%%/ost/table.pyc
+%%PYTHON_SITELIBDIR%%/ost/table_selector.py
+%%PYTHON_SITELIBDIR%%/ost/table_selector.pyc
+%%PYTHON_SITELIBDIR%%/ost/testutils.py
+%%PYTHON_SITELIBDIR%%/ost/testutils.pyc
+%%PYTHON_SITELIBDIR%%/ost/xmlrunner.py
+%%PYTHON_SITELIBDIR%%/ost/xmlrunner.pyc
+libexec/openstructure/gosty
+libexec/openstructure/ost_config
+%%DATADIR%%/atom_scattering_properties.txt
+%%DATADIR%%/gui/icons/add_icon.png
+%%DATADIR%%/gui/icons/close_icon.png
+%%DATADIR%%/gui/icons/critical_icon.png
+%%DATADIR%%/gui/icons/delete_icon.png
+%%DATADIR%%/gui/icons/distance_icon.png
+%%DATADIR%%/gui/icons/find_icon.png
+%%DATADIR%%/gui/icons/information_icon.png
+%%DATADIR%%/gui/icons/map_icon.png
+%%DATADIR%%/gui/icons/menubar_icon.png
+%%DATADIR%%/gui/icons/refresh.png
+%%DATADIR%%/gui/icons/rigid_body_manipulator_icon.png
+%%DATADIR%%/gui/icons/selection_icon.png
+%%DATADIR%%/gui/icons/show_sidebar_icon.png
+%%DATADIR%%/gui/icons/site_icon.png
+%%DATADIR%%/gui/icons/split_icon.png
+%%DATADIR%%/gui/icons/warning_icon.png
+%%DATADIR%%/gui/images/logo-small.png
+%%DATADIR%%/scene/gradients.xml
+%%DATADIR%%/scene/icons/color_icon.png
+%%DATADIR%%/scene/icons/preset_icon.png
+%%DATADIR%%/scene/icons/render_icon.png
+%%DATADIR%%/scene/icons/tool_icon.png
+%%DATADIR%%/scene/presets.xml
+%%DATADIR%%/stereo_chemical_props.txt
+%%DATADIR%%/textures/glyph_texture.png
+%%DATADIR%%/textures/test_texture.png