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Date:      Mon, 9 Jul 2018 04:41:17 +0000 (UTC)
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r474223 - in head/science: . openstructure openstructure/files
Message-ID:  <201807090441.w694fH7G043339@repo.freebsd.org>

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Author: yuri
Date: Mon Jul  9 04:41:17 2018
New Revision: 474223
URL: https://svnweb.freebsd.org/changeset/ports/474223

Log:
  New port: science/openstructure: Molecular modelling and visualization environment

Added:
  head/science/openstructure/
  head/science/openstructure/Makefile   (contents, props changed)
  head/science/openstructure/distinfo   (contents, props changed)
  head/science/openstructure/files/
  head/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake   (contents, props changed)
  head/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake   (contents, props changed)
  head/science/openstructure/files/patch-cmake__support_FindPython.cmake   (contents, props changed)
  head/science/openstructure/files/patch-cmake__support_OST.cmake   (contents, props changed)
  head/science/openstructure/files/patch-modules_config_base.hh   (contents, props changed)
  head/science/openstructure/files/patch-modules_db_src_sqlite3.c   (contents, props changed)
  head/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh   (contents, props changed)
  head/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt   (contents, props changed)
  head/science/openstructure/files/patch-modules_gui_src_gosty.cc   (contents, props changed)
  head/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc   (contents, props changed)
  head/science/openstructure/pkg-descr   (contents, props changed)
  head/science/openstructure/pkg-plist   (contents, props changed)
Modified:
  head/science/Makefile

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Mon Jul  9 03:33:35 2018	(r474222)
+++ head/science/Makefile	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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

Added: head/science/openstructure/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/Makefile	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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>

Added: head/science/openstructure/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/distinfo	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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

Added: head/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-cmake__support_CopyDependencies.cmake	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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})

Added: head/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-cmake__support_FindOPENSTRUCTURE.cmake	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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 ()

Added: head/science/openstructure/files/patch-cmake__support_FindPython.cmake
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-cmake__support_FindPython.cmake	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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

Added: head/science/openstructure/files/patch-cmake__support_OST.cmake
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-cmake__support_OST.cmake	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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}

Added: head/science/openstructure/files/patch-modules_config_base.hh
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_config_base.hh	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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)

Added: head/science/openstructure/files/patch-modules_db_src_sqlite3.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_db_src_sqlite3.c	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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))

Added: head/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_gfx_src_offscreen__buffer.hh	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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

Added: head/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_gui_src_CMakeLists.txt	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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})
+            

Added: head/science/openstructure/files/patch-modules_gui_src_gosty.cc
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_gui_src_gosty.cc	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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";

Added: head/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/files/patch-modules_img_base_src_raster__image_raster__image.cc	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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>

Added: head/science/openstructure/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/pkg-descr	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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/

Added: head/science/openstructure/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/openstructure/pkg-plist	Mon Jul  9 04:41:17 2018	(r474223)
@@ -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
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+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
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+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
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+lib/libost_mol_alg.so
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+lib/libost_seq.so
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+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

*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***



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