From 65da7c03589d1019eb265ed731413070e0654a64 Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 5 Jul 2010 09:01:41 +0000
Subject: [PATCH] optimising dir structure for examples/demos
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2507 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
.../code_fragments}/dokk/KEYS | 0
.../code_fragments}/dokk/config.py | 0
.../code_fragments}/dokk/datafiles/dengue/level.ini | 0
.../dokk/datafiles/dengue/levelF.ini | 0
.../dokk/datafiles/dengue/ligand.sdf | 0
.../dokk/datafiles/dengue/protein.pdb | 0
.../dokk/datafiles/dengue/surface.face | 0
.../dokk/datafiles/dengue/surface.vert | 0
.../dokk/datafiles/dengue/top_ten.ini | 0
.../dokk/datafiles/glyoxalase/level.ini | 0
.../dokk/datafiles/glyoxalase/levelF.ini | 0
.../dokk/datafiles/glyoxalase/ligand.sdf | 0
.../dokk/datafiles/glyoxalase/protein.pdb | 0
.../dokk/datafiles/glyoxalase/surface.face | 0
.../dokk/datafiles/glyoxalase/surface.vert | 0
.../dokk/datafiles/glyoxalase/top_ten.ini | 0
.../code_fragments}/dokk/datafiles/hud.ini | 0
.../code_fragments}/dokk/datafiles/hudF.ini | 0
.../dokk/datafiles/retinol/level.ini | 0
.../dokk/datafiles/retinol/levelF.ini | 0
.../dokk/datafiles/retinol/ligand.sdf | 0
.../dokk/datafiles/retinol/protein.pdb | 0
.../dokk/datafiles/retinol/surface.face | 0
.../dokk/datafiles/retinol/surface.vert | 0
.../dokk/datafiles/retinol/top_ten.ini | 0
.../dokk/datafiles/thrombin/level.ini | 0
.../dokk/datafiles/thrombin/levelF.ini | 0
.../dokk/datafiles/thrombin/ligand.sdf | 0
.../dokk/datafiles/thrombin/protein.pdb | 0
.../dokk/datafiles/thrombin/surface.face | 0
.../dokk/datafiles/thrombin/surface.vert | 0
.../dokk/datafiles/thrombin/top_ten.ini | 0
.../dokk/datafiles/tutorial_1/level.ini | 0
.../dokk/datafiles/tutorial_1/levelF.ini | 0
.../dokk/datafiles/tutorial_1/ligand.sdf | 0
.../dokk/datafiles/tutorial_1/protein.pdb | 0
.../dokk/datafiles/tutorial_1/surface.face | 0
.../dokk/datafiles/tutorial_1/surface.vert | 0
.../dokk/datafiles/tutorial_1/top_ten.ini | 0
.../dokk/datafiles/tutorial_2/level.ini | 0
.../dokk/datafiles/tutorial_2/levelF.ini | 0
.../dokk/datafiles/tutorial_2/ligand.sdf | 0
.../dokk/datafiles/tutorial_2/protein.pdb | 0
.../dokk/datafiles/tutorial_2/surface.face | 0
.../dokk/datafiles/tutorial_2/surface.vert | 0
.../dokk/datafiles/tutorial_2/top_ten.ini | 0
.../code_fragments}/dokk/dokk | 0
.../code_fragments}/dokk/dokk.py | 0
.../code_fragments}/dokk/glwin.py | 0
.../code_fragments}/dokk/hud.py | 0
.../code_fragments}/dokk/images/openstructure.png | Bin
.../code_fragments}/dokk/images/rotation.png | Bin
.../code_fragments}/dokk/images/translation.png | Bin
.../code_fragments}/dokk/level.py | 0
.../code_fragments}/dokk/level_info.py | 0
.../code_fragments}/dokk/level_intro.py | 0
.../code_fragments}/dokk/level_messages.py | 0
.../code_fragments}/dokk/ligand.py | 0
.../code_fragments}/dokk/name_enter.py | 0
.../code_fragments}/dokk/protein.py | 0
.../code_fragments}/dokk/score_updater.py | 0
.../code_fragments}/dokk/spacenav_connect.py | 0
.../code_fragments}/dokk/spnav_input.py | 0
.../code_fragments}/dokk/start_dokk.py | 0
.../code_fragments}/dokk/surface.py | 0
.../code_fragments}/entity/color_by_property.py | 0
.../code_fragments}/entity/fragment.pdb | 0
.../code_fragments}/entity/fragment2.pdb | 0
.../code_fragments}/entity/gfx_selection.py | 0
.../code_fragments}/entity/gfx_symmetry.py | 2 +-
.../code_fragments}/entity/gradient.py | 0
.../code_fragments}/entity/pdb1ake.ent | 0
.../code_fragments}/entity/pdb4ake.ent | 0
.../code_fragments}/entity/primitives.py | 0
.../code_fragments}/entity/random_lines.py | 0
.../code_fragments}/entity/sdh.pdb | 0
.../code_fragments}/entity/superpose.py | 0
.../code_fragments}/harmony/glwin.py | 0
.../code_fragments}/harmony/harmony | 0
.../code_fragments}/harmony/harmony.py | 0
.../code_fragments}/img/circle.png | Bin
.../code_fragments}/img/create_split_image.py | 0
.../code_fragments}/img/fft_li.py | 0
.../code_fragments}/img/modulate_image.py | 0
.../code_fragments}/img/spoke_pattern.py | 0
.../code_fragments}/img/square.png | Bin
.../code_fragments}/img/tone1.png | Bin
.../code_fragments}/img/tone2.png | Bin
.../code_fragments}/img/tone3.png | Bin
.../code_fragments}/img/tone4.png | Bin
.../code_fragments}/img/tone5.png | Bin
.../code_fragments}/img/view_phase_diff.py | 0
.../code_fragments}/map/1ppt.map | Bin
.../code_fragments}/map/1ppt.pdb | 0
.../code_fragments}/map/gfx_mapiso.py | 0
.../code_fragments}/misc/bitmap_export.py | 0
.../code_fragments}/misc/export_pov.py | 0
.../code_fragments}/misc/fragment.face | 0
.../code_fragments}/misc/fragment.pdb | 0
.../code_fragments}/misc/fragment.vert | 0
.../code_fragments}/modelling/roll_helix.py | 0
.../code_fragments}/modelling/sdh.pdb | 0
.../code_fragments}/modelling/strip_sidechains.py | 0
.../code_fragments}/seq/seq_viewer.py | 0
.../code_fragments}/surf/fragment.pdb | 0
.../code_fragments}/surf/sdh.face | 0
.../code_fragments}/surf/sdh.pdb | 0
.../code_fragments}/surf/sdh.vert | 0
.../code_fragments}/surf/test_surf.py | 0
.../code_fragments}/surf/test_surf_pov.py | 0
.../code_fragments}/trj/fragment.pdb | 0
.../code_fragments}/trj/mpor_trj.crd | 0
.../code_fragments}/trj/mpor_trj_short.trj | Bin
.../code_fragments}/trj/test_trj.py | 0
.../code_fragments}/ui/board.py | 0
.../code_fragments}/ui/color_tool.py | 0
.../code_fragments}/ui/mdi_example.py | 0
.../code_fragments}/ui/menubar_example.py | 0
.../code_fragments}/ui/widget_example.py | 0
{demos => examples/demos}/bbox.py | 4 +++-
{demos => examples/demos}/conservation.py | 6 +++---
{demos => examples/demos}/gfx_mapslab.py | 0
{demos => examples/demos}/load_and_display.py | 2 +-
{demos => examples/demos}/rendermodes.py | 2 +-
{demos => examples/demos}/sample.dcd | Bin
{demos => examples/demos}/sample.pdb | 0
{demos => examples/demos}/sdh.pdb | 0
{demos => examples/demos}/sh2.aln | 0
{demos => examples/demos}/sh2.face | 0
{demos => examples/demos}/sh2.pdb | 0
{demos => examples/demos}/sh2.vert | 0
{demos => examples/demos}/test_trj_blur.py | 3 ++-
{demos => examples/demos}/the_hammer.py | 0
133 files changed, 11 insertions(+), 8 deletions(-)
rename {code_fragments => examples/code_fragments}/dokk/KEYS (100%)
rename {code_fragments => examples/code_fragments}/dokk/config.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/dengue/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/glyoxalase/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/hud.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/hudF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/retinol/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/thrombin/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_1/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/level.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/levelF.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/ligand.sdf (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/protein.pdb (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/surface.face (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/surface.vert (100%)
rename {code_fragments => examples/code_fragments}/dokk/datafiles/tutorial_2/top_ten.ini (100%)
rename {code_fragments => examples/code_fragments}/dokk/dokk (100%)
rename {code_fragments => examples/code_fragments}/dokk/dokk.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/glwin.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/hud.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/images/openstructure.png (100%)
rename {code_fragments => examples/code_fragments}/dokk/images/rotation.png (100%)
rename {code_fragments => examples/code_fragments}/dokk/images/translation.png (100%)
rename {code_fragments => examples/code_fragments}/dokk/level.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/level_info.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/level_intro.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/level_messages.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/ligand.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/name_enter.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/protein.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/score_updater.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/spacenav_connect.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/spnav_input.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/start_dokk.py (100%)
rename {code_fragments => examples/code_fragments}/dokk/surface.py (100%)
rename {code_fragments => examples/code_fragments}/entity/color_by_property.py (100%)
rename {code_fragments => examples/code_fragments}/entity/fragment.pdb (100%)
rename {code_fragments => examples/code_fragments}/entity/fragment2.pdb (100%)
rename {code_fragments => examples/code_fragments}/entity/gfx_selection.py (100%)
rename {code_fragments => examples/code_fragments}/entity/gfx_symmetry.py (91%)
rename {code_fragments => examples/code_fragments}/entity/gradient.py (100%)
rename {code_fragments => examples/code_fragments}/entity/pdb1ake.ent (100%)
rename {code_fragments => examples/code_fragments}/entity/pdb4ake.ent (100%)
rename {code_fragments => examples/code_fragments}/entity/primitives.py (100%)
rename {code_fragments => examples/code_fragments}/entity/random_lines.py (100%)
rename {code_fragments => examples/code_fragments}/entity/sdh.pdb (100%)
rename {code_fragments => examples/code_fragments}/entity/superpose.py (100%)
rename {code_fragments => examples/code_fragments}/harmony/glwin.py (100%)
rename {code_fragments => examples/code_fragments}/harmony/harmony (100%)
rename {code_fragments => examples/code_fragments}/harmony/harmony.py (100%)
rename {code_fragments => examples/code_fragments}/img/circle.png (100%)
rename {code_fragments => examples/code_fragments}/img/create_split_image.py (100%)
rename {code_fragments => examples/code_fragments}/img/fft_li.py (100%)
rename {code_fragments => examples/code_fragments}/img/modulate_image.py (100%)
rename {code_fragments => examples/code_fragments}/img/spoke_pattern.py (100%)
rename {code_fragments => examples/code_fragments}/img/square.png (100%)
rename {code_fragments => examples/code_fragments}/img/tone1.png (100%)
rename {code_fragments => examples/code_fragments}/img/tone2.png (100%)
rename {code_fragments => examples/code_fragments}/img/tone3.png (100%)
rename {code_fragments => examples/code_fragments}/img/tone4.png (100%)
rename {code_fragments => examples/code_fragments}/img/tone5.png (100%)
rename {code_fragments => examples/code_fragments}/img/view_phase_diff.py (100%)
rename {code_fragments => examples/code_fragments}/map/1ppt.map (100%)
rename {code_fragments => examples/code_fragments}/map/1ppt.pdb (100%)
rename {code_fragments => examples/code_fragments}/map/gfx_mapiso.py (100%)
rename {code_fragments => examples/code_fragments}/misc/bitmap_export.py (100%)
rename {code_fragments => examples/code_fragments}/misc/export_pov.py (100%)
rename {code_fragments => examples/code_fragments}/misc/fragment.face (100%)
rename {code_fragments => examples/code_fragments}/misc/fragment.pdb (100%)
rename {code_fragments => examples/code_fragments}/misc/fragment.vert (100%)
rename {code_fragments => examples/code_fragments}/modelling/roll_helix.py (100%)
rename {code_fragments => examples/code_fragments}/modelling/sdh.pdb (100%)
rename {code_fragments => examples/code_fragments}/modelling/strip_sidechains.py (100%)
rename {code_fragments => examples/code_fragments}/seq/seq_viewer.py (100%)
rename {code_fragments => examples/code_fragments}/surf/fragment.pdb (100%)
rename {code_fragments => examples/code_fragments}/surf/sdh.face (100%)
rename {code_fragments => examples/code_fragments}/surf/sdh.pdb (100%)
rename {code_fragments => examples/code_fragments}/surf/sdh.vert (100%)
rename {code_fragments => examples/code_fragments}/surf/test_surf.py (100%)
rename {code_fragments => examples/code_fragments}/surf/test_surf_pov.py (100%)
rename {code_fragments => examples/code_fragments}/trj/fragment.pdb (100%)
rename {code_fragments => examples/code_fragments}/trj/mpor_trj.crd (100%)
rename {code_fragments => examples/code_fragments}/trj/mpor_trj_short.trj (100%)
rename {code_fragments => examples/code_fragments}/trj/test_trj.py (100%)
rename {code_fragments => examples/code_fragments}/ui/board.py (100%)
rename {code_fragments => examples/code_fragments}/ui/color_tool.py (100%)
rename {code_fragments => examples/code_fragments}/ui/mdi_example.py (100%)
rename {code_fragments => examples/code_fragments}/ui/menubar_example.py (100%)
rename {code_fragments => examples/code_fragments}/ui/widget_example.py (100%)
rename {demos => examples/demos}/bbox.py (78%)
rename {demos => examples/demos}/conservation.py (93%)
rename {demos => examples/demos}/gfx_mapslab.py (100%)
rename {demos => examples/demos}/load_and_display.py (91%)
rename {demos => examples/demos}/rendermodes.py (98%)
rename {demos => examples/demos}/sample.dcd (100%)
rename {demos => examples/demos}/sample.pdb (100%)
rename {demos => examples/demos}/sdh.pdb (100%)
rename {demos => examples/demos}/sh2.aln (100%)
rename {demos => examples/demos}/sh2.face (100%)
rename {demos => examples/demos}/sh2.pdb (100%)
rename {demos => examples/demos}/sh2.vert (100%)
rename {demos => examples/demos}/test_trj_blur.py (93%)
rename {demos => examples/demos}/the_hammer.py (100%)
diff --git a/code_fragments/dokk/KEYS b/examples/code_fragments/dokk/KEYS
similarity index 100%
rename from code_fragments/dokk/KEYS
rename to examples/code_fragments/dokk/KEYS
diff --git a/code_fragments/dokk/config.py b/examples/code_fragments/dokk/config.py
similarity index 100%
rename from code_fragments/dokk/config.py
rename to examples/code_fragments/dokk/config.py
diff --git a/code_fragments/dokk/datafiles/dengue/level.ini b/examples/code_fragments/dokk/datafiles/dengue/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/level.ini
rename to examples/code_fragments/dokk/datafiles/dengue/level.ini
diff --git a/code_fragments/dokk/datafiles/dengue/levelF.ini b/examples/code_fragments/dokk/datafiles/dengue/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/levelF.ini
rename to examples/code_fragments/dokk/datafiles/dengue/levelF.ini
diff --git a/code_fragments/dokk/datafiles/dengue/ligand.sdf b/examples/code_fragments/dokk/datafiles/dengue/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/dengue/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/dengue/protein.pdb b/examples/code_fragments/dokk/datafiles/dengue/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/protein.pdb
rename to examples/code_fragments/dokk/datafiles/dengue/protein.pdb
diff --git a/code_fragments/dokk/datafiles/dengue/surface.face b/examples/code_fragments/dokk/datafiles/dengue/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/surface.face
rename to examples/code_fragments/dokk/datafiles/dengue/surface.face
diff --git a/code_fragments/dokk/datafiles/dengue/surface.vert b/examples/code_fragments/dokk/datafiles/dengue/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/surface.vert
rename to examples/code_fragments/dokk/datafiles/dengue/surface.vert
diff --git a/code_fragments/dokk/datafiles/dengue/top_ten.ini b/examples/code_fragments/dokk/datafiles/dengue/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/dengue/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/dengue/top_ten.ini
diff --git a/code_fragments/dokk/datafiles/glyoxalase/level.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/level.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/level.ini
diff --git a/code_fragments/dokk/datafiles/glyoxalase/levelF.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/levelF.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/levelF.ini
diff --git a/code_fragments/dokk/datafiles/glyoxalase/ligand.sdf b/examples/code_fragments/dokk/datafiles/glyoxalase/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/glyoxalase/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/glyoxalase/protein.pdb b/examples/code_fragments/dokk/datafiles/glyoxalase/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/protein.pdb
rename to examples/code_fragments/dokk/datafiles/glyoxalase/protein.pdb
diff --git a/code_fragments/dokk/datafiles/glyoxalase/surface.face b/examples/code_fragments/dokk/datafiles/glyoxalase/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/surface.face
rename to examples/code_fragments/dokk/datafiles/glyoxalase/surface.face
diff --git a/code_fragments/dokk/datafiles/glyoxalase/surface.vert b/examples/code_fragments/dokk/datafiles/glyoxalase/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/surface.vert
rename to examples/code_fragments/dokk/datafiles/glyoxalase/surface.vert
diff --git a/code_fragments/dokk/datafiles/glyoxalase/top_ten.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/glyoxalase/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/top_ten.ini
diff --git a/code_fragments/dokk/datafiles/hud.ini b/examples/code_fragments/dokk/datafiles/hud.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/hud.ini
rename to examples/code_fragments/dokk/datafiles/hud.ini
diff --git a/code_fragments/dokk/datafiles/hudF.ini b/examples/code_fragments/dokk/datafiles/hudF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/hudF.ini
rename to examples/code_fragments/dokk/datafiles/hudF.ini
diff --git a/code_fragments/dokk/datafiles/retinol/level.ini b/examples/code_fragments/dokk/datafiles/retinol/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/level.ini
rename to examples/code_fragments/dokk/datafiles/retinol/level.ini
diff --git a/code_fragments/dokk/datafiles/retinol/levelF.ini b/examples/code_fragments/dokk/datafiles/retinol/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/levelF.ini
rename to examples/code_fragments/dokk/datafiles/retinol/levelF.ini
diff --git a/code_fragments/dokk/datafiles/retinol/ligand.sdf b/examples/code_fragments/dokk/datafiles/retinol/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/retinol/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/retinol/protein.pdb b/examples/code_fragments/dokk/datafiles/retinol/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/protein.pdb
rename to examples/code_fragments/dokk/datafiles/retinol/protein.pdb
diff --git a/code_fragments/dokk/datafiles/retinol/surface.face b/examples/code_fragments/dokk/datafiles/retinol/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/surface.face
rename to examples/code_fragments/dokk/datafiles/retinol/surface.face
diff --git a/code_fragments/dokk/datafiles/retinol/surface.vert b/examples/code_fragments/dokk/datafiles/retinol/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/surface.vert
rename to examples/code_fragments/dokk/datafiles/retinol/surface.vert
diff --git a/code_fragments/dokk/datafiles/retinol/top_ten.ini b/examples/code_fragments/dokk/datafiles/retinol/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/retinol/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/retinol/top_ten.ini
diff --git a/code_fragments/dokk/datafiles/thrombin/level.ini b/examples/code_fragments/dokk/datafiles/thrombin/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/level.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/level.ini
diff --git a/code_fragments/dokk/datafiles/thrombin/levelF.ini b/examples/code_fragments/dokk/datafiles/thrombin/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/levelF.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/levelF.ini
diff --git a/code_fragments/dokk/datafiles/thrombin/ligand.sdf b/examples/code_fragments/dokk/datafiles/thrombin/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/thrombin/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/thrombin/protein.pdb b/examples/code_fragments/dokk/datafiles/thrombin/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/protein.pdb
rename to examples/code_fragments/dokk/datafiles/thrombin/protein.pdb
diff --git a/code_fragments/dokk/datafiles/thrombin/surface.face b/examples/code_fragments/dokk/datafiles/thrombin/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/surface.face
rename to examples/code_fragments/dokk/datafiles/thrombin/surface.face
diff --git a/code_fragments/dokk/datafiles/thrombin/surface.vert b/examples/code_fragments/dokk/datafiles/thrombin/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/surface.vert
rename to examples/code_fragments/dokk/datafiles/thrombin/surface.vert
diff --git a/code_fragments/dokk/datafiles/thrombin/top_ten.ini b/examples/code_fragments/dokk/datafiles/thrombin/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/thrombin/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/top_ten.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_1/level.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/level.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/level.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_1/levelF.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/levelF.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/levelF.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_1/ligand.sdf b/examples/code_fragments/dokk/datafiles/tutorial_1/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/tutorial_1/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/tutorial_1/protein.pdb b/examples/code_fragments/dokk/datafiles/tutorial_1/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/protein.pdb
rename to examples/code_fragments/dokk/datafiles/tutorial_1/protein.pdb
diff --git a/code_fragments/dokk/datafiles/tutorial_1/surface.face b/examples/code_fragments/dokk/datafiles/tutorial_1/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/surface.face
rename to examples/code_fragments/dokk/datafiles/tutorial_1/surface.face
diff --git a/code_fragments/dokk/datafiles/tutorial_1/surface.vert b/examples/code_fragments/dokk/datafiles/tutorial_1/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/surface.vert
rename to examples/code_fragments/dokk/datafiles/tutorial_1/surface.vert
diff --git a/code_fragments/dokk/datafiles/tutorial_1/top_ten.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_1/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/top_ten.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_2/level.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/level.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/level.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/level.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_2/levelF.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/levelF.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/levelF.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/levelF.ini
diff --git a/code_fragments/dokk/datafiles/tutorial_2/ligand.sdf b/examples/code_fragments/dokk/datafiles/tutorial_2/ligand.sdf
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/tutorial_2/ligand.sdf
diff --git a/code_fragments/dokk/datafiles/tutorial_2/protein.pdb b/examples/code_fragments/dokk/datafiles/tutorial_2/protein.pdb
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/protein.pdb
rename to examples/code_fragments/dokk/datafiles/tutorial_2/protein.pdb
diff --git a/code_fragments/dokk/datafiles/tutorial_2/surface.face b/examples/code_fragments/dokk/datafiles/tutorial_2/surface.face
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/surface.face
rename to examples/code_fragments/dokk/datafiles/tutorial_2/surface.face
diff --git a/code_fragments/dokk/datafiles/tutorial_2/surface.vert b/examples/code_fragments/dokk/datafiles/tutorial_2/surface.vert
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/surface.vert
rename to examples/code_fragments/dokk/datafiles/tutorial_2/surface.vert
diff --git a/code_fragments/dokk/datafiles/tutorial_2/top_ten.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/top_ten.ini
similarity index 100%
rename from code_fragments/dokk/datafiles/tutorial_2/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/top_ten.ini
diff --git a/code_fragments/dokk/dokk b/examples/code_fragments/dokk/dokk
similarity index 100%
rename from code_fragments/dokk/dokk
rename to examples/code_fragments/dokk/dokk
diff --git a/code_fragments/dokk/dokk.py b/examples/code_fragments/dokk/dokk.py
similarity index 100%
rename from code_fragments/dokk/dokk.py
rename to examples/code_fragments/dokk/dokk.py
diff --git a/code_fragments/dokk/glwin.py b/examples/code_fragments/dokk/glwin.py
similarity index 100%
rename from code_fragments/dokk/glwin.py
rename to examples/code_fragments/dokk/glwin.py
diff --git a/code_fragments/dokk/hud.py b/examples/code_fragments/dokk/hud.py
similarity index 100%
rename from code_fragments/dokk/hud.py
rename to examples/code_fragments/dokk/hud.py
diff --git a/code_fragments/dokk/images/openstructure.png b/examples/code_fragments/dokk/images/openstructure.png
similarity index 100%
rename from code_fragments/dokk/images/openstructure.png
rename to examples/code_fragments/dokk/images/openstructure.png
diff --git a/code_fragments/dokk/images/rotation.png b/examples/code_fragments/dokk/images/rotation.png
similarity index 100%
rename from code_fragments/dokk/images/rotation.png
rename to examples/code_fragments/dokk/images/rotation.png
diff --git a/code_fragments/dokk/images/translation.png b/examples/code_fragments/dokk/images/translation.png
similarity index 100%
rename from code_fragments/dokk/images/translation.png
rename to examples/code_fragments/dokk/images/translation.png
diff --git a/code_fragments/dokk/level.py b/examples/code_fragments/dokk/level.py
similarity index 100%
rename from code_fragments/dokk/level.py
rename to examples/code_fragments/dokk/level.py
diff --git a/code_fragments/dokk/level_info.py b/examples/code_fragments/dokk/level_info.py
similarity index 100%
rename from code_fragments/dokk/level_info.py
rename to examples/code_fragments/dokk/level_info.py
diff --git a/code_fragments/dokk/level_intro.py b/examples/code_fragments/dokk/level_intro.py
similarity index 100%
rename from code_fragments/dokk/level_intro.py
rename to examples/code_fragments/dokk/level_intro.py
diff --git a/code_fragments/dokk/level_messages.py b/examples/code_fragments/dokk/level_messages.py
similarity index 100%
rename from code_fragments/dokk/level_messages.py
rename to examples/code_fragments/dokk/level_messages.py
diff --git a/code_fragments/dokk/ligand.py b/examples/code_fragments/dokk/ligand.py
similarity index 100%
rename from code_fragments/dokk/ligand.py
rename to examples/code_fragments/dokk/ligand.py
diff --git a/code_fragments/dokk/name_enter.py b/examples/code_fragments/dokk/name_enter.py
similarity index 100%
rename from code_fragments/dokk/name_enter.py
rename to examples/code_fragments/dokk/name_enter.py
diff --git a/code_fragments/dokk/protein.py b/examples/code_fragments/dokk/protein.py
similarity index 100%
rename from code_fragments/dokk/protein.py
rename to examples/code_fragments/dokk/protein.py
diff --git a/code_fragments/dokk/score_updater.py b/examples/code_fragments/dokk/score_updater.py
similarity index 100%
rename from code_fragments/dokk/score_updater.py
rename to examples/code_fragments/dokk/score_updater.py
diff --git a/code_fragments/dokk/spacenav_connect.py b/examples/code_fragments/dokk/spacenav_connect.py
similarity index 100%
rename from code_fragments/dokk/spacenav_connect.py
rename to examples/code_fragments/dokk/spacenav_connect.py
diff --git a/code_fragments/dokk/spnav_input.py b/examples/code_fragments/dokk/spnav_input.py
similarity index 100%
rename from code_fragments/dokk/spnav_input.py
rename to examples/code_fragments/dokk/spnav_input.py
diff --git a/code_fragments/dokk/start_dokk.py b/examples/code_fragments/dokk/start_dokk.py
similarity index 100%
rename from code_fragments/dokk/start_dokk.py
rename to examples/code_fragments/dokk/start_dokk.py
diff --git a/code_fragments/dokk/surface.py b/examples/code_fragments/dokk/surface.py
similarity index 100%
rename from code_fragments/dokk/surface.py
rename to examples/code_fragments/dokk/surface.py
diff --git a/code_fragments/entity/color_by_property.py b/examples/code_fragments/entity/color_by_property.py
similarity index 100%
rename from code_fragments/entity/color_by_property.py
rename to examples/code_fragments/entity/color_by_property.py
diff --git a/code_fragments/entity/fragment.pdb b/examples/code_fragments/entity/fragment.pdb
similarity index 100%
rename from code_fragments/entity/fragment.pdb
rename to examples/code_fragments/entity/fragment.pdb
diff --git a/code_fragments/entity/fragment2.pdb b/examples/code_fragments/entity/fragment2.pdb
similarity index 100%
rename from code_fragments/entity/fragment2.pdb
rename to examples/code_fragments/entity/fragment2.pdb
diff --git a/code_fragments/entity/gfx_selection.py b/examples/code_fragments/entity/gfx_selection.py
similarity index 100%
rename from code_fragments/entity/gfx_selection.py
rename to examples/code_fragments/entity/gfx_selection.py
diff --git a/code_fragments/entity/gfx_symmetry.py b/examples/code_fragments/entity/gfx_symmetry.py
similarity index 91%
rename from code_fragments/entity/gfx_symmetry.py
rename to examples/code_fragments/entity/gfx_symmetry.py
index bfef9fb1b..a0d795ece 100644
--- a/code_fragments/entity/gfx_symmetry.py
+++ b/examples/code_fragments/entity/gfx_symmetry.py
@@ -8,7 +8,7 @@ ent=io.LoadEntity(filename)
edi=ent.RequestXCSEditor()
m=geom.Mat4()
-m.PasteTranslation(-ent.bounds.min)
+m.PasteTranslation(-ent.GetGeometricStart())
edi.ApplyTransform(m)
edi.UpdateICS()
frag=gfx.Entity('frag', ent)
diff --git a/code_fragments/entity/gradient.py b/examples/code_fragments/entity/gradient.py
similarity index 100%
rename from code_fragments/entity/gradient.py
rename to examples/code_fragments/entity/gradient.py
diff --git a/code_fragments/entity/pdb1ake.ent b/examples/code_fragments/entity/pdb1ake.ent
similarity index 100%
rename from code_fragments/entity/pdb1ake.ent
rename to examples/code_fragments/entity/pdb1ake.ent
diff --git a/code_fragments/entity/pdb4ake.ent b/examples/code_fragments/entity/pdb4ake.ent
similarity index 100%
rename from code_fragments/entity/pdb4ake.ent
rename to examples/code_fragments/entity/pdb4ake.ent
diff --git a/code_fragments/entity/primitives.py b/examples/code_fragments/entity/primitives.py
similarity index 100%
rename from code_fragments/entity/primitives.py
rename to examples/code_fragments/entity/primitives.py
diff --git a/code_fragments/entity/random_lines.py b/examples/code_fragments/entity/random_lines.py
similarity index 100%
rename from code_fragments/entity/random_lines.py
rename to examples/code_fragments/entity/random_lines.py
diff --git a/code_fragments/entity/sdh.pdb b/examples/code_fragments/entity/sdh.pdb
similarity index 100%
rename from code_fragments/entity/sdh.pdb
rename to examples/code_fragments/entity/sdh.pdb
diff --git a/code_fragments/entity/superpose.py b/examples/code_fragments/entity/superpose.py
similarity index 100%
rename from code_fragments/entity/superpose.py
rename to examples/code_fragments/entity/superpose.py
diff --git a/code_fragments/harmony/glwin.py b/examples/code_fragments/harmony/glwin.py
similarity index 100%
rename from code_fragments/harmony/glwin.py
rename to examples/code_fragments/harmony/glwin.py
diff --git a/code_fragments/harmony/harmony b/examples/code_fragments/harmony/harmony
similarity index 100%
rename from code_fragments/harmony/harmony
rename to examples/code_fragments/harmony/harmony
diff --git a/code_fragments/harmony/harmony.py b/examples/code_fragments/harmony/harmony.py
similarity index 100%
rename from code_fragments/harmony/harmony.py
rename to examples/code_fragments/harmony/harmony.py
diff --git a/code_fragments/img/circle.png b/examples/code_fragments/img/circle.png
similarity index 100%
rename from code_fragments/img/circle.png
rename to examples/code_fragments/img/circle.png
diff --git a/code_fragments/img/create_split_image.py b/examples/code_fragments/img/create_split_image.py
similarity index 100%
rename from code_fragments/img/create_split_image.py
rename to examples/code_fragments/img/create_split_image.py
diff --git a/code_fragments/img/fft_li.py b/examples/code_fragments/img/fft_li.py
similarity index 100%
rename from code_fragments/img/fft_li.py
rename to examples/code_fragments/img/fft_li.py
diff --git a/code_fragments/img/modulate_image.py b/examples/code_fragments/img/modulate_image.py
similarity index 100%
rename from code_fragments/img/modulate_image.py
rename to examples/code_fragments/img/modulate_image.py
diff --git a/code_fragments/img/spoke_pattern.py b/examples/code_fragments/img/spoke_pattern.py
similarity index 100%
rename from code_fragments/img/spoke_pattern.py
rename to examples/code_fragments/img/spoke_pattern.py
diff --git a/code_fragments/img/square.png b/examples/code_fragments/img/square.png
similarity index 100%
rename from code_fragments/img/square.png
rename to examples/code_fragments/img/square.png
diff --git a/code_fragments/img/tone1.png b/examples/code_fragments/img/tone1.png
similarity index 100%
rename from code_fragments/img/tone1.png
rename to examples/code_fragments/img/tone1.png
diff --git a/code_fragments/img/tone2.png b/examples/code_fragments/img/tone2.png
similarity index 100%
rename from code_fragments/img/tone2.png
rename to examples/code_fragments/img/tone2.png
diff --git a/code_fragments/img/tone3.png b/examples/code_fragments/img/tone3.png
similarity index 100%
rename from code_fragments/img/tone3.png
rename to examples/code_fragments/img/tone3.png
diff --git a/code_fragments/img/tone4.png b/examples/code_fragments/img/tone4.png
similarity index 100%
rename from code_fragments/img/tone4.png
rename to examples/code_fragments/img/tone4.png
diff --git a/code_fragments/img/tone5.png b/examples/code_fragments/img/tone5.png
similarity index 100%
rename from code_fragments/img/tone5.png
rename to examples/code_fragments/img/tone5.png
diff --git a/code_fragments/img/view_phase_diff.py b/examples/code_fragments/img/view_phase_diff.py
similarity index 100%
rename from code_fragments/img/view_phase_diff.py
rename to examples/code_fragments/img/view_phase_diff.py
diff --git a/code_fragments/map/1ppt.map b/examples/code_fragments/map/1ppt.map
similarity index 100%
rename from code_fragments/map/1ppt.map
rename to examples/code_fragments/map/1ppt.map
diff --git a/code_fragments/map/1ppt.pdb b/examples/code_fragments/map/1ppt.pdb
similarity index 100%
rename from code_fragments/map/1ppt.pdb
rename to examples/code_fragments/map/1ppt.pdb
diff --git a/code_fragments/map/gfx_mapiso.py b/examples/code_fragments/map/gfx_mapiso.py
similarity index 100%
rename from code_fragments/map/gfx_mapiso.py
rename to examples/code_fragments/map/gfx_mapiso.py
diff --git a/code_fragments/misc/bitmap_export.py b/examples/code_fragments/misc/bitmap_export.py
similarity index 100%
rename from code_fragments/misc/bitmap_export.py
rename to examples/code_fragments/misc/bitmap_export.py
diff --git a/code_fragments/misc/export_pov.py b/examples/code_fragments/misc/export_pov.py
similarity index 100%
rename from code_fragments/misc/export_pov.py
rename to examples/code_fragments/misc/export_pov.py
diff --git a/code_fragments/misc/fragment.face b/examples/code_fragments/misc/fragment.face
similarity index 100%
rename from code_fragments/misc/fragment.face
rename to examples/code_fragments/misc/fragment.face
diff --git a/code_fragments/misc/fragment.pdb b/examples/code_fragments/misc/fragment.pdb
similarity index 100%
rename from code_fragments/misc/fragment.pdb
rename to examples/code_fragments/misc/fragment.pdb
diff --git a/code_fragments/misc/fragment.vert b/examples/code_fragments/misc/fragment.vert
similarity index 100%
rename from code_fragments/misc/fragment.vert
rename to examples/code_fragments/misc/fragment.vert
diff --git a/code_fragments/modelling/roll_helix.py b/examples/code_fragments/modelling/roll_helix.py
similarity index 100%
rename from code_fragments/modelling/roll_helix.py
rename to examples/code_fragments/modelling/roll_helix.py
diff --git a/code_fragments/modelling/sdh.pdb b/examples/code_fragments/modelling/sdh.pdb
similarity index 100%
rename from code_fragments/modelling/sdh.pdb
rename to examples/code_fragments/modelling/sdh.pdb
diff --git a/code_fragments/modelling/strip_sidechains.py b/examples/code_fragments/modelling/strip_sidechains.py
similarity index 100%
rename from code_fragments/modelling/strip_sidechains.py
rename to examples/code_fragments/modelling/strip_sidechains.py
diff --git a/code_fragments/seq/seq_viewer.py b/examples/code_fragments/seq/seq_viewer.py
similarity index 100%
rename from code_fragments/seq/seq_viewer.py
rename to examples/code_fragments/seq/seq_viewer.py
diff --git a/code_fragments/surf/fragment.pdb b/examples/code_fragments/surf/fragment.pdb
similarity index 100%
rename from code_fragments/surf/fragment.pdb
rename to examples/code_fragments/surf/fragment.pdb
diff --git a/code_fragments/surf/sdh.face b/examples/code_fragments/surf/sdh.face
similarity index 100%
rename from code_fragments/surf/sdh.face
rename to examples/code_fragments/surf/sdh.face
diff --git a/code_fragments/surf/sdh.pdb b/examples/code_fragments/surf/sdh.pdb
similarity index 100%
rename from code_fragments/surf/sdh.pdb
rename to examples/code_fragments/surf/sdh.pdb
diff --git a/code_fragments/surf/sdh.vert b/examples/code_fragments/surf/sdh.vert
similarity index 100%
rename from code_fragments/surf/sdh.vert
rename to examples/code_fragments/surf/sdh.vert
diff --git a/code_fragments/surf/test_surf.py b/examples/code_fragments/surf/test_surf.py
similarity index 100%
rename from code_fragments/surf/test_surf.py
rename to examples/code_fragments/surf/test_surf.py
diff --git a/code_fragments/surf/test_surf_pov.py b/examples/code_fragments/surf/test_surf_pov.py
similarity index 100%
rename from code_fragments/surf/test_surf_pov.py
rename to examples/code_fragments/surf/test_surf_pov.py
diff --git a/code_fragments/trj/fragment.pdb b/examples/code_fragments/trj/fragment.pdb
similarity index 100%
rename from code_fragments/trj/fragment.pdb
rename to examples/code_fragments/trj/fragment.pdb
diff --git a/code_fragments/trj/mpor_trj.crd b/examples/code_fragments/trj/mpor_trj.crd
similarity index 100%
rename from code_fragments/trj/mpor_trj.crd
rename to examples/code_fragments/trj/mpor_trj.crd
diff --git a/code_fragments/trj/mpor_trj_short.trj b/examples/code_fragments/trj/mpor_trj_short.trj
similarity index 100%
rename from code_fragments/trj/mpor_trj_short.trj
rename to examples/code_fragments/trj/mpor_trj_short.trj
diff --git a/code_fragments/trj/test_trj.py b/examples/code_fragments/trj/test_trj.py
similarity index 100%
rename from code_fragments/trj/test_trj.py
rename to examples/code_fragments/trj/test_trj.py
diff --git a/code_fragments/ui/board.py b/examples/code_fragments/ui/board.py
similarity index 100%
rename from code_fragments/ui/board.py
rename to examples/code_fragments/ui/board.py
diff --git a/code_fragments/ui/color_tool.py b/examples/code_fragments/ui/color_tool.py
similarity index 100%
rename from code_fragments/ui/color_tool.py
rename to examples/code_fragments/ui/color_tool.py
diff --git a/code_fragments/ui/mdi_example.py b/examples/code_fragments/ui/mdi_example.py
similarity index 100%
rename from code_fragments/ui/mdi_example.py
rename to examples/code_fragments/ui/mdi_example.py
diff --git a/code_fragments/ui/menubar_example.py b/examples/code_fragments/ui/menubar_example.py
similarity index 100%
rename from code_fragments/ui/menubar_example.py
rename to examples/code_fragments/ui/menubar_example.py
diff --git a/code_fragments/ui/widget_example.py b/examples/code_fragments/ui/widget_example.py
similarity index 100%
rename from code_fragments/ui/widget_example.py
rename to examples/code_fragments/ui/widget_example.py
diff --git a/demos/bbox.py b/examples/demos/bbox.py
similarity index 78%
rename from demos/bbox.py
rename to examples/demos/bbox.py
index 242ba49b1..ea49aef60 100644
--- a/demos/bbox.py
+++ b/examples/demos/bbox.py
@@ -1,4 +1,4 @@
-sdh=io.LoadPDB('sdh.pdb')
+sdh=io.LoadPDB('data/sdh.pdb')
helix=sdh.Select('rnum=99:128 and cname=A and aname=CA,C,N,O')
go=gfx.Entity('helix', gfx.SIMPLE, helix)
scene.Add(go)
@@ -10,6 +10,8 @@ def RenderBBox(bbox):
bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
scene.Add(bb)
+print 'Center:',(helix.GetGeometricStart()+helix.GetGeometricEnd())*.5
+
RenderBBox(bbox)
scene.center=go.center
print 'Demo2: Translucent bounding box around an OpenStructure entity'
diff --git a/demos/conservation.py b/examples/demos/conservation.py
similarity index 93%
rename from demos/conservation.py
rename to examples/demos/conservation.py
index 8399ef05b..fa1e2a6cb 100644
--- a/demos/conservation.py
+++ b/examples/demos/conservation.py
@@ -2,9 +2,9 @@ from ost.seq import alg
#-------------------------------------------------------------------------------
# Loading structure and alignment
#-------------------------------------------------------------------------------
-m=io.LoadPDB('sh2.pdb')
+m=io.LoadPDB('data/sh2.pdb')
mp=m.Select('ishetatm=false')
-aln=io.LoadAlignment('sh2.aln')
+aln=io.LoadAlignment('data/sh2.aln')
aln.AttachView(0, mp)
#-------------------------------------------------------------------------------
# Calculate conservation of alignment
@@ -16,7 +16,7 @@ alg.Conservation(aln)
# Setup Graphical Objects for Rendering
#-------------------------------------------------------------------------------
g=gfx.Entity('SH2', m)
-s=io.LoadSurface('sh2.vert')
+s=io.LoadSurface('data/sh2.vert')
gs=gfx.Surface('SH2-surf', s)
scene.Add(gs)
scene.Add(g)
diff --git a/demos/gfx_mapslab.py b/examples/demos/gfx_mapslab.py
similarity index 100%
rename from demos/gfx_mapslab.py
rename to examples/demos/gfx_mapslab.py
diff --git a/demos/load_and_display.py b/examples/demos/load_and_display.py
similarity index 91%
rename from demos/load_and_display.py
rename to examples/demos/load_and_display.py
index 382197ea7..94ec016e2 100644
--- a/demos/load_and_display.py
+++ b/examples/demos/load_and_display.py
@@ -1,5 +1,5 @@
# Load chain A of SDH
-ent=io.LoadPDB('sdh.pdb', restrict_chains='A')
+ent=io.LoadPDB('data/sdh.pdb', restrict_chains='A')
# create graphics object
go=gfx.Entity('SDH', ent)
diff --git a/demos/rendermodes.py b/examples/demos/rendermodes.py
similarity index 98%
rename from demos/rendermodes.py
rename to examples/demos/rendermodes.py
index b45cd500c..0c5077b01 100644
--- a/demos/rendermodes.py
+++ b/examples/demos/rendermodes.py
@@ -1,5 +1,5 @@
# load pdb file
-eh=io.LoadEntity("sdh.pdb")
+eh=io.LoadEntity("data/sdh.pdb")
sdh_go=gfx.Entity("SDH2", eh.Select("cname=A"))
diff --git a/demos/sample.dcd b/examples/demos/sample.dcd
similarity index 100%
rename from demos/sample.dcd
rename to examples/demos/sample.dcd
diff --git a/demos/sample.pdb b/examples/demos/sample.pdb
similarity index 100%
rename from demos/sample.pdb
rename to examples/demos/sample.pdb
diff --git a/demos/sdh.pdb b/examples/demos/sdh.pdb
similarity index 100%
rename from demos/sdh.pdb
rename to examples/demos/sdh.pdb
diff --git a/demos/sh2.aln b/examples/demos/sh2.aln
similarity index 100%
rename from demos/sh2.aln
rename to examples/demos/sh2.aln
diff --git a/demos/sh2.face b/examples/demos/sh2.face
similarity index 100%
rename from demos/sh2.face
rename to examples/demos/sh2.face
diff --git a/demos/sh2.pdb b/examples/demos/sh2.pdb
similarity index 100%
rename from demos/sh2.pdb
rename to examples/demos/sh2.pdb
diff --git a/demos/sh2.vert b/examples/demos/sh2.vert
similarity index 100%
rename from demos/sh2.vert
rename to examples/demos/sh2.vert
diff --git a/demos/test_trj_blur.py b/examples/demos/test_trj_blur.py
similarity index 93%
rename from demos/test_trj_blur.py
rename to examples/demos/test_trj_blur.py
index eedba6bb3..4619374a7 100644
--- a/demos/test_trj_blur.py
+++ b/examples/demos/test_trj_blur.py
@@ -18,7 +18,7 @@ class Anim(QtCore.QTimer):
self.cg_.CopyFrame(self.frame_)
go.UpdatePositions()
-cg = io.LoadCHARMMTraj("sample.pdb","sample.dcd")
+cg = io.LoadCHARMMTraj("data/sample.pdb","data/sample.dcd")
eh=cg.GetEntity()
ev=eh.Select("not ele=H")
go=gfx.Entity("mol",gfx.SIMPLE, ev)
@@ -29,5 +29,6 @@ scene.SetCenter(go.GetCenter())
scene.AutoAutoslab(True)
anim=Anim(cg,go)
+
print 'Demo 6: Import of a CHARMM trajectory. Type anim.stop() to halt animation, anim.start(100) to start it again with stepsize 100!Starting animation now....'
anim.start(50)
diff --git a/demos/the_hammer.py b/examples/demos/the_hammer.py
similarity index 100%
rename from demos/the_hammer.py
rename to examples/demos/the_hammer.py
--
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