Game Engine

[MonZop]

BipoBlender is supposed to use the Blender GE to calculate the transitiono fo a molecule from one conformation to another. However, as soon as the 'Run In GE' button is hit, Blender crashes

[zeffii]

there's an import error, in 2.73,

Blender Game Engine Started
Python module can't be imported - object 'Empty', controller 'Python Script':
ImportError: No module named 'BioBlender2'
Blender Game Engine Finished

but it doesn't crash, pressing esc releases it

[zeffii]

in 2.73 using the branch (2.73_Comp_Explore) To my surprise the Game engine does run, but doesn't record anything (no cache) probably because of the failed import. I'll investigate.

[MonZop]

The recorded animation will be stored as keyframes (one KF for every atom, at each frame), starting 500 frames after the last imported model. Pls. pay attention that animation makes sense only with at least two different conformations of a protein. If you use file '01_CaM 3 conformations.pdb', and changed nothing in the import, you will have a KF at frame 1 (conformation= model 1), a KF at frame 100 (conf 2), and another one at frame 200. After recording the GE simulation, all frames between 500 and 800 will be keyframed.

[zeffii]

i'll add some update prints so it shows when a keyframe is added, else it is impossible to tell if it's actually performing useful work

[zeffii]

OK i see, those keyframes are inserted upon .pdb import if there are several conformations present in the file.

[MonZop]

Back to the GE issue: using 273_Comp animations are not recorded, even when the "Record animation" box is checked. Also it presents a set of options that make little sense to me.

[zeffii]

I've noticed this. this worked in 0.6 ? It will be the first thing I look at tomorrow (cross differential between older and newer version of addon)

[zeffii]

The dropdown options comes from this line

split.prop(bpy.context.scene.objects[str(m)].game, "physics_type") 

the options are generic to the physics type, from what I can tell:

http://www.blender.org/api/blender_python_api_2_73_5/bpy.types.GameObjectSettings.html?highlight=physics_type#bpy.types.GameObjectSettings.physics_type (produces the same list)

Perhaps it would be simpler to remove the options and set Rigid Body if the game engine is invoked.

[zeffii]

This however does not seem to be the reason for the GE to fail to do anything, it is an import issue as mentioned here: https://github.com/MonZop/BioBlender/issues/2#issuecomment-72259622

[MonZop]

Yes, if joints are not built, then the recording of GE is not done, as it is meaningless (in biological sense) As you say, Perhaps it would be simpler to remove the options and set Rigid Body if the game engine is invoked., I agree

[zeffii]

could you add a few simple molecules for the purpose of testing the GE , bones / joints ?

[MonZop]

OK, let me prepare a file with a very small protein in 4 conformations

[MonZop]

Done: you'll find it in the Test Molecules folder. It is a small artificial protein made of only 20 aminoacids, for a total of 158 atoms (excluding Hydrogens). The file contains 4 MODELS (conformations), but I noticed that BB2 only imports 3 of them. I also tried to import other proteins that have many conformations, but BB2 imports all models except the last one.

[MonZop]

Back to the Game Engine: In the master_main_first_fixes version of BB, bones are created (they are listed in the Outliner), but the GE is completely still. In the Blender console it says: Blender Game Engine Started Python module can't be imported - object 'Empty', controller 'Python Script': ImportError: No module named 'BioBlender2' Blender Game Engine Finished

[zeffii]

There's recent fixes to the BGE, today this: https://developer.blender.org/rBbf157ce9277ba1011a6e317c7629bab0dd8c36a5 it may relate to the problem.

@mikepan can probably make more sense of the BGE stuff (either the BioBlender Master, or the experiments branch)

[zeffii]

I renamed BioBlender2.py to BioBlender.py and edited the EmptySet.blend to link to BioBlender.recorder, and now the ImportError seems to go away.. Even if this isn't the solution, the naming seems to have caused a problem.

[zeffii]

it seems to be doing some thing..

[MonZop]

I also just tried, but I get an error: Blender Game Engine Started Python module can't be imported - object 'Empty', controller 'Python Script': ImportError: No module named 'BioBlender2' and no recording of motion

[MonZop]

But I am using an old portable, it might be not very updated. I'll check again when I gat back to the office in Pisa (thursday afernoon)

[zeffii]

I am using a latest Buildbot version, as it includes Game Engine fixes (which might be good to have anyway) I've pushed the change to the experimental branch.

further in the right place: https://github.com/MonZop/BioBlender/issues/9#issuecomment-74645953

this will get easier, not harder :)

[MonZop]

I have tested with several combinations, but nothing seems to worrk for me:

any clue?

[zeffii]

I think this happens if the Addon folder is not called BioBlender, which might be the case if you are using the zip. Yours might be called BioBlender-master , or one of the branches. Ideally the addon wouldn't care about the name of the folder inside which it lives.

[zeffii]

So if you are trying the version i'm experimenting with that folder would be called:

BioBlender-master_mff_experiments , but rename it to BioBlender

the content of this version should be:

If any other BioBlender addons are enabled / ticked other than this one untick them, save settings / Ctrl+U to store this preference. Restart Blender. When you navigate to the addons panel again, you can see where it's loading the addon from by viewing the dropdown:

[zeffii]

Now i said:

Ideally the addon wouldn't care about the name of the folder inside which it lives.

Most likely it can be made to be entirely agnostic about folder and file names, but that's a different problem (one I would like to solve soon)

[MonZop]

Oh, finally, I managed! :-)