Molecule import script

Coding Python Support
1

http://www.geocities.com/theeth/Molecule.html

The .blend is documented.

If you have any question/feature request, just ask.

cheers,
Martin

2

:smiley: Got it. :smiley:

3

New release, same URL.

I cleared three bugs regarding XYZ import

first, if the atom number is not included on the line and if the file name is inlcuded on the first line and third, some silly linefeed char that made an error when loading links. If the colors do not show at first, delete the results and reload (it’s a bug in the API). Be sure to delete the molecule between each import (it doesn’t always modify the old one).

thanks for reporting any errors you find, or even enhancing the code if you want (just tell me and post a version of the code when you’re done).

Martin
PS: I’m redoing PDB import. Even if it’s still include, it will only work in some case.

4

In the ImportMol.py:


import Molecule
import Blender
basename=Blender.Get('filename')
basedir=Blender.sys.dirname(basename)+Blender.sys.dirsep
FilePath = basedir+'cyclacene.xyz' # POINTS TO THE FILE YOU WANT TO IMPORT
....

jm

5

I would very much like to import PDB files into Blender. It appears that someone has written a python script (?) to import atomic xyz coords. Would you please direct me in the right direction.
Thanks in advance.

6

Whoa, that’s old! :o

I don’t really have time to dive in molecular import again, so if anyone is up for it, be my guest.

Martin

7

http://www.tb-software.business.t-online.de/format_info.html

http://www.tb-software.business.t-online.de/download.html

Might help

%<

8

Hey, yea I would be interested, at least in the code. But I think the link has a kink. can you repost? or should I email you?

Thanks
Squirrel

9

I looked everywhere and it seems like I don’t have it anymore. :frowning:

Maybe JMS kept it on his HD, maybe you can try asking him.

Martin

10

Is this one: http://www.zoo-logique.org/3D.Blender/scripts_python/snippets/ImportMolecule.zip

11

Yup, that’s the one. Thanks :slight_smile:

Martin

12

I don’t know how to write python scripts, but I appreciate the effort you have put forth to develop an import script for molecules.

There is a very powerful molecular modelling program based on python called PyMOL (pymol.sourceforge.net). It is an open source project. I imagine that since it is based on python and Blender seems to be very python friendly it maight not be too difficult (if you know someting about python) to integrate the two programs. I encourage you to check out the gallery page to see the impressive images that Pymol is capable of. One of the weaknesses of PyMOL is the ability to generate complex animations/movies of your molecules. This is where I think Blender would truely complement PyMOL.

It would be very cool if the types of 3D objects produced in PyMOL could be imported and then animated/rendered etc. in Blender.

Just some thoughts.

13

This is just the sort of thing I have been working on for the past 6 months. The one I am doing just does one “bead”, but it could be changed with out too much work.

Also, theeth and jms, I looked at the importMolecule files, and I have a question. There is a line in there that goes something like
Sphere = Blender.NMesh.GetRaw(“Sphere”)
Then the rest of the code functions as if Sphere contained an NMesh. There is also one that gets a Tube. Were primitives (Spheres, Cylinders, etc) accessible to python in earlier versions? Why aren’t they accessible now? (Or did I just miss something?)

Thanks
Squirrel

14

IIRC, the sphere and cylinder are on an invisible layer.

Martin