[Plugin] MoleculeImporter (1.3.3) – updated 8.10.2017

Aerilius · 6 May 2013, 14:55

The surface representation is probably much more complicated. SketchUp has only faces and edges as primitives and is thus not really appropriate for chemical/biological visualizations (that are more focussed on atom positions, angles and electon density). This plugin just places components of spheres (which is easy) but I have no idea how the surface representation is stored in pdb and how to generate smooth SketchUp geometry from it.

It is probably easier to let a molecule/protein modeler do the surface generation and then export it to faces/edges to do SketchUp stuff with it. I've seen for example pymol can export to vrml (SketchUp Pro) and obj (free SketchUp importer plugin).
http://www.pymolwiki.org/index.php/Surface

Andri · 31 May 2013, 22:59

@andri said:

@aerilius said:

@unknownuser said:

but I cant see that it is workning

Hi, can you tell me what is "not" working? Do you not see a menu item in the Plugins menu (and in File → Import), or do you see it, but when you import a specific file, it seems not to create a model?
The plugin supports SketchUp 8.0 (which is 2 years old, and didn't add/remove anything that easily breaks plugins). It could be that the plugin cannot yet handle every file of the .mol format, in that case, maybe you can send me the file (or a similar file).

Hi and thanks for your replay. I can not see the plugin in the menu (file - import) and when I open the possible types of import I can not see *.mol.

Hi again, I have been away. but now I realy need this going. I have know been able to set the plugin up corectly. I´m using ACD/chemsketch to build models and I export them as *.mol. But when I try to import them I can select the file and when i click ok nothing happens. just a blank screen.
Could I send you the file for try?? but I´m not allowed to put in *.mol file hear.

I realy need to solve this

Aerilius · 2 Jun 2013, 17:52

You can send the file if you put it in a zip file.

jeichholz · 4 Nov 2013, 05:04

Hi Aerilius,

Like Andri (perhaps) I cannot get the plugin to import an mol file-- nothing happens in the Sketchup window. This is for Sketchup 2013. Any solution since that last post?

Thanks John E.

ericschimel · 4 Dec 2014, 20:39

I am seeing the same thing right now on SketchUp 2013 and 2014. I've tried to import several different MOL files.

Is there possibly a bug here?

I am trying to 3D print some molecules and would love to be able to use this...

Aerilius · 5 Dec 2014, 12:33

The importer has been closely designed around the Symyx specification (2010) for Molfile V2000 and V3000 formats. It maybe possible that there is a bug, but I don't have any file that failed so far (would be good if someone who wants this solved can send me such a file). It may also be possible that the file deviates slightly from the specification, or that it is a different version or file format with .mol ending.

From what software / source are these .mol files?

ericschimel · 5 Dec 2014, 14:18

I tried a bunch from ACD/ChemSketch and they all failed no matter what format I saved them in...

Aerilius · 6 Dec 2014, 10:12

I had some unpublished changes pending, can you check the 1.2.0 release? If it shows the issue, please send me a .mol file.

ericschimel · 6 Dec 2014, 14:01

It looks like I'm on the 1.1 release, I got it from the Extension Warehouse. Should I wait for an update there, or just load the one that you have for download here?

Aerilius · 6 Dec 2014, 17:53

I would prefer to update when I know the new version 1.2.0 in the SCF store is good (EW usually takes a week for review, so I couldn't push another revision).

ericschimel · 7 Dec 2014, 13:45

Ok, I just installed the one in the SketchuCation plugin store and it works on my files perfectly so there's something up with the one in the Extension Warehouse.

Ivosh · 23 Aug 2017, 19:11

Dear Aerilius,
thank you very much for great plugin. However I found difficulties, opening larger structures above 100 atoms. Can number of atoms indeed be the problem? Is there a way to solve it?

Thanks a lot!

Ivan

Aerilius · 23 Aug 2017, 19:27

That can indeed be a problem: SketchUp is a line/polygon-based modeler, not a visualizer made for this purpose.
To reduce the polygon count, one can use a more simplified sphere component for the atoms.

The plugin's folder contains two components for atoms.
In the file "molecule_importer.rb" you can change the line 48:
COMPONENT_ATOM = File.join(PLUGIN_ROOT, "skp", "atom_high.skp")
to
COMPONENT_ATOM = File.join(PLUGIN_ROOT, "skp", "atom_low.skp")
or just edit the skp files.

Ivosh · 23 Aug 2017, 20:01

Thanks for the reply. Nope, does not work. Sorry I was not specfic. the 'difficulties' mean, that it refuses to open the file giving message 'import failed'. Just erasing part of the structure enables opening. I am sending the .mol file attached (I changed the extension to .txt as .mol is not allowed by the web interface. Ivan

structure1-2.txt

Aerilius · 24 Aug 2017, 09:34

It was due to the number of atoms taking all the maximum of 3 digits. I fixed a bug where the plugin was not able to separate the number of atoms from the number of bonds. It should now work up to 999 atoms (maximum of Molfile v2000).
https://sketchucation.com/pluginstore?pln=ae_MoleculeImporter
Can you confirm that it works for you?

Ivosh · 24 Aug 2017, 12:44

Works!!! Thank you so much