[Plugin] MoleculeImporter (1.3.3) – updated 8.10.2017

[Plugin] MoleculeImporter (1.3.3) – updated 8.10.2017

Postby Aerilius » Fri Jul 29, 2011 9:01 am

This Plugin imports chemical structures drawn in various [url=http:http://en.wikipedia.org/wiki/Molecule_editor#Standalone_programs]Molecule Editors[/url]. It supports MDL Molfiles (*.mol) or Z-Matrices (*.mop, *.zmt, *.dat, *.mpc).

MoleculeImporter.jpg

Make sure that you first do a 3d optimization and display hydrogenes before exporting.

Version: 1.3.3

Date: 08.10.2017

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Usage:
(Menu) Plugins → Molecule Importer → Import MDL Molfile
(Menu) Plugins → Molecule Importer → Import Z-Matrix
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Last edited by Aerilius on Thu Nov 29, 2018 12:46 am, edited 10 times in total.

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Re: [Plugin] MoleculeImporter

Postby pilou » Fri Jul 29, 2011 10:17 am

That is a task! :thumb:
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Re: [Plugin] MoleculeImporter

Postby mitcorb » Fri Jul 29, 2011 1:06 pm

What determines the imported 3d object's size or scale in the Sketchup model space? Or, how big are these things relative to "Sang" or "Susan"?
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Re: [Plugin] MoleculeImporter

Postby Aerilius » Fri Jul 29, 2011 4:21 pm

Most programs don't use "physical" units like 1 Ångström = 100 Picometer (10-10m), but document-relative units like in a word processor. Formats like the z-matrizes use Ångström which the plugin scales up to 1 meter. So it depends on the source program.

So it's likely that NanoPutian man can eat Bryce:
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Last edited by Aerilius on Sun Nov 18, 2012 12:39 pm, edited 1 time in total.

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Re: [Plugin] MoleculeImporter

Postby mitcorb » Sun Jul 31, 2011 4:24 am

Thanks, Aerilius:
That picture seems to tell me what I was asking.
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Re: [Plugin] MoleculeImporter

Postby thomthom » Mon Aug 22, 2011 10:18 am

I've been looking around at the various ruby based importers for SketchUp and I see that no one uses the Importer class. If this class is used the importer can be found in the native import list which would be very nice.
http://code.google.com/apis/sketchup/do ... orter.html
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Re: [Plugin] MoleculeImporter

Postby Chris Fullmer » Tue Aug 23, 2011 7:53 am

I use the importer class. It is very nice to use, though it is a bit difficult. It does not pop up errors, it just crashes SU. So if you have a small piece of code wrong while loading, it will crash, making it a bit tricky to debug. But it is really nice to have your importer registered in the list of importers.

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Re: [Plugin] MoleculeImporter

Postby thomthom » Tue Aug 23, 2011 8:06 am

Chris Fullmer wrote:I use the importer class. It is very nice to use, though it is a bit difficult. It does not pop up errors, it just crashes SU. So if you have a small piece of code wrong while loading, it will crash, making it a bit tricky to debug. But it is really nice to have your importer registered in the list of importers.

Chris

Really? hm...
Have you tried wrapping the code in an error catching block?
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Re: [Plugin] MoleculeImporter

Postby Chris Fullmer » Tue Aug 23, 2011 11:16 am

I have not. That would probably be a reasonably easy way to make it work.
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Re: [Plugin] MoleculeImporter

Postby DanYHKim » Mon Oct 17, 2011 8:55 pm

Is there any possibility of a protein structural renderer that would calculate sheets and helices, kind of like RasMol does?
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Re: [Plugin] MoleculeImporter

Postby Aerilius » Tue Oct 18, 2011 12:39 am

I don't believe that this would be feasible (or in the scope of this plugin). Since proteins start with 100+ amino acids, they have several thousand atoms which means a model would have at least a million polygons - a number where SketchUp's performance isn't really fun anymore.

A dedicated molecule visualizer or molecule drawing program is probably better for most chemical/biological applications. This plugin may be useful for importing simple molecules and enhancing them with boxes or SketchUp components.

Here is a list of open source protein visualizers that I found:
PyMOL
Garlic Protein Visualizer
(RasMol)
Avogadro
I hope that helps.
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Re: [Plugin] MoleculeImporter

Postby Andri » Thu Feb 07, 2013 5:48 pm

Hi, I have put the folder and file in the plugin folder but I cant see that it is workning. Is this not ok for ver 8.0? Can help and advice me?
Andri
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Re: [Plugin] MoleculeImporter

Postby Aerilius » Fri Feb 08, 2013 11:23 am

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).
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Re: [Plugin] MoleculeImporter

Postby pbacot » Fri Feb 08, 2013 5:29 pm

I am always amazed by the breadth of interests in this forum and uses of SU. I have a biology degree but I hadn't thought of such a scientific tie-in for SU or that people on this forum would be knowledgeable about these things. Well I guess I should not be amazed but just get used to it.

Thanks for the importer!
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Re: [Plugin] MoleculeImporter

Postby Andri » Sun Feb 10, 2013 11:02 am

Aerilius wrote:
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.
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Re: [Plugin] MoleculeImporter

Postby Aerilius » Sun Feb 10, 2013 3:32 pm

Then I assume the plugin is not loaded. Since you didn't mention a popup with "load errors" at the start of SketchUp, we should maybe check that it is installed correctly:

On the OS X operating system that is in: (the system path, not user path)
MacIntosh HD/Library/Application Support/Google SketchUp 8/SketchUp/plugins/
If Windows is installed on your computer, it is in: (depending on language and drive letter)
C:\Program Files\Google\Google SketchUp 8\Plugins\
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Re: [Plugin] MoleculeImporter (1.1.0) – updated 01.03.2013

Postby Aerilius » Fri Mar 01, 2013 3:52 am

Small update (1.1.0):
- converted it into a SketchUp Extension (that you can turn on/off)
- added icon and translations
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Re: [Plugin] MoleculeImporter (1.1.0) – updated 01.03.2013

Postby Oxer » Tue Mar 05, 2013 3:30 am

Thanks!!
I have created the spanish language file:
MoleculeImporter_es.strings.zip
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Re: [Plugin] MoleculeImporter (1.1.1) – updated 26.04.2013

Postby Aerilius » Fri Apr 26, 2013 8:49 am

A new version 1.1.1 has been uploaded. Some regular expressions failed on OS X and have been fixed.
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Re: [Plugin] MoleculeImporter

Postby matthew.robert » Mon May 06, 2013 2:46 pm

DanYHKim wrote:Is there any possibility of a protein structural renderer that would calculate sheets and helices, kind of like RasMol does?


Aerilius, I am probably asking the same thing as DanYHKim, but is it possible to model the pink and yellow things in the attached graphic? I downloaded the .pdb file from rcsb.org, and then exported the file to MOL v3000. That worked fine to model the molecular structure... which I am guessing is by design, but I am trying to find a way to simply model the other stuff.
pinknyellow.png
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby Aerilius » Mon May 06, 2013 3:55 pm

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
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Re: [Plugin] MoleculeImporter

Postby Andri » Fri May 31, 2013 11:59 pm

Andri wrote:
Aerilius wrote:
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 :)
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby Aerilius » Sun Jun 02, 2013 6:52 pm

You can send the file if you put it in a zip file.
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby jeichholz » Mon Nov 04, 2013 6:04 am

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.
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby ericschimel » Thu Dec 04, 2014 9:39 pm

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...
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby Aerilius » Fri Dec 05, 2014 1:33 pm

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?
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby ericschimel » Fri Dec 05, 2014 3:18 pm

I tried a bunch from ACD/ChemSketch and they all failed no matter what format I saved them in...
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Re: [Plugin] MoleculeImporter (1.2.0) – updated 05.12.2014

Postby Aerilius » Sat Dec 06, 2014 11:12 am

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.
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Re: [Plugin] MoleculeImporter (1.1.2) – updated 05.05.2013

Postby ericschimel » Sat Dec 06, 2014 3:01 pm

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?
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Re: [Plugin] MoleculeImporter (1.2.0) – updated 05.12.2013

Postby Aerilius » Sat Dec 06, 2014 6:53 pm

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).
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