Need to create publishable 2D drawings from 3D MOPAC file

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Need to create publishable 2D drawings from 3D MOPAC file

John McKelvey
Hello..

I have 40 or more MOPAC input structures for which I need to create
publishable 2D drawings.  Ultimately they need to be collated onto a
few pages as possible in teh same order as presented (hopefully) to
OPEN-BABEL.  Is this possible?  I use O-B for file format
interchanges, but that's about all I'm familiar with.

Any suggestions most appreciated.

Many thanks!

John

--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
[hidden email]

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Re: Need to create publishable 2D drawings from 3D MOPAC file

Noel O'Boyle
Administrator
Well, you could try a Python script. Here's one I made earlier for an SDF file:

import pybel
for i, mol in enumerate(pybel.readfile("sdf", "bostrom.sdf")):
    mol.draw(show=False, filename=os.path.join("images", "%d.png" % i))

See http://openbabel.org/wiki/Python. You will need to install OASA to
generate the images (see the instructions).

Alternatively, you could convert to ChemDraw files.

The next version of OpenBabel will allow generation of similar images
directly using "babel", AFAIK.

BTW, you may also wish to ask your question over at
http://blueobelisk.shapado.com.

- Noel

On 24 June 2010 13:06, John McKelvey <[hidden email]> wrote:

> Hello..
>
> I have 40 or more MOPAC input structures for which I need to create
> publishable 2D drawings.  Ultimately they need to be collated onto a
> few pages as possible in teh same order as presented (hopefully) to
> OPEN-BABEL.  Is this possible?  I use O-B for file format
> interchanges, but that's about all I'm familiar with.
>
> Any suggestions most appreciated.
>
> Many thanks!
>
> John
>
> --
> John McKelvey
> 10819 Middleford Pl
> Ft Wayne, IN 46818
> 260-489-2160
> [hidden email]
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss