Re: [Rdkit-discuss] (no subject)
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Re: [Rdkit-discuss] (no subject)
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From: Paolo T. <pao...@gm...> - 2019-12-03 17:52:51
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Hi Eric,
as I mentioned, I do not have access to ChemDraw, so I am afraid I can't
help more with that.
A possible workaround is to install OpenBabel in your conda environment
and use that to do a cdx->mol conversion. While it should be possible to
use the openbabel or pybel module, for some reason I couldn't get it
work, so in the example below I am calling the obabel.exe executable.
import subprocess
from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
RDKit WARNING: [17:45:59] Enabling RDKit 2019.09.1 jupyter extensions
proc = subprocess.Popen("obabel.exe -i cdx 1oit_2d.cdx -o mol".split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = proc.communicate()
rdk_mol = Chem.MolFromMolBlock(stdout.decode("UTF-8"))
drawer = rdMolDraw2D.MolDraw2DSVG(400, 400)
Chem.Kekulize(rdk_mol)
rdMolDraw2D.PrepareAndDrawMolecule(drawer, rdk_mol)
drawer.FinishDrawing()
svg = drawer.GetDrawingText()
SVG(svg)
This should allow you to easily automate the SVG (or PNG) generation
process.
HTH, cheers
p.
On 03/12/2019 15:08, Eric Murphy wrote:
> Hi Paolo, all,
>
> Thank you for responding. I tried this out this morning - though I
> could not find chemdraw using the combrowser.
>
> Instead I went to the registry editor grabbed the CLSID from
> HKEY_CLASSES_ROOT\ChemDraw.Application.15.0\CLSID. (As far as I
> understand this should be identical to the GUID) I replaced the GUID
> in
> \Local\Continuum\anaconda3\pkgs\rdkit-2019.09.1-py37h422b363_0\Lib\site-packages\rdkit\utils\chemdraw.py
> - however, I'm not seeing any change in the error when I go to import
> via "from rdkit.utils import chemdraw".
>
> Please let me know if I am doing something wrong.
>
> Regards,
> Eric Murphy, PhD
>
>
> On Tue, Dec 3, 2019 at 3:47 AM Paolo Tosco <pao...@gm...
> <mailto:pao...@gm...>> wrote:
>
> Hi Eric,
>
> it looks like the GUID in rdkit/utils/chemdraw.py might be outdated.
>
> Unfortunately I don't have access to ChemDraw, so I can't test
> this myself, but you might be able to find the current ChemDraw
> GUID as follows.
>
> From a Python prompt, issue the following commands:
>
> |fromwin32com.client importcombrowse combrowse.main()|
>
> This will pop up a COM browser. Expand the "Registered Type
> Libraries" and look for ChemDraw.
> Expand it, and you should find the IID (which is a GUID)
> corresponding to ChemDraw.
> Try replacing 5F646AAB-3B56-48D2-904C-A68D7989C251 in
> rdkit/utils/chemdraw.py and see if it helps.
>
> Cheers,
> p.
>
> On 02/12/2019 21:04, Eric Murphy wrote:
>> Hello all,
>>
>> I'm trying to make use of the rdkit.utils.chemdraw to automate
>> conversion of cdx files to png's. and other formats. However, I'm
>> getting the following error message: ImportError: ChemDraw
>> version (at least version 7) not found.
>>
>> I'm currently using windows 10 with anaconda 3 with rdkit
>> 2019.09.1 installed from conda forge. I do have chemdraw
>> professional 15.0 installed, so I am wondering if there is
>> anything that I need to do to the path, etc.
>>
>> Regards,
>> Eric Murphy, PhD
>> Multiphase Flow Scientist
>> Mechanical Engineer
>> mur...@gm... <mailto:mur...@gm...> |
>> 563-449-6661
>>
>> LinkedIn <https://www.linkedin.com/in/eric-james-murphy/> |
>> ResearchGate
>> <https://www.researchgate.net/profile/Eric_Murphy5> | Google
>> Scholar
>> <https://scholar.google.com/citations?user=3Mu7770AAAAJ&hl=en>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdk...@li... <mailto:Rdk...@li...>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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