Very close to my current work around. Converting reaction schemes from CDX
to RXN in open babel and then with rdkit to png.
The issue with this route, is that openbabel tends to throw out catalysts
that are central to what I'm trying to do. Using reaction smiles produces
the same issue.
example:
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.utils import chemdraw
import os
os.system("obabel -icdx 2683B.cdx -O 2683B.rxn")
rxn = AllChem.ReactionFromRxnFile('2683B.rxn')
k = Draw.ReactionToImage(rxn, subImgSize=(500,500))
k.save('test-2683B.png')
Regards,
Eric Murphy, PhD
Multiphase Flow Scientist
Mechanical Engineer
murphyericja...@gmail.com | 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>
On Tue, Dec 3, 2019 at 11:52 AM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> 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 subprocessfrom rdkit import Chemfrom rdkit.Chem.Draw import
> rdMolDraw2Dfrom 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 <paolo.tosco.m...@gmail.com>
> 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:
>>
>> from win32com.client import combrowse
>> 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
>> murphyericja...@gmail.com | 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
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
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