Hello Fredrik, Sincere thanks for your prompt reply. I'll keep looking around at some other options for Chemical OCR and will continue to enjoy the current functionality of Open Babel.
Ryan On Thu, Sep 26, 2019 at 12:48 PM Fredrik Wallner <fred...@wallner.nu> wrote: > Hi, > > In order for that to work, you need to embed structural information the > png-file in the first step. Open Babel is not able to do “chemical OCR”. > > obabel -:"NC(SC)=N" -o png -O output.png -xO molfile > > > Kind regards, > Fredrik > On 24 Sep 2019, 22:59 +0200, Ryan Bannen < > ryan.ban...@nimbletherapeutics.com>, wrote: > > Hello all, > > I installed Open Babel via conda on my Linux workstation and have been > enjoying what it can do. I do have a question regarding png files however: > > I was please to find that the following command: > > obabel -:"NC(SC)=N" -o png -O output.png > > will create a nice png file of the provided SMILES string. > > From looking at the available formats when typing obabel -L formats it > would appear that png is an acceptable -input- format and that SMILES would > be an acceptable -output- format. However, when I type: > > obabel output.png -i png -o smi -O output.smi > > Open Babel will tell me that it converted 1 molecule, but output.smi will > be a file with 0 bytes. > > Can Open Babel actually extract SMILES information from provided png files > or should I go investigate programs like osra or CLiDE instead? > > Thank you very much, > > Ryan > -- > *Ryan Bannen, PhD* > Senior Bioinformatics Scientist > > Nimble Therapeutics, Inc. > 500 S. Rosa Rd. > Madison WI, 53719 > www.nimbletherapeutics.com > > *Confidentiality Note:* This message is intended only for the use of the > named recipient(s) and may contain confidential and/or proprietary > information. If you are not the intended recipient, please contact the > sender and delete this message. Any unauthorized use of the information > contained in this message is prohibited. > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- *Ryan Bannen, PhD* Senior Bioinformatics Scientist -- Nimble Therapeutics, Inc. 500 S. Rosa Rd. Madison WI, 53719 www.nimbletherapeutics.com <http://www.nimbletherapeutics.com> * * *Confidentiality Note: *This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.
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