Re: [Open Babel] OpenBabel not Working in Python 3.6

I have issues with OpenBabel in Python3.6 - I found an older topic. But the solution suggested by Neil is not working. Please help. http://forums.openbabel.org/OpenBabel-not-Working-in-Python-3-6-td4659717.html -- Sent from: http://forums.openbabel.org/General-discussion-f3090658.html

Re: [Open Babel] OpenBabel for Python 3?

I have issues with OpenBabel in Python3.6 - I found an older topic. But the solution suggested by Neil is not working. Please help. -- Sent from: http://forums.openbabel.org/General-discussion-f3090658.html ___ OpenBabel-discuss mailing list OpenBabe

[Open Babel] Strange behaviour with pdbqt format

Hi, we are using Open Babel 2.4.1 and we have found a very strange behaviour when converting pdbqt format; for instance: a) babel 3CQA.pdbqt 3CQA_2.pdbqt (file is pasted below) it makes unnecessary modifications to several parts of the file or b) babel *.pdbqt -opdbqt test_join.pdbqt in ou

[Open Babel] Using Openbabel with a New Package

Hello, We are currently working on developing a package for predicting the structure of proto-nucleic acids. In this program, users can input arbitrary backbone structure and other parameters. Then, the program performs a conformational search over the dihedral angles of the backbone to predict

Re: [Open Babel] SMILES to PNG and then PNG to SMILES?

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 , wrote: > Hello all, > > I in

Re: [Open Babel] SMILES to PNG and then PNG to SMILES?

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 wrote: > Hi, > > In order for that to work, you need t

Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik Wallner)

I guess you have seen https://cactus.nci.nih.gov/osra/ Chris___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik Wallner)

Helo Chris, Yup! That's next on my list of things to try. CLiDE is on the list after that. Thanks for pointing it out, Ryan On Thu, Sep 26, 2019 at 1:58 PM Chris Swain via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > I guess you have seen https://cactus.nci.nih.gov/o

Re: [Open Babel] Using Openbabel with a New Package

When you compile Open Babel, do the binaries work? e.g. "obabel -: -omol --gen3d" Regarding 3.0 versus 2.4.1, the release is imminent. Whether you wait or not, is up to you. - Noel On Thu, 26 Sep 2019 at 17:54, Asem Alenaizan wrote: > Hello, > > > > We are currently working on developing a

Re: [Open Babel] Using Openbabel with a New Package

I do not compile Open Babel. I use the pre-compiled library provided in conda-forge. And yes, the binaries work if I set BABEL_DATADIR to the correct path. Asim On Thu, Sep 26, 2019 at 3:52 PM Noel O'Boyle wrote: > When you compile Open Babel, do the binaries work? e.g. "obabel -: > -omol -

Re: [Open Babel] Using Openbabel with a New Package

Were those conda packages built with the same compiler? On Thu, 26 Sep 2019, 21:05 Asim Alenaizan, wrote: > I do not compile Open Babel. I use the pre-compiled library provided in > conda-forge. And yes, the binaries work if I set BABEL_DATADIR to the > correct path. > > Asim > > On Thu, Sep 26,

Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik Wallner)

Hi Ryan, Here is another possible choice for structure OCR: https://spotlite.nih.gov/ncats/molvec Vin From: Ryan Bannen Sent: Thursday, September 26, 2019 2:08 PM To: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik Wallner) He