Thanks Steve, That's really helpful. Given that we're unlikely to end up with a decent pip-installable RDkit, I guess the snippet approach would be the best way to go. I will try to make some time for this (or convince iwatobipen to do it) in the reasonably near future.
Best, -greg On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes <kear...@google.com> wrote: > re: rdkit+colab > > In talking with folks outside of Google about rdkit+colab, I haven't been > able to establish that it's worth the trouble of making rdkit a default > dependency. It seems that a rather compact incantation > <https://iwatobipen.wordpress.com/2018/11/01/run-rdkit-and-deep-learning-on-google-colab-rdkit/> > does the job fairly well. This could be compressed even further, or even > turned into a colab snippet <https://stackoverflow.com/a/53875826> for > easier use. > > Also, since colab doesn't play well with conda (as far as pre-installed > deps are concerned), we would at least need a pip-installable rdkit to > consider making this work. > > Thanks, > Steve > > On Mon, Mar 9, 2020 at 4:43 PM JW Feng <jw.a.f...@gmail.com> wrote: > >> Are you sure depictions in GSheet wouldn't be a good GSoC project? I >> will ask around to find volunteers to connect with you on GSheets and >> Colab. >> >> On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum <greg.land...@gmail.com> >> wrote: >> >>> Hi JW, >>> >>> I don't think it's a great GSoC project for a couple of reasons, but I'd >>> love to have RDKit integration in Google Sheets and am willing to do some >>> work to make that happen. I can poke around a bit to see about how we could >>> use the new RDKit-JS wrappers, but having access to someone with experience >>> writing Sheets add-ins would help. If you know someone internally meeting >>> that description, please put them in touch with me. >>> >>> I think making the code easily available in Colab can only be done by >>> someone inside google. I'm happy to help however I can with that if you (or >>> anyone else) can identify the right person. >>> >>> Best, >>> -greg >>> >>> On Sat, Mar 7, 2020 at 2:22 AM JW Feng <jw.a.f...@gmail.com> wrote: >>> >>>> Project suggestion: >>>> >>>> Project 1: >>>> Implement 2D structure depiction in Google Spreadsheets. My colleagues >>>> at Google think this is very doable. Being able to depict structures in >>>> Google Spreadsheets will dramatically increase collaboration between >>>> scientists. Imaging being able to provide comments for a structure, design >>>> idea, or virtual screening hit in a live Google Spreadsheet. While there >>>> are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source >>>> (Datawarrior) packages that can read CSV files containing smiles and depict >>>> structures, none comes close to GSheets for collaboration and ease of use. >>>> >>>> - Cells in columns named SMILES, or have SMILES as a substring in >>>> the header, will be depicted in 2D using RDKit >>>> - Cells with depicted structures move with other columns when >>>> sorting, filtering, etc. >>>> - Optional: depictions update when SMILES string is edited >>>> - Bonus: calculate properties using formulas. Ex: Descriptors.MolWt(A1) >>>> calculates MW of SMILES in A1 >>>> >>>> Project 2: >>>> >>>> - Make it easy to use RDKit in Google Colab >>>> <https://colab.sandbox.google.com/notebooks/intro.ipynb#recent=true> >>>> >>>> - No need to install RDKit, from rdkit import Chem just works out >>>> of the box >>>> >>>> Best, >>>> >>>> JW >>>> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum <greg.land...@gmail.com> >>>> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm happy to share that the RDKit will once again be part of Google >>>>> Summer of Code in 2020. This is a program where Google funds students to >>>>> work on open-source projects for a couple of months over the summer. We've >>>>> participated in each of the last three years and had some cool stuff come >>>>> out of it. >>>>> >>>>> We're looking for a few more project ideas (along with possible >>>>> mentors!) as well as students. >>>>> Applications start in the middle of March. There's more info about >>>>> timelines here: >>>>> https://developers.google.com/open-source/gsoc/timeline >>>>> >>>>> The current set of project ideas is here and we could use a few more: >>>>> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas >>>>> I'm going to try and come up with something, but if you have something >>>>> to add, please let me know. >>>>> >>>>> Best, >>>>> -greg >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rdkit-discuss mailing list >>>>> Rdkit-discuss@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>>> >>>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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