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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