Dear Steve, Greg and All, Recently I moved from clab to Binder to make cloud env with python. However I'll try to make my code more compact and share it. Thanks for following my blog post. ;) https://iwatobipen.wordpress.com/
Best regards, Taka (tiwtter account / iwatobipen) 2020年3月16日(月) 16:03 Greg Landrum <greg.land...@gmail.com>: > 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 >>> >> _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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