iwatobipen blog was where I found instructions for installing RDKit on Colab. It works but I found waiting for miniconda to install to be too annoying. A one line apt-get command to install RDKit is easier and faster (~10 seconds) but it only works with Python 2. Running following command in a Python 3 environment results in the error below. Getting apt-get to install RDKit correctly for Python 3 is a good solution.
!apt-get install python-rdkit librdkit1 rdkit-data from rdkit import Chem ... --------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) <ipython-input-1-96d31abe2ca9> <https://61qi2f4hjw5-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20200318-085600-RC00_301599018#> in <module>() 1 get_ipython().system('apt-get install python-rdkit librdkit1 rdkit-data')----> 2 from rdkit import Chem ModuleNotFoundError: No module named 'rdkit' --------------------------------------------------------------------------- Best, JW On Mon, Mar 16, 2020 at 4:48 AM Taka Seri <serit...@gmail.com> wrote: > 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 >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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