Re: [Rdkit-discuss] new RDKit FAQ
Le 19/12/2022 à 03:12, Francois Berenger a écrit : I _love_ the getting started with RDKit in Python document. I went many times back to it; and it almost always (like 95% of the time) had the example/answer I was looking for. https://www.rdkit.org/docs/GettingStartedInPython.html Dear all, That reminds me I wanted to add some doc too :-) In the meantime some ideas. Some questions for the FAQ (easy ones) : - How to read / write mol2 files ? - Why (and when) do I need to add Hydrogens to molecules - How to perfom 3D generation from SMILES (or other) - What is Daylight cartridge - Where can I find an introduction to CADD -> redirect to "Teach Open CADD" https://volkamerlab.org/projects/teachopencadd/ - How can I study Protein-Ligand Interaction (PLIF) : doc to PLIF or more advanced ones (https://github.com/chemosim-lab/ProLIF) And many more, I was thinking about something like "Planet RDKIT" where not only the official blog is referenced, but also ones from others, including gist from various people on the list... Have nice holidays ! Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Call for documentation writers
Dear all, I had the chance to go to RDKIT UGM last week, and amongst various discussions, I stepped up to provide and/or organize some documentation. During the hackhathon I had the opportunity to set up a raw list of wishes, nothing spectacular, but with in mind the possibility of: - setting up contribution rules for people willing to help in documentation - determine 2/3 topics that could illustrate non-trivial features - allowing to assemble already discussed topics (but long time ago), and/or provide other visuals for specific features (tables, images, etc). We worked on such a project 2 years ago, having in mind Google's sponsored "Season Of Docs", but unfortunately the project could not go further: https://docs.google.com/document/d/1GuhKrAb0biZD3sc1qZWYJXQGUFLFoMgjnoxEx_A6Cvw/edit This is thus officially the new day 1 of documentation contribution to this wonderful project. I'll set up some preliminary data from the notes taken last week, but don't hesitate to reply to this list, and/or to me directly, I know some people have already stepped up, kuddos to them. All the best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2022 RDKit UGM registration open
Le 03/03/2022 à 15:15, Greg Landrum a écrit : This year's RDKit UGM will take place in Berlin, Germany from 12-14 October. The organizers are the Machine Learning Research group from Bayer Pharma. We're planning the UGM as an in-person event, but we will, assuming the technology works, also live stream the sessions. Dear all, Except if I missed the information, I have not seen the exact location of the UGM in Berlin. Is it still ongoing or only not announced? I am trying to register to congresses in fall now to avoid last-minute "rush" of our administration :-) Thanks a lot in advance, and hopefully see you in person in Berlin! Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Looking for additional GSoC co-mentors
Le 01/04/2020 à 08:16, Greg Landrum a écrit : There's more information on the program, including the dates, here: https://summerofcode.withgoogle.com/how-it-works/ GSoC is really a great program and being a mentor/co-mentor is a good way to help move both the open-source community and the RDKit forward. If you're interested or have questions, feel free to send me email, Dear Greg, I'm not sure if I'm the best specifically concerning rdkit internals, but as a teacher, I think I can help. I think I could be more useful on these topics (pick one): - generalized file reader - molecular interaction fields - openMM HTH, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] decomposing products to reactants from an rxn
Le 04/12/2019 à 16:05, Greg Landrum a écrit : Ideas/suggestions are welcome. Dear all (and Gred of course :-), I'd suggest to have: - gist referenced in the blog (a small intro to the question) - and/or a link to a "cookbook" section - a link on the blog to existing blogs (aka planetrdkit?). I found myself quite confused about some concepts, mostly because sometimes I'm lacking them (or the advanced requirements related to the concepts). I have started aggregating knowledge related to these approaches (simplified introduction to concepts+usage): 1 - https://connect.ed-diamond.com/GNU-Linux-Magazine/GLMFHS-094/Recherche-de-molecules-innovantes (in French, but you get the concepts :-) 2 - https://www.steletch.org/spip.php?article91 (rdkit + django) 3 - https://www.mdpi.com/1422-0067/20/20/5062 (how to gather experimental information from ChEMBL+in house lab and docking data from in-house) But I think the documentation is an ever growing problem, you could think to add a "contribute" to the documentation with a list of "requested features". Since I'm using rdkit more and more for my research, and half of my activity is also to teach, I may try to contribute by "small" documentation on topics where I find it usefull for my students :-) HTH, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] missing MolFromSmiles error output in Jupyter
Le 16/10/2019 à 15:47, Andrew Dalke a écrit :
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
mol = Chem.MolFromSmiles("Q")
On my machine I get a red message from stderr:
RDKit ERROR: [15:41:35] SMILES Parse Error: syntax error for input: 'Q'
Dear Andrew,
Did you 'by chance' transmit your presentation in PDF?
This may come from a weird bug in quote management from a PDF file when
you copy/paste double quotes, I'm encountering this very regularly with
my students in Windows while my presentation is produced under Linux
(using LibreOffice and saved in PDF format)...
HTH,
Stéphane
--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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Re: [Rdkit-discuss] Saving chains from PDB file
Le 05/10/2019 à 12:46, Chris Swain via Rdkit-discuss a écrit :
Hi,
I have a number of PDB files (foo.pdb.gz) and I want to separate each chain in
each file out into a separate file. So if a file contains 4 chains it will
generate 4 separate files.
Can I do this using RDKit, if so how?
Cheers
Chris
Dear Chris,
Even this could be performed in rdkit, I would recommend doing it using
an external tool, for instance using Biopython and the Bio.PDB module
(https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ),
or even ProDy (http://prody.csb.pitt.edu/).
Rdkit needs to wrap a lot of atom definitions to load the pdb file
properly, and it takes time (minutes on my machine, which is a decent
workstation :-).
It will be lightning fast using Bio.PDB or prody, compared to rdkit.
If you still want to use rdkit only, and need to reuse rdkit
representation of the PDB file, then (c)pickle it (python2):
import cPickle
from rdkit import Chem
def processReceptor(r):
try:
h=open('receptor.pkl','r')
receptor=cPickle.load(h)
h.close()
except Exception as e:
receptor = Chem.MolFromPDBFile(r)
f=open('receptor.pkl','w')
cPickle.dump(receptor,f)
f.close()
return receptor
HTH,
Stéphane
--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)
Le 18/11/2016 à 09:16, Greg Landrum a écrit : > Fixing the larger problems is a *lot* of work and not something that > is likely to happen quickly, but there is some low-hanging fruit (like > cutting crossed bonds) that I ought to be able to do something about.[1] > > -greg > [1] the trick is to avoid, as much as possible, creating drawings that > look like Möbius strips. Dear Greg, I appreciate your tremendous, and I have always wanted to give back to the community when possible. Do you have any guidelines about getting something better (a draft or links to ideas / papers?), I do have the possibility to mentor some students and this kind of subjects would be a perfect C++ / python project for them ... Just my two cents :-) Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SubstructMatches help
Le 17/11/2016 à 20:12, Paolo Tosco a écrit : > Dear Stéphane, > > I'll look into this tonight and let you know. > > Best, > p. Thanks a lot. To add more input, depending on the input file provide, the rmsd is computed or not ... (change Chem.MolFromPDBFile(sys.argv[1]) for Chem.MolFromMolFile(sys.argv[1])) ./calc_rmsd_simple.py sd_out/carbLactosamineTypeI5.sdf jeu_test.sd sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.669621 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.766064 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.912119 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.120689 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.512118 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 1.899627 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 1.687619 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamineTypeI5.sdf jeu_test.sd carbLactosamineTypeI 0.00 ./calc_rmsd_simple.py sd_out/carbLactosamine5.sdf jeu_test.sd sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.680751 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.264023 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.127012 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.196644 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.176413 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.578994 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.567569 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 0.592443 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamine 1.295632 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 sd_out/carbLactosamine5.sdf jeu_test.sd carbLactosamineTypeI 0.00 Very weird ... so this is not only an orientation issue ... Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)
Le 17/11/2016 à 18:01, David Cosgrove a écrit : > Hi All, > > I'm currently working on transferring the 2 Python functions > GenerateDepictionMatching2DStructure and the 3D equivalent into the C++ > core so they will be available to all users of the toolkit. Can anyone > supply example test cases for me? In particular, I would appreciate > examples of the 2D version using the optional referencePattern argument, > and, for the 3D version, examples where it works well and less well. > SMILES and/or SDFs would be enough, but if you have pictures of the > output and/or comments on them, that would be a bonus. > > Many thanks, > Dave Dear Dave, thanks a lot for the move. One thing which is not very well handled in rdkit (and elsewhere) is carbohydrates. Since you are moving things, do you want test scenarios and examples to adjust it? For instance "classical" representations of carbohydrates: https://en.wikibooks.org/wiki/File:Chairenvelopeboat*.png or better : http://oregonstate.edu/instruct/bb450/450material/stryer7/11/figure_11_07.jpg Actually they look pretty flat in rdkit, unfortunately. This is also true in pubchem for instance : https://pubchem.ncbi.nlm.nih.gov/compound/D-glucose Sorry for this off-topic demand, but if there is room for improvements, I would be intersted :-) Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Struggling with apache + rdkit + django
Le 24/06/2016 à 02:14, Stéphane Téletchéa a écrit :
> http://www.steletch.org/spip.php?article91
>
> Many thanks,
>
> Stéphane
>
>
Just for the record, there was on omission in the web site when you want
to use a bigger project
than just a demo, the WSGI process must contain the directive:
WSGIApplicationGroup %{GLOBAL}
The long reason is here (basically a problem of python initialisation
ordering):
https://code.google.com/archive/p/modwsgi/wikis/ApplicationIssues.wiki#Python_Simplified_GIL_State_API
HTH,
Stéphane
--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design
In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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Re: [Rdkit-discuss] Struggling with apache + rdkit + django
Le 21/06/2016 20:18, TJ O'Donnell a écrit : > I would suggest setting PYTHONPATH in > config or ini files for > Apache or Django or uwsgi > Not sure which is required. Dear all, This is already indicated using a WSGIprocessGroup : WSGIDaemonProcess manageLibrary python-path=/path/to/project/projets/manageLibrary:/path/to/project/projets/manageLibrary/tools/django1.8/lib/python2.7/site-packages:/path/to/project/projets/manageLibrary/tools/rdkit/lib:/path/to/project/projets/manageLibrary/tools/rdkit/lib/python2.7/site-packages display-name=manageLibrary WSGIProcessGroup manageLibrary WSGIScriptAlias /tools/manageLibrary '/path/to/project/projets/manageLibrary/manageLibrary/wsgi.py' See more in detail here: https://www.digitalocean.com/community/tutorials/how-to-serve-django-applications-with-apache-and-mod_wsgi-on-ubuntu-14-04 I have also checked permisisons and files with no luck (and no output in logs ...). I may start from scratch with a simple django project to find if is already works there ... Many Thanks, if you have any direction I'll be happy to test, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Struggling with apache + rdkit + django
Le 21/06/2016 20:05, Bennion, Brian a écrit : > What is the actual problem that is occurring? You have listed what you have > tried to do to fix a problem. > > Brian Dear Brian, I get a 500 error meaning something is not working properly, but no trace in logs (either apache or django), so I can only "assume" it comes from there since in the "developper" mode there is no problem (everything works as expected). Sorry for the confusion, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Struggling with apache + rdkit + django
Dear all, I am willing to incorporate some rdkit functionalities using a django backend for an internal project (basically ligand annotation and comparison with docking studies) which will be published once ready. Using the "developper" mode of django and conda I can properly get all of them working properly, but I'm struggling in translating this into a real web service. For what it counts, I am admin on the machine and for now not a lot of services are up so I can test things... So far I have tried: - installing rdkit with conda + all required dependencies + wsgi file pointing to it - installing django + dependencies using pip + install from scratch of rkdit (Ubuntu Linux 14.04 LTS, 64bits): a) using a custom location, works with django manage.py runserver but not when launched from apache b) building rdkit using different locations (adding /etc/ld.so.conf.d/rdkit.conf + ldconfig -> libraries are correctly detected) c) adding various path in the wsgi.py configuration file d) and many more ... There are other django services working fine on the machine so it does not come from there. I have also tried to run only this service with no better luck. I think it is the combination of externally adding LD_LIBRARY_PATH + PYTHONPATH that is the culprit, since the web server responds to the requested address, but after "a certain amout of time", I see in apache2 logs: ~~~ End of script output before headers: wsgi.py ~~~ Unfortunately there is no other error message, so I am unable to trace the rest of the error. Does it rings a bell to someone? Thanks a lot in advance, Stéphane Téletchéa -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] link RDKit C++ libraries when using g++ on linux
Le 30/05/2016 15:36, Yingfeng Wang a écrit : > It looks to me is a linking problem, but I don't know how to figure it > out. Dear Yingfeng, I would suspect an underlinking problem and/or a missing include in your code (or in rdkit). See: https://wiki.openmandriva.org/en/Underlinking You should also consider a makefile for you project :-) Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Exact sub-structure match
Le 03/05/2016 07:40, Greg Landrum a écrit : > If there's interest, I can explain what is going on here, but maybe > the solution is enough? > > -greg Dear Greg, Thanks a lot for the explanation and sorry for the delay. Yes this fits my needs, and I think the rationale comes from the "misc chemoinformatics topics" in section 4.1 (I printed and read all the manual before posting). If possible I'd be happy to have a warning (in the documentation) concerning this feature, because I suspected this behaviour before posting to the list, so other users may be confused too ... Thanks a lot, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Exact sub-structure match
Le 02/05/2016 16:02, Greg Landrum a écrit :
Does that help answer your question?
-greg
Dear Greg,
Unfortunately yes an no. I sent my mail before adding that I had already
tested that option,
and in my tests using substructureMatch, various fingerprints, etc ...
does not work if I start
from an SDF file read:
Here is my code excerpt:
>>> from rdkit import Chem
>>> glucose=Chem.MolFromMolFile('Beta-D-Glucose_Structure3D_CID_5793.sdf')
>>> lactose=Chem.MolFromMolFile('Lactose_Structure3D_CID_6134.sdf')
>>>
galactose=Chem.MolFromMolFile('Beta-D-Galactose_Structure3D_CID_6036.sdf')
>>> lactose.GetSubstructMatch(galactose,useChirality=True)
(1, 6, 5, 4, 0, 10, 17, 16, 19, 15, 13, 22)
>>> lactose.GetSubstructMatch(glucose,useChirality=True)
(1, 6, 5, 4, 0, 10, 17, 16, 19, 15, 13, 22)
>>> lactose.GetSubstructMatch(glucose)
(1, 6, 5, 4, 0, 10, 17, 16, 19, 15, 13, 22)
Does the MolFromMolFile removes the chirality?
The files in 2D does not display the chirality (image attached).
Do I have to use the canonical smiles?
Thanks a lot in advance, just ask if you need more info ...
Stéphane
--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design
In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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[Rdkit-discuss] Exact sub-structure match
Dear all,
I am trying to work on sub-structure match using rdkit, my goal is to
identify unambiguously
a carbohydrate moiety in carbohydrates, for example glucose or galactose
in lactose.
I have tried using the built-in functions from the doc, using "ideal"
structures from pubchem as starting structures:
gal = Chem.MolFromMolFile('Beta-D-Galactose_Structure3D_CID_6036.sdf')
glu = Chem.MolFromMolFile('Beta-D-Glucose_Structure3D_CID_5793.sdf')
lactose = Chem.MolFromMolFile('Lactose_Structure3D_CID_6134.sdf')
However, I am not able to distinguish between galactose and glucose
(they are isomers on the c4 position)
during the SubStructure search:
ms=[gal,glu]
fps = [FingerprintMols.FingerprintMol(x) for x in ms]
DataStructs.FingerprintSimilarity(fps[0],fps[1])
1.0
I *understand* that a fingerprint is meant to find the maximum
sub-structure,
but how could I distinguish between glu and gal in such a simple
molecule like lactose?
Is it possible in rdkit? Is is a bug (or a misusage)?
Thanks a lot in advance,
Stéphane
--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design
In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
--
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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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