Re: [Rdkit-discuss] Counting amide groups in rotatable bond counts
Hi Toby,
One additional note on what Greg wrote:
you can define another smarts pattern for the identification of rotatable
bonds:
Lipinski.RotatableBondSmarts = Chem.MolFromSmarts("...")
Some smarts from the literature:
Daylight:
[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]-&!@[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]
Chemaxon: [!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]
Best,
Grégori
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Re: [Rdkit-discuss] Compound Neutralization
Hi Yingfeng, Let me remind you some chemistry basics: Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it requires 1 electron to complete octet. Hence it's valency is 1. Thus it's not a surprise that your smiles is generating an error. In order to check for get the charge state of a compound, you should loop through every atom of the molecule and check its charge; you will find all useful function here: http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Atom-class.html (For instance GetFormalCharge). Some readings for you: http://www.rdkit.org/docs/GettingStartedInPython.html Best, Gregori -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to import RDkit into the ipython notebook
A set of walkthrough notes for RDKit and iPython notebook installation on a Debian based Linux machine. Build RDkit from source. Instructions take from page http://www.rdkit.org/docs/Install.html#building-from-source [1] First Install these dependencies on Debian based Linux system. apt-get update apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev libboost-python-dev libboost-regex-dev => boost libraries installed to /usr/lib [2] Download rdkit 2013 Q3 release from Download RDkit source from http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2013/ Unzip and untar to ~/apps/rdkit/ => Directory ~/apps/rdkit/RDKit_2013_09_1 Ensure these lines in ~/.bashrc file to set environment variables export RDBASE=/home/chemuser/apps/ rdkit/RDKit_2013_09_1 export LD_LIBRARY_PATH=$RDBASE/lib:/usr/lib/:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$RDBASE/lib/:$PYTHONPATH Open new bash shell, then build source. cd $RDBASE mkdir build cd build cmake .. make sudo make install Run RDkit build tests cd $RDBASE/build ctest => 77 out of 78 tests passed (99%) => only test number 78 failed - pythonTestDirChem [3] Install ipython notebook (as root) apt-get install ipython-notebook [4] Run simple python script test for presence of RDkit Create script ~/code/rdkit/test-rdkit.py with 2 lines of code from rdkit import rdBase print rdBase.rdkitVersion => prints version 2013.09.1 [5] Start ipython notebook with command line ipython notebook Select option to create new notebook, paste two lines of code from above into input box. Use shift-enter to run code => prints version 2013.09.1 The ipython notebook and RDkit are installed and ready for use. On Mon, Dec 23, 2013 at 2:09 PM, George Papadatos wrote: > Hi Mark, > > Good to hear the workshop was effective! > Not sure what OS you use or how your python is set up but try adding the > RDKit folder path to your PYTHONPATH. Then launch a python prompt and type: > >>from rdkit import rdBase > >>print rdBase.rdkitVersion > > if this works fine, then you'd be able to use RDKit with ipython and > ipython notebook. > > Hope this helps. > > George > > --- > George Papadatos > EMBL-EBI > > > > > On 23 December 2013 12:42, Mark Forster wrote: > >> RDkit team and users >> >> I have just joined the RDkit discuss mailing list and as a newbie to >> RDkit I have some entry level questions. >> I did a quick search of the mailing list and some google searching, but >> no clear solution popped up. >> Can I get some pointers to this simple question? >> >> If the RDkit tools are installed as described here: >> http://rdkit.readthedocs.org/en/latest/Install.html >> >> What additional steps are required to get the RDkit functionality working >> in an ipython notebook? >> >> Experience suggests it might be something like setting PYTHONPATH but >> does a step by step guide exist? >> I saw the functionality demonstrated and used extensively at a recent EBI >> training workshop. Fantastic stuff. >> It is available with the MyCHEMBL virtual machine download, but at 18GB >> this is a network hog. >> Hence I would just like to get the installation steps needed to get RDkit >> and iPython NB working in harmony. >> >> regards >> >> Mark Forster >> >> >> -- >> Rapidly troubleshoot problems before they affect your business. Most IT >> organizations don't have a clear picture of how application performance >> affects their revenue. With AppDynamics, you get 100% visibility into your >> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics >> Pro! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to import RDkit into the ipython notebook
George Thanks for the course and for the RDkit advice. I was having a few issues, which I traced down to the PYTHONPATH environment variables. I made the mistake of setting them within .bashrc in the following form export RDBASE=/home/chemuser/apps/rdkit/RDKit_2013_09_1 export PYTHONPATH=$PYTHONPATH:$RDBASE:$RDBASE/lib Since PYTHONPATH was not initially set I ended up with an environment variable that started with : and seemed not to work. If I put $PYTHONPATH at the end with the following line, it all seems OK. export PYTHONPATH=$RDBASE:$RDBASE/lib:$PYTHONPATH For my Debian based system (Crunchbang Linux 32 bit VM) I documented the installation for RDKit and the ipython notebook as completely as I could. I will send these notes shortly, just in case they are useful to other users. Mark On Mon, Dec 23, 2013 at 2:09 PM, George Papadatos wrote: > Hi Mark, > > Good to hear the workshop was effective! > Not sure what OS you use or how your python is set up but try adding the > RDKit folder path to your PYTHONPATH. Then launch a python prompt and type: > >>from rdkit import rdBase > >>print rdBase.rdkitVersion > > if this works fine, then you'd be able to use RDKit with ipython and > ipython notebook. > > Hope this helps. > > George > > --- > George Papadatos > EMBL-EBI > > > > > On 23 December 2013 12:42, Mark Forster wrote: > >> RDkit team and users >> >> I have just joined the RDkit discuss mailing list and as a newbie to >> RDkit I have some entry level questions. >> I did a quick search of the mailing list and some google searching, but >> no clear solution popped up. >> Can I get some pointers to this simple question? >> >> If the RDkit tools are installed as described here: >> http://rdkit.readthedocs.org/en/latest/Install.html >> >> What additional steps are required to get the RDkit functionality working >> in an ipython notebook? >> >> Experience suggests it might be something like setting PYTHONPATH but >> does a step by step guide exist? >> I saw the functionality demonstrated and used extensively at a recent EBI >> training workshop. Fantastic stuff. >> It is available with the MyCHEMBL virtual machine download, but at 18GB >> this is a network hog. >> Hence I would just like to get the installation steps needed to get RDkit >> and iPython NB working in harmony. >> >> regards >> >> Mark Forster >> >> >> -- >> Rapidly troubleshoot problems before they affect your business. Most IT >> organizations don't have a clear picture of how application performance >> affects their revenue. With AppDynamics, you get 100% visibility into your >> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics >> Pro! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
