Hi Stuart, Sorry for the late reply
Finally, while I was hoping it would easy to use CDK right in > PyCharm/Python I now see that I will have to install it separately and use > the command line. > I guess I don’t know, is there command line functionality built into the > CDK jar file? You don't need to go via the command line, IDEA <https://www.jetbrains.com/idea/> is the equivalent of PyCharm, in fact I think it came first and I believe PyCharm reuses most of the UI :-). We don't have any command line utilities and what you're trying to do is quite specific so couldn't imagine having a utility for it if we did provide those. It's best to think of CDK like NumPy - it's a set of tools for you build something with. Since you sound like you're more familiar with Python so why not use RDKit or Open Babel? So, I have a project where I am converting a lot of data to RDF and as a > result I am adding compounds to a graph DB with lots of descriptors and > identifiers. > Thus, the first thing I want to do with CDK is to get descriptors for > compounds, preferably using the InChIKey (but other identifiers if needed). I presume you mean Resource Description Framework (RDF) but note CTfile Reaction Data File (RDF) <http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/reference/ctfileformats2016.pdf> is common cheminformatics format so can get confusing. Egon knows more about RDF but I believe Apache JENA <https://jena.apache.org/> will help here - I think we actually use in the CDK already. Thus, the first thing I want to do with CDK is to get descriptors for > compounds, preferably using the InChIKey (but other identifiers if needed). You can't read InChI-Key but perhaps I misunderstand. Second, I want to store the atoms and bonds of the molecular graph in the > data (as RDF). I am therefore really interested in either: > - getting access to the InChI canonicalization algorithm (if CDK has a > version of that outside of the InChI code) OR - obtaining a .mol file where the connection layer atoms are labelled with > the atom numbers from the canonicalization routine > My idea is to see if I can generate the InChI string from the molecular > graph using semantic inferencing We call into the standard InChI native code, however we do provide convenient access to the InChI atoms numbers: http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/graph/invariant/InChINumbersTools.html. It's not too hard to pull these out and set them on a MOLfile or SMILES. John On Thu, 25 Jun 2020 at 18:08, Chalk, Stuart <sch...@unf.edu> wrote: > John > > Thanks for reply. > > So, I have a project where I am converting a lot of data to RDF and as a > result I am adding compounds to a graph DB with lots of descriptors and > identifiers. > Thus, the first thing I want to do with CDK is to get descriptors for > compounds, preferably using the InChIKey (but other identifiers if needed). > > Second, I want to store the atoms and bonds of the molecular graph in the > data (as RDF). I am therefore really interested in either: > - getting access to the InChI canonicalization algorithm (if CDK has a > version of that outside of the InChI code) OR > - obtaining a .mol file where the connection layer atoms are labelled with > the atom numbers from the canonicalization routine > My idea is to see if I can generate the InChI string from the molecular > graph using semantic inferencing > > Finally, while I was hoping it would easy to use CDK right in > PyCharm/Python I now see that I will have to install it separately and use > the command line. > I guess I don’t know, is there command line functionality built into the > CDK jar file? > > Any advice much appreciated… > Stuart > > On Jun 24, 2020, at 7:26 PM, John Mayfield <john.wilkinson...@gmail.com> > wrote: > > Hi Stuart, > > We have some small snippets here ( > https://github.com/cdk/cdk/wiki/Toolkit-Rosetta > <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcdk%2Fcdk%2Fwiki%2FToolkit-Rosetta&data=02%7C01%7Cschalk%40unf.edu%7Cbb26e68251c14bbe4c7708d818961a29%7Cdf29b2fa8929482f9dbb60ff4df224c4%7C1%7C0%7C637286380256993241&sdata=uQmREXtAYy7PI9JEqDH%2Fest4GyQN5modZ4PsmUx8Roo%3D&reserved=0>) > but most of our doc is geared towards having at least some familiarity with > writing and using Java libraries. Saying you don't see a plugin in the IDE > for CDK is like saying you don't see a petrol cap on an electric car. > Removing the Python vs JAVA issues - CDK is a chemistry toolkit (distinctly > not an application) - you link in the JAR file to your own code and use > it's components. IDE plugins help you code, formatting, syntax highlighting > etc. > > Now skipping over a lot of details you can link a Java JAR in different > ways either manually via the classpath or more commonly via a build tool > (e.g. maven/gradle/ant). Before going further I think it would be better to > start from what you hope to do, i.e. why CDK within the PyCharm IDE? Are > you just wanting to have a play around or was there a task you wanted > to accomplish? > > John > > On Wed, 24 Jun 2020 at 23:26, Chalk, Stuart <sch...@unf.edu> wrote: > >> Markus >> >> Thanks for that great idea! >> >> Sadly, I don’t find CDK in the Plugin marketplace for PyCharm. >> All the plugins are coding related of course... >> >> Regards, >> Stuart >> >> On Jun 24, 2020, at 5:35 PM, Markus Sitzmann <markus.sitzm...@gmail.com> >> wrote: >> >> Hi Stuart, >> >> Pycharm is a specialized version of the IntelliJ IDE for python, Intelij >> itself (and pycharm) is written in Java, so the solution for CDK should be >> using Intelij. I am not sure if you can get Java extensions for pycharm >> (the professional versions of pycharm and IntelliJ even require separate >> licenses, but there is a community version of both) >> >> Markus >> >> ----------- >> Markus Sitzmann >> >> >> On 24. Jun 2020, at 23:20, Chalk, Stuart <sch...@unf.edu> wrote: >> >> I am interested in using CDK within the PyCharm IDE. I see that the >> recommendation on the CDK website is to use Cinfony, however the package on >> PyPi does not work and there does not seem to be a version after 2012. >> If anyone has expertise/advise/suggestions please let me know… >> >> I hope everyone out there in CDK land is doing OK given the current >> situation... >> >> Stuart Chalk, Ph.D. >> Professor of Chemistry >> Department of Chemistry, Building 50, Room 3514, >> University of North Florida >> 1 UNF Drive, Jacksonville, FL 32224 USA >> ORCID: 0000-0002-0703-7776 >> P: 904-620-1938 >> F: 904-620-3535 >> E: sch...@unf.edu >> W: http://www.unf.edu/coas/chemistry/ >> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.unf.edu%2Fcoas%2Fchemistry%2Ffaculty%2FStuart_Chalk.aspx&data=02%7C01%7Cschalk%40unf.edu%7Cbb26e68251c14bbe4c7708d818961a29%7Cdf29b2fa8929482f9dbb60ff4df224c4%7C1%7C0%7C637286380256993241&sdata=y7H6vlTCYiZFw4lXNWYPyhUfU0h%2FW%2BbMtBxa30v%2BDTs%3D&reserved=0> >> faculty/Stuart_Chalk.aspx >> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.unf.edu%2Fcoas%2Fchemistry%2Ffaculty%2FStuart_Chalk.aspx&data=02%7C01%7Cschalk%40unf.edu%7Cbb26e68251c14bbe4c7708d818961a29%7Cdf29b2fa8929482f9dbb60ff4df224c4%7C1%7C0%7C637286380256993241&sdata=y7H6vlTCYiZFw4lXNWYPyhUfU0h%2FW%2BbMtBxa30v%2BDTs%3D&reserved=0> >> >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcdk-user&data=02%7C01%7Cschalk%40unf.edu%7Cbb26e68251c14bbe4c7708d818961a29%7Cdf29b2fa8929482f9dbb60ff4df224c4%7C1%7C0%7C637286380257003199&sdata=5%2Bxg0xUaczPuaHhpbfJIVBEFz8M1A94PuyiVM3pRbTQ%3D&reserved=0> >> >> >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcdk-user&data=02%7C01%7Cschalk%40unf.edu%7Cbb26e68251c14bbe4c7708d818961a29%7Cdf29b2fa8929482f9dbb60ff4df224c4%7C1%7C0%7C637286380257003199&sdata=5%2Bxg0xUaczPuaHhpbfJIVBEFz8M1A94PuyiVM3pRbTQ%3D&reserved=0> >> > >
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