Re: [Rdkit-discuss] Code efficiency improvement
On 12/19/19 7:27 PM, Francois Berenger wrote: > > You should parallelize the processing of molecules, since each can be > worked at independently. > Well, for "a lot" of conformers on "a lot" of molecules that'll work if you have access to a compute cluster and/or are willing to pay for spinning up a bunch of VMs on amazon etc. Otherwise the best you can hope for is to run maybe two per CPU core. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand
On 12/16/19 10:35 AM, Illimar Hugo Rekand wrote: > Fair point. > > But when working in the 100s and 1000s range of PDB-files it would be nice to > have some fewer steps when designing a pipeline. But what's the selection criteria? NMR structures are usually deposited with 20 models, do you want the ligand from every one? Only from the representative one? There's at least one PDB ID (forget which) with 3 stable conformers, i.e. model 1 is not the representative structure. Structures annotated by PDB will have HETATM instead of ATOM for non-standards and ligands, but if your files haven't been processed by them, all bets are off. And so on -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand
On 12/16/2019 10:07 AM, Illimar Hugo Rekand wrote: Would it be viable to create a function where you could create a mol object from specific lines within a pdb-file? PDB file is simple text. There's any number of utilities to extract the lines you want, incl. a plain text editor, why spend time on reinventing the wheel? Dima ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Saving chains from PDB file
On 10/5/2019 10:34 AM, Maciek Wójcikowski wrote: Paolo and Chris, There actually is Rdkit function to do this very task: SplitMolByPDBChainId Why, though? -- It's a punch-card format with chain id in specific column, you just read the lines and sort them into buckets on line[X]. Unless you have NMR multi-model ones where you need to keep track of model/endmdl Dima ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] drawing code
On 8/14/19 3:42 PM, Nicola Zonta wrote: > Hi Greg, > yeah, coordgen issues are probably the best way to keep track of where we > perform poorly. So... is it "schrodinger/coordgenlibs"? I can open an issue and upload the sdf. (And yes, since we actually need all the protons with labels, I am painfully aware of how crowded the image becomes. Perhaps some day I'll manage to persuade my spectroscopist to use a 3D image instead -- her argument is that having to move the mouse to the other screen to rotate that thing all the time is too distracting.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] drawing code
PS I played with it a bit: the least ugly version is if you MMFF94-optimize it after rdkit.Chem.rdCoordGen.AddCoords() It's still far from perfect. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] drawing code
Hi all, for our workflow we need molecule drawings with all atoms (incl. Hs) explicitly labeled. And every once in a while we run into molecules that don't look so good. I wonder if it's worth collecting them somewhere, maybe another github repo under rdkit? -- for future developers of 2D layout algorithms. Here's out latest one for example. The thing about this one is, the molecule itself is not that bad, it not clear why the picture isn't any better. Enjoy. (Try it in OB if you think RDKit's pix is bad. ;) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu CID_10955174_alatised.sdf Description: application/vnd.kinar signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] High-quality matplotlib drawing?
On 8/9/19 12:42 PM, Wout Bittremieux wrote: > Alternatively I could export both the spectrum plot and the molecule to > SVG files and then combine them afterwards. But in that case it's not > possible to manipulate both elements in a single matplotlib figure. Yeah, that's what I meant but you're right: getting that to work in an interactive display in a notebook would be a hassle. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] High-quality matplotlib drawing?
On 8/7/2019 7:20 PM, Wout Bittremieux wrote: ... Unfortunately the quality of the molecule drawing is rather poor (see attachment; nonsensical spectrum and molecule). This seems to be true for non-SVG drawing in general, and unfortunately it's not really possible to combine SVG output with Matplotlib functionality. Hmm... have you tried wrapping the molecule svg in a `transform="translate(x,y)"` or something along those lines? Dima ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Read only first model of a pdb-file
On 5/29/19 3:31 PM, David Cosgrove wrote: > Biopython is excellent for extracting particular models from a PDB file. As > Dimitri suggests, you can then pass the result into your processing script. > It is quite straightforward to write the relevant PDB model to a string in > PDB format and parse with RDKit’s PDB reader, for example. Just to add more confusion, if you are working with PDB entries, you may also want to look at """ REMARK 210 CONFORMERS, NUMBER CALCULATED : REMARK 210 CONFORMERS, NUMBER SUBMITTED: REMARK 210 CONFORMERS, SELECTION CRITERIA : REMARK 210 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : """ (the last one is the one I mentioned earlier) You would typically have "lowest energy" as selection criteria and "best reperesentative" is the minimized average of those submitted. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Read only first model of a pdb-file
On 5/29/19 8:19 AM, Illimar Hugo Rekand wrote: > Hey, RDKitters! > > > I am currently trying to figure out how to only read in the first model of a > pdb-file. I've designed a script that performs calculations on a per-atom > basis, and this is very slow when it tries to account for multiple models, > for example with a NMR-structure. Pre-process the PDB file to cut out the model you want. In the files annotated by PDB it should be the first model and I belive tehre is a REMARK something-or-other "best model in this ensemble". However this fails for multiple conformers in one file, there is at least one in PDB. (It's been a while since I did this so I don't remember the remark number, nor the multi-conormer entry id off the top of my head.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit Release 2018.09.2 available
On 2/22/19 5:01 PM, Markus Sitzmann wrote: > It is odd, but one thing I learned from using conda is, sometimes it helps > to ignore problems and wait for a bit and they might go away ... well, I > have similar experiences with maven :-) ... but most likely I do something > stupid which I don't see right now :-) Simple test is to make a clean one and install only rdkit and nothing else and see what happens. It's pretty common for packagers to do something-that-may-or-may-not-be-stupid and have a dependency on an specific version of some other package that depends on a specific version of another package that depends on... turtles all the way down. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Warning as error
On 1/21/19 1:42 PM, Jean-Marc Nuzillard wrote:
> sys.stderr.write("Bad: %s\n" % (mol.GetProp("_Name"),))
> I know which bond has a problem but I still do not know in which molecule.
Are you sure they all have _Name's? I'd just print the count outside of
the try/catch block and ignore ones not followed by the warning message.
(And run with #!/usr/bin/python -u and/or flush sys.stdout/stderr on
every iteration for good measure.)
--
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Re: [Rdkit-discuss] InChI to Mol to InChi
On 12/18/18 1:57 PM, JEAN-MARC NUZILLARD wrote: > Dimitri, how can alatis help me to find a first draft of 3D structure > for a few ten thousands of compounds from InChI strings? It won't, you have to feed it a 3D structure. However its InChI string and/or MOL block will give you the same 3D structure with the same atom labels on round-trip, *as long as you don't removeH/addH/recalculate conformers etc.* (At least on all molecules they tried and I think that includes the entire PubChem.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI to Mol to InChi
On 12/18/18 11:34 AM, JEAN-MARC NUZILLARD wrote: > Molecules m1 and m2 have identical SMILES representations > but different InChI representations, which I find odd. *shrug* this is precisely why they came up with alatis: take a molecule in any input format, round-trip it through any cheminformatics program, there's 50% chance you'll get a different molecule out. That's how chemistry works when it meets compsci. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI to Mol to InChi
On 12/17/18 4:50 PM, JEAN-MARC NUZILLARD wrote: > Is there any more deterministic procedure than the one of trying until > success is obtained? > > How do I determine the InChI string of a conformer obtained after > multiple embedding? This representation keeps 3D config: http://alatis.nmrfam.wisc.edu/ Generally speaking the problem with InChI is that the only *required* layer is the formula. Therefore *an* InChI string cannot be used to differentiate conformers, you need the InChI string with all the relevant layers and all the protons. https://www.nature.com/articles/sdata201773 -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 回复： 回复： Help: How to set timeout for the function namedRunReactants
On 11/15/2018 11:41 AM, Francis Atkinson wrote: > products = rxn.RunReactants([mol], maxProducts=1) > Boost.Python.ArgumentError: Python argument types in > ChemicalReaction.RunReactants(ChemicalReaction, list) > did not match C++ signature: > RunReactants(RDKit::ChemicalReaction*, boost::python::list) > RunReactants(RDKit::ChemicalReaction*, boost::python::tuple) > > I presume I am missing something, but what?! It doesn't list a candidate w/ the 3rd parameter so I'd say maxProducts is not exposed to python in your version. ICBW, though: c++ - boost - swig - python is not something I'd want to ever become familiar with... -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svg: next question
On 11/02/2018 12:19 AM, Greg Landrum wrote: > On Fri, Nov 2, 2018 at 12:32 AM Dimitri Maziuk via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> wrote: > >> Does anyone know where TH does >> >> >> >> come from? -- > > > assuming you're using the RDKit's MolDraw2DSVG class, that comes from here: > https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp#L53 Should it be changed to utf-8? I suspect any system where RDKit builds at this point is using that, and I believe technically element can contain unicode. E.g. you should be able to render your amino-acids with atoms labeled w/ Greek alphas, betas, etc. as per IUPAC. >> I have two SVGs generated by the same container running on >> the same linux host and one has the above, the other has >> >> >> > > No idea where that might have come from, but it's not MolDraw2DSVG Weird. I'll see if I get any more of those... -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Plotting values next to atoms
On 11/02/2018 07:59 AM, Eric Jonas wrote: > Hello! I'm trying to figure out if there's any known or sane way to > automatically plot numerical values adjacent to atoms using the rdkit > drawing machinery. Ideally I'd like to annotate certain atoms > programmatically with values. This draws atom labels: op = dr.drawOptions() for i in range( self._mol.GetNumAtoms() ) : op.atomLabels[i] = self._mol.GetAtomWithIdx( i ).GetSymbol() + str( (i + 1) ) HTH, -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] svg: next question
Does anyone know where TH does come from? -- I have two SVGs generated by the same container running on the same linux host and one has the above, the other has The host is on utf-8, of course, and I can double-check the container thought I don't see it using anything else... certainly not cp1252. Any ideas? -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] svg transparent background
Hi all, I finally got around to playing w/ drawing code in the current version and I like it, but how do I set background colour to transparent? dr = rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG( 1000, 1000 ) results in in the output, which for now I'll just post-process away. Thx, -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compilation Errors on RHEL7
On 10/24/2018 12:10 PM, Dimitri Maziuk via Rdkit-discuss wrote: > Yes. I once spent a couple of hours trying and ended up installing docer docker -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compilation Errors on RHEL7
On 10/24/2018 11:32 AM, Oellien, Frank wrote: > Hi, > > I am trying to compile RDKit on a RHEL7 system using Python 2.7 and Boost > 1.68 ... > Has somebody already seen this error? Yes. I once spent a couple of hours trying and ended up installing docer and pulling a conda/rdkit container instead. I strongly recommend doing that, or finding a singularity version of the same. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
On 10/03/2018 03:23 PM, Peter St. John wrote: > Ah, well I suppose the follow up question is then does 'AddHs' add > hydrogens in a deterministic fashion? It should, what's not guaranteed is that it will be the right order. Obviously, if (using my previous example) L- and D-alanine is the "same molecule" for your purposes, then it doesn't matter. If it does mater, then alatis (the link I sent earlier) is the best option that I know of. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
On 10/02/2018 03:32 PM, Peter St. John wrote: > I.e., if I create a new rdkit Molecule with rdkit.Chem.MolFromSmiles(xxx), > will the bond ordering always be the same? If not, does anyone know a a > robust way of specifying a bond within a molecule as a string-based > representation? https://www.nature.com/articles/sdata201773 -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Creating Mol Object From SD File
On 08/29/2018 01:54 PM, Chris Murphy wrote: > Hi, > > I finally realized that when passing an sdf string to Chem.MolFromMolBlock, > the Mol object will not retain the properties from the sdf. Ugh. You're right. +1 for a MolFromSdfBlock() that doesn't lose the properties. > Also, it seems that SDMolSupplier.next() does not work anymore? if sys.version_info[0] == 2 : next() elif sys.version_info[0] == 3 : __next()__ else : raise Exception( "Go! is looking better every day" ) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 06/13/2018 01:10 PM, Greg Landrum wrote: > You don't excerpt the earlier message where I explained how to get things > working without needing X installed. Was that not clear? If you don't want > to have X installed but would still like to use the conda builds, you can > just install the two packages from the RDKit channel. There's more to it than that. Conda as packaged for a given distro has itself a set of dependencies. As I said before, *for example* installing conda on a centos 6 server will take it off the network at the next maintenance reboot, unless the installer knows they're doing and watches the whole ting very carefully. No, it's not your problem, you're doing the best you can, and thank you for that. But the end result is that ready-made builds are getting increasingly too bloated to be of use, and custom builds are too "non-trivial" to attempt. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 06/13/2018 11:44 AM, Geoffrey Hutchison wrote: > > No, you can compile RDKit yourself if you don't want to use X11 features. You > wanted to install through conda, which has a set of packages for 'most use' - > YMMV. Sadly, MM does indeed V. On my box I can't, not without also compiling boost myself -- and I haven't looked further. Wouldn't be surprised if it takes me all the way to compiling GNU Compiler Collection myself too. Some day I'll get a round tuit to set up an alpine build VM and see if it compiles there... so I can roll it into a reasonable-sized docker container, but compiling it on my desktop is simply not worth my time. (And our compute nodes are the same or older as my desktop, so if it doesn't work on my box, we can't deploy it anywhere.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 6/13/2018 10:06 AM, Greg Landrum wrote: Note that my answer assumes that there is a reason that you don't have X11 installed on your linux box. If that's not the case, you should be able to fix things "more easily" by installing X Quite frankly, this is rapidly becoming unusable as a software platform. I need to install X11 to UUF-optimize a MOL? Seriously? E.g. on centos anaconda installs NetworkManager (why?) which comes in "enabled at boot" but not configured, so next time you reboot, perhaps weeks later, tada! -- you've lost the network. And don't get me started on having several versions of boost coexist... Dima -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] convert a smiles file to a xyz file
On 5/23/2018 10:23 AM, Chenyang Shi wrote: A separate question is that is the converted molecular structure from SMILES the same as that taken from a crystal structure? Provided there's no undefined/different stereochemistry on SMILES side, no quirks with added protons, and so on and so forth... for a small simple molecule... maybe. Dima -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
