Re: [Rdkit-discuss] Possible rotatable bonds replacement
> I could add the new descriptor as Toby provided it. People are then > free to pick between NumRotatableBonds() and NumStrictRotatableBonds > (). This has the advantage of maintaining strict backwards > compatibility, but I could imagine it being confusing/irritating to > people using the code to have to choose between them (or, worse, using both). > > Another option is to just replace the current NumRotatableBonds() > SMARTS with the new one. > This loses backwards compatibility, but replaces NumRotableBonds() > with something more correct. > > Finally, I could take a hybrid approach: replace the default > NumRotatableBonds() with the new one, but add an extra argument that > allows the old one to be used. > > I'm leaning towards the second option. I'd normally go with the > third, but I almost view this as a bug fix for the rotatable bonds definition. > > Comments? suggestions? Other options? I like your idea of your hybrid approach which would mean backwards compatibility. paul This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Possible rotatable bonds replacement
Dear all, A question for the community: Toby Wright submitted a pull request this week that introduces a new, stricter, rotatable bond definition: https://github.com/rdkit/rdkit/pull/211/files The new SMARTS, re-formatted to be somewhat more readable, is: [!$(*#*)&\ !D1&\ !$(C(F)(F)F)&\ !$(C(Cl)(Cl)Cl)&\ !$(C(Br)(Br)Br)&\ !$(C([CH3])([CH3])[CH3])&\ !$([CD3](=[N,O,S])-!@[#7,O,S!D1])&\ !$([#7,O,S!D1]-!@[CD3]=[N,O,S])&\ !$([CD3](=[N+])-!@[#7!D1])&\ !$([#7!D1]-!@[CD3]=[N+])]\ -!@\ [!$(*#*)&\ !D1&\ !$(C(F)(F)F)&\ !$(C(Cl)(Cl)Cl)&\ !$(C(Br)(Br)Br)&\ !$(C([CH3])([CH3])[CH3])] Toby was quite careful and added a new descriptor - NumStrictRotatableBonds() - that uses this SMARTS. I see a few options to deal with this: I could add the new descriptor as Toby provided it. People are then free to pick between NumRotatableBonds() and NumStrictRotatableBonds(). This has the advantage of maintaining strict backwards compatibility, but I could imagine it being confusing/irritating to people using the code to have to choose between them (or, worse, using both). Another option is to just replace the current NumRotatableBonds() SMARTS with the new one. This loses backwards compatibility, but replaces NumRotableBonds() with something more correct. Finally, I could take a hybrid approach: replace the default NumRotatableBonds() with the new one, but add an extra argument that allows the old one to be used. I'm leaning towards the second option. I'd normally go with the third, but I almost view this as a bug fix for the rotatable bonds definition. Comments? suggestions? Other options? -greg -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI roundtrip
Hi George, Don’t quote me on this but I’m guessing the reason Indigo does better is probably because they parse the input coordinates and wedge/hatch labels to the InChI API where as RDKit sets the winding. That is in Indigo’s case - InChI will look at the depiction and interpret where the stereo centres are whilst RDKit tells it explicitly. Basically RDKit is actually round tripping through it’s object model it whilst Indigo isn’t. Anyways a little on InChI and stereochemistry…. Tl;DR; 200/90,000 (0.2%) ain’t bad. When stereochemistry is validated (for https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL287254) the tetrahedral centre on the ring will be removed - it does not have a configuration. In that depiction it doesn’t matter whether the bond is up or down because the centre is dependant on the configuration of the other stereo centre in the ring. Since the other stereo centre doesn’t have a configuration it doesn’t mater want configuration this one has. Formally, a stereo centre is not a stereo centre if there is a permutation that inverts only it’s [the stereo centre] configuration. Clearly this is only the case when both have a configuration. For a more concise example consider these structures. InChI=1S/C8H16/c1-7-3-5-8(2)6-4-7/h7-8H,3-6H2,1-2H3/t7-,8? InChI=1S/C8H16/c1-7-3-5-8(2)6-4-7/h7-8H,3-6H2,1-2H3 Load the first one into your favourite structure diagram editor and invert the wedge/hatch bond. Generating a new InChI will give the same InChI string. Hmm... but didn't inverted the stereo centre? If we got the same InChI it must not matter configuration it is. But the InChI does encode this as seen above. Clearly we do want the two stereoisomers to be different but I’m not sure how useful it is that the above two are not the same. InChI=1S/C8H16/c1-7-3-5-8(2)6-4-7/h7-8H,3-6H2,1-2H3/t7-,8+ InChI=1S/C8H16/c1-7-3-5-8(2)6-4-7/h7-8H,3-6H2,1-2H3/t7-,8- Anyways this isn’t really a problem with RDKit, check out the OEChem release notes: http://www.eyesopen.com/docs/toolkits/current/html/OEChem_TK-csharp/releasenotes/version1_9_2.html They did have page showing exactly what they disagree with but that seems to of gone missing… thankfully PubChem also do it :-)… CID 2375263 : InChI=1S/C17H11Cl3FN3/c1-10-14(9-22-12-4-7-16(21)15(19)8-12)17(20)24(23-10)13-5-2-11(18)3-6-13/h2-9H,1H3 (notice standard InChI = 1S). If you feed InChI the depiction it will add a stereo configuration for the double bond so you’ll get one of the following (depending on depiction) InChI=1S/C17H11Cl3FN3/c1-10-14(9-22-12-4-7-16(21)15(19)8-12)17(20)24(23-10)13-5-2-11(18)3-6-13/h2-9H,1H3/b22-9+ InChI=1S/C17H11Cl3FN3/c1-10-14(9-22-12-4-7-16(21)15(19)8-12)17(20)24(23-10)13-5-2-11(18)3-6-13/h2-9H,1H3/b22-9- Testing last august I found ~250,000 (0.5%) differences in PubChem-Compound. The InChI is great but it’s not perfect and there will always be differences based on what toolkits agree on. There is of course an argument that the InChI is something they can agree on… InChI version 2 is where things get get really fun. J On 30 Jan 2014, at 19:55, George Papadatos wrote: > I agree; that's why I tried to minimise 'doctoring' as much as I could in > this case. > George > > > On 30 January 2014 19:46, Dimitri Maziuk wrote: > On 01/30/2014 01:07 PM, George Papadatos wrote: > > OK just to add some fuel to this fire: A colleague of mine and I looked at > > the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and > > rdkit nodes. > > > Rdkit had 10 times more discrepancies > > If it's any consolation OpenBabel stereo perception does not do CIP > ordering so any input that didn't have correct stereochemistry or it was > removed during whatever processing you did, its output InChi will have a > wrong stereo layer. I expect with properly doctored input you'll get > 100% discrepancies there. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > -- > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > -- > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://puba
Re: [Rdkit-discuss] InChI roundtrip
On 01/30/2014 01:55 PM, George Papadatos wrote: > I agree; that's why I tried to minimise 'doctoring' as much as I could in > this case. What I meant by "doctoring" is select only the inputs that are known to produce discrepancies. One of the features that makes inchi useless is that formula is the only layer that's required. Everything else is optional. Let's say you read in InChI=1/C2H6O and print out InChI=1/C2H6O/c1-2-3. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI roundtrip
I agree; that's why I tried to minimise 'doctoring' as much as I could in this case. George On 30 January 2014 19:46, Dimitri Maziuk wrote: > On 01/30/2014 01:07 PM, George Papadatos wrote: > > OK just to add some fuel to this fire: A colleague of mine and I looked > at > > the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and > > rdkit nodes. > > > Rdkit had 10 times more discrepancies > > If it's any consolation OpenBabel stereo perception does not do CIP > ordering so any input that didn't have correct stereochemistry or it was > removed during whatever processing you did, its output InChi will have a > wrong stereo layer. I expect with properly doctored input you'll get > 100% discrepancies there. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > > -- > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI roundtrip
On 01/30/2014 01:07 PM, George Papadatos wrote: > OK just to add some fuel to this fire: A colleague of mine and I looked at > the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and > rdkit nodes. > Rdkit had 10 times more discrepancies If it's any consolation OpenBabel stereo perception does not do CIP ordering so any input that didn't have correct stereochemistry or it was removed during whatever processing you did, its output InChi will have a wrong stereo layer. I expect with properly doctored input you'll get 100% discrepancies there. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI roundtrip
Hi Igor, Thanks for the quick reply. I just did in my workflow. The number of discrepancies increased from 200 to 950 :( George On 30 January 2014 19:19, Igor Filippov wrote: > George, > > Have you added coordinates to the mols converted from InChI? > It made a huge difference for the examples I've tried. > > Igor > > > On Thu, Jan 30, 2014 at 2:07 PM, George Papadatos wrote: > >> OK just to add some fuel to this fire: A colleague of mine and I looked >> at the inchi roundtrip using KNIME 2.9 and the latest versions of indigo >> and rdkit nodes. We used ~90,000 inchis from chembl_17, converted them to >> mols (sanitise + remove Hs), removed the ones that fail to convert, and >> then we converted back to inchis (standard ones, no extra parameters). We >> assessed the discrepancies between indigo and rdkit inchis compared to the >> original input inchis that are stored in chembl. >> Rdkit had 10 times more discrepancies with 200 failures as opposed to 21 >> from indigo. This rate (~0.2%) was also confirmed using ~1 million inchis. >> >> I had a closer look to a couple of cases here: >> http://nbviewer.ipython.org/gist/madgpap/8715974 >> >> It seems that there is more that one reason for the failure. I totally >> understand Greg's caution about the inchi2mol conversion, but given the >> difference between rdkit and indigo, there might room for improvement. Any >> insights would be very much appreciated. >> >> Btw, the KNIME workflow and full list of fails are available to you. >> >> Cheers, >> >> George >> >> >> >> On 30 January 2014 04:11, Greg Landrum wrote: >> >>> Yeah, I have been tempted several times to remove the InChI->RDKit >>> functionality entirely >>> >>> >>> >>> On Thu, Jan 30, 2014 at 5:05 AM, Igor Filippov < >>> igor.v.filip...@gmail.com> wrote: >>> Thank you, Greg! Very nice explanation and I think this issue has confused people before me as well. I am going to have to keep reminding myself about it as the subject comes up every now and then. Igor On Jan 29, 2014 10:59 PM, "Greg Landrum" wrote: > Hi Igor, > > On Wed, Jan 29, 2014 at 2:04 PM, Igor Filippov < > igor.v.filip...@gmail.com> wrote: > >> Greg et al, >> >> Here is a little script that demonstrates a problem with fingerprints >> after the roundtrip through InChI. >> My input mol file is also attached. >> As you can see the similarity between "before" and "after" is not 1 >> in 45 out of 100 cases. >> In one case it is as low as 0.29. Could someone take a look and tell >> me what I'm doing wrong? >> > > Ah! Now I see what you're doing and understand the problem. > > It's really important when using InChI to remember that InChI is > designed to be an identifier, not an interchange format. The InChI > algorithm modifies the molecule as part of its canonicalization step. This > modification includes standardizing tautomers. > > Here's an example of the type of substructure modification that > happens in your molecules: > input smiles c1c1C(=O)Nc1c1 on begin converted to InChI and > back yields: OC(=Nc1c1)c1c1 > > Basically: If you think you know what your molecules are, you probably > should be building them from SMILES or CTAB, not InChI. > > Apologies that I didn't think of this before; I was just focusing on > the stereochemistry. > > -greg > >>> >>> >>> -- >>> WatchGuard Dimension instantly turns raw network data into actionable >>> security intelligence. It gives you real-time visual feedback on key >>> security issues and trends. Skip the complicated setup - simply import >>> a virtual appliance and go from zero to informed in seconds. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >>> ___ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>> >> >> >> -- >> WatchGuard Dimension instantly turns raw network data into actionable >> security intelligence. It gives you real-time visual feedback on key >> security issues and trends. Skip the complicated setup - simply import >> a virtual appliance and go from zero to informed in seconds. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedb
Re: [Rdkit-discuss] InChI roundtrip
George, Have you added coordinates to the mols converted from InChI? It made a huge difference for the examples I've tried. Igor On Thu, Jan 30, 2014 at 2:07 PM, George Papadatos wrote: > OK just to add some fuel to this fire: A colleague of mine and I looked at > the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and > rdkit nodes. We used ~90,000 inchis from chembl_17, converted them to mols > (sanitise + remove Hs), removed the ones that fail to convert, and then we > converted back to inchis (standard ones, no extra parameters). We assessed > the discrepancies between indigo and rdkit inchis compared to the original > input inchis that are stored in chembl. > Rdkit had 10 times more discrepancies with 200 failures as opposed to 21 > from indigo. This rate (~0.2%) was also confirmed using ~1 million inchis. > > I had a closer look to a couple of cases here: > http://nbviewer.ipython.org/gist/madgpap/8715974 > > It seems that there is more that one reason for the failure. I totally > understand Greg's caution about the inchi2mol conversion, but given the > difference between rdkit and indigo, there might room for improvement. Any > insights would be very much appreciated. > > Btw, the KNIME workflow and full list of fails are available to you. > > Cheers, > > George > > > > On 30 January 2014 04:11, Greg Landrum wrote: > >> Yeah, I have been tempted several times to remove the InChI->RDKit >> functionality entirely >> >> >> >> On Thu, Jan 30, 2014 at 5:05 AM, Igor Filippov > > wrote: >> >>> Thank you, Greg! >>> Very nice explanation and I think this issue has confused people before >>> me as well. I am going to have to keep reminding myself about it as the >>> subject comes up every now and then. >>> >>> Igor >>> On Jan 29, 2014 10:59 PM, "Greg Landrum" wrote: >>> Hi Igor, On Wed, Jan 29, 2014 at 2:04 PM, Igor Filippov < igor.v.filip...@gmail.com> wrote: > Greg et al, > > Here is a little script that demonstrates a problem with fingerprints > after the roundtrip through InChI. > My input mol file is also attached. > As you can see the similarity between "before" and "after" is not 1 in > 45 out of 100 cases. > In one case it is as low as 0.29. Could someone take a look and tell > me what I'm doing wrong? > Ah! Now I see what you're doing and understand the problem. It's really important when using InChI to remember that InChI is designed to be an identifier, not an interchange format. The InChI algorithm modifies the molecule as part of its canonicalization step. This modification includes standardizing tautomers. Here's an example of the type of substructure modification that happens in your molecules: input smiles c1c1C(=O)Nc1c1 on begin converted to InChI and back yields: OC(=Nc1c1)c1c1 Basically: If you think you know what your molecules are, you probably should be building them from SMILES or CTAB, not InChI. Apologies that I didn't think of this before; I was just focusing on the stereochemistry. -greg >>> >> >> >> -- >> WatchGuard Dimension instantly turns raw network data into actionable >> security intelligence. It gives you real-time visual feedback on key >> security issues and trends. Skip the complicated setup - simply import >> a virtual appliance and go from zero to informed in seconds. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > > > -- > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://l
Re: [Rdkit-discuss] InChI roundtrip
OK just to add some fuel to this fire: A colleague of mine and I looked at the inchi roundtrip using KNIME 2.9 and the latest versions of indigo and rdkit nodes. We used ~90,000 inchis from chembl_17, converted them to mols (sanitise + remove Hs), removed the ones that fail to convert, and then we converted back to inchis (standard ones, no extra parameters). We assessed the discrepancies between indigo and rdkit inchis compared to the original input inchis that are stored in chembl. Rdkit had 10 times more discrepancies with 200 failures as opposed to 21 from indigo. This rate (~0.2%) was also confirmed using ~1 million inchis. I had a closer look to a couple of cases here: http://nbviewer.ipython.org/gist/madgpap/8715974 It seems that there is more that one reason for the failure. I totally understand Greg's caution about the inchi2mol conversion, but given the difference between rdkit and indigo, there might room for improvement. Any insights would be very much appreciated. Btw, the KNIME workflow and full list of fails are available to you. Cheers, George On 30 January 2014 04:11, Greg Landrum wrote: > Yeah, I have been tempted several times to remove the InChI->RDKit > functionality entirely > > > > On Thu, Jan 30, 2014 at 5:05 AM, Igor Filippov > wrote: > >> Thank you, Greg! >> Very nice explanation and I think this issue has confused people before >> me as well. I am going to have to keep reminding myself about it as the >> subject comes up every now and then. >> >> Igor >> On Jan 29, 2014 10:59 PM, "Greg Landrum" wrote: >> >>> Hi Igor, >>> >>> On Wed, Jan 29, 2014 at 2:04 PM, Igor Filippov < >>> igor.v.filip...@gmail.com> wrote: >>> Greg et al, Here is a little script that demonstrates a problem with fingerprints after the roundtrip through InChI. My input mol file is also attached. As you can see the similarity between "before" and "after" is not 1 in 45 out of 100 cases. In one case it is as low as 0.29. Could someone take a look and tell me what I'm doing wrong? >>> >>> Ah! Now I see what you're doing and understand the problem. >>> >>> It's really important when using InChI to remember that InChI is >>> designed to be an identifier, not an interchange format. The InChI >>> algorithm modifies the molecule as part of its canonicalization step. This >>> modification includes standardizing tautomers. >>> >>> Here's an example of the type of substructure modification that happens >>> in your molecules: >>> input smiles c1c1C(=O)Nc1c1 on begin converted to InChI and back >>> yields: OC(=Nc1c1)c1c1 >>> >>> Basically: If you think you know what your molecules are, you probably >>> should be building them from SMILES or CTAB, not InChI. >>> >>> Apologies that I didn't think of this before; I was just focusing on the >>> stereochemistry. >>> >>> -greg >>> >> > > > -- > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] standardiser tool, again
I should have mentioned that the HTML version of the documentation is also available at... http://wwwdev.ebi.ac.uk/chembl/extra/francis/standardiser/ Original Message Subject: standardiser tool Date: 2014-01-29 13:05 From: Francis Atkinson To: rdkit-discuss@lists.sourceforge.net Hello, Those who attended the RDKit UGM at the EBI may remember that I gave a talk on a structure standardisation tool I'd been working on. A few people expressed an interest, so I said I'd see about open-sourcing it. Well, I've done some work to tidy it up a bit, and it's now available from GitHub at 'https://github.com/flatkinson/standardiser'. Hopefully it's clear enough how it works, but I'd be happy to answer any questions. Any feedback on the tool itself or the documentation provided would would also be much appreciated. Thanks, Francis -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
