Activity for John May
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John May posted a comment on ticket #1384
Yes this is possible but please post this in the appropriate place (cdk-user mailing...
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Resolved
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Inchi with nonstandard options generates standard InChI in CDK 1.5.14
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It will be different if there's stereochemistry, it would be possible to make them...
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BTW martin if you want to fix your example either generate the depiction using SDG...
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nullpointer in circular fingerprinter
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Fixed - problem was more subtle though: https://github.com/cdk/cdk/pull/259 On 5...
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Odd will investigate. BTW we're wanting to move to github for issues.
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Hi Nina, Do you have a test molecule? Also I likely know where the problem is I had...
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Hmmm I did respond by EMail but looks like SF doesn't handled that anymore. Anyways...
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AtomContainerManipulator.convertImplicitToExplicitHydrogens does not treat correctly the chiral atoms with H atom ligand
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Resolved
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Easy to fix so did it now - https://github.com/cdk/cdk/pull/230
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Ahhh! Good find Nikolay, I'll get that patched right away.
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Hi Dale, JChemPaint is no longer in active development, Egon was refering to the...
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Okay I know what's happening now, fix imminent. It's a curious case actually so will...
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Okay I know what's happening now, fix imminent. It's a curious case actually so will...
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Strange bug parsing SDF file and SMARTS matching
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Probably an aromaticity problem. Regards, John W May john.wilkinsonmay@gmail.com...
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With the new API this is controlled explicity with Atom and Bond matching functions.Checkout...
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UIT should mention which Flags are used and overwritten
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It works now providing you have hydrogen counts.
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Kekulisation fails when SDF bond order is 4
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http://efficientbits.blogspot.co.uk/2015/08/mmff-partial-charges-improvements-in...
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ModelBuilder3D bug - incorrect MMFF94 NO_2 atom type
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~~~~~ https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=C1(=C(C(C2(C(C1(C2([H])[H])[H])(C([H])([H])[H])[H])[H])([H])[H])C([H])([H])[H])C([H])([H])[H]&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none...
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[C1(=C(C(C2(C(C1(C2([H])[H])[H])(C([H])([H])[H])[H])[H])([H])[H])C([H])([H])[H])...
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It's not aromatic, we do now support trans bonds in macrocycles (which is what this...
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Hmmm not sure... Group Abbreviation [ISIS/Desktop - not used in current products]...
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Sure you just set the order of the input atoms and generate a 'Generic' or 'Isomeric'...
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Sure is.
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That sounds like the correct fix. Thanks!
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Hmm... maybe via MDLV2000Reader but not SDFReader. TBH if someone has this input...
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SMILESGenerator Canonicity should be switchable
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SMILES parser doesn't deduce radical centres
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Using CXSMILES: CC[CH2] |^2:1| CC[CH] |^2:2| CC[CH] |^2:3|
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Tricky... these would be possible but CC[CH] for example, is that a singlet or t...
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Seven Membered ring preferably in different orientation
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Depends which way I hold my screen :p. Some of this comes down to personal preference,...
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Ahh yes... I'll look into it. A bit crypic but basically you can use the new substructure...
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New template code accounts for this :-)
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Reopenning - was getting round to this,this week
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Error when parsing particular SMILES
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SMARTS: Reaction not supported
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Sure does!
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2D template handling uses fingerprint screens
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No longer relavent, we do SDG tables via canonical SMILES so you can have a huge...
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Update .travis.yml
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I have (previously) redone the Beam double-bond assignment algorithm that should...
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Hmm only one way right? If Chem4Word were LGPL all would be fine :-)
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On 11 March 2016 at 10:53, Nina Jeliazkova vedina@users.sf.net wrote: https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL2369356...
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Much better in ChEMBL 21. Directional Bonds: Cl.Cl.Cc1cccc2\C(=C/3\Nc4ccccc4/C/3=N\OCCN5CCNCC5)\C(=O)Nc12...
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Hmm, This is somewhat an artifacts of the CDK design being based on CML which was...
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Correct, absolute is the only option at the moment and is backed by the InChI (Noel's...
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MDL2000Reader settings
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Closing - test already present. https://github.com/cdk/cdk/blob/master/storage/i...
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Okay, i'll add a test for the IO settings though as it should be possible to turn...
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Nina, can you provide examples for discrepencies please. IIRC the only cases should...
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Merge pull request #196 from tomas-pluskal/master
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Thanks for the hint about the the strict flag. I don't think it's expsoed so would...
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Thanks Louisa. I couldn't remember when I sent the help message but makes sense if...
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[beam:canon] error, Ring closure bonds did not match. Ring was opened with '\' and...
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24 in ChEMBL right? Another case is a tetravalent aromatic carbon anion. Cc1ccc(OC[CH+]n2c3ccccc3n[c-]2CCNC(=O)C4CCCCC4)cc1...
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Grrr ChEMBL and their crappy SMILES. These are bugs in which ever program they use...
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Grrr ChEMBL and their crappy SMILES. These are bugs in which ever program they use...
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Merge pull request #194 from rajarshi/master
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Merge pull request #188 from egonw/patch/dataFe...
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Merge pull request #190 from tomas-pluskal/master
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Merge pull request #186 from egonw/patch/remove...
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Merge pull request #185 from egonw/fix/missingJ...
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NullPointerException when generating depiction of molecule
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Localization of CDK Depictions
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Resolved - https://github.com/cdk/cdk/pull/184
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Patched - https://github.com/cdk/cdk/pull/183
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Thanks for pointing this out, should be an easy fix. John Regards, John W May john.wilkinsonmay@gmail.com...
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ClassCastExpection when creating fingerprint
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Resolved
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Hmm.. solution here would be load as silent for clean up (listener would not be present)....
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absolute smiles generator fails again
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InChITautomerGeneratorTest regressions
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Now resolved
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SmilesParser throws ArrayIndexOutOfBoundsException on invalid smiles
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Resolved https://github.com/cdk/cdk/pull/179
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Hmm, kind of tempted just to put a catch all around the Beam parsing... it's not...
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Oh nope I goofed on the assertion. Ah well - I can prep release notes etc and will...
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Okay will hold off release for now. The SMILES failure I think is just a clean needed...
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Hmm sounds very fragile. Maybe time I finish off this branch - https://github.com/johnmay/cdk/tree/sd-tautomer....
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Merge pull request #177 from egonw/fix/bondMani...
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Merge pull request #176 from egonw/patch/evenFa...
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Merge pull request #175 from egonw/patch/faster...
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Merge pull request #170 from egonw/patch/faster...
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kekulization fails when parsing smiles
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No problem...
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Hi Martin, The SMILES is invalid, if you really want to try and handle it you can...
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Refine a layout after generation.
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Merge pull request #162 from egonw/fixes/various
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Merge pull request #154 from egonw/patch/unitTests
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Nope, but we should add a clearProperties() method. mol.setProperties(new LinkedHashMap<>());...
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AtomContainer properties are returned as unmodifiable collection in 1.5.11
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