[Cdk-user] Fwd: Fwd: CDKPsearch speed

Also useful for others.. -- Forwarded message -- From: John M john.wilkinson...@gmail.com Date: 29 April 2015 at 10:10 Subject: Re: [Cdk-user] Fwd: CDKPsearch speed To: Rajarshi Guha rajarshi.g...@gmail.com Great to hear - ​lots more to come of course. Some points for an extra

Re: [Cdk-user] XlogP descriptor query

Regards, John W May john.wilkinson...@gmail.com On 11 May 2015 at 10:03, John M john.wilkinson...@gmail.com wrote: Hi Rahul, Just to check for the CDKUI, do you mean CDK Descriptor Calculator GUI, Padel, Knime? Which version of CDK are you using. There were some bug fixes between 1.4

Re: [Cdk-user] Fwd: CDKPsearch speed

Just to clarify to the rest of the list on this, the pattern would be [$(N1(a)CCNCC1)] or being more specific and faster - restrict attachments to the piperizine ring. [0Nv3D3+0$(*(a)1[CD2v4][CD2v4][ND2v3][CD2v4][CD2v4]1)] Rereading now I read $pipN=N(c)(C)(C) as having an N=N but I guess

Re: [Cdk-user] XlogP descriptor query

Hi Rahul, Please post questions to list rather than directly. CDK 1.5.x uses the AtomContainer class. There is also the AtomContainerSet for collections of molecules but TBH you're better off using SetIAtomContainer for most uses. J

Re: [Cdk-user] Fwd: XlogP descriptor query

You're call aromaticity on a compound and then discarding it and a different point of the code. You should load your compounds into memory as the table model. mol = (IAtomContainer)mdlreader.next(); // aromaticity perception goes here dr = (DoubleResult)weight.calculate(mol).getValue(); J

Re: [Cdk-user] Fwd: XlogP descriptor query

​Ah right, yes Rahul the latest version for CDK is 1.5.10 (use Maven central). J -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications

Re: [Cdk-user] [cdk:bugs] Re: #1368 Error identifying aromatic bonds in fused rings

I'm still unsure on this but I believe it is correct. Consider biphenyl - a bond between aromatic atoms is not always aromatic. We could perhaps say then a bond between aromatic atoms that is in a ring is aromatic but then consider biphenylene? In your example it is the outer envelope ring that

Re: [Cdk-user] IChemObjectListener

On 6 August 2015 at 17:36, Edmund Duesbury lip1...@sheffield.ac.uk wrote: it's an iterator having an addition/removal somewhere Not a thread collision. Do you have your calculateImplicitHydrogens method. Also note implicit H on a query atom is currently superfluous unless you use it your self.

Re: [Cdk-user] [cdk:bugs] Re: #1368 Error identifying aromatic bonds in fused rings

images 3] Regards, John W May john.wilkinson...@gmail.com On 7 August 2015 at 10:01, John M john.wilkinson...@gmail.com wrote: I'm still unsure on this but I believe it is correct. Consider biphenyl - a bond between aromatic atoms is not always aromatic. We could perhaps say then a bond between

Re: [Cdk-user] IChemObjectListener

Though the code you've quoted is the part that's causing the bug. Can you provide the full stack place please. -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net

Re: [Cdk-user] problems with calculating partial charge with cdk

to fix. Regards, John W May john.wilkinson...@gmail.com On 13 July 2015 at 22:28, John M john.wilkinson...@gmail.com wrote: Do you have a molecule it fails for? John Regards, John W May john.wilkinson...@gmail.com On 13 July 2015 at 21:21, Zheng Shi zs...@ualberta.ca wrote: Hi, I'm

[Cdk-user] CDK Depict

Hi All, I've wanted a write depict service for a while (note we already have https://apps.ideaconsult.net/ambit2/depict which I now see is updated to the new renderers). More so since the Daylight one is now dead. Anyways, just deployed one to OpenShift running the latest CDK SnapShot with some

Re: [Cdk-user] CDK Depict

Pushed - https://github.com/cdk/depict Regards, John W May john.wilkinson...@gmail.com On 25 October 2015 at 16:04, Egon Willighagen wrote: > On Sun, Oct 25, 2015 at 5:02 PM, John May > wrote: > > GitHub can attach binaries to releases,

Re: [Cdk-user] no aromaticity detected for compound O=s1cncc1

; ambit-smarts. Chemaxon had apparently a similar aromaticity concept as > daylight, and the reaction rules have been defined accordingly. Some cannot > be applied when using the standard cdk aromaticity. > > Regards, > Martin > > > > > > > Am 10.11.2015

Re: [Cdk-user] retain unfilled valences

Simple, don't change the molecule :-). You only need atom types here to add hydrogens and you don't need to add hydrogens they're there already when read from SMILES. String smiles = "C[N]C(=O)C(=O)C=O"; IAtomContainer mol = new

[Cdk-user] Molecular Weight

Hi All, Looking around the manipulators is it correct in saying we don't currently have a method to get correct (based on my understanding) molecular weight? My understanding of MW is, if the isotope isn't defined (e.g. null in our case) use the natural mass, however if it is explicitly defined

Re: [Cdk-user] Molecular Weight

On 3 November 2015 at 12:53, John M <john.wilkinson...@gmail.com> wrote: > two closest methods Sorry just to clarify there is one implement on the AtomContainerManipulator and one on the MolecularFormulaManipulator. Regards, John W May john.wilkinson...@

Re: [Cdk-user] Fingerprints in 1.4 und 1.5

Hi Till, Have you found one? Nothing immediately jumps out from recent history - https://github.com/cdk/cdk/blob/master/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java Further history I see count fingerprints introduced but that shouldn't change the bits -

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

manually. So is there a reasonable way to do that? can we just generate canonical form for molecules (like SMILES, then compare the SMILES)? Is it reasonable for this? Or other methods? Thanks. On Mon, Jul 6, 2015 at 3:17 AM, John M john.wilkinson...@gmail.com wrote: Hit send too soon

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

Hi John, If the reader produces and IQueryAtomContainer IQueryAtoms/IQueryBonds then it's simply a matter of passing it into the Pattern class (of UIT). This will do a test of the query against real molecules - if you want to check if one query equals another that's more tricky (I think RDKit has

Re: [Cdk-user] inchi conversion changes compound

-canonical but store stereochemistry. IAtomContainer mol = SmilesGenerator.isomeric().create(container); John Regards, John W May john.wilkinson...@gmail.com On 2 September 2015 at 19:54, John M <john.wilkinson...@gmail.com> wrote: > Hi Martin, > > The InChI is an identifier and

Re: [Cdk-user] inchi conversion changes compound

Can this be avoided? > > > although possible you should perhaps store and index (unique check) you > structures separately. > > Thats what we try to not do, if possible. > > Martin > > > Am 03.09.2015 um 11:32 schrieb John M: > > Hi Martin, > > B

Re: [Cdk-user] Molecule Validation

Hi, One approach would be to try and assign atom types and check for null.. or it might even throw an exception. AtomContainerManipulator.perceiveAndConfigureAtomTypes(mol); // or something similar The atom types are finite opposed to empirical rules so might be too strict depending on your use

[Cdk-user] Preserving public API

Hi all, Wanted a quick poll of thoughts on API changes. CDK does/has gone with the linux kernal style versioning (which they actually dropped in 2003) on odd numbers for unstable (dev version) and even numbers for stable (e.g. 1.4.x=stable,1.5.x=unstable). I've been making an effort in 1.5.x to

Re: [Cdk-user] canonical chiral smiles with free electron pair

> > I have to imagine the electron pair between the "@" and the "]", right? Yep that's correct. It's technically an extension but is widely supported at least by CDK, Open Babel, ChemAxon, ChemDraw, OpenEye, CACTVS. It looks RDKit doesn't support it, not Indigo (at least in the version I have

Re: [Cdk-user] canonical chiral smiles with free electron pair

Hmm, actually from that screenshot it looks like Indigo supports @@ but not @... CCC[S@](C)=O CCC[S@@](C)=O Regards, John W May john.wilkinson...@gmail.com On 26 November 2015 at 18:14, John M <john.wilkinson...@gmail.com> wrote: > I have to imagine the electron pai

[Cdk-user] CDK Release 1.5.12

Hi all, CDK 1.5.12 is now available - https://github.com/cdk/cdk/wiki/1.5.12-Release-Notes. Regards, John W May john.wilkinson...@gmail.com -- ___ Cdk-user mailing list

Re: [Cdk-user] absolute smiles error?

Nice molecules BTW - have added them to my depiction benchmark. -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user

Re: [Cdk-user] canonical chiral smiles with free electron pair

Hi, I'm not entirely sure what the question was but - The lone-pair is treated like an implicit hydrogen and is placed where the central atom is. In the internal representation this means one of the neighbours will also be the central atom. For example in (your email client might cut the tail

[Cdk-user] Structure 2D Layout: generateExperimentalCoordinates

Hi All, Just making some more patches to the 2D layout, and I am tempted to deprecate the method: 'generateExperimentalCoordinates'. Essentially this method first deletes hydrogens, lays out the rest of the structure then adds them back in with a specialised HydrogenPlacer. Anyone know the

Re: [Cdk-user] DepictionGenerator - changing Visibility properties

rs sincerely, > > Nikita > -- > *От:* John M <john.wilkinson...@gmail.com> > *Отправлено:* 3 июня 2016 г. 20:29 > *Кому:* Nikita Kozhukhov > *Тема:* Re: [Cdk-user] DepictionGenerator - changing Visibility properties > > Hi Nikita

Re: [Cdk-user] Reading Mol2 format

Or actually if the hydrogens are explicit in the input they are preserved. Looking this up briefly looks to be the case. Regards, John W May john.wilkinson...@gmail.com On 22 June 2016 at 10:52, John M <john.wilkinson...@gmail.com> wrote: > Hmm, > > That shouldn't be the ca

Re: [Cdk-user] Reading Mol2 format

as when I added the implicit hydrogens and then > exported to smiles then the smiles contains all those hydrogens (as > Explicit/Expanded/Sprouted in your terminology). So to me it looks like it > added explicit hydrogens. > > Tim > > On 22/06/2016 10:08, John M wrote: >

Re: [Cdk-user] Reading Mol2 format

rote: > John > > Thanks for that. Adding implicit hydrogens does indeed resolve the problem. > But does this mean that for formats like this you MUST add IMPLICIT > hydrogens everywhere (there's no way for them to be explicit)? That's ugly! > > Tim > > On 21/06/2016 1

Re: [Cdk-user] Reading Mol2 format

eon...@gmail.com> wrote: > Yes, that's right. They are there in the mol2 file. > > Strange that you need to "add" them again! > > Tim > > On 22/06/2016 11:10, John M wrote: > > Or actually if the hydrogens are explicit in the input they are preserved. >

Re: [Cdk-user] Reading Mol2 format

licit hydrogens, they are real > (explicit) ones. > So presumably they would need to be deleted and then implicit ones adding > back? > > Tim > > On 22/06/2016 11:42, John M wrote: > > Well you can just zero all the counts, > > for (IAtom atom : mol.atoms()) > atom.s

Re: [Cdk-user] PDB reading (repost)

Don't really use that functionality but... 1. Aren't there no bonds in a PDBFile so getting separate fragments isn't clear cut? If you have a sample file would help. 2. For the residue information you can cast the atoms to PDBAtom and access info from there. Regards, John W May

Re: [Cdk-user] SDFile Renderer

On 16 January 2016 at 19:14, John M <john.wilkinson...@gmail.com> wrote: > didn't set properties even John -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Moni

[Cdk-user] Fwd: Clarification about LargestChainDescriptor behavior

h the first could be parametrized >> on element, in which case we'd only need one) >> >> On Thu, Feb 11, 2016 at 1:06 PM, John M <john.wilkinson...@gmail.com> >> wrote: >> >>> Hmm.. should we deprecate one of LargestChainDescriptor >>> or LongestA

Re: [Cdk-user] ICountFingerprint usage question

on this ? Supporting this on the interface > level would be nice as well . (I have a different use case and not > particularly interested in the index building capabilities at the moment ). > > Best regards, > Nina > > > > > > On 3 February 2016 at 12:17

Re: [Cdk-user] DepictionGenerator - unregistered generator?

There are about three different generators which have separate parameters - the depiction generator is intended to hide this, here the withParam is really an expert mode... I should give a better error message though. The depiction generator uses the StandardGenerator and and BasicSceneGenerator

Re: [Cdk-user] Hydrogen display with DepictionGenerator

You can't exactly replicate that because I really think the 'none' hydrogen display is completely wrong as it changes the valence of atoms. However you can choose which atoms have their symbol displayed and by definition hydrogens which allows you to have the 'all', 'heteroterm', and 'hetero'.

Re: [Cdk-user] DepictionGenerator - unregistered generator?

Yep - I'll add a better error message to reflect this. Regards, John W May john.wilkinson...@gmail.com On 26 January 2016 at 16:03, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > So this means that options like this can't be used with DepictionGenerator? > > > On 26/01/2016 1

Re: [Cdk-user] Hydrogen display with DepictionGenerator

Tim Dudgeon <tdudgeon...@gmail.com> wrote: > > > On 26/01/2016 14:57, John M wrote: > > You can't exactly replicate that because I really think the 'none' > hydrogen display is completely wrong as it changes the valence of atoms. > > Not sure what you mean her

Re: [Cdk-user] DepictionGenerator - unregistered generator?

Dudgeon <tdudgeon...@gmail.com> wrote: > Any chance to change this? > Displaying explicit H is pretty important when dealing with query > structures. > Not sure if there are other "critical" "advanced" parameters. > > Tim > > > On 26/01/2016 1

Re: [Cdk-user] inconsistency in ready molfiles

Hi Tim, V3000 reader doesn't accept ChemFiles, if you want to be squeaky clean try ' reader.accepts(IChemFile.class)': https://github.com/cdk/cdk/blob/39e87cafae1f044c16dd101e7a8bd7e1ccb00fa3/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java#L130-L139 Although it could read

Re: [Cdk-user] DepictionGenerator - unregistered generator?

is option do: > > http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/renderer/generators/BasicAtomGenerator.ShowExplicitHydrogens.html > > Is it just a way to turn off display off explicit H with the default being > to display them? > > Tim > > > > > On 26/01/

Re: [Cdk-user] Clarification about LargestChainDescriptor behavior

It's a simple change but it makes sense to me a chain is length>1 John Regards, John W May john.wilkinson...@gmail.com On 18 February 2016 at 14:52, Giovanni Cincilla wrote: > Hi guys, > I just had the possibility to test the corrected version. In general the >

Re: [Cdk-user] Clarification about LargestChainDescriptor behavior

Hopefully soon, I'm in the process of moving house this/next month but one that's settled I'll make it ASAP. John Regards, John W May john.wilkinson...@gmail.com On 18 February 2016 at 16:40, Giovanni Cincilla wrote: > Guys, > Thanks for your quick answers. More than

Re: [Cdk-user] Clarification about LargestChainDescriptor behavior

Cheers for patch Rajarshi, added some clean up the code: https://github.com/cdk/cdk/pull/195 but get a test failure on, "CC=CC(C)=O" expected longest path is 6 but I get 5? 5 looks correct to me? John Regards, John W May john.wilkinson...@gmail.com On 11 February 2016 at 17:03, Rajarshi Guha

Re: [Cdk-user] Reaction depiction

Hi Scooter, This is now much easier, for most use-cases you use the new DepictionGenerator abstract (module cdk-depict will be bundled but needs to be load separately). Lots of tweaks you can do

Re: [Cdk-user] Reaction depiction

On 5 March 2016 at 09:51, John M <john.wilkinson...@gmail.com> wrote: > will be bundled *will be bundled in future but at the moment you need to include it explicitly Regards, John W May john.wilkinson...@

Re: [Cdk-user] create amino acide

Hi Hanouna, Sorry I didn't see your other messages, they were marked as spam due the writing style and yahoo.fr authentication failures. If you're still having trouble building/using the CDK in an IDE (e.g. Eclipse) I put together a guide here: https://github.com/cdk/cdk/wiki/Building-CDK I've

Re: [Cdk-user] create amino acide

Regards, John W May john.wilkinson...@gmail.com On 27 April 2016 at 19:39, hanouna nouna wrote: > hello > i have to create an amino acide from a library of fragment acide and a > library of fragments amine if you can help me with packages of CDK that i > have to use

Re: [Cdk-user] [URGENT] Help needed for processing of aromatic compounds and Structure Search

Hi Yannick, This should be much similar now. First off, you're using some old APIs, SQT still works but it's preferred now to go through 'Pattern'. The SmartsPattern does all the setup needed, other implementations can be faster and more customisable (see later) if you have many SMARTS against

[Cdk-user] Interest in metabolic reaction depictions.

Hey all, I've been doing a fair bit on reaction depictions recently. It's tended to focus on organic chemistry but was wondering how much interest there would be in specialised metabolic reaction depictions. We do much better with the introduction of abbreviations: SMILES:

Re: [Cdk-user] create amino acide

; the amines from ChemSpider database in mol format, and i wont to make a > novel amino acid from this two fragments , and i will use the first way > (using SMARTS) to create it . > > > Le Lundi 2 mai 2016 21h21, John M <john.wilkinson...@gmail.com> a écrit : > > > What do

Re: [Cdk-user] create amino acide

for (IAtomContainer fused : fuse(amineMol, acidMol)) { > System.out.println(smigen.create(fused)); > } > } > } > > } > } > > Regards, John W May john.wilkinson...@gmail.com On 2 May 2016 at 22:38, han

Re: [Cdk-user] Resonance isomers - Aromatic species

Hi Florence, That code is quite old, given it looks like it doesn't work so I'll probably deprecate it... If I understand correctly there are three problems: 1) Not all resonance forms are generated 2) Non transitivity/round tripping, that is if I have resonsance forms a,b,c,d,etc I only get

[Cdk-user] Reaction Agents

Hi All, Lots of the ReactionManipulator methods don't consider agents. Guessing they may have been written before an API change. Is there any objection to me updating the semantics such that getAllMolecules and getAtomCount etc don't ignore agents? Example of current implementations:

[Cdk-user] Project Versioning

This has come up before, but wanted to hear from users. Currently the project versioning system is 1.{odd/even}.{number} where by 1 is fixed for now, odd/even for stability (e.g. 1.4.x stable, 1.5.x unstable), the last number just increments. This system hints that 1.4 is the preferred version as

Re: [Cdk-user] Merge molecules

My mistake, the method add() already does what you need... just can be more efficient. IAtomContainer a; IAtomContainer b; a.add(b); John On 26 November 2016 at 16:56, John M <john.wilkinson...@gmail.com> wrote: > No convenience method, curiously addAtom() does a unique check (

Re: [Cdk-user] Merge molecules

Ahh okay, merge via MCS. Yes you'll need to do that on your own, UniversalIsomorphismTester should help or perhaps something in the SMSD - but as you know NP-Complete so not generally something you want to be doing. John

Re: [Cdk-user] molecule fragments

Hi Tim, You've already used it... see message from 28 Sep. Documentation is out of date (MoleculeSet was deleted) but essentially - http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/graph/ConnectivityChecker.html John On 24 November 2016 at 15:04, Tim Dudgeon

[Cdk-user] CDK 1.5.14 Release

Been live for a couple of days but took a while to write the release notes: https://github.com/cdk/cdk/wiki/1.5.14-Release-Notes -- Check out the vibrant tech community on one of the world's most engaging tech sites,

Re: [Cdk-user] Free QSAR service powered by the CDK

Looks cool. Any chance of updating the depictions? [image: Inline images 3] That's the old code and the renderer that didn't but hydrogens on the atoms by default. John On 3 January 2017 at 12:08, Martin Gütlein wrote: > Hi, > > Based on the awesome CDK, we built a free

Re: [Cdk-user] Free QSAR service powered by the CDK

For comparison: [image: Inline images 1] On 3 January 2017 at 12:13, John M <john.wilkinson...@gmail.com> wrote: > Looks cool. Any chance of updating the depictions? > > [image: Inline images 3] > That's the old code and the renderer that didn't but hydrogens on the > atoms

Re: [Cdk-user] Free QSAR service powered by the CDK

gt; 150=3,4,5,9=true=true=true > > This is why I did not use the new DepictionGenerator yet, because I > thought it might require some effort to change the code. But I will keep > this in mind. > > Martin > > > Am 03.01.2017 um 13:13 schrieb John M: > > For compar

Re: [Cdk-user] Get chain between ringsystems

There isn't a utility function but it's quite simple. Get the fragments as you are already doing, then for each fragment delete all the the cyclic bonds. In practise it's more efficient to build a new molecule and only include the acyclic bonds. Code:

Re: [Cdk-user] XMLIsotope class file missing

Hello team, I have CDK checkout of version 1.4.19 for JChemPaint. But it seems XMLIsotope class file is missing. Is it that I am not using the correct CDK version for JChemPaint ? Please help me with this.Thank you. Regards,karuk Hi Karuk, The JChemPaint master branch is using the CDK 1.5.8.

[Cdk-user] cdk-jar including java sources

Just to follow up on this, I might do include such a jar in the next release. We currently only create an *aggregate* for the JavaDoc but this is also possible for the source - http://maven.apache.org/plugins/maven-source-plugin/aggregate-mojo.html. Regards, John W May john.wilkinson...@gmail.com

Re: [Cdk-user] Stereochemistry during 2D generation of SMILES structure

Patch is now done https://github.com/cdk/cdk/pull/115. Regards, John W May john.wilkinson...@gmail.com On 17 January 2015 at 10:14, Oscar Mora oscarmorape...@gmail.com wrote: Thanks for your message. The workaround works nice. Oscar 2015-01-16 14:52 GMT+01:00 John M john.wilkinson

Re: [Cdk-user] [CDK] Urgent issue : Adding/Removing Explicit Hydrogen atoms

without errors. However, using the first snippet, I could not remove the hydrogen atoms. Could you examine this and let me know where the problem might come from and how to fix it? Regards, Yannick On Tue, Jan 27, 2015 at 3:32 PM, John M john.wilkinson...@gmail.com wrote: Hi Yannick

Re: [Cdk-user] Getting Screen Coordinates for each Atom

Hi Zach, *Renderer.toScreenCoordinates should do what you need https://github.com/cdk/cdk/blob/master/display/renderbasic/src/main/java/org/openscience/cdk/renderer/AbstractRenderer.java#L180-L184 If not I'll look into adding this, but essentially you should just need to consider the scale

Re: [Cdk-user] convert ecfp fingerprint to fragments

Hi Martin, Try here - http://www.jcheminf.com/content/5/1/26 J ​ -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub

Re: [Cdk-user] First property missing from SD file

Hi Egon, In 1.5.x you don't need to remove the name for the SMILES parser it stops at termination characters - note SMILES with tabs is common :-). Is there any ability in the format matcher to use extensions? For example '.smi,.iso,.csmi'. J

Re: [Cdk-user] Generating smiles / query smarts string for QueryAtomContainer

This functionality is not currently available but I think AMBIT might have something? John Regards, John W May john.wilkinson...@gmail.com On 1 July 2015 at 06:28, T. V. Siva Kumar tvsivaku...@gmail.com wrote: Deal All, Is there a way to get the string representation of QueryAtomContainer,

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

Hi, The CDK has always been intended as a toolbox (Lego like) rather than an application. There are a couple of reasons for this but primarily there isn't always a single or best way to accomplish a particular task. If you would like such functionality I believe workflow tools (Knime-CDK) offer a

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

. So is there a reasonable way to do that? can we just generate canonical form for molecules (like SMILES, then compare the SMILES)? Is it reasonable for this? Or other methods? Thanks. On Mon, Jul 6, 2015 at 3:17 AM, John M john.wilkinson...@gmail.com wrote: Hit send too soon... ​ b

Re: [Cdk-user] Old versions from Maven?

Hi Tim, We switched to maven in 1.5.6, http://efficientbits.blogspot.co.uk/2014/02/cdk-now-built-using-maven.html. I think AMBIT might have some in their repo but modules won't match 100%. Nina will be able to confirm.. the repo moved recently and all the links I can find are to the old one.

Re: [Cdk-user] InChI with \KET and \15T options from JAVA

gon Willighagen <egon.willigha...@gmail.com> wrote: > I think this is important for Bioclipse too... > > -- Forwarded message -- > From: John M <john.wilkinson...@gmail.com> > Date: Tue, Oct 4, 2016 at 4:15 PM > Subject: Re: [Cdk-user] InChI with \KET and \

Re: [Cdk-user] InChI with \KET and \15T options from JAVA

tautomer handling) > > Cheers! > Antoni > > On Wed, Oct 5, 2016 at 10:13 AM, John M <john.wilkinson...@gmail.com> > wrote: > >> Okay support added for 15T and KET options. Hopefully the new version of >> InChI is released soon and I can rebuild JNI-InChI and p

Re: [Cdk-user] DepictionGenerator - unregistered IGenerator when in jar

@cdkuser list - resolved due to downstream project including the CDK 1.5.11. Regards, John W May john.wilkinson...@gmail.com On 23 August 2016 at 09:37, John M <john.wilkinson...@gmail.com> wrote: > Nothing odd there... do you have the projected hosted? If not, are you > able to

Re: [Cdk-user] DepictionGenerator - unregistered IGenerator when in jar

Nothing odd there... do you have the projected hosted? If not, are you able to send the zip just to me? Pretty sure I can work out what's interfering but difficult remotely. Could maybe also try the snapshot build? Repository: *https://oss.sonatype.org/content/repositories/snapshots/

Re: [Cdk-user] DepictionGenerator - unregistered IGenerator when in jar

gt; [INFO] | \- org.freehep:freehep-graphicsio-pdf:jar:2.4:compile > [INFO] +- org.javatuples:javatuples:jar:1.2:compile > [INFO] +- com.itextpdf:itextpdf:jar:5.5.9:compile > [INFO] \- org.apache.directory.studio:org.apache.commons.io:jar:2.4: > compile > [INFO]\- commons-io:commons-io:jar:2.4:

Re: [Cdk-user] Complex Molecule Rendering

Steve, You can do this now, no reorganization. Just double checking, you're comping from SMILES right? If you only care about getting an image and not the layout skip the StructureDiagramGenerator entirely. > SmilesParser smipar = new > SmilesParser(SilentChemObjectBuilder.getInstance());