You can also use a different electron donation model which doesn’t need atom types.- JohnOn 12 Oct 2023, at 02:07, Uli Fechner wrote:Hi,Welcome to the CDK community.Atom types can be determined withAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);If you do this before
Hi Tom,
Can you open an issue on GitHub and I will fix it. Andrew has given a good
explanation. My view is the simple fix is we add the flag in (1), or I could
write a better canonicalisation algorithm (2). I did recently present to inchi
the “how” on inorganic stereochemistry (octahedral
Yep that’s correct, they are just integers and there are different ways to
encode them.
- John
> On 25 Jul 2022, at 17:42, #NG WOON YEE# wrote:
>
>
> Hi Egon,
>
> I have tried the getFingerprint() method but the outputs are not a series of
> fixed-length integers too. The output remains
Use RDKit
- John
> On 25 Jul 2022, at 14:25, dpoly wrote:
>
>
> Thank you.. That’s helpful (I guess).
>
> So can you suggest where I should look? Open Babel? I guess I could use C++,
> although it’s a lot less convenient.
>
> Regards
> David M Bennett FACS
>
> Polygamo – Programming
Which parts does it depend on? A better way to do the versioning is to use the
“” in maven - no need to modify the ambit props
- John
> On 22 Jul 2022, at 09:26, Uli Fechner wrote:
>
>
> Thank you for your reply, John.
>
> I bumped the cdk dependency in the POM of ambit by changing the
Also Java 8/11 are preferred
- John
> On 30 Dec 2020, at 06:25, Winod Dhamnekar
> wrote:
>
>
> Hello,
> I have java , java development kit 32 bit and 64 bit installed on my laptop.
> I have installed apache maven 3.6.3 and its path is C: \Program
> Files\apache-maven-3.6.3. I have
You need to run mvn install from the CDK directory, the install just builds the
code and puts the JAR files in the maven repo directory (~/.m2/repository on
Linux not sure where it is on Windows).
If you just want to use the CDK you can actually just download the release jar
from GitHub or let
I try and find time
- John
> On 22 Dec 2020, at 12:20, Egon Willighagen wrote:
>
>
>
> Yes, half yearly releases would be nice. I second the usefulness of being
> able to cite a specific version, ideally one on Zenodo with DOI, and that
> -SNAPSHOT is not something I would like in a paper
So the source was always going to be the primary dist, but it is convenient to
have the WAR download.
GitHub can attach binaries to releases, we do it already:
https://github.com/cdk/cdk/releases/tag/cdk-1.5.11. Given the whole SourceForge
Gimp fiasco I’m wary of using it.
John
On Oct 25,
the same between them.JBegin forwarded message:From: John May john.wilkinson...@gmail.comSubject: Re: [Cdk-devel] Images from Smiles StringsDate: May 2, 2015 at 6:52:35 PM GMT+1To: John Sterling j...@johnksterling.comCc: "Developers forum for discussion about the Chemistry Development Kit (CDK)&qu
, 2015, at 7:35 PM, John May john...@ebi.ac.uk wrote:
Aromatic bonds (bond order 4) are a query feature and should NOT be used to
store structures. The reason is otherwise the implicit hydrogen placement
must be guessed. It’s easier to demonstrate this error propagation with
SMILES, same
Aromatic bonds (bond order 4) are a query feature and should NOT be used to
store structures. The reason is otherwise the implicit hydrogen placement must
be guessed. It’s easier to demonstrate this error propagation with SMILES, same
structure in, different structures out:
[hal ~]: obabel
Slight correction, CircularFingerprint does actually store the all the atoms in
the feature. It’s a simple patch to expose this if you want to add it.
J
On Mar 4, 2015, at 7:42 PM, John May john.wilkinson...@gmail.com wrote:
Hi Martin,
Yes and no. The CDK has two morgan/radial/circular
Hi Tim,
You want MDLV2000Reader instead of MDLReader.
J
On Jan 6, 2015, at 6:27 PM, Tim Dudgeon tdudgeon...@gmail.com wrote:
I'm just starting to use CDK, so may not be doing things right, but it
seems to me like the first property in a SD file is missing.
I have code like this:
HI all,
I’m pleased to announce that the CDK is now available on the central maven
repo. I’ve just pushed a new release (1.5.10 - will add notes tomorrow) but you
can use it right now.
http://repo1.maven.org/maven2/org/openscience/cdk/
It might take a few hours for the various search indices
Hi All,
Just released CDK 1.5.9 to maven and sourceforge. This is the first release
built with Java 7 and will required Java Runtime SE 7 or later.
The full release notes are available here:
https://github.com/cdk/cdk/wiki/1.5.9-Release-Notes.
Best wishes,
Hi Zheng,
That second molecule looks 2D rather than just the off change of having perfect
planar conformation. You need to add/generate 3D coordinates for the molecule,
the CDK can not reliable do this.
Thanks,
J
On Dec 21, 2014, at 5:25 PM, Zheng Shi zs...@ualberta.ca wrote:
It's a
Hi Scooter,
Glad you managed to get it working. JNI is always a bit painful. Not really
familiar with OSGI workings but xom should only be used for writing CML
(libiocml) if you’re not writing CML then this module isn’t needed and I would
just exclude that.
Things also get fun with jnati if
No. Only 1.5 - actually the main reason the SMILES rewrite. 1.4 will write
stereo if given a molecule with 2D coordinates and wedges but since you can’t
generate a depiction from SMILES with this (in 1.5) it’s not possible. The
stereo written from the 2D depiction also isn’t always corrected.
Hi Martin,
You need a javacc connecter or something… there has been other posts but since
I’m not an eclipse user I’m not really sure. I’ll try an figure it out tonight
and will add it to the Wiki.
https://github.com/cdk/cdk/wiki/Building-CDK
J
On Dec 2, 2014, at 9:31 AM, Martin Gütlein
Please pull the latest version and try -
https://github.com/cdk/cdk/wiki/Building-CDK#eclipse
On Dec 2, 2014, at 7:33 PM, John May john.wilkinson...@gmail.com wrote:
--
Download BIRT iHub F-Type - The Free Enterprise
Hi Both,
Mass/isotope has never been set by atom typing or the AtomContainerManipulator
convince method you need to use Istopes (or XMLIsotopedFactory). These were
IsotopedFactory in CDK 1.4. You might have have found this already.
Istopes.getInstance().configureAtoms(container);
In fact
Hi Oscar,
We could add this as a convince function but the following would work:
for (IAtom atom : container.atoms()) {
atom.setAtomicMass(null);
}
J
On 7 Oct 2014, at 12:39, Oscar Mora oscarmorape...@gmail.com wrote:
Hi,
I use CDK 1.5.8 to read and pre-process a set of molecules
Actually… If you really do want the most abundant isotope replace this with a
call to Istopes.getMajorIsotope()
http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/config/Isotopes.html;
J
On 28 Nov 2014, at 09:29, John May j...@nextmovesoftware.com wrote:
Hi Oscar,
We
Begin forwarded message:
Subject: Re: [Cdk-user] questions about the hash fingerprinters
From: John May j...@nextmovesoftware.com
Date: 28 November 2014 09:55:56 GMT
To: Andrew Dalke da...@dalkescientific.com
Hi Andrew,
Firstly it should be noted the fingerprint module is in need
Begin forwarded message:
From: John May j...@nextmovesoftware.com
Subject: Re: [Cdk-user] Double bond stereochemistry
Date: 28 November 2014 09:34:27 GMT
To: Santiago Fraga santi...@mestrec.com
Hi Santiago,
Please use the most recent CDK substructure/isomorphism matchers (Pattern
Okay I've added a section for the source jar. The JavaDoc was already there but
for some reason isn't working at the moment. Will debug and update if needed.
Sent from my iPhone
On 28 Nov 2014, at 13:28, Oliver Stueker ostue...@gmail.com wrote:
+1
And maybe the commands to create a
Hi Oscar,
Sorry for the delay I’ve missed almost two months of cdk-user mail without
realising it. It’s a simple fix due to an oversight by me (I missed out an if)
and will add the patch tonight.
J
--
Download BIRT
, Sep 29, 2014 at 11:14 AM, John May john.wilkinson...@gmail.com
wrote:
Hi Kevin,
Glad you’re finding Stephan’s fix up useful.
Input from SMILES/InChI/molfile will set the hydrogen count allowing correct
output for any compound. Drawing the compound in JChemPaint uses the CDK atom
types
:35, John May john.wilkinson...@gmail.com wrote:
Hi Martin,
The mykekule() example as it is will preserve 3D coordinates. All properties
(except bond order) remain unchanged from the input. Using the SMILES output
just simplifies the code a little. The input to SMILES must already have
AtomPair that = (AtomPair) obj;
return this.a.equals(that.a) this.b.equal(that.b) ||
this.a.equals(that.b) this.b.equal(that.a);
}
}
J
Begin forwarded message:
From: Zheng Shi zs...@ualberta.ca
Date: 13 September 2014 22:34:39 BST
To: John May john...@ebi.ac.uk
Subject
:40, Cyrus Harmon ch-...@bobobeach.com wrote:
Looks cool. Any chance of seeing some of these bits in CDK itself?
thanks,
Cyrus
On Sep 12, 2014, at 7:01 AM, John May john...@ebi.ac.uk wrote:
Hi all,
In the release there is a new generator for rendering diagrams. For those
who need
Could someone answer this pls. On holiday.
Sent from my iPhone
Begin forwarded message:
From: Zheng Shi zs...@ualberta.ca
Date: 13 September 2014 22:34:39 BST
To: John May john...@ebi.ac.uk
Subject: questions about adding implicit hydrogen and get paths of a certain
length in a molecule
Hi all,
In the release there is a new generator for rendering diagrams. For those who
need to display I would recommend it’s use and have written up with an example
project how to size diagrams correctly for publication
http://efficientbits.blogspot.co.uk/2014/09/not-to-scale.html.
Best
Hi all,
1.5.8 was release yesterday. Release notes are available on the GitHub Wiki:
https://github.com/cdk/cdk/wiki/1.5.8-Release-Notes. This is the first citable
(via DOI) release. We can perform these in retrospect - if you have a specific
realease you would like cite let use know and we’ll
:57 AM, John May john...@ebi.ac.uk wrote:
Hi all,
1.5.8 was release yesterday. Release notes are available on the GitHub Wiki:
https://github.com/cdk/cdk/wiki/1.5.8-Release-Notes. This is the first
citable (via DOI) release. We can perform these in retrospect - if you have a
specific
not contain the classes of this dependency.
thanks for your time.
Oscar
2014-09-03 20:32 GMT+02:00 John May john...@ebi.ac.uk:
Hi Oscar,
Just a hunch but might also need to exclude xom also - xom depends on
xml-apis (see here http://mvnrepository.com/artifact/xom/xom/1.2.5).
[WARNING
:03 GMT+02:00 John May john...@ebi.ac.uk:
Hi Oscar,
Thanks for the example of configuring shade to exclude it.
I guess the issue you were having was it was clashing with the JDK class (see
below). XML APIs is not really my domain but I'll see if we can remove
dependence on xmlapis from
Hi Oscar,
Just a hunch but might also need to exclude xom also - xom depends on xml-apis
(see here http://mvnrepository.com/artifact/xom/xom/1.2.5).
[WARNING] xml-apis-1.3.03.jar, xpp3-1.1.4c.jar define 1 overlappping classes:
[WARNING] - javax.xml.namespace.QName
[WARNING] xom-1.2.5.jar,
...@cgl.ucsf.edu wrote:
Hi John,
Cytoscape 3.2 will require Java 7, so moving CDK to Java 7 makes
good sense.Cytoscape 3.2 should be releasing sometime this fall.
-- scooter
On 8/31/14, 11:19 AM, John May wrote:
Hi Scooter,
Is cytoscape on Java 7?
J
On Aug 29, 2014, at 5:20
Hi all,
I was thinking we should move off 1.6 since it’s no longer supported. I would
like to hop 1.7 and go straight to 1.8 since it’s been out a while but wanted
some opinions. Would changing the JDK version cause problems for anyone?
Cheers,
John
,
Cyrus
On Aug 29, 2014, at 4:38 AM, John May john...@ebi.ac.uk wrote:
Hi all,
I was thinking we should move off 1.6 since it’s no longer supported. I
would like to hop 1.7 and go straight to 1.8 since it’s been out a while
but wanted some opinions. Would changing the JDK version cause
and update procedures are a bit conservative (read it
make take couple of years for the IT department to roll out an update).
Regards,
Nina
On 29 Aug 2014 15:59, John May john...@ebi.ac.uk wrote:
Hi Till,
True - but then there are a lot of companies still use IE 5 and Windows XP.
Java 1.7
On Fri, Aug 8, 2014 at 5:40 PM, John May john...@ebi.ac.uk wrote:
(on list)
Hi Zheng,
Aromaticity is stored as a flag on atoms and bonds (CDKConstants.ISAROMATIC).
When given an aromatic compound one needs to kekulise or dearomatise the
structure. There are multiple ways of doing
Hi Zheng,
Works fine for me. I think your problem is you have old version of CDK on the
class path. The method that is throwing the exception doesn’t have an array in
it, but it did in 1.4.x. Do you have another version on your class path? It may
be there indirectly, i.e. from padel (which
is false. So I just wonder how to
use aromaticity class to perceive this property. Thanks,
On Tue, Aug 12, 2014 at 2:18 PM, Zheng Shi zs...@ualberta.ca wrote:
Here it is.
On Tue, Aug 12, 2014 at 2:16 PM, John May john...@ebi.ac.uk wrote:
Do you for .mol file rather than a screen shot
(on list)
Hi Zheng,
Aromaticity is stored as a flag on atoms and bonds (CDKConstants.ISAROMATIC).
When given an aromatic compound one needs to kekulise or dearomatise the
structure. There are multiple ways of doing this (see the API) the most recent
is the ‘Kekulise’ class.
However one
Hi Zheng,
Some fingerprints might do this internally but I don’t think they (all) expose
it. Depending on what you need, signatures may be an option. These capture the
circular / layer information of atoms (and molecules). The relevant class is
AtomSignature.
J
On 31 Jul 2014, at 22:45,
in the molecule? Thanks.
On Thu, Jul 31, 2014 at 3:51 PM, John May john...@ebi.ac.uk wrote:
Hi Zheng,
Some fingerprints might do this internally but I don’t think they (all)
expose it. Depending on what you need, signatures may be an option. These
capture the circular / layer information of atoms
https://github.com/cdk/cdk/wiki/1.5.7-Release-Notes--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software
/on-the-myth-of-chemical-structure-format-conversion/.
There are pragmatic solutions to most of his listed shortcomings but then I’m
definitely more informatician then chemist :-).
J
On 13 May 2014, at 22:06, John May john...@ebi.ac.uk wrote:
Hi Asad,
You are generating a generic SMILES, you
p.s. nice oneliner for debug….
new MDLV2000Writer(System.out).write(mol);
On 13 May 2014, at 22:06, John May john...@ebi.ac.uk wrote:
Hi Asad,
You are generating a generic SMILES, you probably want an isomeric SMILES.
Both and non-canonical and intended for storage, canonical
Hi Mikael,
Could you give an approximation of when cdk 1.6 will be released?
This year, hopefully summer time.
How finished/polished/bugfree/tested is it?
Almost/well/almost/well.
There are a couple more features I want to add and optimise some will probably
wait till 1.6. In terms of
, the 'AtomTypeAwareSaturationChecker' solves these cases. I'll
use it until the new kekulisation process will be ready
Thanks
Oscar
2014-04-26 20:36 GMT+02:00 John May john...@ebi.ac.uk:
Hi Oscar,
I have an improved kekulisation almost done that handles a lot more cases but
it's not ready yet
Hi all,
Just released 1.5.6, brief details available here:
https://github.com/cdk/cdk/wiki/1.5.6-Release-Notes.
Download is available from sourceforge and the EBI maven repository.
J--
Start Your Social Network Today -
Hi Oscar,
I have an improved kekulisation almost done that handles a lot more cases but
it's not ready yet I’m afraid.
AtomTypeAwareSaturationChecker is probably your best bet but there are known
issues with it.
I thought it might be possible to go via SMILES and use the atom typer to add
Hi Lochana,
You need to close the buffer before getting the output.
J
public static String toSDfileString(ListIAtomContainer ms) throws
IOException, CDKException {
StringWriter sw = new StringWriter();
SDFWritersdw = new SDFWriter(sw);
for (IAtomContainer m : ms){
1.5.6 will hopefully be release this week but the ECFP (and FCFP) is already
available for use on the SNAPSHOTS. Alex and Krishna have done a really good
job and the fingerprint is robust and fast. We actually found we can make it
even faster by using the recent CDK ring perception improvements
Hi all,
I had a question about how to start using the CDK (from Scala). Since I’ve been
meaning to do this for a while, I wrote up some examples from the Dalke’s CTR.
With the exception of ’sbt’, the project should be self contained.
https://github.com/cdk/cdk-scala-examples
You can script the CDK in python using -
http://baoilleach.blogspot.co.uk/2011/12/cinfony-11-released.html
There is also:
R http://cran.r-project.org/web/packages/rcdk/index.html
ABCL https://github.com/slyrus/abcl-cdk
J
On 28 Mar 2014, at 05:37, Egon Willighagen egon.willigha...@gmail.com
) - [Help 1]
On Sun, Mar 9, 2014 at 7:53 AM, John May john...@ebi.ac.uk wrote:
Okay,
The ebi-repo metadata was being updated on deployment but the
ebi-repo-snapshots was not. Reading around a bit it looks like LATEST is
really only for plugins and there are other ways to get the newest
] For more information about the errors and possible solutions, please
read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
On Sat, Mar 8, 2014 at 5:03 PM, John May john...@ebi.ac.uk wrote:
Yep - it pulls down
Have you got the project hosted anywhere? Or zip it up and I’ll see what’s
missing.
J
On 8 Mar 2014, at 17:57, Rajarshi Guha gu...@mail.nih.gov wrote:
I have project (CDKDescUI) that depends on the CDK and uses an ant build.
Since it only uses a few CDK modules, I figured it's time to
I actually want to remove that option :-). I couple of people have sent me some
example code that had turned it off. I only really added that for debugging.
Anyways, the latest IteratingSMILESReader in the snapshot won’t stop and dumps
the problem input in a property of an empty container -
On Mon, Feb 24, 2014 at 2:15 PM, John May john...@ebi.ac.uk wrote:
Sorry, I was going on what you had and presumed ruby was loading Order
directly. The full name is IBond.Order.SINGLE.
Bond.new(mol.getAtom(0), mol.getAtom(1), IBond.Order.SINGLE)
- John
On 24 Feb 2014, at 21:10
?
In the current example, mol.getAtom(2).getAtomTypeName() and
mol.getAtom(2).getCharge() both return nil.
Cheers,
Yannick
On Mon, Feb 24, 2014 at 3:46 PM, John May john...@ebi.ac.uk wrote:
Yes - that would not make sense, the bond holds atom references and knows
nothing about
Hi all,
As you may have seen the CDK is now built with maven. I’ve written a blog post
with a few more details here and what changes:
http://efficientbits.blogspot.co.uk/2014/02/cdk-now-built-using-maven.html.
Thanks,
these. Note - I’m just deploy now so the
below may not work for 5 mins or so.
$ cd bundle
$ mvn package
$ ls target/cdk-1.5.5-SNAPSHOT.jar
J
On 18 Feb 2014, at 22:58, John May john...@ebi.ac.uk wrote:
Todo I’m afraid but I’ll add the relevant bit first thing tomorrow. If you
can’t wait just add
Hmm… Extended should do it. Let me try and see what I get.
You could also try the prototype generator I posted the other week.
J
On 19 Feb 2014, at 14:25, Rajarshi Guha gu...@mail.nih.gov wrote:
Hi, I have some code renders molecules, but when the input ( say [CH2+] ) is
a charged species
Confirmed, could you post a bug on the tracker. Here’s what I get for basic, extended and smooth (the prototype).--
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid
does that work in the latest CDK?
UniversalIsomorphismTester.getOverlaps no longer exists (?)
On Wed, Feb 19, 2014 at 9:36 AM, John May john...@ebi.ac.uk wrote:
Do you get the correct answer with the UIT?
The SMSD code hasn’t been maintained in a long time and I’ve seen quite a few
bugs
to get the
prototype into master (the inter symbol spacing certainly looks nice)
On Wed, Feb 19, 2014 at 9:48 AM, John May john...@ebi.ac.uk wrote:
Confirmed, could you post a bug on the tracker. Here’s what I get for basic,
extended and smooth (the prototype
Actually the opposite… kekulisation should always be on.
You will get the same result if you parse, ‘C1=CC=CC=C1’ and the perceive
aromaticity.
I think the issue is the RingGenerator and BondGenerator both draw the parts. I
would not use the ring generator.
J
On 19 Feb 2014, at 15:11,
the same set of heavy atoms and switching the target and query does
give the other MCS based on the query molecule.
Using the UIT gives me [CH2]CNC independent of the order of the target and
query molecules
On Wed, Feb 19, 2014 at 9:52 AM, John May john...@ebi.ac.uk wrote:
It’s now
Todo I’m afraid but I’ll add the relevant bit first thing tomorrow. If you
can’t wait just add the snip it below to the plugins in the cdk/pom.xml - don’t
need the main class obv.
mvn assembly:assemble
is the cmd line goal.
Hi Lochana,
You may only be looking at an index of your local repo. I’ve tried an netbeans
and it won’t let me index the ebi repo.
If you add the repository/dependencies to your pom it will work, the Netbeans
viewer is only for browsing.
J
On 9 Feb 2014, at 13:58, lochana menikarachchi
to download/explore the entire repository (tens of GBs).
Sorry,
J
On 9 Feb 2014, at 18:53, John May john...@ebi.ac.uk wrote:
Hi Lochana,
You may only be looking at an index of your local repo. I’ve tried an
netbeans and it won’t let me index the ebi repo.
If you add the repository
: John May [john...@ebi.ac.uk]
Sent: Friday, February 07, 2014 6:48 PM
To: Nick Vandewiele
Cc: cdk-user@lists.sourceforge.net
Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
conversion and SSSRing finder
Okay now I’ve actually tracked it down - the issue is to do
the 1.5.4 or master branch?
Regards,
Nick
From: John May [mailto:john...@ebi.ac.uk]
Sent: Friday, February 07, 2014 5:28 PM
To: Nick Vandewiele
Cc: cdk-user@lists.sourceforge.net
Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
conversion and SSSRing finder
Confirm - I’ll look into it tonight.
For now if you don’t need the SMARTS stereochemistry you can actually use the
Pattern directly with the query container. This gives the correct answer:
Pattern pattern = Pattern.findSubstructure(SMARTSParser.parse(smarts, blr));
for (IAtomContainer
Hi Nick,
So it is hard coded in Beam - we can change it there but I don’t think it’s
needed. Firstly the new parser will accept ‘$’ for quadruple bond as per
OpenSMILES specification.
The most portal way of encoding extra semantics with SMILES is use an auxiliary
suffix. This is basically
Hi all,
I’ve just made a release of CDK 1.5.5. This is a developer (unstable) release
and includes a couple of new features.
Download: Sourceforge
Release notes: https://github.com/cdk/cdk/wiki/1.5.5-Release-Notes
Maven artefacts: available soon (currently deploying)
We getting very close to
at 12:49 PM, John May john...@ebi.ac.uk wrote:
Hi Yingfeng,
In short, no. I don’t think it’s easy to provide a comprehensive solution for
neutralisation. However approximations such as the RDKit SMARTS you’ve tried
offer a good approach for most cases.
What might be easier is to understand
Hi Yingfeng,
In short, no. I don’t think it’s easy to provide a comprehensive solution for
neutralisation. However approximations such as the RDKit SMARTS you’ve tried
offer a good approach for most cases.
What might be easier is to understand why you need to neutralise the compounds?
Hi All,
I made the 1.5.4 release yesterday and have just finished the release notes:
https://github.com/cdk/cdk/wiki/1.5.4-Release-Notes. There are several new
features and improvements all of which have examples in the release notes.
:25 PM, John May john...@ebi.ac.uk wrote:
Hi Christophe,
The InChI stores coordinates in the AuxInfo and without that the IUPAC binary
(called by the CDK) won’t set structure coordinates. To obtain a depiction
you need to generate coordinates from scratch. The 2D coordinates are
generated
No problem - it should say in the error message but I think it is be bing
suppressed (wrapped exceptions) I’ll double check that.
On 8 Nov 2013, at 04:29, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Thanks for the explaination - much clearer now!
On Thu, Nov 7, 2013 at 1:05 PM, John May
Right I'm going to call the poll finished now as there hasn't been any change
in a day or two. Results of both shown below.
Original Poll
Molecule: 13, AtomContainer: 4, AtomAndBondCloud: 0 -
http://strawpoll.me/501772/r
Updated Poll
Molecule: 13, ChemicalEntity: 6, AtomContainer: 1,
which is actually
useful.
J
On 7 Oct 2013, at 08:28, Egon Willighagen egon.willigha...@gmail.com wrote:
On Fri, Oct 4, 2013 at 4:32 PM, John May john...@ebi.ac.uk wrote:
There is no more Molecule in new CDK versions only AtomContainer, this could
be confusing - vote here: http://strawpoll.me
)) {
...
}
On 7 Oct 2013, at 09:09, Egon Willighagen egon.willigha...@gmail.com wrote:
John,
On Mon, Oct 7, 2013 at 9:59 AM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
On 7 October 2013 10:28, Egon Willighagen egon.willigha...@gmail.com
wrote:
On Fri, Oct 4, 2013 at 4:32 PM, John May
Any projects you know that make heavy use of IPolymer (excluding Bioclipse)?
J
On 7 Oct 2013, at 09:16, Egon Willighagen egon.willigha...@gmail.com wrote:
On Mon, Oct 7, 2013 at 10:11 AM, John May john.wilkinson...@gmail.com wrote:
It's much better to do one thing really well then to do many
We're using proportional representation right? :-)
Molecule 3, ChemicalEntity 3 - http://strawpoll.me/514829/r
Molecule 13, AtomContainer 4 - http://strawpoll.me/501772/r
On 7 Oct 2013, at 09:27, John May john.wilkinson...@gmail.com wrote:
Any projects you know that make heavy use of IPolymer
of
chemistry
but it shouldn't try to encode an ontology in the classes.
J
On 7 Oct 2013, at 10:18, Egon Willighagen egon.willigha...@gmail.com wrote:
On Mon, Oct 7, 2013 at 11:00 AM, John May john.wilkinson...@gmail.com wrote:
We're using proportional representation right? :-)
Molecule 3
'physicsy' libraries might doing useful
things.
Cheers,
J
On 6 Oct 2013, at 22:08, Egon Willighagen egon.willigha...@gmail.com wrote:
On Sun, Oct 6, 2013 at 11:01 PM, John May john.wilkinson...@gmail.com wrote:
http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/Crystal.html
, lochana menikarachchi locha...@yahoo.com wrote:
My biggest concern is the charge column. One of our programs uses a
proprietary program that relies on this information.
From: John May john...@ebi.ac.uk
To: lochana menikarachchi locha...@yahoo.com
Cc: cdk-user@lists.sourceforge.net cdk
Hi Martin,
My application is building QSAR models. I am not a chemist, but my
feeling is that the clean but complicated solution would be to have
'set-valued features' (a set of values instead of a single value) for
multi-compound molecules.
The trouble is one has to detect the and split
Hi All,
Currently in the CDK tetrahedral centres are represented by a central atoms and
four neighbours. Representing chiral centres with only three neighbours has
previously been achieved by adding an explicit hydrogen atom. It is not
currently possible to represent centres involving a
Sounds cool,Not aware of any open alternatives I'm afraid but might have an idea.One way I can think of is to iteratively collapse edges of the graph to find two adjacent tetrahedral centres which share 3 vertices. You could restrict this to only collapsecyclic parts - perhaps restricted to a
Hi all,
Debugging some CDK tests and I want to try an work out what the original Kekulé
form of a structure is. Any help is greatly appreciated. I think the structure
in question is 'SID 48855' which has been revoked - probably related to the
these issues. The original bug reports are here:
Info on build stuff below...
Begin forwarded message:
From: John May john...@ebi.ac.uk
Subject: Re: [Cdk-user] ant dist-large after adding custom classes to cdk?
Date: 24 July 2013 21:15:16 BST
To: Nick Vandewiele nick.vandewi...@ugent.be
Hi Nick,
Would you be willing to submit
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