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.
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
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 of
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
I have also added 'configure' call in addition to
'Istopes.getMajorIsotope();'
IsotopeFactory isotopeFactory = Isotopes.getInstance();
for (IAtom iAtom : pIAtomContainer.atoms()) {
IIsotope iIsotope =
isotopeFactory.getMajorIsotope(iAtom.getAtomicNumber());
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
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