Re: [Cdk-user] CDK v2.2

[Syed A. R. <s9...@gm...>]

Thanks.

I have started to play with the new release.
Got few regression which is fine with API changes.

Any pointer please?

Q1) What is the equivalent of GeometryTools.getRectangle2D in the new GeometryUtil?
import static org.openscience.cdk.geometry.GeometryTools.getRectangle2D;
Q2)
IAtomContainer clone = org.clone();

Throws java.lang.ClassCastException: java.util.ArrayList cannot be cast to org.openscience.cdk.sgroup.SgroupBracket
java.lang.ClassCastException: java.util.ArrayList cannot be cast to org.openscience.cdk.sgroup.SgroupBracket
                at org.openscience.cdk.tools.manipulator.SgroupManipulator.copy(SgroupManipulator.java:108)
                at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1408)

From: John Mayfield <joh...@gm...>
Date: Tuesday, 30 October 2018 at 15:39
To: Syed Asad Rahman <s9...@gm...>
Cc: cdkuser <cdk...@li...>
Subject: Re: [Cdk-user] CDK v2.2

Yes, but there has been no changes to SilentChemObjectBuilder...?

- I did try testing RDT with the new AtomContainer APIs but your tests took too long to run and I have stuff to do :-).
- Likewise I did the same with Ambit but there are integration tests with dependencies on DBs etc so difficult to see if there is actually anything wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer) which needs to implement some new methods. Often trivial stuff convenience stuff that could be resolved with Java 8 and default method implementations on interfaces, but we're currently on Java 7 so not an option.

John

On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman <s9...@gm...<mailto:s9...@gm...>> wrote:
Thank you John and Developers!


This is a fantastic news!

One quick question before I pull it into SMSD and RDT - Is SilentChemObjectBuilder thread safe?
Best wishes,
-Asad

From: John Mayfield <joh...@gm...<mailto:joh...@gm...>>
Date: Tuesday, 30 October 2018 at 12:01
To: cdkuser <cdk...@li...<mailto:cdk...@li...>>
Subject: [Cdk-user] CDK v2.2

Dear CDK users,

CDK 2.2 is now released and can be obtained from Maven central or the GitHub<https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full release notes<https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details on the new features and changes.

As noted in v2.1/v2.1.1 the AtomContainer2<https://github.com/cdk/cdk/wiki/AtomContainer2> is now the default so if you didn't try running v2.1/v2.1.1 with the flag CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on the wiki page<https://github.com/cdk/cdk/wiki/AtomContainer2> this normally just requires addAtom/Bond statements be reordered and using ``Objects.equals(container1, container2)`` instead of reference comparison (container1 == container2).

- John