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 <[email protected]>
Date: Tuesday, 30 October 2018 at 15:39
To: Syed Asad Rahman <[email protected]>
Cc: cdkuser <[email protected]>
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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>>
Date: Tuesday, 30 October 2018 at 12:01
To: cdkuser
<[email protected]<mailto:[email protected]>>
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
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