1) You can just include cdk-legacy and use the existing, but the functionality was just a connivence the same as getMinMax(container) but without the Java AWT dependency which caused problems for Andriod/SWT. IIRC this was the only place AWT was use in the core package. If you just want the width/height use: get2DDimension. Note this was 4+ years ago :-) https://github.com/cdk/cdk/commit/214785ce18e2d06f1ba7d9fddc82c0ea9753a385#diff-9a119f1ec045c70b21aa694d01bbc773 2) Looks like a bug, but you really really really should not be using clone.
On Tue, 30 Oct 2018 at 15:51, Syed Asad Rahman <[email protected]> wrote: > 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]> 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]> > *Date: *Tuesday, 30 October 2018 at 12:01 > *To: *cdkuser <[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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