Thanks! 1. Great- perhaps I was out of touch 😊 2. As of now, I will perhaps remove the S-groups flag. What would be a preferred way to circumvent clone? -Asad
From: John Mayfield <john.wilkinson...@gmail.com> Date: Tuesday, 30 October 2018 at 16:15 To: Syed Asad Rahman <s9a...@gmail.com> Cc: cdkuser <cdk-user@lists.sourceforge.net> Subject: Re: [Cdk-user] CDK v2.2 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 <s9a...@gmail.com<mailto:s9a...@gmail.com>> 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 <john.wilkinson...@gmail.com<mailto:john.wilkinson...@gmail.com>> Date: Tuesday, 30 October 2018 at 15:39 To: Syed Asad Rahman <s9a...@gmail.com<mailto:s9a...@gmail.com>> Cc: cdkuser <cdk-user@lists.sourceforge.net<mailto:cdk-user@lists.sourceforge.net>> 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 <s9a...@gmail.com<mailto:s9a...@gmail.com>> 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 <john.wilkinson...@gmail.com<mailto:john.wilkinson...@gmail.com>> Date: Tuesday, 30 October 2018 at 12:01 To: cdkuser <cdk-user@lists.sourceforge.net<mailto:cdk-user@lists.sourceforge.net>> 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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