I agree that a customised constructor is good and efficient though sometimes there is an overhead in doing so. Itβs a choice between driving ones car or taking a public transport to work π
From: John Mayfield <john.wilkinson...@gmail.com> Date: Tuesday, 30 October 2018 at 17:00 To: Christoph Steinbeck <christoph.steinb...@uni-jena.de> Cc: Syed Asad Rahman <s9a...@gmail.com>, cdkuser <cdk-user@lists.sourceforge.net> Subject: Re: [Cdk-user] CDK v2.2 It's more that clone() is an indication of bad style. Unfortunately a lot of the CDK (particularly the QSAR code) is built on the premise this is easy and cheap. Also all out clone() implementations throw CloneNotSupported when they shouldn't this leads to ugly try/catch down stream. It is true there isn't a viable alternative for a deep copy and having a AtomContainerManipulator.copy() for example would help, ideally the copy constructor should have been a deep copy (it's currently a shallow). John On Tue, 30 Oct 2018 at 16:50, Christoph Steinbeck <christoph.steinb...@uni-jena.de<mailto:christoph.steinb...@uni-jena.de>> wrote: > On 30. Oct 2018, at 17:15, John Mayfield > <john.wilkinson...@gmail.com<mailto:john.wilkinson...@gmail.com>> wrote: > > 2) Looks like a bug, but you really really really should not be using clone. You also say that in https://github.com/cdk/cdk/wiki/AtomContainer2, which is a great guidance, apart from indicating alternatives cloning for the less enlightened :) The only alternative to cloning is to write code which comes down to a custom clone method, or not? i.e. you create a new AtomContainer and copy over the objects that you need for your algorithm, by, say, instantiating new atoms with identical properties, and adding them to the AC. Is your argument that clone does a lot more work than one might need in one's specific case? Kind regards, Chris β Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3..
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