{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2006/04/12/cdk-data-classes-and-change.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/3xsm0-bt478", "url": "https://chem-bla-ics.linkedchemistry.info/2006/04/12/cdk-data-classes-and-change.html", "title": "The CDK data classes and change notifications", "content_html": "

The data classes of the Chemistry Development Kit are mutable, unlike those of\nOctet. This means that other classes may need to respond when\nthe content updates. For example, a render class. CDK’s ChemObject\nprovides a notifyChanged() and addListener() methods for this. However, as was\nrecently pointed out,\nwhile this is useful in editors, such as JChemPaint, this is a performance killer in high-throughput\nsitations, such as descriptor calculation, or structure diagram generation runs.

\n\n

To address this, the IChemObject\ninterface has been extended with the methods setNotification(boolean) and getNotification(), which allow to temporarily\ndisable change notifications. There are no helper methods yet to disable it for a complete data structure, like\nChemModelManipulator.setNotification(ChemModel, boolean), but I expect these to be written soon.

\n\n

Alternatively, special data classes may be used if notification is never needed for a special setup, for example, in case the QSAR descriptor calculation. In such cases, the new NoNotificationChemObjectBuilder\ncan be used:

\n\n
IChemObjectReader reader = new MDLReader(new FileInputStream(new File(\"some.mol\")));\nIChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();\nIMolecule molecule = reader.read(builder.newMolecule());\n// then perform some operation in which the molecule changes a lot\n
\n\n

The advantage is that you do not have to manually disable notification for each class you instantiate. This should give a considerable speed up, and I hope soon to give some statistics.

", "summary": "The data classes of the Chemistry Development Kit are mutable, unlike those of Octet. This means that other classes may need to respond when the content updates. For example, a render class. CDK’s ChemObject provides a notifyChanged() and addListener() methods for this. However, as was recently pointed out, while this is useful in editors, such as JChemPaint, this is a performance killer in high-throughput sitations, such as descriptor calculation, or structure diagram generation runs.", "date_published": "2006-04-12T00:00:00+00:00", "date_modified": "2025-02-13T00:00:00+00:00", "tags": ["cdk","cheminf","jchempaint"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }