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cdk / nwo-openscience-2024

Repository to track the progress of the NWO Open Grant accepted for the CDK in 2023.
https://www.nwo.nl/en/projects/osf232097
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update SmartCyp to CDK 2.9 (or better) #22

Open tdudgeon opened 10 months ago

tdudgeon commented 10 months ago

SmartCyp uses the 1.4 API and 1.5+ can't be used. https://smartcyp.sund.ku.dk/mol_to_som

egonw commented 10 months ago

Source code: http://smartcyp2.sund.ku.dk/download.php

egonw commented 8 months ago

~Also needs JChemPaint.~

Also needs the JChemPaint-originating rendering stack, but that is actually part of the CDK.

egonw commented 8 months ago

Downstream users: Bioclipse (Bacting!) and this: https://github.com/christinadebruynkops/GLORYx/tree/a1f4a8246e09eb971aac88d29123f59f2ad33944

egonw commented 8 months ago

We're running into character encoding issues:

[ERROR] /home/egonw/var/Projects/Other/smartcyp/src/main/java/smartcyp/MoleculeKU.java:[1084,118] unmappable character (0x96) for encoding UTF-8
[ERROR] /home/egonw/var/Projects/Other/smartcyp/src/main/java/smartcyp/MoleculeKU.java:[1084,1388] unmappable character (0x96) for encoding UTF-8
[ERROR] /home/egonw/var/Projects/Other/smartcyp/src/main/java/smartcyp/MoleculeKU.java:[1088,140] unmappable character (0x96) for encoding UTF-8
[ERROR] /home/egonw/var/Projects/Other/smartcyp/src/main/java/smartcyp/MoleculeKU.java:[1092,120] unmappable character (0x96) for encoding UTF-8
[ERROR] /home/egonw/var/Projects/Other/smartcyp/src/main/java/smartcyp/MoleculeKU.java:[1096,515] unmappable character (0x96) for encoding UTF-8
jmillanacosta commented 8 months ago
egonw commented 7 months ago

I started this monitoring report: https://github.com/cdk/nwo-openscience-2024/blob/main/monitoring/smartcyp.md

egonw commented 7 months ago

Update to CDK 2.1 fails with a missing dependency:

[ERROR] Failed to execute goal on project smartcyp: Could not resolve dependencies for project io.github.cdk.smartcyp:smartcyp:jar:2.5.0-SNAPSHOT: The following artifacts could not be resolved: uk.ac.ebi.beam:beam-core:jar:1.1-SNAPSHOT, uk.ac.ebi.beam:beam-func:jar:1.1-SNAPSHOT: Could not find artifact uk.ac.ebi.beam:beam-core:jar:1.1-SNAPSHOT in ossrh (https://oss.sonatype.org/content/repositories/snapshots) -> [Help 1]
egonw commented 7 months ago

Update to CDK 2.2 fails with the following, which will be fixed when I further clean up the use of builders and a single (silent?) data model implementation: 

Exception in thread "main" java.lang.ClassCastException: class org.openscience.cdk.AtomContainer2$BaseAtomRef cannot be cast to class org.openscience.cdk.Atom (org.openscience.cdk.AtomContainer2$BaseAtomRef and org.openscience.cdk.Atom are in unnamed module of loader 'app')
        at smartcyp.MoleculeKU.assignAtomEnergies(MoleculeKU.java:229)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:210)
egonw commented 7 months ago

Okay, I got it compiling with CDK 2.9 and the calculations seem to run okay, but the rendering worked still okay with 2.2 but is not ideal with 2.9:

image

egonw commented 7 months ago

Task: https://github.com/cdk/nwo-openscience-2024/issues/26

egonw commented 7 months ago

@tdudgeon, this would be a good time to give the new a first spin.

egonw commented 5 months ago

Look up past code examples: https://github.com/cdk/nwo-openscience-2024/issues/30