cdk / nodes4knime Goto Github PK

The plugin specifies the max version is 4.0 and needs to be changed to 5.0.

I can submit a pull request for this if you'd like?

Reported on https://forum.knime.com/t/substructure-node-cannot-deal-with-explicit-hydrogens/45155:

I would like to use your substructure search node.
Unfortunately it cannot deal with explicit hydrogens. But that is really crucial to my search, as I need to limit in which direction my molecule is “growing”.

here examples for query and molecule:

[H]OC(=O)c1ccccc1

O=C(O)c1c(cccc1)C(=O)C

is this a bug or a missing feature? :slight_smile:

@sithmein, can you have a look at this too?

Checks needed:

• is everything included to open this in Eclipse
• does it compile
• does it run in KNIME from within the SDK
• does an export lead to proper installable product

CdkTestConnectivity test workflow appears to be failing

Node 'SDF Reader 0:3' has unexpected warning message: Cannot access 'knime://knime.workflow/../CdkTestData/Connectivity.sdf%20': /var/lib/jenkins/jobs/org.openscience.cdk.knime.update-3.6/workspace/tmp/knime_temp/KNIME Testflow63081/Testflows/3.6/CDK/CdkTestConnectivity/../CdkTestData/Connectivity.sdf (No such file or directory)

Having issues loading the SDF from the relative directory.

• port nodes4knime from SVN to Git
• extract the CDK nodes
• push to this repository

The node dialog won't open unless a column compatible with the atom highlight/bond highlight is provided.

A user may not want highlighting and shouldn't be forced to provide this column.

This was an oversight when I wrote the node. I'll submit a pull request with an fix for this issue.

This turns out to be a bit harder than expected, as it simultaneously needs updating of JChemPaint and AMBIT ...

... including how to develop the plugins, but also where to find, download and run the test workflows.

Raising here for visibility.

KNIME community builds now have OWASP dependency checker run against them and fail on critical security issues.

Legacy CDK fails on:

• CVE-2019-17571, CVE-2020-9493, CVE-2022-23305 (shaded: log4j:log4j:1.2.17) - this can be switched to reload4j
• CVE-2022-28890: (shaded: org.apache.jena:jena-core:2.7.4)
• CVE-2022-28890: (shaded: org.apache.jena:jena-iri:0.9.4)

The KNIME plugin has a bundled jar for CDK 1.5.13 so it's not possible to simply replace the libs provided.

For the reaction decoder tool integration I updated the dependencies (CDK 2.4 -> 2.7) and then had to update some of the CDK dependencies to work around security issues.

I'll try submit a fix for this, will need to make sure CDK 1.5 tests pass with updated JENA deps

CDK Substructure Search node: when a flow variable is used one cannot open the configuration dialogue again because of a null pointer exception (see attached KNIME workflow
CDK_Substructure_bug.knwf.zip
).

Hi,

I suppose the issue is with the URLs in the getMoleculeFromCAS(String cas) method in InsertTextPanel.java. As NCBI switched to HTTPS, this method now returns null. I could get the method working with the following changes:

Edit 1:
String firstURL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound&term=" + cas;
(change to https)

Edit 2:
Pattern pattern = Pattern.compile("http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi\\?cid=(\\d*)");
(change the regex string to https://pubchem.ncbi.nlm.nih.gov/compound/(\\d*))

Edit 3:
String secondURL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?tool=jcppubchem&db=pccompound&id=" + cid;
(change to https)

Edit 4:
pattern = Pattern.compile("<Item Name=\"CanonicalSmile\" Type=\"String\">([^\\s]*?)</Item>");
(change CanonicalSmile to CanonicalSmiles)

Is it possible to release a new version of jchempaint-hotfix-3.4.jar? I would like to use the sketcher panel in the development of a new KNIME node.

Thank you,
Vishal