ReactionDecoder

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Mapping Difference

4

Hi, I am trying to map atoms of molecules supported by Recon 3D. In [Recon 3D study](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840010/) Reaction Decoder tool have been also used, and the mapped reactions can be...

selcenari

``` java -cp dist/*:lib/* aamtool.ReactionDecoder -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -j AAM -f TEXT ``` zsh: no matches found: dist/_:lib/_ see: http://stackoverflow.com/a/10230446/2714931

twz915

The tests give PNGs with labeled compounds. Is it possible to run from command line, define SMILES and include labels to overwrite the default M0001, M0002, M0003....?

saleha1wer

[WARNING] The POM for org.openscience.cdk:cdk-bundle:jar:2.4-SNAPSHOT is missing, no dependency information available

2

mvn install fails due to a missing dependency [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.039 s [INFO] Finished at: 2022-10-26T18:03:49+01:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute...

rmtfleming

I am new to this field and I have a conceptual question related to the ReactionDecoder tool. I am running the tool in the Annotation mode. In the resulting XML...

kumarsaurabh20