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Add a reader for cdxml format#145

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mojaie merged 6 commits intomojaie:masterfrom
hhaensel:hh-cdxml
Feb 28, 2026
Merged

Add a reader for cdxml format#145
mojaie merged 6 commits intomojaie:masterfrom
hhaensel:hh-cdxml

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@hhaensel
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@hhaensel hhaensel commented Feb 4, 2026

added a reader for cdxml format that supports

  • bond stereo information via 'notation' analog to sdfilereader
  • aromaticity from bond order '1.5'

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hhaensel commented Feb 4, 2026

@mojaie would be great if you could review

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@mojaie sorry for pinging you once more on this. I had the impression that you liked the idea of adding a cdxml reader?
If it's just lack of time, you might leave a short note.

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mojaie commented Feb 25, 2026

I'm sorry for the late response.
It looks good to me. If there is any specific reason why you chose LightXML.jl instead of EzXML.jl, please let me know.
I’m ready to merge whenever you are.

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LightXML was a pick from the AI, but as EzXML is meanwhile hosted by JuliaIO, it's probably the better choice, moreover we're using it in GenieFramework.
So I took some time to switch to EzXML and cleaned up the code a bit.
The only two functions to be exported are cdxmltomol and cdxmltomols. They have similar syntax as sdftomol. Morevover, there are CDXMLAtom, CDXMLBond and CDXMLMolGraph.
So I guess it's ready for merging.

@mojaie mojaie merged commit 5e015a8 into mojaie:master Feb 28, 2026
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mojaie commented Feb 28, 2026

Thank you very much!

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2 participants