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As we observed in a test case, it might happen, that Inchi strings get annotated which differ in charge with the charge that is encoded in the SBML model for the metabolite. This could lead to problem…
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**Describe the bug**
`"[H:5][S:3]#[N+:2][S:1][H:4]"` is a molecule that cannot be turned into an InChI due to what looks like an internal software error in the inchi code itself. However, the too…
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It seems that the InChI for `CH3SO2`
(https://mcm.york.ac.uk/MCM/species/CH3SO2) is incorrect. It should have
3 H atoms, not 4. The correct InChI is probably
`InChI=1S/CH3O2S/c1-4(2)3/h1H3`, see:
…
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If a molecule consists out of multiple fragments but no other fragement the InChI should only be calculated based on 1 fragment. In case you multiple identical fragments but any other fragment in addi…
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During my research, I came across a phenomenon in InChI. The -RecMet
flag does not work for the following compounds (all chlorides):
magnesium chloride, MgCl2
InChI=1S/2ClH.Mg/h2*1H;/q;;+2/p-2
I…
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I have been using both the `rcdk` and the `rinchi` packages in my work. Thank you for creating them. The other day I decided to download the latest version of the `rcdklibs` package. I encountered a p…
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Currently we don't specify which InChI flavor should be provided in 6.5.6. inchi
http://hupo-psi.github.io/mzTab/2_0-metabolomics-draft/mzTab_format_specification_2_0-M_draft.html#small-molecule-evid…
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Datagrok uses [RDKit minimal lib](https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib) for cheminformatics related calculations. Minimal lib is limited to a subset of features presented in [RDK…
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I wonder if there is already a way to create a reaction InChI or am I just not finding it.
Or is it planned to integrate this in future, since RInChI is part of the JNA InChI?
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During some testing I came across a few smaller things/inconsistencies/bugs in the filtering pipeline.
1. `repair_not_matching_annotation`
- sometimes gave the following warning: ```WARNING:match…