Make use of isotope label information in InChi values in transition lists and .msp files #3230
Conversation
…s, e.g. the "1D3" in "InChI=1S/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3/i1D3" which tells us that three of the hydrogens in C8H8O are deuterium
…k/20241102_use_InChi_labels
|
@nickshulman this one's pretty nerdy, but it needs the blessing |
| { | ||
| Dictionary<string, int> result = null; | ||
| var inchi = GetInChI(); | ||
| if (!string.IsNullOrEmpty(inchi)) |
There was a problem hiding this comment.
I'd recommend doing something like:
if (string.IsNullOrEmpty(inchi))
return result;
so that the main body of the function is less indented.
| @@ -102,6 +102,16 @@ public static Dictionary<string, string> FormatAccessionNumbers(string keysTSV, | |||
| return keys; | |||
| } | |||
|
|
|||
| public static MoleculeAccessionNumbers Create(Dictionary<string, string> accessions) | |||
| { | |||
| if (accessions==null || accessions.Count == 0) | |||
There was a problem hiding this comment.
The spacing around the "==" is incorrect.
| } | ||
| if (Adduct.DICT_ADDUCT_ISOTOPE_NICKNAMES.TryGetValue(isotope, out var skylineIsotope)) // e.g. "C13" => "C'" | ||
| { | ||
| if (result == null) |
There was a problem hiding this comment.
I'd recommend replacing this "if" and the two subsequent two "else" clauses with:
result ??= new Dictionary<string, int>();
result.TryGetValue(skylineIsotope, out var existing);
result[skylineIsotope] = existing + count;
| @@ -344,4 +344,7 @@ | |||
| <data name="NistLibraryBase_GetMod_Unknown_modification__0__at_line__1_" xml:space="preserve"> | |||
| <value>Unknown modification {0} at line {1}</value> | |||
| </data> | |||
| <data name="NistLibraryBase_CreateCache_Missing_details_for__0__at_line__1___ignored" xml:space="preserve"> | |||
| <value>Missing details for {0} at line {1}, ignored</value> | |||
There was a problem hiding this comment.
Could this warning message be rephrased so that it is more clear how big of a thing is being ignored?
Is just the line which has the missing details being ignored, or is the entire spectrum for the molecule being excluded from the spectral library?
There was a problem hiding this comment.
OK, updated to say that the entry is being ignored
I'll have a look, thanks. I always appreciate your thoughtful reviews. |
Sometimes isotope label information can be found in InChi descriptions, e.g. the "/i1D3" in "InChI=1S/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3/i1D3" which tells us that three of the hydrogens in C8H8O are deuterated