Keywords: Signals Notebook, salt, solvate, metadata, bulk, import, material, library, mapping
Details:
It is possible to map salt and solvate information from the source .sdf file. In the attached code block at the bottom of this article, there is an example of two compounds with different salts. This is how it should look like in the sdf file, for Signals Notebook to recognize salt or solvate metadata correctly.
Basically, the field that makes the difference is <Batch_Metadata>. If you import this file in SNB and map all required fields, you will notice how the salt information will be displayed in the batch level.
This will be only for Bulk import. Bulk update didn’t take the salt information.
For updates, use the following API:
Where “Fragments” refer to salts and solvates, you should be able to edit this information using that API. In the swagger page there is an example you can use as reference:
Attachment:
Source .sdf file example
SignalsN02222320092D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 10 10 0 0 0
M V30 BEGIN ATOM
M V30 1 C -1.428854 0.412500 0.000000 0
M V30 2 C -1.428854 -0.412500 0.000000 0
M V30 3 C -0.714427 -0.825000 0.000000 0
M V30 4 C -0.000000 -0.412500 0.000000 0
M V30 5 C -0.000000 0.412500 0.000000 0
M V30 6 C -0.714427 0.825000 0.000000 0
M V30 7 C 0.714427 0.825000 0.000000 0
M V30 8 N 1.428854 0.412500 0.000000 0
M V30 9 O 0.714427 1.650000 0.000000 0
M V30 10 O -0.714427 -1.650000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 1
M V30 7 1 5 7
M V30 8 1 7 8
M V30 9 2 7 9
M V30 10 1 3 10
M V30 END BOND
M V30 END CTAB
M END
> <ID>
C-111-001
> <Chemical_Name>
3-hydroxybenzamide
> <Molecular_Weight>
137.14 g/mol
> <Exact_Mass>
137.04768
> <Molecular_Formula>
C7H7NO2
> <Amount>
12.000 g
> <Purity_(_)>
90 %
> <Batch_Chemical_Name>
3-hydroxybenzamide, Acetate
> <Batch_Molecular_Formula>
C7H7NO2·C2H3O2-
> <Formula_Mass>
196.18 g/mol
> <Submitter_(Name)>
Standard user
> <Submitter_(E_mail)>
user@mail.com
> <Submission_Date>
2023-01-16T17:23:50.053Z
> <Batch_Metadata>
{"fragments":{"salts":[{"type":"SALT","name":"Acetate","mf":"C2H3O2-","mw":{"rawValue":"59.0445","displayValue":"59.0445 g/mol"},"id":"SALT:3","coefficient":1.0}],"solvates":[]}}
$$$$
SignalsN02222320092D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 10 10 0 0 0
M V30 BEGIN ATOM
M V30 1 C -1.428854 0.412500 0.000000 0
M V30 2 C -1.428854 -0.412500 0.000000 0
M V30 3 C -0.714427 -0.825000 0.000000 0
M V30 4 C -0.000000 -0.412500 0.000000 0
M V30 5 C -0.000000 0.412500 0.000000 0
M V30 6 C -0.714427 0.825000 0.000000 0
M V30 7 C 0.714427 0.825000 0.000000 0
M V30 8 N 1.428854 0.412500 0.000000 0
M V30 9 O 0.714427 1.650000 0.000000 0
M V30 10 O -0.714427 -1.650000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 1
M V30 7 1 5 7
M V30 8 1 7 8
M V30 9 2 7 9
M V30 10 1 3 10
M V30 END BOND
M V30 END CTAB
M END
> <ID>
C-112-001
> <Chemical_Name>
3-hydroxybenzamide
> <Molecular_Weight>
137.14 g/mol
> <Exact_Mass>
137.04768
> <Molecular_Formula>
C7H7NO2
> <Amount>
12.000 g
> <Purity_(_)>
90 %
> <Batch_Chemical_Name>
3-hydroxybenzamide, Chloride
> <Batch_Molecular_Formula>
C7H7NO2·Cl-
> <Formula_Mass>
172.59 g/mol
> <Submitter_(Name)>
Standard User
> <Submitter_(E_mail)>
user@mail.com
> <Submission_Date>
> <Batch_Metadata>
{"fragments":{"salts":[{"type":"SALT","name":"Chloride","mf":"Cl-","mw":{"rawValue":"35.4505","displayValue":"35.4505 g/mol"},"id":"SALT:10","coefficient":1.0}],"solvates":[]}}
$$$$