Depict app file upload menu

[jeremyjyang]

The Depict file upload menu should support two formats, based on RDKit capabilities:

1. SMILES
2. MDL Molfile

The SMILES format is specified with some variation by Daylight, ChemAxon, and RDKit. However, at minimum we should support a file with lines which begin with SMILES, and optionally, followed by a whitespace (space or tab) and name/ID.

[Priyansh-Kedia]

@jeremyjyang I have fixed the CSV file variations as mentioned.

I could not find multi molecule Mol Files over the internet to test the variations with MDL file. Please let me know where I can find such files to test.

Thanks

[jeremyjyang]

See the rdkit repo for lots of example files, such as https://github.com/rdkit/rdkit/blob/master/Projects/DbCLI/testData/pubchem.200.sdf, and https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/test_data/compounds.smi, and many more SMILES and MDL Molfile (SDF) format files.

[Priyansh-Kedia]

Thank you Professor

On Wed, May 24, 2023, 12:01 Jeremy J Yang @.***> wrote:

See the rdkit repo for lots of example files, such as https://github.com/rdkit/rdkit/blob/master/Projects/DbCLI/testData/pubchem.200.sdf, and https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/test_data/compounds.smi, and many more SMILES and MDL Molfile (SDF) format files.

— Reply to this email directly, view it on GitHub https://github.com/unmtransinfo/CFChemApps/issues/2#issuecomment-1561465858, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMRYYAIZXZB7UWWVAEKUESDXHYWHLANCNFSM6AAAAAAYCXAI7Q . You are receiving this because you commented.Message ID: @.***>

[Priyansh-Kedia]

The code is now fixed so that I can output the multiple compounds along with the structures.

[jeremyjyang]

drugs.smi.gz

The app fails using the attached drugs.smi, due to the line with "CCO" and no space nor name. This should be supported. SMILES files may have only one column, just the SMILES.

[Priyansh-Kedia]

drugs.smi.gz

The app fails using the attached drugs.smi, due to the line with "CCO" and no space nor name. This should be supported. SMILES files may have only one column, just the SMILES.

The SMI and SDF files have a lot of different formats as I checked on the internet. I will confirm this in the meeting tomorrow and work on the fix

Thank you

[jeremyjyang]

Good plan. Please prioritize learning from documentation and examples from cheminformatics community/industry leaders: (1) RDKit, (2) OpenEye, (3) ChemAxon, and (4) Daylight (https://www.daylight.com/), no longer in business, but inventors of SMILES.

[Jack-42]

Although it was being inferred before, pull request #17 allows for explicitly setting the file type for SMILES/MDL MolFile. We're using RDKit to read both kinds of files, which should be robust to differences in formatting (within reason). I'm going to close this as completed for now.