In Fragalysis in silico generated compound poses can be uploaded and will be in the RHS, which can be toggled by a button on the bottom right:
To upload a new set log-in first via pancake stack icon button on the top left:
Once logged in, change the url to:
https://fragalysis.diamond.ac.uk/viewer/upload_cset
The specs for the upload can be found at:
To create a header easily you can use the function generate_header from here:
from gist_import import GistImporter
fmodule = GistImporter.from_github('https://raw.githubusercontent.com/matteoferla/Fragment-hit-follow-up-chemistry/main/followup/prep_fragalysis.py')
generate_header = fmodule['generate_header']
prep = fmodule['prep']
header: Chem.Mol = generate_header(method_name,
ref_url=ref_url,
submitter_name=submitter_name,
submitter_email=submitter_email,
extras=extra_field_definitions
)
prep(df, header, mol_col='minimized_mol', name_col='name', outfile=f'{method_name}.sdf', ref_pdb=ref_pdb, extras=extras)
Where df has to have the columns specified by mol_col and name_col and a string w/ comma-separator ref_mols. These names must exist. If the hit is shown in Fragalysis as X0123_0A:Z00012345, the name will be x0123_0A.
The compound name must be <50 char.
The columns of extra fields have to be numeric and there can be no nans or strings —only the header needs submitter name etc.
