The XChem team has been working hard to allow uploading of SDF files and proper integration into Fragalysis, their fragment analysis site.
In the meanwhile, I have been throwing together interactive views in Michelanglo, which is a site that allows biochemists to make a page with an interactive 3D protein (using NGL like Fragalysis) and a user written narrative about the protein with links that alter its orientation and representations —so not really ideal for this.
Here is an example:
I have added the code to make the totally-off-specs interactive pages with tables to the client-side Python API code, just in case it helps:
Here is code specific for MPro with a XChem-ready SDF file. A few things to note:
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“Basic” users cannot do this to prevent client side exploits. Only approved users can (message me and I’ll approve you).
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the data needs to be stored on GitHub for retrieval: it gets split into
molfiles (getting a user to download 20 MB on a webpage is not okay, especially as 50% of users are on mobile devices). -
A JSON table is made and automatically placed in the same folder
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template.pdbor whatever your column name has (see below) has to be in the same folder (manually placed). -
inspiration hits need to be manually placed in the same folder
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Under T&Cs the content is your responsibility, so if the data is not yours explicitly pass blame/credit to the author.
from michelanglo_api import MikeAPI, MikePage mike = MikeAPI('username','password') # use your username and password assert mike.verify_user()['rank'] != 'basic', 'Only privileged users can add JS'
Make a page via the GUI and copy the uuid part of the URL (the gibberish part).
page = MikePage(mike, 'uuid').retrieve()
Alternatively make one via python (less pretty, especially since the autoView does not change view angle)
page = mike.convert_pdb('6LU7').retrieve()
Then, with appropriate changes run:
gitfolder='/Users/you/path_to_your_github_repo_on_your_machine'
sdfile='/Users/you/path_to_sdfile.sdf'
folder = 'folder_name_within_repo'
targetfolder=f'{gitfolder}/{folder}'
page.description = 'Hello world. '
page.loadfun = ''
page.columns_viewport = 6
page.columns_text = 6
page.sdf_to_mols(sdfile=sdfile,
targetfolder=targetfolder,
skip_first=True) # first row is metadata in a SDF for XChem
page.sdf_to_json(sdfile=sdfile,
keys=('∆∆G', 'comRMSD', 'N_constrained_atoms', 'runtime', 'disregarded', 'smiles'),
key_defaults=(999., 999., 0, 999., 'NA', 'NA'), #what to set stuff that is null
filename=f'{targetfolder}/data.json')
page.make_fragment_table(sdfile=sdfile,
username='matteoferla',
repo_name='Data_for_own_Michelanglo_pages',
foldername=folder,
protein_sele='145:A', # show this on protein. NGL selection
sort_col=2, #sort by column index 2.
sort_dir='asc', #asc or desc
template_row=-1, # is the template a file called `template.pdb` (-1) or a filename in the row n?
fragment_row=1, # the inspiration fragments (-1 for none). The names must match with or without a .mol.
jsonfile='data.json')
page.commit()
# if in a Jupyter notebook
page.show_link()
The files with need to be Git-pushed first.