Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Support for mmCIF Files #127

Open
a-r-j opened this issue Mar 11, 2022 · 1 comment
Open

Support for mmCIF Files #127

a-r-j opened this issue Mar 11, 2022 · 1 comment
Labels
enhancement New feature or request help wanted Extra attention is needed

Comments

@a-r-j
Copy link
Owner

a-r-j commented Mar 11, 2022

Is your feature request related to a problem? Please describe.
Currently, we only support PDB files as inputs for protein structure graphs. Large complexes are now unavailable as PDBs.:

Several type of PDB entries are not offered in the legacy PDB format anymore:
Entries containing multiple character chain ids
Entries containing > 62 chains
Entries containing > 99999 ATOM coordinates
Entries that have complex beta sheet topology, see more details

Describe the solution you'd like
Once BioPandas has support for parsing mmCIF files (BioPandas/biopandas#94) , we can parse the DFs into a format consistent with PDB files. This is the simplest route forward. However, mmCIF files are 'better' (esp wrt how they handle insertions / altlocs) as well as author inconsistencies in the contents. Longer term we may consider refactoring to treat mmCIF as the first class citizen input file format.

@a-r-j a-r-j added enhancement New feature or request help wanted Extra attention is needed labels Mar 11, 2022
@mrauha
Copy link

mrauha commented Aug 29, 2022

The MMCIF -> PDB conversion should be available quite soon in Biopandas, waiting to be merged: BioPandas/biopandas#107

After this is done, using MMCIF's should take couple lines work :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request help wanted Extra attention is needed
Projects
None yet
Development

No branches or pull requests

2 participants