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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.
The text was updated successfully, but these errors were encountered:
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.:
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.
The text was updated successfully, but these errors were encountered: