Skip to content

feature request: correct conversion from three-letter to one-letter AA code (including ncAA correct processing) #2186

@lokapal

Description

@lokapal

Hello, developers!

As far as I understand, there is no built-in prody functions to convert three-letter code to one-letter code correctly, Under "correctly" I mean replacing ncAA to canonical AA counterpart by MODRES and then conversion to one-letter AA code.
This code can extract from PDB three-letter AA code, including ncAA. But I need in BOTH sequences - three-letter with ncAA and one-letter with cAA only.

for currpoly in polymers:                                          
      currid = currpoly.chid                                       
      sequence = currpoly.sequence                                 
      modres = currpoly.modified                                   
fseq.close()

I can process modres and replace by position ncAA to their canonical AA counterparts in sequence, and then use common map, but anyway it would be good to have this functionality from library. I definitely don't want to reparse PDB from the scratch, because the real-life code is more complex, and I need in specific chains sequences (both three- and one-letter).

Metadata

Metadata

Labels

No labels
No labels

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions