[ENH] pdb to String loader using SEQREQ records

[satvshr]

Closes #147

[satvshr]

Renamed the _pfoa_loader.py file to _pfoa.py for consistency.

[fkiraly]

Does this function, at least ideas-wise, not do the same as pdb_to_struct then struct_to_aaseq? Recall that we separated the two intentionally, to separate file manipulation from in-memory objects which are abstract representations.

Instead of adding this new function which would link file manipulation back into the in-memory workflow, why not add features to the existing struct_to_aaseq?

[satvshr]

Instead of adding this new function which would link file manipulation back into the in-memory workflow, why not add features to the existing struct_to_aaseq?

#147 answers your question, essentially 3d data is being captured when biopython converts something to a Structure object using ATOM records, sometimes a part of the sequence cna go missing if the 3d orientation of it is not known. This issue is not faced with SEQRES records, hence the direct converter.

[fkiraly]

let's try to be rst compatible where we can:

• newlines before and after bullet point lists
• double backticks around code like 'chain' (note that markdown uses single backtick, rst wants double backtick)

[fkiraly]

let's call this return_type with two possible values "pd.df" and "list". This makes it more upwards compatible.

[fkiraly]

Instead of adding this new function which would link file manipulation back into the in-memory workflow, why not add features to the existing struct_to_aaseq?

#147 answers your question, essentially 3d data is being captured when biopython converts something to a Structure object using ATOM records, sometimes a part of the sequence cna go missing if the 3d orientation of it is not known. This issue is not faced with SEQRES records, hence the direct converter.

follow-up question: would it be possible to get the sequences from the Structure object instead of the pdb?

[satvshr]

would it be possible to get the sequences from the Structure object instead of the pdb?

I thought I mentioned this but I didnt, so apologies for that.

sometimes a part of the sequence cna go missing (in the Structure object) if the 3d orientation of it is not known.

So when the Structure object is formed, it also misses this 3d information, hence the complete sequence cannot be extracted from it, as the unknown 3 orientation leads to a lack of a complete sequence. If it didnt, I wouldnt have made this PR.

[fkiraly]

Ok, that is concerning. Are you saying the Structure objec tis not an 1:1 in-memory representation of the full pdb?

[satvshr]

Are you saying the Structure objec tis not an 1:1 in-memory representation of the full pdb?

Just to have it on record, yes

[satvshr]

Made the 2 changes requested above and renamed all files to private to prevent weird import errors as discussed in todays meeting.

[fkiraly]

We should rethink what the internal structure is.

SeqIO seems to be loading pdb in a parsable form - so if it is non-lossy, we should add at least a loader that returns the python object (and not a string), see #160