IO

faltwerk.io.is_gz_file(filepath)[source]

https://stackoverflow.com/questions/3703276/how-to-tell-if-a-file-is-gzip-compressed

faltwerk.io.load_bfactor_column(fp)[source]

Load annotation data stored in the bfactor column of a .pdb file

faltwerk.io.load_conserved(fp, ref=None, metric=<function mean_pairwise_similarity>)[source]

If no reference sequence name is provided, assume the first sequence is the reference. Why do we even need to specify the reference? Bc/ in the MSA it can contain gaps, which we’ll omit bc/ we want to be able to map the conservation values to the protein structure, which does not contain gaps and we assume is identical to the reference sequence.

Available functions:

  • mean_pairwise_similarity

  • entropy

faltwerk.io.load_scores(fp)[source]

Expects pLDDT scores as output by ColabFold

faltwerk.io.parse_hyphy(fp, method='meme', direction='positive', skip=[])[source]

hyphy returns endless files with lots and lots of values (granted, it makes the calculations very transparent). Parse them into a human- friendly format.

Optional arguments:

  • skip – use e.g. to mask gaps in an alignment, needs to be some form of binary iterator (eg [0, 0, 0, 1, 0, 0, 0, …])

faltwerk.io.read_pdb(fp: Union[str, Path], name: str = 'x', strict: bool = True, reindex: bool = False, reindex_start_position: int = 1) → <module 'Bio.PDB.Structure' from '/home/docs/checkouts/readthedocs.org/user_builds/faltwerk/conda/latest/lib/python3.10/site-packages/Bio/PDB/Structure.py'>[source]

Return structure AND sequence

https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ

The hierarchy of the PDB parser is this:

>>> p = PDBParser()
>>> structure = p.get_structure("X", "pdb1fat.ent")
>>> for model in structure:
>>>     for chain in model:
>>>         for residue in chain:
>>>             for atom in residue:
>>>                 print(atom)
faltwerk.io.save_pdb(structure: <module 'Bio.PDB.Structure' from '/home/docs/checkouts/readthedocs.org/user_builds/faltwerk/conda/latest/lib/python3.10/site-packages/Bio/PDB/Structure.py'>, out: ~typing.Union[str, ~pathlib.Path, ~_io.StringIO]) → None[source]

Save structure as pdb file.