biofkit 0.0.4

With biofkit, sequence can be easily extract from pdb. And more functions will be added.

biofkit

Biofkit is now containing only one module with one package which can transfer pdb into fasta (or a sequence dictionary) very easily.

How to Install

Conda

conda install -c chou_uken biofkit

Mamba

mamba install -c chou_uken biofkit

Pip

pip install biofkit

How to Use

ProteinKit

from proteinKit import pdbKit

# if argument fasta is True, a fasta file will be created in the same path as the pdb file.
pdbKit.pdb2Seq(pdbFilePath: str, fasta: bool = False, fastaLineLen: int = 80) -> dict[str, str]
    # pdfFilePath: the file path of the pdb you want to transfer.
    # fasta: Whether to transfer into fasta file. If false, pdb will only be transferred to a dictionary.{chainId: Seq}
    # fastaLineLen: How many residues are contained in a single line of the fasta, only work when `fasta` is true.

# load the information of all amino-acid-residue atoms into a list which can be converted to a dataframe with famous `pandas`.
pdbKit.pdb2dfList(pdbFilePath: str, colName: bool = True) -> list[list[int, str, str, int, str, float, float, float]]:
    # pdbFilePath: the file path of the pdb you want to load.
    # colName: a prepared colname list for the output. If colName is true, pdb can be directly transfer to a pandas dataframe.