biofkit 0.0.5

With biofkit you can deal with pdb file (extract sequence, atom information and so on) very easily.

biofkit

Biofkit is now containing only one module with one package which can deal with pdb file (extract sequence, atom information and so on) 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. output[idx] shows the information of an atom.
pdb2List(pdbFilePath: str, csvPath: str = None, colName: bool = False) -> list[list[int, str, str, int, str, float, float, float]]:
    # pdbFilePath: the file path of the pdb you want to load.
    # csvPath: if given, then write a csv file for your atom information.
    # colName: a prepared colname list for the output. If colName is true, the output[0] will be such a list shown below. May help when column names are needed.
    pdbInfoColumns: [str] = ['Serial', 'Atom', 'ResName', 'ResSeq', 'ChainId', 'X', 'Y', 'Z']

# load the information of all amimo-acid-residue atoms into a dictionary, which can be converted into a dataframe with famous `pandas`.
pdb2Dict(pdbFilePath: str) -> dict[str, list]:
    # pdbFilePath: the file path of the pdb you want to load.