Module `library.classes.dataset`

Expand source code

import os
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom

class Dataset:
    """
        A class used to represent a membrane or molecule dataset. Does not contain any data, only metadata.
    """

    def __init__(self, name, path, type, parent=None):
        self.name = name
        self.path = path
        self.parent = parent
        self.type = type


    def __repr__(self) -> str:
        return f'<Dataset {self.name} at {hex(id(self))}>'
    
    def get_structure(self) -> Structure: 
        parser = PDBParser(QUIET=True)
        return parser.get_structure(self.name, self.path)
    
    def get_model(self) -> Model:
        return self.get_structure().get_models()[0]

    def get_chains(self) -> list:
        return self.get_structure().get_chains()

    def get_residues(self) -> list:
        return self.get_structure().get_residues()

Classes

class Dataset (name, path, type, parent=None)

A class used to represent a membrane or molecule dataset. Does not contain any data, only metadata.

Expand source code

class Dataset:
    """
        A class used to represent a membrane or molecule dataset. Does not contain any data, only metadata.
    """

    def __init__(self, name, path, type, parent=None):
        self.name = name
        self.path = path
        self.parent = parent
        self.type = type


    def __repr__(self) -> str:
        return f'<Dataset {self.name} at {hex(id(self))}>'
    
    def get_structure(self) -> Structure: 
        parser = PDBParser(QUIET=True)
        return parser.get_structure(self.name, self.path)
    
    def get_model(self) -> Model:
        return self.get_structure().get_models()[0]

    def get_chains(self) -> list:
        return self.get_structure().get_chains()

    def get_residues(self) -> list:
        return self.get_structure().get_residues()

Methods

def get_chains(self) ‑> list

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def get_chains(self) -> list:
    return self.get_structure().get_chains()

def get_model(self) ‑> Bio.PDB.Model.Model

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def get_model(self) -> Model:
    return self.get_structure().get_models()[0]

def get_residues(self) ‑> list

Expand source code

def get_residues(self) -> list:
    return self.get_structure().get_residues()

def get_structure(self) ‑> Bio.PDB.Structure.Structure

Expand source code

def get_structure(self) -> Structure: 
    parser = PDBParser(QUIET=True)
    return parser.get_structure(self.name, self.path)