Module protkit.file_io.prot_io
Implements class ProtIO to read and write protein structures in the Prot format.
The Prot format enables storage of attributes of the protein structure that are not
part of the PDB format. It closely resembles the internal data structure of the
Protein class.
The Prot format is a JSON format that is compressed using zlib to reduce the file size. The JSON format is used because it is human-readable and can be easily parsed by other programs.
Methods are static and can be called without instantiating the class. The main methods are:
convert()to convert a PDB file to a Prot file.load()to load a Prot file.save()to save a Prot file.
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `ProtIO` to read and write protein structures in the Prot format.
The Prot format enables storage of attributes of the protein structure that are not
part of the PDB format. It closely resembles the internal data structure of the
Protein class.
The Prot format is a JSON format that is compressed using zlib to
reduce the file size. The JSON format is used because it is human-readable and
can be easily parsed by other programs.
Methods are static and can be called without instantiating the class. The main methods
are:
- `convert()` to convert a PDB file to a Prot file.
- `load()` to load a Prot file.
- `save()` to save a Prot file.
"""
import json
import zlib
from typing import List, Dict, Union, Optional
from protkit.file_io import PDBIO
from protkit.structure.protein import Protein
from protkit.structure.chain import Chain
from protkit.structure.residue import Residue
from protkit.structure.atom import Atom
class ProtIO:
@staticmethod
def convert(pdb_file_path: str,
prot_file_path: str,
is_pqr_format: bool = False,
pdb_id: Optional[str] = None,
compress: bool = True,
indent: int = 2) -> Protein:
"""
Converts a PDB file to a Prot file.
Args:
pdb_file_path (str): The path to the PDB file.
prot_file_path (str): The path to the Prot file.
is_pqr_format (bool): Whether the PDB file is in PQR format.
pdb_id (str): The ID of the protein.
compress (bool): Whether to compress the Prot file.
indent (int): The indentation level of the Prot file.
Returns:
Protein: The protein.
Raises:
FileNotFoundError: If the PDB file could not be found.
Examples:
>> ProtIO.convert("1a00.pdb", "1a00.prot")
>> ProtIO.convert("1a00.pdb", "1a00.prot", is_pqr_format=True)
>> ProtIO.convert("1a00.pdb", "1a00.prot", pdb_id="1A00")
"""
protein = PDBIO.load(pdb_file_path, is_pqr_format=is_pqr_format, pdb_id=pdb_id)[0]
ProtIO.save(protein, prot_file_path, compress=compress, indent=indent)
return protein
@staticmethod
def load(file_path: str,
decompress: bool = True) -> List[Protein]:
"""
Loads a protein from a Prot file.
Args:
file_path (str): The path to the Prot file.
decompress (bool): Whether to decompress the Prot file.
Returns:
List[Protein]: The protein(s) in the Prot file.
Raises:
FileNotFoundError: If the Prot file could not be found.
"""
if decompress:
with open(file_path, "rb") as file:
text = file.read()
text = zlib.decompress(text)
else:
with open(file_path, "rt") as file:
text = file.read()
property_list = json.loads(text)
proteins = [ProtIO.protein_from_dict(property_dict) for property_dict in property_list]
return proteins
@staticmethod
def save(protein: Union[Protein, List[Protein]],
file_path: str,
compress: bool = True,
indent: int = 2) -> None:
"""
Saves a protein to a Prot file.
Args:
protein (Union[Protein, List[Protein]]): The protein(s) to save.
file_path (str): The path to the Prot file.
compress (bool): Whether to compress the Prot file.
indent (int): The indentation level of the Prot file.
Returns:
None
"""
if type(protein) is Protein:
protein = [protein]
if compress:
text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=0)
text = zlib.compress(text.encode('utf-8'))
with open(file_path, "wb") as file:
file.write(text)
else:
text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=indent)
with open(file_path, "wt") as file:
file.write(text)
# ------------------------------------------------------------
# Methods to convert between Prot and Python data structures
# - atom_to_dict()
# - atom_from_dict()
# - residue_to_dict()
# - residue_from_dict()
# - chain_to_dict()
# - chain_from_dict()
# - protein_to_dict()
# - protein_from_dict()
# ------------------------------------------------------------
@staticmethod
def atom_to_dict(atom: Atom) -> Dict:
"""
Converts an Atom object to a dictionary.
Args:
atom (Atom): The Atom object.
Returns:
Dict: The dictionary representation of the Atom object.
Raises:
None
"""
props = dict()
var = vars(atom)
exclude = ["_residue"]
for key in var:
if key not in exclude:
props[key[1:]] = var[key]
return props
@staticmethod
def atom_from_dict(props: dict) -> Atom:
"""
Converts a dictionary to an Atom object.
Args:
props (dict): The dictionary representation of the Atom object.
Returns:
Atom: The Atom object created from the dictionary.
Raises:
None
"""
atom = Atom("", "", 0, 0, 0)
for key in props:
atom.set_attribute(key, props[key])
return atom
@staticmethod
def residue_to_dict(residue: Residue) -> Dict:
"""
Converts a Residue object to a dictionary.
Args:
residue (Residue): The Residue object.
Returns:
Dict: The dictionary representation of the Residue object.
Raises:
None
"""
props = dict()
var = vars(residue)
exclude = ["_chain", "_atoms"]
for key in var:
if key not in exclude:
props[key[1:]] = var[key]
# Add atoms
props["atoms"] = {}
for atom in residue.atoms:
props["atoms"][atom.atom_type] = ProtIO.atom_to_dict(atom)
return props
@staticmethod
def residue_from_dict(props: dict) -> Residue:
"""
Converts a dictionary to a Residue object.
Args:
props (dict): The dictionary representation of the Residue object.
Returns:
Residue: The Residue object created from the dictionary.
Raises:
None
"""
residue = Residue("")
exclude = ["chain", "atoms"]
for key in props:
if key not in exclude:
residue.set_attribute(key, props[key])
# Add atoms
for key in props["atoms"]:
atom = ProtIO.atom_from_dict(props["atoms"][key])
residue.add_atom(key, atom)
return residue
@staticmethod
def chain_to_dict(chain: Chain) -> Dict:
"""
Converts a Chain object to a dictionary.
Args:
chain (Chain): The Chain object.
Returns:
Dict: The dictionary representation of the Chain object.
Raises:
None
"""
props = dict()
var = vars(chain)
exclude = ["_protein", "_residues"]
for key in var:
if key not in exclude:
props[key[1:]] = var[key]
# Add residues
props["residues"] = []
for residue in chain.residues:
props["residues"].append(ProtIO.residue_to_dict(residue))
return props
@staticmethod
def chain_from_dict(props: dict) -> Chain:
"""
Converts a dictionary to a Chain object.
Args:
props (dict): The dictionary representation of the Chain object.
Returns:
Chain: The Chain object created from the dictionary.
Raises:
None
"""
chain = Chain("")
exclude = ["protein", "residues"]
for key in props:
if key not in exclude:
chain.set_attribute(key, props[key])
# Add residues
for res in props["residues"]:
residue = ProtIO.residue_from_dict(res)
chain.add_residue(residue)
return chain
@staticmethod
def protein_to_dict(protein: Protein) -> Dict:
"""
Converts a Protein object to a dictionary.
Args:
protein (Protein): The Protein object.
Returns:
Dict: The dictionary representation of the Protein object.
Raises:
None
"""
props = dict()
var = vars(protein)
exclude = ["_chains"]
for key in var:
if key not in exclude:
props[key[1:]] = var[key]
# Add chains
props["chains"] = {}
for chain in protein.chains:
props["chains"][chain.chain_id] = ProtIO.chain_to_dict(chain)
return props
@staticmethod
def protein_from_dict(props: dict) -> Protein:
"""
Converts a dictionary to a Protein object.
Args:
props (dict): The dictionary representation of the Protein object.
Returns:
Protein: The Protein object created from the dictionary.
Raises:
None
"""
protein = Protein(None)
exclude = ["chains"]
for key in props:
if key not in exclude:
protein.set_attribute(key, props[key])
# Add chains
for chain in props["chains"]:
chain = ProtIO.chain_from_dict(props["chains"][chain])
protein.add_chain(chain.chain_id, chain)
return proteinClasses
class ProtIO-
Expand source code
class ProtIO: @staticmethod def convert(pdb_file_path: str, prot_file_path: str, is_pqr_format: bool = False, pdb_id: Optional[str] = None, compress: bool = True, indent: int = 2) -> Protein: """ Converts a PDB file to a Prot file. Args: pdb_file_path (str): The path to the PDB file. prot_file_path (str): The path to the Prot file. is_pqr_format (bool): Whether the PDB file is in PQR format. pdb_id (str): The ID of the protein. compress (bool): Whether to compress the Prot file. indent (int): The indentation level of the Prot file. Returns: Protein: The protein. Raises: FileNotFoundError: If the PDB file could not be found. Examples: >> ProtIO.convert("1a00.pdb", "1a00.prot") >> ProtIO.convert("1a00.pdb", "1a00.prot", is_pqr_format=True) >> ProtIO.convert("1a00.pdb", "1a00.prot", pdb_id="1A00") """ protein = PDBIO.load(pdb_file_path, is_pqr_format=is_pqr_format, pdb_id=pdb_id)[0] ProtIO.save(protein, prot_file_path, compress=compress, indent=indent) return protein @staticmethod def load(file_path: str, decompress: bool = True) -> List[Protein]: """ Loads a protein from a Prot file. Args: file_path (str): The path to the Prot file. decompress (bool): Whether to decompress the Prot file. Returns: List[Protein]: The protein(s) in the Prot file. Raises: FileNotFoundError: If the Prot file could not be found. """ if decompress: with open(file_path, "rb") as file: text = file.read() text = zlib.decompress(text) else: with open(file_path, "rt") as file: text = file.read() property_list = json.loads(text) proteins = [ProtIO.protein_from_dict(property_dict) for property_dict in property_list] return proteins @staticmethod def save(protein: Union[Protein, List[Protein]], file_path: str, compress: bool = True, indent: int = 2) -> None: """ Saves a protein to a Prot file. Args: protein (Union[Protein, List[Protein]]): The protein(s) to save. file_path (str): The path to the Prot file. compress (bool): Whether to compress the Prot file. indent (int): The indentation level of the Prot file. Returns: None """ if type(protein) is Protein: protein = [protein] if compress: text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=0) text = zlib.compress(text.encode('utf-8')) with open(file_path, "wb") as file: file.write(text) else: text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=indent) with open(file_path, "wt") as file: file.write(text) # ------------------------------------------------------------ # Methods to convert between Prot and Python data structures # - atom_to_dict() # - atom_from_dict() # - residue_to_dict() # - residue_from_dict() # - chain_to_dict() # - chain_from_dict() # - protein_to_dict() # - protein_from_dict() # ------------------------------------------------------------ @staticmethod def atom_to_dict(atom: Atom) -> Dict: """ Converts an Atom object to a dictionary. Args: atom (Atom): The Atom object. Returns: Dict: The dictionary representation of the Atom object. Raises: None """ props = dict() var = vars(atom) exclude = ["_residue"] for key in var: if key not in exclude: props[key[1:]] = var[key] return props @staticmethod def atom_from_dict(props: dict) -> Atom: """ Converts a dictionary to an Atom object. Args: props (dict): The dictionary representation of the Atom object. Returns: Atom: The Atom object created from the dictionary. Raises: None """ atom = Atom("", "", 0, 0, 0) for key in props: atom.set_attribute(key, props[key]) return atom @staticmethod def residue_to_dict(residue: Residue) -> Dict: """ Converts a Residue object to a dictionary. Args: residue (Residue): The Residue object. Returns: Dict: The dictionary representation of the Residue object. Raises: None """ props = dict() var = vars(residue) exclude = ["_chain", "_atoms"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add atoms props["atoms"] = {} for atom in residue.atoms: props["atoms"][atom.atom_type] = ProtIO.atom_to_dict(atom) return props @staticmethod def residue_from_dict(props: dict) -> Residue: """ Converts a dictionary to a Residue object. Args: props (dict): The dictionary representation of the Residue object. Returns: Residue: The Residue object created from the dictionary. Raises: None """ residue = Residue("") exclude = ["chain", "atoms"] for key in props: if key not in exclude: residue.set_attribute(key, props[key]) # Add atoms for key in props["atoms"]: atom = ProtIO.atom_from_dict(props["atoms"][key]) residue.add_atom(key, atom) return residue @staticmethod def chain_to_dict(chain: Chain) -> Dict: """ Converts a Chain object to a dictionary. Args: chain (Chain): The Chain object. Returns: Dict: The dictionary representation of the Chain object. Raises: None """ props = dict() var = vars(chain) exclude = ["_protein", "_residues"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add residues props["residues"] = [] for residue in chain.residues: props["residues"].append(ProtIO.residue_to_dict(residue)) return props @staticmethod def chain_from_dict(props: dict) -> Chain: """ Converts a dictionary to a Chain object. Args: props (dict): The dictionary representation of the Chain object. Returns: Chain: The Chain object created from the dictionary. Raises: None """ chain = Chain("") exclude = ["protein", "residues"] for key in props: if key not in exclude: chain.set_attribute(key, props[key]) # Add residues for res in props["residues"]: residue = ProtIO.residue_from_dict(res) chain.add_residue(residue) return chain @staticmethod def protein_to_dict(protein: Protein) -> Dict: """ Converts a Protein object to a dictionary. Args: protein (Protein): The Protein object. Returns: Dict: The dictionary representation of the Protein object. Raises: None """ props = dict() var = vars(protein) exclude = ["_chains"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add chains props["chains"] = {} for chain in protein.chains: props["chains"][chain.chain_id] = ProtIO.chain_to_dict(chain) return props @staticmethod def protein_from_dict(props: dict) -> Protein: """ Converts a dictionary to a Protein object. Args: props (dict): The dictionary representation of the Protein object. Returns: Protein: The Protein object created from the dictionary. Raises: None """ protein = Protein(None) exclude = ["chains"] for key in props: if key not in exclude: protein.set_attribute(key, props[key]) # Add chains for chain in props["chains"]: chain = ProtIO.chain_from_dict(props["chains"][chain]) protein.add_chain(chain.chain_id, chain) return proteinStatic methods
def atom_from_dict(props: dict) ‑> Atom-
Converts a dictionary to an Atom object.
Args
props:dict- The dictionary representation of the Atom object.
Returns
Atom- The Atom object created from the dictionary.
Raises
None
Expand source code
@staticmethod def atom_from_dict(props: dict) -> Atom: """ Converts a dictionary to an Atom object. Args: props (dict): The dictionary representation of the Atom object. Returns: Atom: The Atom object created from the dictionary. Raises: None """ atom = Atom("", "", 0, 0, 0) for key in props: atom.set_attribute(key, props[key]) return atom def atom_to_dict(atom: Atom) ‑> Dict-
Converts an Atom object to a dictionary.
Args
atom:Atom- The Atom object.
Returns
Dict- The dictionary representation of the Atom object.
Raises
None
Expand source code
@staticmethod def atom_to_dict(atom: Atom) -> Dict: """ Converts an Atom object to a dictionary. Args: atom (Atom): The Atom object. Returns: Dict: The dictionary representation of the Atom object. Raises: None """ props = dict() var = vars(atom) exclude = ["_residue"] for key in var: if key not in exclude: props[key[1:]] = var[key] return props def chain_from_dict(props: dict) ‑> Chain-
Converts a dictionary to a Chain object.
Args
props:dict- The dictionary representation of the Chain object.
Returns
Chain- The Chain object created from the dictionary.
Raises
None
Expand source code
@staticmethod def chain_from_dict(props: dict) -> Chain: """ Converts a dictionary to a Chain object. Args: props (dict): The dictionary representation of the Chain object. Returns: Chain: The Chain object created from the dictionary. Raises: None """ chain = Chain("") exclude = ["protein", "residues"] for key in props: if key not in exclude: chain.set_attribute(key, props[key]) # Add residues for res in props["residues"]: residue = ProtIO.residue_from_dict(res) chain.add_residue(residue) return chain def chain_to_dict(chain: Chain) ‑> Dict-
Converts a Chain object to a dictionary.
Args
chain:Chain- The Chain object.
Returns
Dict- The dictionary representation of the Chain object.
Raises
None
Expand source code
@staticmethod def chain_to_dict(chain: Chain) -> Dict: """ Converts a Chain object to a dictionary. Args: chain (Chain): The Chain object. Returns: Dict: The dictionary representation of the Chain object. Raises: None """ props = dict() var = vars(chain) exclude = ["_protein", "_residues"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add residues props["residues"] = [] for residue in chain.residues: props["residues"].append(ProtIO.residue_to_dict(residue)) return props def convert(pdb_file_path: str, prot_file_path: str, is_pqr_format: bool = False, pdb_id: Optional[str] = None, compress: bool = True, indent: int = 2) ‑> Protein-
Converts a PDB file to a Prot file.
Args
pdb_file_path:str- The path to the PDB file.
prot_file_path:str- The path to the Prot file.
is_pqr_format:bool- Whether the PDB file is in PQR format.
pdb_id:str- The ID of the protein.
compress:bool- Whether to compress the Prot file.
indent:int- The indentation level of the Prot file.
Returns
Protein- The protein.
Raises
FileNotFoundError- If the PDB file could not be found.
Examples
ProtIO.convert("1a00.pdb", "1a00.prot") ProtIO.convert("1a00.pdb", "1a00.prot", is_pqr_format=True) ProtIO.convert("1a00.pdb", "1a00.prot", pdb_id="1A00")
Expand source code
@staticmethod def convert(pdb_file_path: str, prot_file_path: str, is_pqr_format: bool = False, pdb_id: Optional[str] = None, compress: bool = True, indent: int = 2) -> Protein: """ Converts a PDB file to a Prot file. Args: pdb_file_path (str): The path to the PDB file. prot_file_path (str): The path to the Prot file. is_pqr_format (bool): Whether the PDB file is in PQR format. pdb_id (str): The ID of the protein. compress (bool): Whether to compress the Prot file. indent (int): The indentation level of the Prot file. Returns: Protein: The protein. Raises: FileNotFoundError: If the PDB file could not be found. Examples: >> ProtIO.convert("1a00.pdb", "1a00.prot") >> ProtIO.convert("1a00.pdb", "1a00.prot", is_pqr_format=True) >> ProtIO.convert("1a00.pdb", "1a00.prot", pdb_id="1A00") """ protein = PDBIO.load(pdb_file_path, is_pqr_format=is_pqr_format, pdb_id=pdb_id)[0] ProtIO.save(protein, prot_file_path, compress=compress, indent=indent) return protein def load(file_path: str, decompress: bool = True) ‑> List[Protein]-
Loads a protein from a Prot file.
Args
file_path:str- The path to the Prot file.
decompress:bool- Whether to decompress the Prot file.
Returns
List[Protein]- The protein(s) in the Prot file.
Raises
FileNotFoundError- If the Prot file could not be found.
Expand source code
@staticmethod def load(file_path: str, decompress: bool = True) -> List[Protein]: """ Loads a protein from a Prot file. Args: file_path (str): The path to the Prot file. decompress (bool): Whether to decompress the Prot file. Returns: List[Protein]: The protein(s) in the Prot file. Raises: FileNotFoundError: If the Prot file could not be found. """ if decompress: with open(file_path, "rb") as file: text = file.read() text = zlib.decompress(text) else: with open(file_path, "rt") as file: text = file.read() property_list = json.loads(text) proteins = [ProtIO.protein_from_dict(property_dict) for property_dict in property_list] return proteins def protein_from_dict(props: dict) ‑> Protein-
Converts a dictionary to a Protein object.
Args
props:dict- The dictionary representation of the Protein object.
Returns
Protein- The Protein object created from the dictionary.
Raises
None
Expand source code
@staticmethod def protein_from_dict(props: dict) -> Protein: """ Converts a dictionary to a Protein object. Args: props (dict): The dictionary representation of the Protein object. Returns: Protein: The Protein object created from the dictionary. Raises: None """ protein = Protein(None) exclude = ["chains"] for key in props: if key not in exclude: protein.set_attribute(key, props[key]) # Add chains for chain in props["chains"]: chain = ProtIO.chain_from_dict(props["chains"][chain]) protein.add_chain(chain.chain_id, chain) return protein def protein_to_dict(protein: Protein) ‑> Dict-
Converts a Protein object to a dictionary.
Args
protein:Protein- The Protein object.
Returns
Dict- The dictionary representation of the Protein object.
Raises
None
Expand source code
@staticmethod def protein_to_dict(protein: Protein) -> Dict: """ Converts a Protein object to a dictionary. Args: protein (Protein): The Protein object. Returns: Dict: The dictionary representation of the Protein object. Raises: None """ props = dict() var = vars(protein) exclude = ["_chains"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add chains props["chains"] = {} for chain in protein.chains: props["chains"][chain.chain_id] = ProtIO.chain_to_dict(chain) return props def residue_from_dict(props: dict) ‑> Residue-
Converts a dictionary to a Residue object.
Args
props:dict- The dictionary representation of the Residue object.
Returns
Residue- The Residue object created from the dictionary.
Raises
None
Expand source code
@staticmethod def residue_from_dict(props: dict) -> Residue: """ Converts a dictionary to a Residue object. Args: props (dict): The dictionary representation of the Residue object. Returns: Residue: The Residue object created from the dictionary. Raises: None """ residue = Residue("") exclude = ["chain", "atoms"] for key in props: if key not in exclude: residue.set_attribute(key, props[key]) # Add atoms for key in props["atoms"]: atom = ProtIO.atom_from_dict(props["atoms"][key]) residue.add_atom(key, atom) return residue def residue_to_dict(residue: Residue) ‑> Dict-
Converts a Residue object to a dictionary.
Args
residue:Residue- The Residue object.
Returns
Dict- The dictionary representation of the Residue object.
Raises
None
Expand source code
@staticmethod def residue_to_dict(residue: Residue) -> Dict: """ Converts a Residue object to a dictionary. Args: residue (Residue): The Residue object. Returns: Dict: The dictionary representation of the Residue object. Raises: None """ props = dict() var = vars(residue) exclude = ["_chain", "_atoms"] for key in var: if key not in exclude: props[key[1:]] = var[key] # Add atoms props["atoms"] = {} for atom in residue.atoms: props["atoms"][atom.atom_type] = ProtIO.atom_to_dict(atom) return props def save(protein: Union[Protein, List[Protein]], file_path: str, compress: bool = True, indent: int = 2) ‑> None-
Saves a protein to a Prot file.
Args
protein:Union[Protein, List[Protein]]- The protein(s) to save.
file_path:str- The path to the Prot file.
compress:bool- Whether to compress the Prot file.
indent:int- The indentation level of the Prot file.
Returns
None
Expand source code
@staticmethod def save(protein: Union[Protein, List[Protein]], file_path: str, compress: bool = True, indent: int = 2) -> None: """ Saves a protein to a Prot file. Args: protein (Union[Protein, List[Protein]]): The protein(s) to save. file_path (str): The path to the Prot file. compress (bool): Whether to compress the Prot file. indent (int): The indentation level of the Prot file. Returns: None """ if type(protein) is Protein: protein = [protein] if compress: text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=0) text = zlib.compress(text.encode('utf-8')) with open(file_path, "wb") as file: file.write(text) else: text = json.dumps([ProtIO.protein_to_dict(prot) for prot in protein], indent=indent) with open(file_path, "wt") as file: file.write(text)