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bioinf_tools.py
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bioinf_tools.py
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#!/usr/bin/python
try:
import platform
import xml.dom.minidom as mnd
import urllib3
except:
print('Necessary libraries not found :/')
if platform.system() == 'Linux':
class Colors:
RED = '\33[31m'
GREEN = '\33[32m'
BLUE = '\33[34m'
YELLOW = '\33[33m'
END = '\033[0m'
else:
class Colors:
RED = ''
GREEN = ''
BLUE = ''
YELLOW = ''
END = ''
# ------------------------------------------------------------------------------------------------------
class Unp_record:
"""Klasa służąca do przechowywania odniesień do bazy danych UniProt znalezionych w plikach PDB."""
def __init__(self, chain_name, unp_accession, unp_id):
try:
self.chain_name : str = str(chain_name).strip()
self.unp_accession : str = str(unp_accession).strip()
self.unp_id : str = str(unp_id).strip()
except:
print(Colors.RED + 'UNP_record: ValueError!' + Colors.END)
raise ValueError
def __repr__(self):
return f'UNP Record -> chain: {self.chain_name}, UNP accession: {self.unp_accession}, ID code: {self.unp_id}'
# ------------------------------------------------------------------------------------------------------
class Pfam_domain:
"""Klasa służąca do przechowywania informacji o domenach białkowych (Pfam)."""
def __init__(self, chain_name, pfam_accession, pfam_id, start, end):
try:
self.chain_name : str = str(chain_name).strip()
self.pfam_accession : str = str(pfam_accession).strip()
self.pfam_id : str = str(pfam_id).strip()
self.start : int = int(start)
self.end : int = int(end)
except:
print(Colors.RED + 'Pfam_domain: ValueError!' + Colors.END)
raise ValueError
def __repr__(self):
return 'Pfam_domain -> {: <10} {: <23} {: <8} ({: <5} - {: >5})'.format(self.pfam_accession, self.pfam_id, self.chain_name, self.start, self.end)
# ------------------------------------------------------------------------------------------------------
class Atom:
"""Klasa służąca do przechowywania informacji o pojedynczych atomach pobranych ze struktury białka (nazwa, symbol, położenie w R^3 [A])."""
def __init__(self, atom_name, element_symbol, x_coordinate, y_coordinate, z_coordinate):
try:
self.atom_name : str = str(atom_name).strip()
self.element_symbol : str = str(element_symbol).strip()
self.x_coordinate : float = float(x_coordinate)
self.y_coordinate : float = float(y_coordinate)
self.z_coordinate : float = float(z_coordinate)
except:
print(Colors.RED + 'Atom: ValueError!' + Colors.END)
raise ValueError
# ------------------------------------------------------------------------------------------------------
class Termination_symbol:
"""Znacznik końca łańcucha aminokwasowego."""
def __init__(self, residue_name, residue_sequence_number):
try:
self.residue_name : str = str(residue_name).strip()
self.residue_sequence_number : int = int(residue_sequence_number)
except:
print(Colors.RED + 'Termination_symbol: ValueError!' + Colors.END)
raise ValueError
# ------------------------------------------------------------------------------------------------------
class Residue:
"""Klasa zawierająca grupę wczytanych atomów (klasa: Atom), stanowiąca reprezentację reszty aminokwasowej."""
def __init__(self, residue_name, residue_sequence_number):
try:
self.residue_name : str = str(residue_name).strip()
self.residue_sequence_number : int = int(residue_sequence_number)
self.ATOMS : list[Atom] = []
except:
print(Colors.RED + 'Residue: ValueError!' + Colors.END)
raise ValueError
def __repr__(self):
return 'Residue -> {} {: <4}'.format(self.residue_name, self.residue_sequence_number)
def push_atom(self, next_atom : Atom):
self.ATOMS.append(next_atom)
# ------------------------------------------------------------------------------------------------------
class Ligand:
"""Klasa zawierająca grupę wczytanych atomów (klasa: Atom), stanowiąca reprezentację cząsteczki liganda."""
def __init__(self, residue_name, residue_sequence_number):
try:
self.residue_name : str = str(residue_name).strip()
self.residue_sequence_number : int = int(residue_sequence_number)
self.ATOMS : list[Atom] = []
except:
print(Colors.RED + 'Ligand: ValueError!' + Colors.END)
raise ValueError
def __repr__(self):
return 'Ligand -> {} {: <8}'.format(self.residue_name, self.residue_sequence_number)
def push_atom(self, next_atom : Atom):
self.ATOMS.append(next_atom)
# ------------------------------------------------------------------------------------------------------
class Chain:
"""Klasa zawierająca grupę wczytanych reszt aminokwasowych (klasa: Residue), stanowiąca reprezentację łańcucha białkowego."""
def __init__(self, chain_name):
try:
self.chain_name : str = str(chain_name).strip()
self.RESIDUES : list[Residue] = []
except:
print(Colors.RED + 'Chain: ValueError!' + Colors.END)
raise ValueError
def __repr__(self):
chain_arrow = f'{Colors.GREEN}CHAIN: {self.chain_name} --> {Colors.END}'
residues_names = ''
for i in range(len(self.RESIDUES)):
residues_names += self.RESIDUES[i].residue_name
if ((i + 1) % 10 == 0):
residues_names += '\n'
residues_names += ''.ljust(len(chain_arrow) - 9)
else:
residues_names += ' '
return f'{chain_arrow}{residues_names}'
def push_residue(self, next_residue : Residue):
self.RESIDUES.append(next_residue)
# ------------------------------------------------------------------------------------------------------
class Structure:
"""Klasa zawierająca grupę wczytanych łańcuchów aminokwasowych (klasa: Chain), stanowiąca reprezentację całego białka."""
def __init__(self, structure_PDB_ID):
try:
self.structure_PDB_ID : str = str(structure_PDB_ID).strip()
self.data_correctnes_flag : bool = True
self.CHAINS : list[Chain] = []
self.LIGANDS : list[Ligand] = []
self.UNP_RECORDS : list[Unp_record] = []
self.PFAM_DOMAINS : list[Pfam_domain] = []
except:
print(Colors.RED + 'Structure: ValueError!' + Colors.END)
raise ValueError
def collect_data_from_Pfam(self, backup_folder):
"""Funkcja pobierająca informacje o architekturach domenowych z bazy danych Pfam (pod warunkiem, że danych tych w postaci plików *.xml nie ma w lokalnym repozytorium)."""
try:
if self.data_correctnes_flag == True:
http = urllib3.PoolManager()
for unp_record in self.UNP_RECORDS:
try:
xml_file = open(f'{backup_folder}/{self.structure_PDB_ID}_{unp_record.chain_name}_{unp_record.unp_accession}.xml', 'r')
decoded_content = xml_file.read()
xml_file.close()
except:
resource = http.request('GET', f'http://pfam.xfam.org/protein?output=xml&acc={unp_record.unp_accession}')
decoded_content = resource.data.decode('utf-8')
xml_file = open(f'{backup_folder}/{self.structure_PDB_ID}_{unp_record.chain_name}_{unp_record.unp_accession}.xml', 'w')
xml_file.write(decoded_content)
xml_file.close()
parser = mnd.parseString(decoded_content)
matches = parser.getElementsByTagName('match')
for match in matches:
for child in match.childNodes:
if child.nodeType == child.ELEMENT_NODE and child.tagName == 'location':
pfam_record = Pfam_domain(
unp_record.chain_name,
match.getAttribute('accession'),
match.getAttribute('id'),
child.getAttribute('start'),
child.getAttribute('end'))
self.PFAM_DOMAINS.append(pfam_record)
except:
self.data_correctnes_flag = False
print(Colors.RED + f'Could not get domain information for structure: {self.structure_PDB_ID}' + Colors.END)
def get_ligands_environment(self) -> list[tuple[Ligand, Residue, str, Pfam_domain]]:
"""Funkcja zwracająca listę znalezionych miejsc kontaktu ligand - białko."""
distance = lambda atom_a, atom_b: (
(atom_a.x_coordinate - atom_b.x_coordinate) ** 2
+ (atom_a.y_coordinate - atom_b.y_coordinate) ** 2
+ (atom_a.z_coordinate - atom_b.z_coordinate) ** 2
) ** 0.5
comparison_tuple = lambda ligand, residue, chain: (
ligand.residue_name,
ligand.residue_sequence_number,
residue.residue_name,
residue.residue_sequence_number,
chain.chain_name
)
fits = lambda domain, residue: domain.start <= residue.residue_sequence_number and domain.end >= residue.residue_sequence_number
ligands_environment : list[tuple[Ligand, Residue, str, Pfam_domain]] = []
ligands_environment_quick_compare = []
for ligand in self.LIGANDS:
for chain in self.CHAINS:
for residue in chain.RESIDUES:
for atom_a in [atom for atom in residue.ATOMS if atom.atom_name[0] != 'H']:
for atom_b in [atom for atom in ligand.ATOMS if atom.atom_name[0] != 'H']:
if distance(atom_a, atom_b) < 5.0:
comp_tuple = comparison_tuple(ligand, residue, chain)
if comp_tuple not in ligands_environment_quick_compare:
ligands_environment_quick_compare.append(comp_tuple)
found_domain = False
for pfam_domain in self.PFAM_DOMAINS:
if pfam_domain.chain_name == chain.chain_name and fits(pfam_domain, residue):
ligands_environment.append( (ligand, residue, chain.chain_name, pfam_domain) )
found_domain = True
if found_domain == False:
ligands_environment.append( (ligand, residue, chain.chain_name, None) )
for ligand in self.LIGANDS:
if (ligand.residue_name, ligand.residue_sequence_number) not in [(m_ligand.residue_name, m_ligand.residue_sequence_number) for (m_ligand, _, _, _) in ligands_environment]:
ligands_environment.append( (ligand, None, None, None) )
return ligands_environment
def get_ligands_binding_domains(self) -> list[tuple[Ligand, Pfam_domain]]:
"""Funkcja zwracająca domeny białkowe wiążące wskazane ligandy (nie uwzględniono wielokrotnych miejsc wiązania dla tego samego liganda w obrębie tej samej domeny)."""
ligands_environment = self.get_ligands_environment()
matched_domains : list[tuple[Ligand, Pfam_domain]] = []
matched_domains_quick_compare = []
for (ligand, _, _, pfam_domain) in ligands_environment:
if pfam_domain != None:
domain = (
ligand.residue_name,
pfam_domain.chain_name,
pfam_domain.pfam_accession,
pfam_domain.pfam_id,
pfam_domain.start,
pfam_domain.end
)
if domain not in matched_domains_quick_compare:
matched_domains_quick_compare.append(domain)
matched_domains.append( (ligand, pfam_domain) )
return matched_domains
def get_ligands_binding_domains_detailed(self) -> list[tuple[Ligand, Pfam_domain]]:
"""Funkcja zwracająca domeny białkowe wiążące wskazane ligandy (uwzględniono wielokrotne miejsca wiązania dla tego samego liganda w obrębie tej samej domeny)."""
ligands_environment = self.get_ligands_environment()
matched_domains : list[tuple[Ligand, Pfam_domain]] = []
matched_domains_quick_compare = []
for (ligand, _, _, pfam_domain) in ligands_environment:
if pfam_domain != None:
domain = (
ligand.residue_name,
ligand.residue_sequence_number,
pfam_domain.chain_name,
pfam_domain.pfam_accession,
pfam_domain.pfam_id,
pfam_domain.start,
pfam_domain.end
)
if domain not in matched_domains_quick_compare:
matched_domains_quick_compare.append(domain)
matched_domains.append( (ligand, pfam_domain) )
return matched_domains
# ------------------------------------------------------------------------------------------------------
def parse_PDB_file(pdb_file_path, ligands : list[str] = []) -> Structure:
"""Funkcja parsująca pliki PDB. Zwraca wczytaną cząsteczkę w postaci obiektu klasy Structure."""
try:
structure = Structure(pdb_file_path[-8 : -4].upper())
pdb_file = open(pdb_file_path, 'r')
line_counter = -1
try:
for DATA in pdb_file:
line_counter += 1
RECORD_TYPE = DATA[0 : 6]
LIGAND_TYPE = DATA[17 : 20]
DATABASE = DATA[26 : 32]
if RECORD_TYPE == 'HETATM' and LIGAND_TYPE.strip() in ligands:
ATOM_NAME = DATA[12 : 16]
ELEM_SYMBOL = DATA[76 : 78]
X_COORD = DATA[30 : 38]
Y_COORD = DATA[38 : 46]
Z_COORD = DATA[46 : 54]
RES_NAME = DATA[17 : 20]
RES_SEQ_NUM = DATA[22 : 26]
next_atom = Atom(ATOM_NAME, ELEM_SYMBOL, X_COORD, Y_COORD, Z_COORD)
if structure.LIGANDS:
if structure.LIGANDS[-1].residue_sequence_number == int(RES_SEQ_NUM):
structure.LIGANDS[-1].push_atom(next_atom)
else:
next_ligand = Ligand(RES_NAME, RES_SEQ_NUM)
structure.LIGANDS.append(next_ligand)
structure.LIGANDS[-1].push_atom(next_atom)
else:
next_ligand = Ligand(RES_NAME, RES_SEQ_NUM)
structure.LIGANDS.append(next_ligand)
structure.LIGANDS[-1].push_atom(next_atom)
elif RECORD_TYPE == 'ATOM ' or RECORD_TYPE == 'HETATM':
ATOM_NAME = DATA[12 : 16]
ELEM_SYMBOL = DATA[76 : 78]
X_COORD = DATA[30 : 38]
Y_COORD = DATA[38 : 46]
Z_COORD = DATA[46 : 54]
CHAIN_IDENT = DATA[21 : 22]
RES_NAME = DATA[17 : 20]
RES_SEQ_NUM = DATA[22 : 26]
next_atom = Atom(ATOM_NAME, ELEM_SYMBOL, X_COORD, Y_COORD, Z_COORD)
if structure.CHAINS:
if structure.CHAINS[-1].chain_name == str(CHAIN_IDENT).strip():
if structure.CHAINS[-1].RESIDUES[-1].residue_sequence_number == int(RES_SEQ_NUM):
structure.CHAINS[-1].RESIDUES[-1].push_atom(next_atom)
else:
next_residue = Residue(RES_NAME, RES_SEQ_NUM)
structure.CHAINS[-1].push_residue(next_residue)
structure.CHAINS[-1].RESIDUES[-1].push_atom(next_atom)
else:
next_chain = Chain(CHAIN_IDENT)
next_residue = Residue(RES_NAME, RES_SEQ_NUM)
structure.CHAINS.append(next_chain)
structure.CHAINS[-1].push_residue(next_residue)
structure.CHAINS[-1].RESIDUES[-1].push_atom(next_atom)
else:
next_chain = Chain(CHAIN_IDENT)
next_residue = Residue(RES_NAME, RES_SEQ_NUM)
structure.CHAINS.append(next_chain)
structure.CHAINS[-1].push_residue(next_residue)
structure.CHAINS[-1].RESIDUES[-1].push_atom(next_atom)
elif RECORD_TYPE == 'TER ':
RES_NAME = DATA[17 : 20]
RES_SEQ_NUM = DATA[22 : 26]
structure.CHAINS[-1].push_residue(Termination_symbol(RES_NAME, RES_SEQ_NUM))
elif RECORD_TYPE == 'DBREF ' and DATABASE == 'UNP ':
CHAIN_IDENT = DATA[12 : 13]
DB_ACCESSION = DATA[33 : 41]
ID_CODE = DATA[42 : 54]
structure.UNP_RECORDS.append(Unp_record(CHAIN_IDENT, DB_ACCESSION, ID_CODE))
pdb_file.close()
try:
chains_to_remove = []
for index in range(len(structure.CHAINS)):
if type(structure.CHAINS[index].RESIDUES[-1]) != Termination_symbol:
chains_to_remove.append(index)
else:
structure.CHAINS[index].RESIDUES.pop(-1)
chains_to_remove.reverse()
for index in chains_to_remove:
structure.CHAINS.pop(index)
except:
structure.data_correctnes_flag = False
print(Colors.RED + f'The file: \'{pdb_file_path}\' contains an error in the marking of amino acid chains :O' + Colors.END)
except:
structure.data_correctnes_flag = False
print(Colors.RED + f'The file \'{pdb_file_path}\' has an error in line: {line_counter} :O' + Colors.END)
except FileNotFoundError:
structure.data_correctnes_flag = False
print(Colors.RED + f'File: \'{pdb_file_path}\' not found :/' + Colors.END)
return structure