comparison COBRAxy/utils/model_utils.py @ 499:a2f7a6dd9d0b draft

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498:df90f40a156c

    
    return model


# Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore)
def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
    """
    Extract metabolite IDs from a reaction formula.
    Robust pattern: tokens ending with _<compartment> (e.g., _c, _m, _e),
    allowing leading digits/underscores.
    """
    metabolites = set()
    # optional coefficient followed by a token ending with _<letters>
    if reaction_formula[-1] == ']' and reaction_formula[-3] == '[':
        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+[[A-Za-z0-9]]+)'
    else:
        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+_[A-Za-z0-9]+)'
    matches = re.findall(pattern, reaction_formula)
    metabolites.update(matches)
    return metabolites


def extract_compartment_from_metabolite(metabolite_id: str) -> str:
    """Extract the compartment from a metabolite ID."""
    if '_' in metabolite_id:

499:a2f7a6dd9d0b

    
    return model


# Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore)
#def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
#    """
#    Extract metabolite IDs from a reaction formula.
#    Robust pattern: tokens ending with _<compartment> (e.g., _c, _m, _e),
#    allowing leading digits/underscores.
#    """
#    metabolites = set()
#    # optional coefficient followed by a token ending with _<letters>
#    if reaction_formula[-1] == ']' and reaction_formula[-3] == '[':
#        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+[[A-Za-z0-9]]+)'
#    else:
#        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+_[A-Za-z0-9]+)'
#    matches = re.findall(pattern, reaction_formula)
#    metabolites.update(matches)
#    return metabolites

import re
from typing import Set

# Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore e [comp])
def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
    """
    Estrae gli ID dei metaboliti da una formula di reazione.
    Gestisce:
      - coefficienti stechiometrici opzionali (interi o decimali)
      - compartimenti sia in forma [c] sia _c, sempre a fine metabolita
    Restituisce gli ID includendo il suffisso di compartimento così come appare.
    """
    pattern = re.compile(
        r'(?:^|(?<=\s)|(?<=\+)|(?<=,)|(?<==)|(?<=:))'              # confine a sinistra
        r'(?:\d+(?:\.\d+)?\s*)?'                                   # coefficiente opzionale
        r'([A-Za-z0-9_]+(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+))'       # metabolita + compartimento
    )
    return {m.group(1) for m in pattern.finditer(reaction_formula)}


def extract_compartment_from_metabolite(metabolite_id: str) -> str:
    """Extract the compartment from a metabolite ID."""
    if '_' in metabolite_id: