def adjust_protons(formula, protons):
"""
@param formula: chemical formula as string
@param protons: number of hydrogens to add/remove as intager
@return: new formula as string
"""
if not protons:
return (formula, "")
protons = int(protons)
Notes = ""
#The whole function assumes that there is a single formula string
#If the formula can be broken into components, it must first be merged
#This is because the proton layer only ever has a single component
if (len(formula.split('.')) > 1):
print(
"Error: you must merge the formula components into a single formula string"
)
print("You can do so using Compounds.mergeFormula()")
return formula, "Unadjustable due to multiple components"
atoms = Compounds.parseFormula(formula)
if "H" in atoms:
atoms['H'] += protons
if atoms['H'] < 0:
Notes = 'Too Many Protons adjusted!'
if atoms['H'] == 0:
del atoms['H']
elif (len(atoms) == 0):
#special case for the proton
atoms['H'] = protons
formula = Compounds.buildFormula(atoms)
return (formula, Notes)
sys.path.append('../../Libs/Python')
from BiochemPy import Reactions, Compounds, InChIs
CompoundsHelper = Compounds()
Compounds_Dict = CompoundsHelper.loadCompounds()
Structures_Dict = CompoundsHelper.loadStructures(["InChI"],["ModelSEED"])
for cpd in sorted(Compounds_Dict.keys()):
if(Compounds_Dict[cpd]['inchikey'] == '' or cpd not in Structures_Dict):
continue
(inchi_formula,inchi_layers) = InChIs.parse(Structures_Dict[cpd]['InChI'])
merged_inchi_formula = CompoundsHelper.mergeFormula(inchi_formula)[0]
adjusted_inchi_formula = (InChIs.adjust_protons(merged_inchi_formula,inchi_layers['p']))[0]
if(adjusted_inchi_formula != Compounds_Dict[cpd]['formula']):
adjusted_inchi_atoms_dict = CompoundsHelper.parseFormula(adjusted_inchi_formula)
if('H' in adjusted_inchi_atoms_dict):
del(adjusted_inchi_atoms_dict['H'])
adjusted_inchi_protonfree_formula = CompoundsHelper.buildFormula(adjusted_inchi_atoms_dict)
original_formula_atoms_dict = CompoundsHelper.parseFormula(Compounds_Dict[cpd]['formula'])
if('H' in original_formula_atoms_dict):
del(original_formula_atoms_dict['H'])
original_formula_protonfree_formula = CompoundsHelper.buildFormula(original_formula_atoms_dict)
if(adjusted_inchi_protonfree_formula != original_formula_protonfree_formula):
print cpd,original_formula_protonfree_formula,adjusted_inchi_protonfree_formula
# break
