import chemparse
import numpy as np
from molmass import Formula
from .constant import valence_dict
[docs]
def check_senior(formula):
from .constant import valence_dict
max_valence = 0
sum_valence = 0
element_count = 0
parsed_formula = chemparse.parse_formula(formula)
for k in parsed_formula.keys():
sum_valence= sum_valence+parsed_formula[k]*valence_dict[k]
element_count = element_count+parsed_formula[k]
if valence_dict[k]>max_valence:
max_valence=valence_dict[k]
# if sum_valence%2 != 0:
# return False
if sum_valence<2*max_valence:
return False
if sum_valence<2*(element_count-1):
return False
return True
[docs]
def check_ratio(formula):
"""
Checks the composition of chemical formula using ratio checks in the "7 golden rules"
('Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry').
Args:
formula (str): The chemical formula to be checked.
Returns:
bool: True if the formula passes all checks, False otherwise.
np.NAN: If the formula is invalid due to non-alphanumeric characters at the end.
The function performs the following checks:
- Checks the number of hydrogen and carbon atoms based on the accurate mass.
- Checks the number of nitrogen and oxygen atoms.
- Ensures the it is not a pure carbon/nitrogen loss (except N2)
- Checks the hydrogen to carbon ratio.
- Checks the fluorine to carbon ratio.
- Checks the chlorine to carbon ratio.
- Checks the bromine to carbon ratio.
- Checks the nitrogen to carbon ratio.
- Checks the oxygen to carbon ratio.
- Checks the phosphorus to carbon ratio.
- Checks the sulfur to carbon ratio.
- Checks the silicon to carbon ratio.
"""
if len(formula)==0:
return False
if formula[-1].isalnum() ==False:
print(f'the formula passes {formula} is not right')
return(np.NAN)
parsed_formula = chemparse.parse_formula(formula)
accurate_mass = Formula(formula).isotope.mass
if accurate_mass >0 and accurate_mass<500:
if 'H' in parsed_formula.keys() and parsed_formula['H']>72:
return False
if 'C' in parsed_formula.keys() and parsed_formula['C']>39:
return False
elif accurate_mass>500 and accurate_mass<1000:
if 'H' in parsed_formula.keys() and parsed_formula['H']>126:
return False
if 'C' in parsed_formula.keys() and parsed_formula['C']>78:
return False
if 'N' in parsed_formula.keys() and parsed_formula['N']>20:
return False
if 'O' in parsed_formula.keys() and parsed_formula['O']>27:
return False
if len(parsed_formula.keys())==1 and next(iter(parsed_formula.keys()))=='C':
#check for pure carbon loss
return(False)
if len(parsed_formula.keys())==1 and next(iter(parsed_formula.keys()))=='N' and next(iter(parsed_formula.values()))!=2:
#check for pure nitrogen loss (while not N2)
return (False)
if 'C' in parsed_formula.keys() and 'H' in parsed_formula.keys():
if parsed_formula['H']/parsed_formula['C']>6 or parsed_formula['H']/parsed_formula['C']<0.1:
# 7 golden rules: HC check
return False
if 'C' in parsed_formula.keys() and 'F' in parsed_formula.keys():
if parsed_formula['F']/parsed_formula['C']>6:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'Cl' in parsed_formula.keys():
if parsed_formula['Cl']/parsed_formula['C']>2:
# 7 golden rules: CCl check
return False
if 'C' in parsed_formula.keys() and 'Br' in parsed_formula.keys():
if parsed_formula['Br']/parsed_formula['C']>2:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'N' in parsed_formula.keys():
if parsed_formula['N']/parsed_formula['C']>4:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'O' in parsed_formula.keys():
if parsed_formula['O']/parsed_formula['C']>3:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'P' in parsed_formula.keys():
if parsed_formula['P']/parsed_formula['C']>2:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'S' in parsed_formula.keys():
if parsed_formula['S']/parsed_formula['C']>3:
# 7 golden rules: CF check
return False
if 'C' in parsed_formula.keys() and 'Si' in parsed_formula.keys():
if parsed_formula['Si']/parsed_formula['C']>1:
# 7 golden rules: CF check
return False
return(True)
[docs]
def check_huristic(formula):
if len(formula)==0:
return False
if formula[-1].isalnum() ==False:
print(f'the formula passes {formula} is not right')
return(np.NAN)
parsed_formula = chemparse.parse_formula(formula)
if 'N' in parsed_formula.keys() and 'O' in parsed_formula.keys() and 'P' in parsed_formula.keys() and 'S' in parsed_formula.keys():
if parsed_formula['N']>=10 or parsed_formula['O']>=20 or parsed_formula['P']>=4 or parsed_formula['S']>=3:
return False
if 'N' in parsed_formula.keys() and 'O' in parsed_formula.keys() and 'P' in parsed_formula.keys():
if parsed_formula['N']>3 or parsed_formula['O']>3 or parsed_formula['P']>3:
if parsed_formula['N']>=11 or parsed_formula['O']>=22 or parsed_formula['P']>=6:
return False
if 'O' in parsed_formula.keys() and 'P' in parsed_formula.keys() and 'S' in parsed_formula.keys():
if parsed_formula['O']>=14 or parsed_formula['P']>=3 or parsed_formula['S']>=3:
return False
if 'P' in parsed_formula.keys() and 'S' in parsed_formula.keys() and 'N' in parsed_formula.keys():
if parsed_formula['P']>=3 or parsed_formula['S']>=3 or parsed_formula['N']>=4:
return False
if 'N' in parsed_formula.keys() and 'O' in parsed_formula.keys() and 'S' in parsed_formula.keys():
if parsed_formula['N']>6 or parsed_formula['O']>6 or parsed_formula['S']>6:
if parsed_formula['N']>=19 or parsed_formula['O']>=14 or parsed_formula['S']>=8:
return False
if 'C' in parsed_formula.keys() and 'H' in parsed_formula.keys() and len(parsed_formula.keys())==2:
if 2*parsed_formula['C']+2<parsed_formula['H']:
return False
return True