How do I parse a chemical formula using a regular expression?

user_14380697 0
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I have a list patterns:

patterns=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
       'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn',
       'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb',
       'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In',
       'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm',
       'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta',
       'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At',
       'Rn']

and I have big dataframe with strings, for example:

str0='Mg0.97Fe0.03B2'
str1='Tl0.5Hg0.5Ba2Ca2Cu3O8'

I am trying this:

keyss=list(filter(None,regex.split("[^a-zA-Z]*",somestring)))
values=list(filter(None,regex.split("[^0-9.0-9]*",somestring)))

Sometimes, this works:

str3='Hg0.75SrBa2Ca2Cu3O8'
keyss=list(filter(None,regex.split("[^a-zA-Z]*",str3)))
values=list(filter(None,regex.split("[^0-9.0-9]*",str3))
['Ba', 'Fe', 'Co', 'Mn', 'As']
['1', '1.832', '0.15', '0.018', '2']

However, if I have a string like this:

str3='Hg0.75SrBa2Ca2Cu3O8'
keyss=list(filter(None,regex.split("[^a-zA-Z]*",str3)))
values=list(filter(None,regex.split("[^0-9.0-9]*",str3)))
['Hg', 'SrBa', 'Ca', 'Cu', 'O']!=['Hg', 'Sr','Ba', 'Ca', 'Cu', 'O']
['0.75', '2', '2', '3', '8']!=['0.75', '1','2', '2', '3', '8']

or this

str4='NbSn3'
keyss=list(filter(None,regex.split("[^a-zA-Z]*",str4)))
values=list(filter(None,regex.split("[^0-9.0-9]*",str4)))
['NbSn']!=['Nb','Sn']
['3']!=['1','3']
str4='Pb1.4Sr4Y1.2Ca0.8Cu4.6O'
...

My code is not working correctly. How I can fix it?

python regex string
2 Answers

I guess you started good with patterns and then dropped the idea which is probably not helpful (you could use it in pyparsing grammar) but there is indeed a simpler approach that follows your latter idea.

I suggest you do something like this:

str3='Hg0.75SrBa2Ca2Cu3O8'
splitted = list(regex.split("([A-Z][a-z]*)",str3))
keyss = list(filter(lambda a: a[0].isupper() if a else False, splitted))
values = list(filter(lambda a: a[0].isdigit() if a else False, splitted))
print(keyss, values)

['Hg', 'Sr', 'Ba', 'Ca', 'Cu', 'O'] ['0.75', '2', '2', '3', '8']

user_65739020

Use

import pandas as pd

patterns=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
       'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn',
       'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb',
       'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In',
       'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm',
       'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta',
       'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At',
       'Rn']
rx = fr'({"|".join(sorted(patterns, key=len,reverse=True))})(\d+(?:\.\d+)?)?'
df = pd.DataFrame({'formulas' : ['Mg0.97Fe0.03B2', 'Tl0.5Hg0.5Ba2Ca2Cu3O8', 'Hg0.75SrBa2Ca2Cu3O8', 'NbSn3']})
df['result'] = df['formulas'].str.findall(rx)
df['result'] = df['result'].apply(lambda m: [(x,y) if y else (x,1) for x,y in m])

Results

>>> df
                formulas                                                     result
0         Mg0.97Fe0.03B2                           [(Mg, 0.97), (Fe, 0.03), (B, 2)]
1  Tl0.5Hg0.5Ba2Ca2Cu3O8  [(Tl, 0.5), (Hg, 0.5), (Ba, 2), (Ca, 2), (Cu, 3), (O, 8)]
2    Hg0.75SrBa2Ca2Cu3O8   [(Hg, 0.75), (Sr, 1), (Ba, 2), (Ca, 2), (Cu, 3), (O, 8)]
3                  NbSn3                                         [(Nb, 1), (Sn, 3)]
user_113298900
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