A strict regular expression for matching chemical formulae - regex

Question

In the course of processing a large textual chemical database with Perl, I had been faced with the problem of using a regex to match chemical formulae. I have seen these two previous topics, but the suggested answers there are too loose for my requirements.
Specifically, my (admittedly limited) research has led me to this posting that gives a regex for the currently accepted chemical symbols, which I'll copy here for reference
[BCFHIKNOPSUVWY]|[ISZ][nr]|[ACELP][ru]|A[cglmst]|B[aehikr]|C[adeflos]|D[bsy]|Es|F[elmr]|G[ade]|H[efgos]|Kr|L[aiv]|M[cdgnot]|N[abdehiop]|O[gs]|P[abdmot]|R[abe-hnu]|S[bcegim]|T[abcehilms]|Xe|Yb
(Thus e.g. C, Cm, and Cn will pass, but not Cg or Cx.)
As with the previous questions, I also need to match numbers, complete sets of parentheses and complete sets of square brackets, so that both e.g. C2H6O and (CH3)2CFCOO(CH2)2Si(CH3)2Cl are matched.
So how do I combine the previous solutions with the grand regex for matching valid chemical elements to strictly match a chemical formula?
(If it's not too much trouble to add, a blow-by-blow account of how to humanly parse the regex would be appreciated greatly, though not strictly necessary.)

Answer 1

Brief
I decided why not create a massive regex to do what you want (but still maintain a clean regex). This regex would be used in conjunction with a loop to go over matches for bracket or parentheses groups.
Assumptions
I am assuming the following since the OP has not given a full list of positive and negative matches:
Nested parentheses aren't possible
Nested square brackets aren't possible
Square bracket groups that surround a single parentheses group are redundant and therefore incorrect
Square bracket groups must contain at least 2 groups, of which 1 such group must be a parentheses group
If any of these assumptions are incorrect, please let me know so that I may fix the regex accordingly
Answer
View this regex in use here
Code
(?(DEFINE)
(?# Periodic elements )
(?<Hydrogen>H)
(?<Helium>He)
(?<Lithium>Li)
(?<Beryllium>Be)
(?<Boron>B)
(?<Carbon>C)
(?<Nitrogen>N)
(?<Oxygen>O)
(?<Fluorine>F)
(?<Neon>Ne)
(?<Sodium>Na)
(?<Magnesium>Mg)
(?<Aluminum>Al)
(?<Silicon>Si)
(?<Phosphorus>P)
(?<Sulfur>S)
(?<Chlorine>Cl)
(?<Argon>Ar)
(?<Potassium>K)
(?<Calcium>Ca)
(?<Scandium>Sc)
(?<Titanium>Ti)
(?<Vanadium>V)
(?<Chromium>Cr)
(?<Manganese>Mn)
(?<Iron>Fe)
(?<Cobalt>Co)
(?<Nickel>Ni)
(?<Copper>Cu)
(?<Zinc>Zn)
(?<Gallium>Ga)
(?<Germanium>Ge)
(?<Arsenic>As)
(?<Selenium>Se)
(?<Bromine>Br)
(?<Krypton>Kr)
(?<Rubidium>Rb)
(?<Strontium>Sr)
(?<Yttrium>Y)
(?<Zirconium>Zr)
(?<Niobium>Nb)
(?<Molybdenum>Mo)
(?<Technetium>Tc)
(?<Ruthenium>Ru)
(?<Rhodium>Rh)
(?<Palladium>Pd)
(?<Silver>Ag)
(?<Cadmium>Cd)
(?<Indium>In)
(?<Tin>Sn)
(?<Antimony>Sb)
(?<Tellurium>Te)
(?<Iodine>I)
(?<Xenon>Xe)
(?<Cesium>Cs)
(?<Barium>Ba)
(?<Lanthanum>La)
(?<Cerium>Ce)
(?<Praseodymium>Pr)
(?<Neodymium>Nd)
(?<Promethium>Pm)
(?<Samarium>Sm)
(?<Europium>Eu)
(?<Gadolinium>Gd)
(?<Terbium>Tb)
(?<Dysprosium>Dy)
(?<Holmium>Ho)
(?<Erbium>Er)
(?<Thulium>Tm)
(?<Ytterbium>Yb)
(?<Lutetium>Lu)
(?<Hafnium>Hf)
(?<Tantalum>Ta)
(?<Tungsten>W)
(?<Rhenium>Re)
(?<Osmium>Os)
(?<Iridium>Ir)
(?<Platinum>Pt)
(?<Gold>Au)
(?<Mercury>Hg)
(?<Thallium>Tl)
(?<Lead>Pb)
(?<Bismuth>Bi)
(?<Polonium>Po)
(?<Astatine>At)
(?<Radon>Rn)
(?<Francium>Fr)
(?<Radium>Ra)
(?<Actinium>Ac)
(?<Thorium>Th)
(?<Protactinium>Pa)
(?<Uranium>U)
(?<Neptunium>Np)
(?<Plutonium>Pu)
(?<Americium>Am)
(?<Curium>Cm)
(?<Berkelium>Bk)
(?<Californium>Cf)
(?<Einsteinium>Es)
(?<Fermium>Fm)
(?<Mendelevium>Md)
(?<Nobelium>No)
(?<Lawrencium>Lr)
(?<Rutherfordium>Rf)
(?<Dubnium>Db)
(?<Seaborgium>Sg)
(?<Bohrium>Bh)
(?<Hassium>Hs)
(?<Meitnerium>Mt)
(?<Darmstadtium>Ds)
(?<Roentgenium>Rg)
(?<Copernicium>Cn)
(?<Nihonium>Nh)
(?<Flerovium>Fl)
(?<Moscovium>Mc)
(?<Livermorium>Lv)
(?<Tennessine>Ts)
(?<Oganesson>Og)
(?# Regex )
(?<Element>(?&Actinium)|(?&Silver)|(?&Aluminum)|(?&Americium)|(?&Argon)|(?&Arsenic)|(?&Astatine)|(?&Gold)|(?&Barium)|(?&Beryllium)|(?&Bohrium)|(?&Bismuth)|(?&Berkelium)|(?&Bromine)|(?&Boron)|(?&Calcium)|(?&Cadmium)|(?&Cerium)|(?&Californium)|(?&Chlorine)|(?&Curium)|(?&Copernicium)|(?&Cobalt)|(?&Chromium)|(?&Cesium)|(?&Copper)|(?&Carbon)|(?&Dubnium)|(?&Darmstadtium)|(?&Dysprosium)|(?&Erbium)|(?&Einsteinium)|(?&Europium)|(?&Iron)|(?&Flerovium)|(?&Fermium)|(?&Francium)|(?&Fluorine)|(?&Gallium)|(?&Gadolinium)|(?&Germanium)|(?&Helium)|(?&Hafnium)|(?&Mercury)|(?&Holmium)|(?&Hassium)|(?&Hydrogen)|(?&Indium)|(?&Iridium)|(?&Iodine)|(?&Krypton)|(?&Potassium)|(?&Lanthanum)|(?&Lithium)|(?&Lawrencium)|(?&Lutetium)|(?&Livermorium)|(?&Moscovium)|(?&Mendelevium)|(?&Magnesium)|(?&Manganese)|(?&Molybdenum)|(?&Meitnerium)|(?&Sodium)|(?&Niobium)|(?&Neodymium)|(?&Neon)|(?&Nihonium)|(?&Nickel)|(?&Nobelium)|(?&Neptunium)|(?&Nitrogen)|(?&Oganesson)|(?&Osmium)|(?&Oxygen)|(?&Protactinium)|(?&Lead)|(?&Palladium)|(?&Promethium)|(?&Polonium)|(?&Praseodymium)|(?&Platinum)|(?&Plutonium)|(?&Phosphorus)|(?&Radium)|(?&Rubidium)|(?&Rhenium)|(?&Rutherfordium)|(?&Roentgenium)|(?&Rhodium)|(?&Radon)|(?&Ruthenium)|(?&Antimony)|(?&Scandium)|(?&Selenium)|(?&Seaborgium)|(?&Silicon)|(?&Samarium)|(?&Tin)|(?&Strontium)|(?&Sulfur)|(?&Tantalum)|(?&Terbium)|(?&Technetium)|(?&Tellurium)|(?&Thorium)|(?&Titanium)|(?&Thallium)|(?&Thulium)|(?&Tennessine)|(?&Uranium)|(?&Vanadium)|(?&Tungsten)|(?&Xenon)|(?&Ytterbium)|(?&Yttrium)|(?&Zirconium)|(?&Zinc))
(?<Num>(?:[1-9]\d*)?)
(?<ElementGroup>(?:(?&Element)(?&Num))+)
(?<ElementParenthesesGroup>\((?&ElementGroup)+\)(?&Num))
(?<ElementSquareBracketGroup>\[(?:(?:(?&ElementParenthesesGroup)(?:(?&ElementGroup)|(?&ElementParenthesesGroup))+)|(?:(?:(?&ElementGroup)|(?&ElementParenthesesGroup))+(?&ElementParenthesesGroup)))\](?&Num))
)
^((?<Brackets>(?&ElementSquareBracketGroup))|(?<Parentheses>(?&ElementParenthesesGroup))|(?<Group>(?&ElementGroup)))+$
Explanation
The first part of the (?(DEFINE)) section lists each periodic element (ordered by atomic number for easy lookup).
The Element group acts as a simple or | between each of the elements listed in 1. ensuring that each element's symbol is ordered alphabetically by the first character, and then by symbol character length (so as not to catch, for example, Carbon C instead of Calcium Ca)
ElementGroup specifies a group of chemicals in the format: one or more Element followed by zero or more digits, excluding zero (specified by the group Num)
Valid Examples
C - Element
CH - Element followed by another Element
CH3 -Element followed by another Element and a Num
O2 - Element followed by a Num
Invalid Examples
N0 - 0 cannot be used explicitly
N01 - Num group specifies the number must begin with 1-9 or not have a number
A - Element does not exist
c - Element does not exist - case sensitive regex
ElementParenthesesGroup specifies one or more groupings of ElementGroup between parentheses ( ) but containing at least one ElementGroup
Valid Examples
(CH) - ElementGroup surrounded by parentheses
(CH3) - ElementGroup surrounded by parentheses
(CH3NO4) - multiple ElementGroup surrounded by parentheses
(CH3N04)2 - multiple ElementGroup surrounded by parentheses followed by a Num
Invalid Examples
(CH[NO4]) - Only ElementGroup is valid inside ElementParenthesesGroup
ElementSquareBracketGroup specifies a grouping of ElementParenthesesGroup or ElementGroup between square brackets [ ] but containing at least one ElementParenthesesGroup and one other group (ElementParenthesesGroup or ElementGroup)
Valid Examples
[CH3(NO4)] - Contains at least one ElementParenthesesGroup and one other ElementParenthesesGroup or ElementGroup
[(NO4)CH]2 - Contains at least one ElementParenthesesGroup and one other ElementParenthesesGroup or ElementGroup followed by Num
[(NO4)(CH3)] - Contains at least one ElementParenthesesGroup and one other ElementParenthesesGroup or ElementGroup
Invalid Examples
[(NO4)] - Does not contain second group, brackets [ ] are redundant
[NO4] - Does not contain ElementParenthesesGroup
Additional Information
I realize this is a very long answer, but the OP is asking a very specific question and wants to ensure specific criteria are met.
Ensure the following flags are set:
g - ensures global matches
x - ensures whitespace is ignored
if the data is across multiple lines (separated by a newline character) use m for multi line
Note: Regex will only capture the last group of type X that it finds (and overwrite the previously captured group of said type X. This is the default behaviour of regex and there is no way to currently override this behaviour. This may give you undesirable results. You can see this with the last example in the linked regex as well as with your example of (CH3)2CFCOO(CH2)2Si(CH3)2Cl since there are multiple of each group type.

Answer 2

It is best not to assemble such a large regex manually. Instead, let's assume we have an array of atoms #atoms. We can then create a regex matching any of these atoms like:
my ($atoms_regex) = map qr/$_/, join '|', map quotemeta, sort #atoms;
(Sort all items so that shorter atom names come first, then escape all items with quotemeta, join them with a | for alternatives, and compile the regex.)
You can add any used abbreviations to the #atoms array.
Next, we can write a regex that allows grouping and numbering. Our regex will match any number of items, where an item may be an atom or a group, and may be followed by a number:
my $chemical_formula_regex = qr/
(?&item)++
(?(DEFINE)
(?<item> (?: \((?&item)++\) | \[(?&item)++\] | $atoms_regex ) [0-9]* )
)
/x;
Within the (?(DEFINE) ...) group we can define named subpatterns with (?<name> ...). A subpattern is like a subroutine for a regex. We can call those subpatterns with (?&name). This allows us to structure the regex without unnecessary repetition.
The /x flag allows us to use whitespace and linebreaks and comments to lay out the regex in a more readable fashion. Regexes don't have to be an incomprehensible mess!
The ++ quantifier instead of + is not strictly necessary, but prevents unwanted backtracking. That may be a bit faster when a match fails.

Answer 3

Since this post is a top result for "regex chemistry symbols", I would also like to submit a solution. It is a python script that uses a regex to match chemistry formulas of the type A#B#, where A and B are chemical symbols and # is a number. The script as implemented matches and then surrounds the matches with \ce{} for use in LaTeX. It also includes the ability to exclude matches if the capture is in a user-defined list, which means words such as "I" and "In" will not be matched. Gist Link.
#!/usr/bin/env python3
# Find chemical symbols and surround them with \ce{ Symbol }
# Problem words: I, HOW, In, degrees K. Add words to exlist to ignore them.
import re, sys
if len(sys.argv) < 2 :
print('Usage:> {} <filename>'.format(sys.argv[0]))
sys.exit(1)
ptable =" H He "
ptable+=" Li Be B C N O F Ne "
ptable+=" Na Mg Al Si P S Cl Ar "
ptable+=" K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr "
ptable+=" Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe "
ptable+=" Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn "
ptable+=" Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og "
ptable+=" Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu "
ptable+=" Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr "
exlist = ['C','I','In','K','HOW'] # exclude these words from being replaced
orsyms = '|'.join(ptable.split())
resyms = re.compile(r'\b'+'((?:(?:{})\d*)+)'.format(orsyms)+r'\b')
latexfile=sys.argv[1]
with open(latexfile,'r') as fd:
for line in fd:
for m in list(set(resyms.findall(line))):
if m not in exlist :
line = re.sub(r'\b'+m+r'\b', r'\ce{'+m+r'}', line)
print(line,end='')