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regexperlpcre

A strict regular expression for matching chemical formulae

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.)

Solution

  • 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

    1. The first part of the (?(DEFINE)) section lists each periodic element (ordered by atomic number for easy lookup).
    2. 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)
    3. 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
    4. 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
    5. 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.