Add mhchem.lua filter.

Author: jgm

mhchem/Makefile

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+DIFF ?= diff --strip-trailing-cr -u
+PANDOC ?= pandoc
+
+test:
+	@$(PANDOC) --lua-filter=mhchem.lua test.txt -o test.docx
+	@rm -f test.native
+
+.PHONY: test

mhchem/README.md

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+# mhchem
+
+[mhchem] is a widely-used LaTeX package for chemical notation.
+It is not understood natively by pandoc's LaTeX reader. This
+filter replaces any `\ce{}` commands in RawInline, RawBlock,
+and Math elements, with Math elements that can be reliably
+converted to other formats by pandoc.
+
+## Usage
+
+To convert a LaTeX document containing mhchem macros
+to docx, do
+
+    pandoc -f latex+raw_tex -L mhchem.lua input.tex -o output.docx
+
+The `-f latex+raw_tex` part is essential; it ensures that
+bare `\ce{}` commands will be included in the pandoc AST as
+raw TeX, so that this filter can see them.
+
+Related work:
+
+- <https://github.com/mhchem/mhchemParser/>
+

mhchem/mhchem.lua

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+-- For better performance we put these functions in local variables:
+local P, S, R, Cf, Cc, Ct, V, Cs, Cg, Cb, B, C, Cmt =
+  lpeg.P, lpeg.S, lpeg.R, lpeg.Cf, lpeg.Cc, lpeg.Ct, lpeg.V,
+  lpeg.Cs, lpeg.Cg, lpeg.Cb, lpeg.B, lpeg.C, lpeg.Cmt
+
+local whitespacechar = S(" \t\r\n")
+local number = (R"09"^1 * (P"." * R"09"^1)^-1)
+local symbol = C(S"()[],;") + (P"\\" * C(S"{}"))
+
+local function escapeTeX(x)
+  return x:gsub("%%","\\%")
+          :gsub("\\","\\\\")
+          :gsub("([{}])", "\\%1")
+end
+
+local arrows = {
+  ["->"] = "\\longrightarrow",
+  ["<-"] = "\\longleftarrow",
+  ["<->"] = "\\longleftrightarrow",
+  ["<-->"] = "\\longleftrightarrow", -- for now; we don't have a longer arrow
+  ["<=>"] = "\\rightleftharpoons",
+  ["<=>>"] = "\\longRightleftharpoons",
+  ["<<=>"] = "\\longLeftrightharpoons"
+}
+
+local bonds = {
+  ["-"] = "{-}",
+  ["="] = "{=}",
+  ["#"] = "{\\equiv}",
+  ["1"] = "{-}",
+  ["2"] = "{=}",
+  ["3"] = "{\\equiv}",
+  ["..."] = "{\\cdot}{\\cdot}{\\cdot}",
+  ["...."] = "{\\cdot}{\\cdot}{\\cdot}{\\cdot}",
+  ["->"] = "{\\rightarrow}",
+  ["<-"] = "{\\leftarrow}",
+  ["~"] = "{\\tripledash}",
+  ["~-"] = "{\\rlap{\\lower.1em{-}}\\raise.1em{\\tripledash}}",
+  ["~--"] = "{\\rlap{\\lower.2em{-}}\\rlap{\\raise.2em{\\tripledash}}-}",
+  ["~="] = "{\\rlap{\\lower.2em{-}}\\rlap{\\raise.2em{\\tripledash}}-}",
+  ["-~-"] = "{\\rlap{\\lower.2em{-}}\\rlap{\\raise.2em{-}}\\tripledash}"
+}
+
+-- math mode renderer
+local render =
+  { str = function(x)
+      if #x > 0 then
+        return "\\mathrm{" .. escapeTeX(x) .. "}"
+      else
+        return ""
+      end
+    end,
+    element = function(x) return "\\mathrm{" .. escapeTeX(x) .. "}" end,
+    superscript = function(x) return "^{" .. x .. "}" end,
+    subscript = function(x) return "_{" .. x .. "}" end,
+    number = function(x) return x end,
+    math = function(x) return x end,
+    fraction = function(n,d) return "\\frac{" .. n .. "}{" .. d .. "}" end,
+    fractionparens = function(n,d) return "(" .. n .. "/" .. d .. ")" end,
+    greek = function(x) return "\\mathrm{" .. x .. "}" end,
+    arrow = function(arr, above, below)
+      local result = arrows[arr]
+      if above then
+        result = "\\overset{" .. above .. "}{" .. result .. "}"
+      end
+      if below then
+        result = "\\underset{" .. below .. "}{" .. result .. "}"
+      end
+      return result
+    end,
+    precipitate = function() return "\\downarrow " end,
+    gas = function() return "\\uparrow " end,
+    circa = function() return "{\\sim}" end,
+    grouped = function(...)
+      return "{" .. table.concat(table.pack(...)) .. "}"
+    end
+  }
+
+Mhchem = P{ "Formula",
+  Formula = Ct( V"FormulaPart"^0 ) * P(-1) / table.concat;
+  FormulaPart =  V"Molecule"
+               + V"ReactionArrow"
+               + V"Bond"
+               + V"Sup"
+               + V"Sub"
+               + V"Charge"
+               + V"Fraction"
+               + V"Number"
+               + V"Math"
+               + V"Precipitate"
+               + V"Gas"
+               + V"Letters"
+               + V"GreekLetter"
+               + V"Circa"
+               + V"Text"
+               + V"EquationOp"
+               + V"Space"
+               + V"TeXCommand"
+               + V"Times"
+               + V"Symbol" ;
+
+  Molecule = V"StoichiometricNumber"^-1 * V"MoleculePart"^1 ;
+  MoleculePart = (V"Element" + V"Group") * V"ElementSub"^-1 / render.grouped ;
+  Group = Cs(P"(" * V"MoleculePart"^1 * P")") ;
+  StoichiometricNumber = (V"Number" + C(R"az") + V"Math" + V"Fraction") *
+                          Cc("\\;") * whitespacechar^0 ;
+  Element = C(R"AZ" * R"az"^0) / render.element ;
+  Charge = B(R"AZ" + R"az" + S")]}") * (S"+-") * #-R"AZ" /
+    render.superscript ;
+  ElementSub = C(R"09"^1) / render.str / render.subscript ;
+  Precipitate = whitespacechar^0 * (P"(v)" + P"v") * whitespacechar^0 /
+    render.precipitate ;
+  Gas = whitespacechar^0 * (P"(^)" + P"^") * whitespacechar^0 /
+    render.gas ;
+  Bond = (C(S"#=-") * #R"AZ" / bonds) +
+         (P"\\bond{" * Cmt(C((P(1) - P"}")^0),
+                       function(subj,pos,capt)
+                         local b = bonds[capt]
+                         if b then
+                           return pos, b
+                         else
+                           return false
+                         end
+                       end) * P"}") ;
+  Letters = R"az"^1 / render.str ;
+  Number = C(number) / render.number;
+  NumberOrLetter = V"Number" + V"Letters" ;
+  Fraction = (P"(" * V"NumberOrLetter"^1 * P"/" * V"NumberOrLetter"^1 * P")"
+              / render.fractionparens) +
+             (V"NumberOrLetter" * P"/" * V"NumberOrLetter" / render.fraction);
+  Sup = P"^" * (V"InBracesSuper" +
+        (C(S"+-"^-1 * R"09"^0 * S"+-"^-1) / render.str)) / render.superscript ;
+  Sub = P"_" * (V"InBraces" + (C(S"+-"^-1 * R"09"^0 * S"+-"^-1) / render.str)) /
+    render.subscript ;
+  TeXCommand = C(P"\\" * (R"AZ" + R"az")^1 * whitespacechar^0 * V"InBraces"^0) ;
+  Math = P"$" * Cs((V"MathPart" + V"CEPart")^1) * P"$" / render.math ;
+  MathPart = C((P(1) - (P"$" + V"CEPart"))^1) ;
+  CEPart = P"\\ce{" * Ct((V"FormulaPart" - P"}")^0) * P"}" / table.concat ;
+  GreekLetter = C(P"\\" *
+    (( P"alpha" + P"beta" + P"gamma" + P"delta" + P"epsilon" +
+      P"zeta" + P"eta" + P"theta" + P"iota" + P"kappa" +
+      P"mu" + P"nu" + P"xi" + P"omicron" + P"pi" + P"rho" + P"sigma" +
+      P"tau" + P"upsilon" + P"phi" + P"xi" + P"psi" + P"omega"
+     ) +
+    (( P"Alpha" + P"Beta" + P"Gamma" + P"Delta" + P"Epsilon" +
+      P"Zeta" + P"Eta" + P"Theta" + P"Iota" + P"Kappa" +
+      P"Mu" + P"Nu" + P"Xi" + P"Omicron" + P"Pi" + P"Rho" + P"Sigma" +
+      P"Tau" + P"Upsilon" + P"Phi" + P"Xi" + P"Psi" + P"Omega" )))) *
+      whitespacechar^0 / render.greek ;
+  EquationOp = whitespacechar^0 *
+      C(P"+" + P"-" + P"=" + (P"\\pm")) *
+      whitespacechar^0 /
+      render.math;
+  ReactionArrow =
+    whitespacechar^0 *
+    C(P"->" +
+      P"<-->" +
+      P"<->" +
+      P"<-" +
+      P"<=>>" +
+      P"<=>" +
+      P"<<=>") *
+      (P"[" * Cs((V"FormulaPart" - P"]")^0) * P"]")^-2 *
+      whitespacechar^0 / render.arrow ;
+  Text = V"InBraces" ;
+  Circa = P"\\ca" * whitespacechar^0 / render.circa ;
+  Space = C(whitespacechar^1) / "~" ;
+  Times =  S".*" / "\\cdot " ;
+  Symbol = symbol / render.str;
+  InBraces = P"{" * Ct((((V"FormulaPart" - S"{}")^1) + V"InBraces")^0) * P"}" /
+    table.concat ;
+  InBracesSuper = P"{"
+                * Ct(((( ((P"." / "\\bullet ") + V"FormulaPart") - S"{}")^1)
+                        + V"InBraces")^0)
+                * P"}" / table.concat
+  }
+
+function handleCe(s)
+  local inner = s:sub(5,-2) -- strip off \ce{ and }
+  local result = lpeg.match(Mhchem, inner)
+  if not result then
+    io.stderr:write("Could not parse mhchem formula " .. inner .. "\n")
+    return "\\text{Could not parse}"
+  end
+  return result
+end
+
+function RawInline(el)
+  if (el.format == "latex" or el.format == "tex") and
+      el.text:match("\\ce{") then
+    local result = handleCe(el.text)
+    if result then
+      return pandoc.Math("InlineMath", handleCe(el.text))
+    end
+  end
+end
+
+function RawBlock(el)
+  local il = RawInline(el)
+  if il then
+    return pandoc.Para(il)
+   end
+end
+
+function Math(el)
+  el.text = string.gsub(el.text, "(\\ce%b{})", handleCe)
+end