pandoc-chem-struct

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pandoc-chem-struct

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Simple pandoc filter for formatting of chemical structures.

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# pandoc-chem-struct: A pandoc filter for easier, more legible chemical structures

pandoc-chem-struct is a little [pandoc][] filter that converts simple chemical structures into the
proper formatting. In principle, the markdown is easier to read and longer structures are much
easier to type. The syntax is loosely based on the (infinitely more powerful) [mhchem][] LaTeX
package.

## Installation

Use as any other pandoc filter (i.e., `pandoc --filter pandoc-chem-struct`). For LaTeX (or pdf)
output, must have mhchem installed.

## Usage

Within a pandoc markdown document, chemical structures are written as `s:{formula}`. Numbers
are automatically subscripted. Charges at the end of the formula are superscripted. If the species
is multiply charged, this can be indicated with `^`.

When converting to non-LaTeX documents, result is simply:
- `s:{CH3CH2OH}` → `CH~3~CH~2~OH`
- `s:{NH4+}` → `NH~4~^+^`
- `s:{SO3^2-}` → `SO~3~^2−^`

When converting to LaTeX documents, chemical formulas are simply typeset with mhchem. That is:
- `s:{CH3CH2OH}` → `\ce{CH3CH2OH}`

Obviously, this package must be loaded in the LaTeX preamble.

[pandoc]: http://pandoc.org
[mhchem]: https://www.ctan.org/pkg/mhchem?lang=en

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