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Chem plugin

Compatible with DokuWiki

2006/11/06 or later

Format a molecular formula

Last updated on: 2008-09-29
Provides: Syntax

The missing download url means that this extension cannot be installed via the Extension Manager. Please see Publishing a Plugin on dokuwiki.org. Recommended are public repository hosts like GitHub, GitLab or Bitbucket.

This extension has not been updated in over 2 years. It may no longer be maintained or supported and may have compatibility issues.

Tagged with chemistry, formula, science

By Ikuo Obataya

Details and Download page

ZIP file
chem.zip (1KB)

This DokuWiki plugin formats a molecular formula easily.

Appearance	C₂H₅O₂^-Na⁺
Without the plugin	C<sub>2</sub>H<sub>5</sub>O<sub>2</sub><sup>-</sup>Na<sup>+</sup>
Using Chem plugin	<chem>C2H5O2-Na+</chem>

The latest version supports to export Open Document format using ODT plugin.

Examples

C₂H₆

<chem>C2H6</chem>

Na₂HPO₄ 12H₂O

<chem>Na2HPO4 12H2O</chem>

C₂H₅O₂^-Na⁺

<chem>C2H5O2|-Na+</chem>    // | is a splitter.

Cl₂H₆N₂Pt²⁺

<chem>Cl2H6N2Pt2+</chem>

Al₂(SO₄)₃

<chem>Al2(SO4)3</chem>

another Version

The original plugin works very fine.

For those of you who have to write more chemical formulars and have some extra wishes like easier syntax, nuclid-number, and a nicer output in DokuWiki pages the following suggestion could help you.

Syntax:

92|235U3|2+

would appear as <html>²³⁵_92<sub>3²⁺</html>; the single numbers are optional so expressions like U2+, U2, 235U or 92|235U are recognized as well as all the brackets.

Unfortunately there are some limitations:

Due to many preg_matches the entering and leaving of DokuWiki editmenu takes quite long
ODT-Support doesn't work - but that´s just due to a lack of regular expressions to get the formatting out. (May someone could give me a hand here)
if you use ions and have multiple elements the shifting breaks as I just optimized it for one digit. (May someone could give me a hand here)

I'll work on it soon (in Apr, maybe — iobataya 2010/04/04 22:23

I'd like to apply a new syntax for notation of isotopes in order to simplify either the DW syntax and the regular expressions.

Put on ^ before nucleons within a <chem> element. (→ superscript)
Put on _ before atomic number within a <chem> element. (→ subscript)

#EXAMPLE
^14_6C        (carbon-14)
^235_92U      (uranium-235)

What do you think ? — iobataya 2010/04/21 05:45

syntax.php:

<?php
/*
description : Plugin Chem: formatting chemical format
author      : Ikuo Obataya
email       : ikuo_obataya@symplus.co.jp
lastupdate  : 2008-09-29
license     : GPL 2 (http://www.gnu.org/licenses/gpl.html)
*/
if(!defined('DOKU_INC')) die();
if(!defined('DOKU_PLUGIN')) define('DOKU_PLUGIN',DOKU_INC.'lib/plugins/');
require_once(DOKU_PLUGIN.'syntax.php');
class syntax_plugin_chem extends DokuWiki_Syntax_Plugin {
  function getInfo(){
    return array(
        'author' => 'Ikuo Obataya',
        'email'  => 'I.Obataya@gmail.com',
        'date'   => '2008-9-29',
        'name'   => 'Chemical Formula Plugin',
        'desc'   => 'Format chemical formula',
        'url'    => 'http://wiki.symplus.co.jp/computer/en/chem_plugin',
    );
}
 
  function getType(){ return 'formatting'; }
  function getAllowedTypes() { return array('formatting', 'substition', 'disabled'); }   
  function getSort(){ return 158; }
  function connectTo($mode) { $this->Lexer->addEntryPattern('<chem>(?=.*?</chem>)',$mode,'plugin_chem'); }
  function postConnect() { $this->Lexer->addExitPattern('</chem>','plugin_chem'); }
 
  function handle($match, $state, $pos, &$handler){
    switch ($state) {
        case DOKU_LEXER_ENTER     :return array($state, '');
        case DOKU_LEXER_UNMATCHED :return array($state, $match);
        case DOKU_LEXER_EXIT      :return array($state, '');
    }
    return array();
  }
 
  function render($mode, &$renderer, $data) {
    if($mode == 'xhtml' || $mode=='odt'){
      list($state, $match) = $data;
      switch ($state) {
        case DOKU_LEXER_ENTER:break;
        case DOKU_LEXER_UNMATCHED:
          if($mode=='xhtml'){
            // xhtml
            $renderer->doc .= $this->getChemFormat($match);
          }
		  if($mode == 'odt'){
            // Open document format
            $renderer->doc.= $this->getOdtChemFormat($match);
          }
          break;
        case DOKU_LEXER_EXIT:break;
      }
      return true;
    }
    return false;
  }
 
   function getChemFormat($raw){
    $pattern = array(	"/([A-Z][a-z]?|\)|\])([1-9][0-9]*)[\|](([\-\+][0-9]*)|([0-9]*[\-\+]))/",	/* sub+ sup: Al2|2+ , H2 , )2 , ]2 */
						"/([A-Ze][a-z]?|\)|\])(([\-\+][0-9]*)|([0-9]*[\-\+]))/",					/* only sup: Al2- , H2+ , )2+ , ]2- */
						"/([A-Z][a-z]?|\)|\])([1-9][0-9]*)/",										/* only sub: Al2 , H2 , )2 , ]2 */
						"/([0-9]*)[\|]([0-9]*)([A-Z][a-z]?)/",										/* sup + sub: 92|235U */
						"/([0-9]*)([A-Z][a-z]?)/",													/* only sup: 235U */
 
						"/Neutron/",
						"/Elektron/",
						"/Proton/",
 
						"/alpha/",
						"/beta/",
						"/gamma/");
    $replace = array(	"\${1}<sub style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>\${2}</sub><sup style='position: relative; left: -0.5em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>\${3}</sup>",
						"\${1}<sup>\${2}</sup>",
						"\${1}<sub>\${2}</sub>",
						"<sup style='position: relative; right: -1.0em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>\${2}</sup><sub style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>\${1}</sub>\${3}",
						"<sup>\${1}</sup>\${2}",
 
						"<sup style='position: relative; right: -0.5em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>1</sup><sub style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>0</sub>n",
						"<sup style='position: relative; right: -1.0em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>0</sup><sub style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>-1</sub>e",
						"<sup style='position: relative; right: -1.0em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>0</sup><sub style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>+1</sub>p",
 
						"<sub style='position: relative; right: -0.5em;font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>2</sub><sup style='position: relative; font-family: Arial, Helvetica, sans-serif; font-size: 70%;'>4</sup>He",
						"e<sup>-</sup>",
						"&gamma;");
    return preg_replace($pattern,$replace,$raw);
  }
 
 
  function getOdtChemFormat($raw){
    $c = $this->getChemFormat($raw);
    $pattern = array(	"/<sup([^>]*)>([^<]+)<\/sup>/",
						"/<sub([^>]*)>([^<]+)<\/sub>/");
    $replace = array(	"<text:span text:style-name=\"sup\">\${2}</text:span>",
						"<text:span text:style-name=\"sub\">\${2}</text:span>"); 
    return preg_replace($pattern,$replace,$c);
  }
 
 
 }
?>

Table of Contents

Chem plugin

Examples

another Version