Help:Extension/MolFunctions

Extension Information
Implementation
Description
Author(s)	K, Suwa
Version	0.1
MediaWiki	1.11.1
License
Hooks used
Token type

Extension to obtain molecular formula, exact mass, and others from MOL-format files. Prepare a MOL-format file with a trailer like:

 S  SKP  5
 ID	FL3FECGS0010
 FORMULA	C20H18O11
 EXACTMASS	434.084911418
 AVERAGEMASS	434.35032
 SMILES	C(O)C(C1O)(COC1Oc(c2O)cc(O3)c(C(=O)C=C3c(c4)cc(c(O)c4)O)c2O)O
 M  END

Since the number of MOL-format files can be large, create directories whose names are the upper 4 digits of the filenames. For example, in the case of FL3FECGS0010, the location will be /path to mol directory/FL3F/FL3FECGS0010.mol.

The system assumes the location of the MOL directory as $_SERVER["DOCUMENT_ROOT"].
For this reason, the extension fails when called from outside of www, such as jobs by maintenance/runJobs.php. In this case, set the DocumentRoot as $spath (line 121).

Requirements

None

Download

version	source	md5
0.1(September 26,2008)	MolFunctions.phps	5e2e923d24534af51c4884751e28ec46

Installtion

1. Download the source code and rename it to MolFunctions.php.
2. Place it in the extensions/ directory.
3. Insert the follow lines to LocalSettings.php

   require_once( "$IP/extensions/MolFunctions.php" );
   $egMolPath = "path to mol directory from DocumentRoot"; // ex. "/data/mol"

   If $egMolPath is nil, the extention stops.

Function

1. formula
2. avemass
3. extmass
4. smiles