Help:Extension/MolFunctions
From Metabolomics.JP
(Difference between revisions)
m (Doc:Extension/MolFunctions moved to Help:Extension/MolFunctions) |
|||
| Line 7: | Line 7: | ||
__TOC__ | __TOC__ | ||
| − | Extension to obtain molecular formula, exact mass, and others from MOL-format files. | + | Extension to obtain molecular formula, exact mass, and others from MOL-format files. Prepare a MOL-format file with a trailer like: |
| − | + | ||
| − | + | ||
<pre> | <pre> | ||
S SKP 5 | S SKP 5 | ||
| Line 20: | Line 18: | ||
</pre> | </pre> | ||
| − | Since the number of MOL-format files | + | 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 <tt>/path to mol directory/FL3F/FL3FECGS0010.mol</tt>. |
| − | For example, in the case of FL3FECGS0010, the location will be <tt>/path to mol directory/FL3F/FL3FECGS0010.mol</tt>. | + | |
The system assumes the location of the MOL directory as $_SERVER["DOCUMENT_ROOT"].<br> | The system assumes the location of the MOL directory as $_SERVER["DOCUMENT_ROOT"].<br> | ||
| − | For this reason, the extension fails when called from outside of www, such as jobs by maintenance/runJobs.php. | + | 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 $spath (line 121). |
== Requirements == | == Requirements == | ||
| Line 37: | Line 34: | ||
== Installtion == | == Installtion == | ||
<ol> | <ol> | ||
| − | <li>Download source and rename to MolFunctions.php.</li> | + | <li>Download the source code and rename it to MolFunctions.php.</li> |
| − | <li> | + | <li>Place it in the extensions/ directory.</li> |
| − | <li>Insert follow | + | <li>Insert the follow lines to LocalSettings.php |
<pre>require_once( "$IP/extensions/MolFunctions.php" ); | <pre>require_once( "$IP/extensions/MolFunctions.php" ); | ||
$egMolPath = "path to mol directory from DocumentRoot";</pre> | $egMolPath = "path to mol directory from DocumentRoot";</pre> | ||
Revision as of 17:49, 20 September 2008
| Extension Information | |
| Implementation | |
| Description | |
| Author(s) | K, Suwa |
| Version | 0.1 |
| MediaWiki | 1.11.1 |
| License | |
| Hooks used | |
| Token type | |
Contents |
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 $spath (line 121).
Requirements
None
Download
| version | source | size |
| 0.1(September 11,2008) | MolFunctions.phps |
Installtion
- Download the source code and rename it to MolFunctions.php.
- Place it in the extensions/ directory.
- Insert the follow lines to LocalSettings.php
require_once( "$IP/extensions/MolFunctions.php" ); $egMolPath = "path to mol directory from DocumentRoot";
If $egMolPath is nil, the extention stops.
