Help:Extension/MolFunctions
From Metabolomics.JP
(Difference between revisions)
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__TOC__ | __TOC__ | ||
| − | + | Extension to obtain molecular formula, exact mass, and others from MOL-format files. | |
| − | + | ||
| − | + | ||
| + | You need to prepare a MOL-format file with a trailer like the following. | ||
| + | <pre> | ||
S SKP 5 | S SKP 5 | ||
ID FL3FECGS0010 | ID FL3FECGS0010 | ||
| Line 18: | Line 18: | ||
SMILES C(O)C(C1O)(COC1Oc(c2O)cc(O3)c(C(=O)C=C3c(c4)cc(c(O)c4)O)c2O)O | SMILES C(O)C(C1O)(COC1Oc(c2O)cc(O3)c(C(=O)C=C3c(c4)cc(c(O)c4)O)c2O)O | ||
M END | M END | ||
| + | </pre> | ||
| − | + | Since the number of MOL-format files is large, create directories whose names are the upper 4 digits of the filenames. <br> | |
| − | + | 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> | |
| − | + | For this reason, the extension fails when called from outside of www, such as jobs by maintenance/runJobs.php.<br> In this case, assign the path of DocumentRoot in $spath (line 121). | |
| − | + | ||
== Requirements == | == Requirements == | ||
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<pre>require_once( "$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> | ||
| − | $ | + | If $egMolPath is nil, the extention stops.</li> |
</ol> | </ol> | ||
== Function == | == Function == | ||
| − | # [[ | + | # [[Help:Extensions#.7B.7B.23formula:id.3D.27.27.7D.7D|formula]] |
| − | # [[ | + | # [[Help:Extensions#.7B.7B.23avemass:id.3D.27.27.7D.7D|avemass]] |
| − | # [[ | + | # [[Help:Extensions#.7B.7B.23extmass:id.3D.27.27.7D.7D|extmass]] |
| − | # [[ | + | # [[Help:Extensions#.7B.7B.23smiles:id.3D.27.27.7D.7D|smiles]] |
Revision as of 17:12, 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.
You need to prepare a MOL-format file with a trailer like the following.
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 is 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, assign the path of DocumentRoot in $spath (line 121).
Requirements
None
Download
| version | source | size |
| 0.1(September 11,2008) | MolFunctions.phps |
Installtion
- Download source and rename to MolFunctions.php.
- Put in extensions/ directory.
- Insert follow line to LocalSettings.php
require_once( "$IP/extensions/MolFunctions.php" ); $egMolPath = "path to mol directory from DocumentRoot";
If $egMolPath is nil, the extention stops.
