Help:Extension/MolFunctions - Revision history

Editor at 08:33, 26 September 2008

2008-09-26T08:33:04Z

Editor at 08:25, 26 September 2008

2008-09-26T08:25:30Z

Editor at 08:03, 26 September 2008

2008-09-26T08:03:38Z

Editor at 08:49, 20 September 2008

2008-09-20T08:49:05Z

Editor: Doc:Extension/MolFunctions moved to Help:Extension/MolFunctions

2008-09-20T08:22:44Z

Doc:Extension/MolFunctions moved to Help:Extension/MolFunctions

Editor at 08:12, 20 September 2008

2008-09-20T08:12:24Z

Editor at 02:35, 18 September 2008

2008-09-18T02:35:46Z

Editor: New page: {{Extension |author=K, Suwa |version=0.1 |mediawiki=1.11.1 }} TOC Molfiles形式のSKP部に、適切なデータを入れたmolファイルを用意することで、組成式、平...

2008-09-11T06:55:21Z

New page: {{Extension |author=K, Suwa |version=0.1 |mediawiki=1.11.1 }} __TOC__ Molfiles形式のSKP部に、適切なデータを入れたmolファイルを用意することで、組成式、平...

New page

{{Extension
|author=K, Suwa
|version=0.1
|mediawiki=1.11.1
}}

__TOC__

Molfiles形式のSKP部に、適切なデータを入れたmolファイルを用意することで、組成式、平均質量、精密質量、smilesを取得できるようになるextensionです。

例えば、以下のような記述です。各値のペアはタブ区切りです。

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

molファイルの格納されたディレクトリはファイル数が多くなってしまうため、IDの上位4文字のディレクトリを作成し、その中へグループ分けして格納して下さい。<br>
例えば上記の「FL3FECGS0010」であれば、IDの上位4文字は「FL3F」なので「/path to mol directory/FL3F/FL3FECGS0010.mol」というパスになります。

molディレクトリへは、$_SERVER["DOCUMENT_ROOT"]の値を使用してアクセスします。<br>
そのため、Web経由以外からこのextensionが呼び出されると失敗します(例えば、maintenance/runJobs.phpによるjobの一括処理)。<br>
そのため、121行目の「$path」にDocumentRootの絶対パスを書いておくと、正しく処理されます。

== Requirements ==
None

== Download ==
<table border="1" cellpadding="3" cellspacing="1">
<tr><td>version</td><td>source</td><td>size</td></tr>
<tr><td>0.1(September 11,2008)</td><td>MolFunctions.phps</td><td></td></tr>
</table>

== Installtion ==
<ol>
<li>Download source and rename to MolFunctions.php.</li>
<li>Put in extensions/ directory.</li>
<li>Insert follow line to LocalSettings.php
<pre>require_once( "$IP/MolFunctions.php" );
$ugMolPath = "path to mol directory from DocumentRoot"; (default: "/mol" )</pre></li>
</ol>

== Function ==
# [[Doc:Extensions#.7B.7B.23formula:id.3D.27.27.7D.7D|formula]]
# [[Doc:Extensions#.7B.7B.23avemass:id.3D.27.27.7D.7D|avemass]]
# [[Doc:Extensions#.7B.7B.23extmass:id.3D.27.27.7D.7D|extmass]]
# [[Doc:Extensions#.7B.7B.23smiles:id.3D.27.27.7D.7D|smiles]]

@@ Line 29: / Line 29: @@
 <table border="1" cellpadding="3" cellspacing="1">
   <tr><td>version</td><td>source</td><td>size</td></tr>
-  <tr><td>0.1(September 11,2008)</td><td>MolFunctions.phps</td><td></td></tr>
+  <tr><td>0.1(September 17,2008)</td><td>{{#ifexistfile:/data/src/MolFunctions/MolFunctions.phps}}</td><td><pre style="border: 0px; background-color: white; padding: 0em; line-height: 0em">5e2e923d24534af51c4884751e28ec46</pre></td></tr>
 </table>
@@ Line 38: / Line 38: @@
   <li>Insert the follow lines to LocalSettings.php
   <pre>require_once( "$IP/extensions/MolFunctions.php" );
-$egMolPath = "path to mol directory from DocumentRoot";</pre>
+$egMolPath = "path to mol directory from DocumentRoot"; // ex. "/data/mol"</pre>
 If $egMolPath is nil, the extention stops.</li>
 </ol>

@@ Line 7: / Line 7: @@
 __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:
-−
-You need to prepare a MOL-format file with a trailer like the following.
 <pre>
   S  SKP  5
@@ Line 20: / Line 18: @@
 </pre>
-Since the number of MOL-format files is large, create directories whose names are the upper 4 digits of the filenames. <br>
+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>
-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).
+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 $spath (line 121).
 == Requirements ==
@@ Line 37: / Line 34: @@
 == Installtion ==
 <ol>
-  <li>Download source and rename to MolFunctions.php.</li>
+  <li>Download the source code and rename it to MolFunctions.php.</li>
-  <li>Put in extensions/ directory.</li>
+  <li>Place it in the extensions/ directory.</li>
-  <li>Insert follow line to LocalSettings.php
+  <li>Insert the follow lines to LocalSettings.php
   <pre>require_once( "$IP/extensions/MolFunctions.php" );
 $egMolPath = "path to mol directory from DocumentRoot";</pre>

@@ Line 7: / Line 7: @@
 __TOC__
-Molfiles形式のSKP部に、適切なデータを入れたmolファイルを用意することで、組成式、平均質量、精密質量、smilesを取得できるようになるextensionです。
+Extension to obtain molecular formula, exact mass, and others from MOL-format files.
-−
-例えば、以下のような記述です。各値のペアはタブ区切りです。
   S  SKP  5
   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
   M  END
-molファイルの格納されたディレクトリはファイル数が多くなってしまうため、IDの上位4文字のディレクトリを作成し、その中へグループ分けして格納して下さい。<br>
+Since the number of MOL-format files is large, create directories whose names are the upper 4 digits of the filenames. <br>
-例えば上記の「FL3FECGS0010」であれば、IDの上位4文字は「FL3F」なので「/path to mol directory/FL3F/FL3FECGS0010.mol」というパスになります。
+For example, in the case of FL3FECGS0010, the location will be <tt>/path to mol directory/FL3F/FL3FECGS0010.mol</tt>.
-molディレクトリへは、$_SERVER["DOCUMENT_ROOT"]の値を使用してアクセスします。<br>
+The system assumes the location of the MOL directory as $_SERVER["DOCUMENT_ROOT"].<br>
-そのため、Web経由以外からこのextensionが呼び出されると失敗します(例えば、maintenance/runJobs.phpによるjobの一括処理)。<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 $spath (line 121).
-そのため、121行目の「$path」にDocumentRootの絶対パスを書いておくと、正しく処理されます。
 == Requirements ==
@@ Line 42: / Line 42: @@
   <pre>require_once( "$IP/extensions/MolFunctions.php" );
 $egMolPath = "path to mol directory from DocumentRoot";</pre>
-$egMolPathを設定しなかった場合、処理は実行されません。</li>
+If $egMolPath is nil, the extention stops.</li>
 </ol>
 == Function ==
-# [[Doc:Extensions#.7B.7B.23formula:id.3D.27.27.7D.7D|formula]]
+# [[Help:Extensions#.7B.7B.23formula:id.3D.27.27.7D.7D|formula]]
-# [[Doc:Extensions#.7B.7B.23avemass:id.3D.27.27.7D.7D|avemass]]
+# [[Help:Extensions#.7B.7B.23avemass:id.3D.27.27.7D.7D|avemass]]
-# [[Doc:Extensions#.7B.7B.23extmass:id.3D.27.27.7D.7D|extmass]]
+# [[Help:Extensions#.7B.7B.23extmass:id.3D.27.27.7D.7D|extmass]]
-# [[Doc:Extensions#.7B.7B.23smiles:id.3D.27.27.7D.7D|smiles]]
+# [[Help:Extensions#.7B.7B.23smiles:id.3D.27.27.7D.7D|smiles]]

@@ Line 28: / Line 28: @@
 == Download ==
 <table border="1" cellpadding="3" cellspacing="1">
-  <tr><td>version</td><td>source</td><td>size</td></tr>
+  <tr><td>version</td><td>source</td><td>md5</td></tr>
   <tr><td>0.1(September 26,2008)</td><td>{{#ifexistfile:/data/src/MolFunctions/MolFunctions.phps}}</td><td><pre style="border: 0px; background-color: white; padding: 0em; line-height: 0em">5e2e923d24534af51c4884751e28ec46</pre></td></tr>
 </table>