Difference between revisions of "Inlined MDL Molfile"

From Jmol
Jump to navigation Jump to search
(move comments to Talk/Discussion page)
Line 49: Line 49:
 
   </jmolApplet>
 
   </jmolApplet>
 
</jmol>
 
</jmol>
−
 
−
<!--  This problem was solved on 8-9 Dec. 2008
 
−
This page does not currently display correctly.  the problem seems to be the first three lines of the Molfile.
 
−
If lines  2 and 3 are left blank, the current system strips these lines out entirely, invalidating the Molfile.
 
−
A title in line  2 preserves it, but  we are currently finding out what line 3 should be!
 
−
 
−
The solution is to preserve blank lines in inlined data files.--[[User:Rzepa|Rzepa]] 08:58, 8 June 2006 (CEST)
 
−
:I get it working when commenting out the following line in JmolExtension.php:<br/><code>$this->mValInlineContents = preg_replace("/\n/", "\\n'+\n'", $this->mValInlineContents);</code><br/>--[[User:SHL|SHL]] 06:13, 21 February 2007 (CET)
 
−
 
−
I think the problem is not in the contents of the first 3 lines, but in the MediaKiwi extension parsing incorrectly the newline characters (the code mentioned above by SHL and belonging to Jmol.body.php),
 
−
which inserts literal single quotes in the call to jmolAppletInline() that remain there after being passed through Jmol.js. Since this latter inserts a vertical bar (pipe, |) in every new line, I think that the quotes and the excess \n are not needed any longer. The same ought to happen with an [[Inlined PDB File]]. [[Inlined CML File]] works I guess because it does not depend on newlines, or maybe because of the CDATA tags. I cannot test it since I don't have a WikiMedia implementation of my own. --[[User:AngelHerraez|AngelHerraez]] 21:32, 30 November 2008 (CET)
 
−
: OK, I have confirmed this in a local wiki. Commenting out the line in Jmol.body.php solves the problem for inline MOL data. I guess the change may have been raised by a new Jmol.js version. Once I double-check this, I will commit a fix to SVN and have it implemented in this wiki. --[[User:AngelHerraez|AngelHerraez]] 13:51, 7 December 2008 (CET)
 
−
-->
 

Revision as of 19:30, 23 November 2010

Inlined MDL Molfile

Contributors

AngelHerraez, Rzepa, SHL