Inlined MDL Molfile - Revision history

AngelHerraez: add to Category

2010-11-23T20:38:56Z

add to Category

AngelHerraez: merging test with more code from Sandbox

2010-11-23T19:56:52Z

merging test with more code from Sandbox

AngelHerraez: move comments to Talk/Discussion page

2010-11-23T19:30:49Z

move comments to Talk/Discussion page

AngelHerraez at 22:56, 9 December 2008

2008-12-09T22:56:47Z

AngelHerraez: /* Inlined MDL Molfile */

2008-12-07T12:51:03Z

‎Inlined MDL Molfile

AngelHerraez at 20:32, 30 November 2008

2008-11-30T20:32:12Z

SHL at 05:13, 21 February 2007

2007-02-21T05:13:17Z

SHL at 05:12, 21 February 2007

2007-02-21T05:12:12Z

Rzepa: /* Inlined MDL Molfile */

2006-06-08T06:58:26Z

‎Inlined MDL Molfile

Rzepa: /* Inlined MDL Molfile */

2006-06-08T06:51:08Z

‎Inlined MDL Molfile

← Older revision		Revision as of 20:38, 23 November 2010
Line 62:		Line 62:
	</jmolApplet>		</jmolApplet>
	</jmol>		</jmol>
		+
		+	[[Category:Pages Using Jmol MW Extension]]

@@ Line 1: / Line 1: @@
 == Inlined MDL Molfile ==
 <jmol>
@@ Line 46: / Line 47: @@
 18  1  0  0  0
 M  END
 </inlineContents>
    </jmolApplet>
 </jmol>

← Older revision		Revision as of 19:30, 23 November 2010
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)
−	~~-->~~

@@ Line 50: / Line 50: @@
 </jmol>
 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.
@@ Line 60: / Line 61: @@
 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)

← Older revision		Revision as of 12:51, 7 December 2008
Line 59:		Line 59:
	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),		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)		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)

← Older revision		Revision as of 20:32, 30 November 2008
Line 56:		Line 56:
	The solution is to preserve blank lines in inlined data files.--[[User:Rzepa\|Rzepa]] 08:58, 8 June 2006 (CEST)		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'", $this->mValInlineContents);</code><br/>--[[User:SHL\|SHL]] 06:13, 21 February 2007 (CET)		:I get it working when commenting out the following line in JmolExtension.php:<br/><code>$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)

← Older revision		Revision as of 05:13, 21 February 2007
Line 55:		Line 55:

	The solution is to preserve blank lines in inlined data files.--[[User:Rzepa\|Rzepa]] 08:58, 8 June 2006 (CEST)		The solution is to preserve blank lines in inlined data files.--[[User:Rzepa\|Rzepa]] 08:58, 8 June 2006 (CEST)
−	:I get it ~~to work if I~~ commenting out the following line in JmolExtension.php:<br/><code>$this->mValInlineContents = preg_replace("/\n/", "\\n'+\n'", $this->mValInlineContents);</code><br/>--[[User:SHL\|SHL]] 06:12, 21 February 2007 (CET)	+	:I get it working when commenting out the following line in JmolExtension.php:<br/><code>$this->mValInlineContents = preg_replace("/\n/", "\\n'+\n'", $this->mValInlineContents);</code><br/>--[[User:SHL\|SHL]] 06:13, 21 February 2007 (CET)

← Older revision		Revision as of 05:12, 21 February 2007
Line 55:		Line 55:

	The solution is to preserve blank lines in inlined data files.--[[User:Rzepa\|Rzepa]] 08:58, 8 June 2006 (CEST)		The solution is to preserve blank lines in inlined data files.--[[User:Rzepa\|Rzepa]] 08:58, 8 June 2006 (CEST)
		+	:I get it to work if I commenting out the following line in JmolExtension.php:<br/><code>$this->mValInlineContents = preg_replace("/\n/", "\\n'+\n'", $this->mValInlineContents);</code><br/>--[[User:SHL\|SHL]] 06:12, 21 February 2007 (CET)

← Older revision		Revision as of 06:58, 8 June 2006
Line 50:		Line 50:
	</jmol>		</jmol>

−	This page does not currently display	+	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)

@@ Line 6: / Line 6: @@
 <color>green</color>
   <inlineContents>chair.mol
+Conformational analysis
-−
 18  0  0  0                 1 V2000
 .6881    2.1572   -3.0193 C   0  0  0  0  0