Inlined CML File
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Inlined CML File
 Jmol._Canvas2D (Jmol) "JSmol_1"[x] script 1 started pdbGetHeader = true loadScript /extensions/Jmol/j2s/core/coretext.z.js JSmol exec JSmol_2 start applet null Jmol JavaScript applet JSmol_2__8463274113553854__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_2__8463274113553854__) vwrOptions: { "name":"JSmol_2","applet":true,"documentBase":"http://wiki.jmol.org/index.php/Inlined_CML_File","platform":"J.awtjs2d.Platform","fullName":"JSmol_2__8463274113553854__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8463274113553854","bgcolor":"orange" } setting document base to "http://wiki.jmol.org/index.php/Inlined_CML_File" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 java.vendor: Java2Script (HTML5) java.version: 2018-01-28 23:38:52 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:JSmol_2 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor orange backgroundColor = "orange" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue AUDIOCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet JSmol_2__8463274113553854__ ready |
This inline example is of a datafile in XML format, but fully carried in a declared namespace of xmlns:cml="http://www.xml-cml.org/schema/cml2/core. In theory, this XML should be processable separately from e.g. the jmol default namespace. Does Mediawiki honour such namespaces?
The next example is the same datafile, but fully escaped.
Jmol._Canvas2D (Jmol) "JSmol_2"[x] loadScript /extensions/Jmol/j2s/core/package.js loadScript /extensions/Jmol/j2s/core/corejmol.z.js loadScript /extensions/Jmol/j2s/J/translation/PO.js loadScript /extensions/Jmol/j2s/core/corescript.z.js JSmol exec JSmol_1 start applet null Jmol JavaScript applet JSmol_1__8463274113553854__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(JSmol_1__8463274113553854__) vwrOptions: { "name":"JSmol_1","applet":true,"documentBase":"http://wiki.jmol.org/index.php/Inlined_CML_File","platform":"J.awtjs2d.Platform","fullName":"JSmol_1__8463274113553854__","codePath":"http:/extensions/Jmol/j2s/","display":"JSmol_1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8463274113553854","bgcolor":"red" } setting document base to "http://wiki.jmol.org/index.php/Inlined_CML_File" (C) 2015 Jmol Development Jmol Version: 14.29.32 2019-01-29 14:30 java.vendor: Java2Script (HTML5) java.version: 2018-01-28 23:38:52 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:JSmol_1 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor red backgroundColor = "red" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue AUDIOCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet JSmol_1__8463274113553854__ ready script 1 started pdbGetHeader = true Loading...|Please wait. Loading...|Please wait. platformSpeed = 5 loadScript /extensions/Jmol/j2s/core/corescriptcmd.z.js The Resolver thinks XmlCml loadScript /extensions/Jmol/j2s/J/adapter/readers/xml/XmlReader.js loadScript /extensions/Jmol/j2s/J/adapter/readers/xml/XmlCmlReader.js File Error:No atoms found for file null type XmlCml loadScript /extensions/Jmol/j2s/JV/DataManager.js loadScript /extensions/Jmol/j2s/J/api/JmolDataManager.js script ERROR: No atoms found for file null type XmlCml ---- data "model" |<cml:molecule xmlns:cml="http://www.xml-cml.org/schema/cml2/core" title="chair.mol">|<cml:metadataList title="generated automatically from Openbabel">|<cml:metadata name="dc:creator" content="OpenBabel version 1-100.1"/>|<cml:metadata name="dc:description" content="Conversion of legacy filetype to CML"/>|<cml:metadata name="dc:identifier" content="Unknown"/>|<cml:metadata name="dc:content"/>|<cml:metadata name="dc:rights" content="unknown"/>|<cml:metadata name="dc:type" content="chemistry"/>|<cml:metadata name="dc:contributor" content="unknown"/>|<cml:metadata name="dc:creator" content="Openbabel V1-100.1"/>|<cml:metadata name="dc:date" content="Tue Jun 06 19:11:23 BST 2006"/>|<cml:metadata name="cmlm:structure" content="yes"/>|</cml:metadataList>|<cml:atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18" elementType="C C C C C C H H H H H H H H H H H H" formalCharge="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" x3="1.688100 2.148400 2.936100 2.092700 1.632900 0.853200 2.580700 1.089700 1.257800 2.779100 3.872500 3.241300 1.200500 2.683500 0.995700 2.524000 0.564200 -0.091900" y3="2.157200 3.621700 3.912600 3.576900 2.112000 1.810200 1.488700 1.971100 4.292700 3.847400 3.305300 4.986100 4.246700 3.770000 1.892800 1.442600 0.732200 2.403900" z3="-3.019300 -2.979700 -1.694200 -0.455700 -0.489800 -1.777800 -3.065200 -3.943000 -3.028200 -3.872700 -1.684400 -1.668500 -0.422400 0.471400 0.400200 -0.429400 -1.803100 -1.787800"/>|<cml:bondArray atomRef1="a1 a1 a1 a1 a2 a2 a2 a3 a3 a3 a4 a4 a4 a5 a5 a5 a6 a6" atomRef2="a2 a6 a7 a8 a3 a9 a10 a4 a11 a12 a5 a13 a14 a6 a15 a16 a17 a18" order="1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1"/>|</cml:molecule>| end <<<<"model" Script completed Jmol script terminated platformSpeed = 5 The Resolver thinks XmlCml chair.mol reading 18 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 18 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Time for creating model: 9 ms chair.mol Script completed Jmol script terminated |
Both of these examples display if (and only if) the CML contents is put inside <![CDATA[ and ]]> tags.
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