ChemAxon Forum Archive » Drawing & visualization: Marvin/Sketch /View /Space

MarvinView freezes/won't launch with compressed MOL

User 870ab5b546

20-01-2016 15:34:40

Hi,


We have a feature that allows users to launch MarvinView with a particular structure. When the structure is in compressed MOL format, as in the following case:


  Marvin  05200618592D          



  5  4  0  0  0  0            999 V2000

PCxVdD2W60

DE-VdD2W70

7F1WdD2W60

JDzVdD2W60

JDzVjC0W10

10401

40202

20301

40501

M  END

then MarvinView fails to launch; the structure never appears, although no error appears in the browser console. If the structure is in MRV format, as in this case:


<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="N" x2="-3.0917600000000007" y2="1.4000000000000001" lonePair="1"/><atom id="a2" elementType="C" x2="-1.5517600000000003" y2="1.4000000000000001"/><atom id="a3" elementType="R" x2="-0.51176" y2="0.19166666666666665" sgroupRef="sg1"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1" id="b1"/><bond atomRefs2="a2 a3" order="1" id="b2"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="CN"><atomArray><atom id="a4" elementType="C" x2="-0.51176" y2="0.19166666666666665" sgroupAttachmentPoint="1"/><atom id="a5" elementType="N" x2="0.25824000000000014" y2="-1.1420666666666668"/></atomArray><bondArray><bond atomRefs2="a4 a5" order="3" id="b3"/></bondArray></molecule></molecule></MChemicalStruct><MElectronContainer occupation="0 0" radical="0" id="o1"><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/></MElectronContainer></MDocument></cml>

then MarvinView launches just fine. Here is the code that launches MarvinView:


function launchMView_1() {

	startMView(250, 

			113,

			'\n  Marvin  05200618592D          \n\n  5  4  0  0  0  0            999 V2000\nPCxVdD2W60\nDE-VdD2W70\n7F1WdD2W60\nJDzVdD2W60\nJDzVjC0W10\n10401\n40202\n20301\n40501\nM  END\n',

			0, 

			0, 

			'fig1', 

			-1,

			'marvin');

	setInnerHTML('launchMViewCell1', 'MarvinView&trade;');

} // launchMView_1()



/* Method for initiating MarvinView in a jsp page. Requires an

 * HTML element with ID = elementId.  */

function startMView(width, height, mol, displayFlags, mviewNum, elementId,

		qdNum, marvinVersion) {

	"use strict";

	var isQDatum = !isNaN(qdNum) && qdNum >= 0,

		appletBld = new String.builder(),

		molParts = (mol + ' ').split('<\/MDocument>'),

		numMols = molParts.length - 1,

		numCols = (numMols > 2 ? 2 : numMols),

		newWidth = width * numCols,

		numRows;

	if (isQDatum) {

		appletBld.append('<table><tr><td class="boldtext" ' +

					'style="text-align:right;font-style:italic;">' +

					'MarvinView&trade;' +

					'<input type="hidden" id="mviewNumOfQD').

				append(qdNum).

				append('" value="').

				append(mviewNum).

				append('" /><\/td><\/tr><tr><td class="whiteTable">');

	} // if is qDatum

	// multidocument structure to display in table?

	if (numMols === 0) {

		numMols = 1;

	}

	if (newWidth < 0) {

		newWidth *= -1;

	} else if (newWidth > 300) {

		newWidth = 300;

	}

	mview_name = 'marvinView' + mviewNum;

	mview_begin('/nosession/' + marvinVersion, newWidth, height);

	if (numMols > 1) {

		numRows = (numMols + (numMols % 2)) / 2;

		mview_param('rows', numRows);

		mview_param('cols', numCols);

		mview_param('border', 1);

	} // if there's more than one molecule to display

	mview_param('mol', mol);

	mview_param('molbg', '#FFFFFF');

	mview_param('rendering', 'wireframe');

	mview_param('valenceErrorVisible', 'true');

	mview_param('valencePropertyVisible', 'false');

	mview_param('implicitH', getHVisibility(displayFlags));

	mview_param('viewCarbonVisibility', getCVisibility(displayFlags));

	mview_param('lonePairsVisible', getLonePairsVisible(displayFlags));

	mview_param('atomPropertiesVisible', 'false');

	mview_param('chiralitySupport', getRSLabelsVisible(displayFlags));

	mview_param('atomMappingVisible', getAtomMapping(displayFlags));

	// if (width < 0) mview_param('tabScale', 30);

	appletBld.append(mview_end_to_string());

	if (isQDatum) {

		appletBld.append('<\/td><\/tr><\/table>');

	}

	setInnerHTML(elementId, appletBld.toString());

} // startMView()

Does MarvinView no longer support compressed MOL format?


P.S. MarvinSketch loads the compressed MOL files just fine. It's only MarvinView that chokes.

ChemAxon d26931946c

22-01-2016 14:04:36

Hi Bob,


 


I've created a simple MView applet that loads the molecule from compressed mdl:


https://marvin-demo.chemaxon.com/applet/GLUON/deploy/master/examples/applets/view/embed2.html


It works on my machine, could you try it out?


BRs,


Peter

User 870ab5b546

22-01-2016 15:14:51

Yes, it works for me. So, try this:



  1. Go to https://epoch.uky.edu/ace and login as student2, password doh! (with the exclamation point).

  2. Click on Test course, then Assignments, then MarvinView test.

  3. Next to question 1, press Solve.

  4. Click on Launch MarvinView. The SVG picture should be replaced with a MarvinView applet containing the same structure, but it's not.

  5. Now navigate to question 2. MarvinView launches and displays the structure properly!


The only difference I can see between structures for which MarvinView launches properly, and those for which it doesn't, is the format in which they are saved.

User 870ab5b546

26-01-2016 19:19:58

Can you change your example to launch MarvinView the way we do, with the user pressing a button to replace an image with the MarvinView applet? We do it this way because some students may be using a computer that does not have Java enabled.


function startMView(width, height, mol, displayFlags, mviewNum, elementId,

        qdNum, marvinVersion) {

    "use strict";

    var isQDatum = !isNaN(qdNum) && qdNum >= 0,

        appletBld = new String.builder(),

        molParts = (mol + ' ').split('<\/MDocument>'),

        numMols = molParts.length - 1,

        numCols = (numMols > 2 ? 2 : numMols),

        newWidth = width * numCols,

        numRows;

    if (isQDatum) {

        appletBld.append('<table><tr><td class="boldtext" ' +

                    'style="text-align:right;font-style:italic;">' +

                    'MarvinView&trade;' +

                    '<input type="hidden" id="mviewNumOfQD').

                append(qdNum).

                append('" value="').

                append(mviewNum).

                append('" /><\/td><\/tr><tr><td class="whiteTable">');

    } // if is qDatum

    // multidocument structure to display in table?

    if (numMols === 0) {

        numMols = 1;

    }

    if (newWidth < 0) {

        newWidth *= -1;

    } else if (newWidth > 300) {

        newWidth = 300;

    }

    mview_name = 'marvinView' + mviewNum;

    mview_begin('/nosession/' + marvinVersion, newWidth, height);

    if (numMols > 1) {

        numRows = (numMols + (numMols % 2)) / 2;

        mview_param('rows', numRows);

        mview_param('cols', numCols);

        mview_param('border', 1);

    } // if there's more than one molecule to display

    mview_param('mol', mol);

    mview_param('molbg', '#FFFFFF');

    mview_param('rendering', 'wireframe');

    mview_param('valenceErrorVisible', 'true');

    mview_param('valencePropertyVisible', 'false');

    mview_param('implicitH', getHVisibility(displayFlags));

    mview_param('viewCarbonVisibility', getCVisibility(displayFlags));

    mview_param('lonePairsVisible', getLonePairsVisible(displayFlags));

    mview_param('atomPropertiesVisible', 'false');

    mview_param('chiralitySupport', getRSLabelsVisible(displayFlags));

    mview_param('atomMappingVisible', getAtomMapping(displayFlags));

    // if (width < 0) mview_param('tabScale', 30);

    appletBld.append(mview_end_to_string());

    if (isQDatum) {

        appletBld.append('<\/td><\/tr><\/table>');

    }

    setInnerHTML(elementId, appletBld.toString());

} // startMView()





function launchMView_1() {

	startMView(250, 

		113,

		'\n  Marvin  05200618592D          \n\n  5  4  0  0  0  0            999 V2000\nPCxVdD2W60\nDE-VdD2W70\n7F1WdD2W60\nJDzVdD2W60\nJDzVjC0W10\n10401\n40202\n20301\n40501\nM  END\n',

		0, 

		0, 

		'fig1', 

		-1,

		'marvin');

	setInnerHTML('launchMViewCell1', 'MarvinView&trade;');

} // launchMView_1()

<table class="regtext" style="border-collapse:collapse; border-style:none; border-color:black;

border-width:1px; margin-left:0px; margin-right:0px; background-color:#FFFFFF;

color:#000000;">

	<tr style="background-color:#f6f7ed; border-style:none;">

		<td id="launchMViewCell1" class="boldtext" colspan="2"

				style="text-align:right; padding-left:10px; font-style:italic;">

			<a onclick="launchMView_1();"><u>Launch MarvinView</u></a>&trade;

			or click image to copy source

		</td>

	

	</tr>

	<tr style="background-color:white; border-style:solid; border-width:1px;">

	<td id="fig1" colspan="1"

			style="text-align:center; border-style:solid; border-width:1px;">

		

			<a onclick="showSource(1);"><svg fill-opacity="1" xmlns:xlink="http://www.w3.org/1999/xlink" color-rendering="auto" color-interpolation="auto" text-rendering="auto" stroke="black" stroke-linecap="square" width="250" stroke-miterlimit="10" shape-rendering="auto" stroke-opacity="1" fill="black" stroke-dasharray="none" font-weight="normal" stroke-width="1" height="113" xmlns="http://www.w3.org/2000/svg" font-family="&apos;Dialog&apos;" font-style="normal" stroke-linejoin="miter" font-size="12" stroke-dashoffset="0" image-rendering="auto">

  <!--Generated by Marvin with Batik SVG Generator

MolSource:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_12_01.xsd" version="ChemAxon file format v14.12.01, generated by v15.11.23.0">

<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5" elementType="C N C C H" x2="-3.6749066666666668 -0.5949066666666667 0.9450933333333335 -2.1349066666666667 -2.1349066666666667" y2="1.6917600000000002 1.6917600000000002 1.6917600000000002 1.6917600000000002 0.15176"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a4" order="1"></bond><bond id="b2" atomRefs2="a4 a2" order="2"></bond><bond id="b3" atomRefs2="a2 a3" order="1"></bond><bond id="b4" atomRefs2="a4 a5" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>

</cml>

-->

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ChemAxon d26931946c

27-01-2016 12:03:08

I couldn't find where you call mview_end() to start the applet.


I can see that the applet does not start on your site. I will try to reproduce the behavior on our server.

User 870ab5b546

27-01-2016 13:31:17










gezapeti wrote:

I couldn't find where you call mview_end() to start the applet.


I can see that the applet does not start on your site. I will try to reproduce the behavior on our server.

The applet normally starts when the setInnerHTML() step is executed, that is, when the HTML that invokes the applet is inserted into the page. Notice that there is a call to mview_end_to_string().


Note also that the applet does start on the second example on our site, in which the applet loads an MRV instead of compressed MOL. Note also that these are not the only two examples of this behavior.


We now always save drawings as MRV, never as MOL, but we still have a lot of older data that is in MOL or compressed MOL.

ChemAxon d26931946c

28-01-2016 08:54:32

Hi Bob,


The good news is that the applet actually stats in both cases.


The difference is that the width of the applet is set to 0 in case of the compressed molfile (See attached files)


I did not found the reason for this but I guess it has to do something with this:




        molParts = (mol + ' ').split('<\/MDocument>'),

 



This will return 1 in case of mol files as there is no MDocument tag in them and therefore  



numMols

will become 0.


 


Peter

User 870ab5b546

28-01-2016 13:35:45

Aha! Thanks for your help!