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

image generation bug

User 870ab5b546

23-03-2016 19:53:40

There appears to be a change from JChem version 16.2.15 to 16.2.29 in how Unicode characters are handled in image generation. We are generating an image from an MRV that contains Unicode bullet characters. 


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<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<propertyList>

<property dictRef="is Lewis Structure?" title="is Lewis Structure?">

<scalar>

true</scalar>

</property>

</propertyList>

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<bondArray>

<bond id="b1" atomRefs2="a1 a2" order="1"></bond>

<bond id="b2" atomRefs2="a1 a3" order="1"></bond>

<bond id="b3" atomRefs2="a1 a4" order="1"></bond>

<bond id="b4" atomRefs2="a1 a5" order="1"></bond>

<bond id="b5" atomRefs2="a5 a6" order="1"></bond>

</bondArray>

</molecule>

</MChemicalStruct>

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<Field name="text"><![CDATA[{fg=#ff0000}\\u2022  ]]></Field>

<MPoint x="13.144444444444442" y="-7.1"></MPoint>

<MPoint x="15.144444444444442" y="-7.1"></MPoint>

<MPoint x="15.144444444444442" y="-9.1"></MPoint>

<MPoint x="13.144444444444442" y="-9.1"></MPoint>

</MTextBox>

<MTextBox id="o3" fontScale="10.0" halign="LEFT" valign="TOP" autoSize="false">

<Field name="text"><![CDATA[{fg=#ff0000}\\u2022  ]]></Field>

<MPoint x="13.144444444444442" y="-5.766666666666666"></MPoint>

<MPoint x="15.144444444444442" y="-5.766666666666666"></MPoint>

<MPoint x="15.144444444444442" y="-7.766666666666666"></MPoint>

<MPoint x="13.144444444444442" y="-7.766666666666666"></MPoint>

</MTextBox>

<MTextBox id="o4" fontScale="10.0" halign="LEFT" valign="TOP" autoSize="false">

<Field name="text"><![CDATA[{fg=#ff0000}\\u2022  ]]></Field>

<MPoint x="12.81111111111111" y="-7.1"></MPoint>

<MPoint x="14.81111111111111" y="-7.1"></MPoint>

<MPoint x="14.81111111111111" y="-9.1"></MPoint>

<MPoint x="12.81111111111111" y="-9.1"></MPoint>

</MTextBox>

<MTextBox id="o5" fontScale="10.0" halign="LEFT" valign="TOP" autoSize="false">

<Field name="text"><![CDATA[{fg=#ff0000}\\u2022  ]]></Field>

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<MPoint x="14.81111111111111" y="-5.766666666666666"></MPoint>

<MPoint x="14.81111111111111" y="-7.766666666666666"></MPoint>

<MPoint x="12.81111111111111" y="-7.766666666666666"></MPoint>

</MTextBox>

</MDocument>

</cml>

JChem 16.2.15 correctly renders the Unicode bullets in the SVG drawing. (Scroll to the bottom and look for the lines beginning with <text>; the lines end with &#8226.)


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MolSource:

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      <text xml:space="preserve" x="149.57489013671875" y="43.611244201660156" clip-path="url(#21839662815-clipPath1)" stroke="none">&#8226;  

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JChem 16.2.29, by contrast, renders the Unicode bullets as " characters.


Mar 23, 2016 3:43:24 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: updateFigure.jsp: imgXML:

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MolSource:

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      >"  </text

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      >"  </text

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>

(Not to mention the strange placement of the return characters, which makes the document more difficult to read.) Can you fix?

ChemAxon cbb451ac1e

29-03-2016 07:07:16

Thanks for reporting. We are investigating the issue. 

User 870ab5b546

29-03-2016 15:16:23

Here are some other potentially relevant discussions about using non-ASCII characters in MRV and image URIs.


https://www.chemaxon.com/forum/viewpost1051.html (2004)


https://www.chemaxon.com/forum/viewpost4036.html (2005)


https://www.chemaxon.com/forum/viewpost53626.html (2013)

ChemAxon 7936325a45

30-03-2016 09:46:58

Dear Bob,


With Marvin the SVG export generates source with bullet characters. I try to reproduce this with JChem.


Sadly we can't do anything about the return characters, the SVG image is generated with a third party software.


Best regards,
István 

User 870ab5b546

15-04-2016 12:48:29

Any progress on this bug?

ChemAxon cbb451ac1e

25-04-2016 09:14:45

will keep you posted when fixed.


best,


Krisztian

User 870ab5b546

12-05-2016 16:20:44

FYI, I have come across this problem again, this time in the context of a Greek character (nu) in a textbox in a Marvin JS drawing. The MRV is:


<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="Cl" x2="-6.375" y2="4.291666666666667" lonePair="3"/><atom id="a2" elementType="C" x2="-4.835" y2="4.291666666666667"/><atom id="a3" elementType="Cl" x2="-4.835" y2="2.751666666666667" lonePair="3"/><atom id="a4" elementType="Br" x2="-3.295" y2="4.291666666666667" lonePair="3"/><atom id="a5" elementType="Cl" x2="-4.835" y2="5.831666666666667" lonePair="3"/><atom id="a6" elementType="C" x2="-5.958333333333333" y2="-0.41666666666666663"/><atom id="a7" elementType="C" x2="-4.624654211505297" y2="0.3533333333333332"/><atom id="a8" elementType="R" x2="-3.2909750896772616" y2="-0.4166666666666667" sgroupRef="sg1"/><atom id="a9" elementType="C" x2="5.083333333333335" y2="2.25"/><atom id="a10" elementType="C" x2="6.4170124551613705" y2="3.0199999999999996"/><atom id="a11" elementType="R" x2="7.750691576989406" y2="2.25" sgroupRef="sg2"/><atom id="a12" elementType="Br" x2="6.4170124551613705" y2="4.56" lonePair="3"/><atom id="a13" elementType="C" x2="3.7496542115052995" y2="3.0200000000000005"/><atom id="a14" elementType="Cl" x2="3.7496542115052995" y2="4.5600000000000005" lonePair="3"/><atom id="a15" elementType="Cl" x2="2.2096542115052995" y2="3.0200000000000005" lonePair="3"/><atom id="a16" elementType="Cl" x2="2.9796542115053" y2="1.6863208781719647" lonePair="3"/></atomArray><bondArray><bond atomRefs2="a2 a3" order="1" id="b1"/><bond atomRefs2="a2 a5" order="1" id="b2"/><bond atomRefs2="a6 a7" order="2" id="b3"/><bond atomRefs2="a7 a8" order="1" id="b4"/><bond atomRefs2="a9 a10" order="1" id="b5"/><bond atomRefs2="a10 a11" order="1" id="b6"/><bond atomRefs2="a9 a13" order="1" id="b7"/><bond atomRefs2="a13 a16" order="1" id="b8"/><bond atomRefs2="a13 a15" order="1" id="b9"/><bond atomRefs2="a13 a14" order="1" id="b10"/><bond atomRefs2="a10 a12" order="1" id="b11"/><bond atomRefs2="a1 a2" order="1" id="b12"/><bond atomRefs2="a2 a4" order="1" id="b13"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a17" elementType="C" x2="-3.2909750896772616" y2="-0.4166666666666667" sgroupAttachmentPoint="1"/><atom id="a18" elementType="C" x2="-1.957428433678968" y2="-1.1866666605066667"/><atom id="a19" elementType="C" x2="-1.957428433678968" y2="-2.726666648186667"/><atom id="a20" elementType="C" x2="-3.2909750896772616" y2="-3.4966666420266668"/><atom id="a21" elementType="C" x2="-4.624708412340729" y2="-2.726666648186667"/><atom id="a22" elementType="C" x2="-4.624708412340729" y2="-1.1866666605066667"/></atomArray><bondArray><bond atomRefs2="a17 a18" order="2" id="b14"/><bond atomRefs2="a17 a22" order="1" id="b15"/><bond atomRefs2="a18 a19" order="1" id="b16"/><bond atomRefs2="a19 a20" order="2" id="b17"/><bond atomRefs2="a20 a21" order="1" id="b18"/><bond atomRefs2="a21 a22" order="2" id="b19"/></bondArray></molecule><molecule id="sg2" molID="m3" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a23" elementType="C" x2="7.750691576989406" y2="2.25" sgroupAttachmentPoint="1"/><atom id="a24" elementType="C" x2="9.0842382329877" y2="1.4800000061599998"/><atom id="a25" elementType="C" x2="9.0842382329877" y2="-0.0599999815200003"/><atom id="a26" elementType="C" x2="7.750691576989406" y2="-0.8299999753600003"/><atom id="a27" elementType="C" x2="6.416958254325939" y2="-0.0599999815200003"/><atom id="a28" elementType="C" x2="6.416958254325939" y2="1.4800000061599998"/></atomArray><bondArray><bond atomRefs2="a23 a24" order="2" id="b20"/><bond atomRefs2="a23 a28" order="1" id="b21"/><bond atomRefs2="a24 a25" order="1" id="b22"/><bond atomRefs2="a25 a26" order="2" id="b23"/><bond atomRefs2="a26 a27" order="1" id="b24"/><bond atomRefs2="a27 a28" order="2" id="b25"/></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><MElectronContainer occupation="0 0" radical="0" id="o2"><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o3"><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a1" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o4"><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o5"><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o6"><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a3" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o7"><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o8"><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o9"><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a4" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o10"><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o11"><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o12"><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o13"><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o14"><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o15"><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a12" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o16"><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o17"><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o18"><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a14" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o19"><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o20"><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o21"><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a15" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o22"><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o23"><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o24"><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a16" difLoc="0.0 0.0 0.0"/></MElectronContainer><MTextBox toption="NOROT" fontScale="14.0" halign="LEFT" valign="TOP" autoSize="true" id="o25"><Field name="text">{italic}h{noitalic}\\u03bd</Field><MPoint x="-0.5" y="3.6666666666666665"/><MPoint x="-0.5" y="3.6666666666666665"/><MPoint x="-0.5" y="3.6666666666666665"/><MPoint x="-0.5" y="3.6666666666666665"/></MTextBox><MPolyline headLength="0.6" headWidth="0.4" id="o26"><MPoint x="-0.9583333333333334" y="2.7083333333333335"/><MPoint x="0.6666666666666666" y="2.7083333333333335"/></MPolyline></MDocument></cml>

The key part is:


<Field name="text">{italic}h{noitalic}\\u03bd</Field>

Here's the SVG generated by JChem. The nu is rendered as &#65533;, which appears as a question mark on a black diamond in the image.


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><!--Generated by Marvin with Batik SVG Generator

MolSource:

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order="1"></bond><bond id="b5" atomRefs2="a9 a10" order="1"></bond><bond id="b6" atomRefs2="a10 a11" order="1"></bond><bond id="b7" atomRefs2="a9 a13" order="1"></bond><bond id="b8" atomRefs2="a13 a16" order="1"></bond><bond id="b9" atomRefs2="a13 a15" order="1"></bond><bond id="b10" atomRefs2="a13 a14" order="1"></bond><bond id="b11" atomRefs2="a10 a12" order="1"></bond><bond id="b12" atomRefs2="a1 a2" order="1"></bond><bond id="b13" atomRefs2="a2 a4" order="1"></bond></bondArray><molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2"><atomArray atomID="a17 a18 a19 a20 a21 a22" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-3.2909750896772616 -1.957428433678968 -1.957428433678968 -3.2909750896772616 -4.624708412340729 -4.624708412340729" y2="-0.4166666666666667 -1.1866666605066667 -2.726666648186667 -3.4966666420266668 -2.726666648186667 -1.1866666605066667"></atomArray><bondArray><bond id="b14" atomRefs2="a17 a18" 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User 870ab5b546

06-06-2016 20:29:15

I wanted to check in on this problem again. It's pretty serious that the image generator cannot properly render Greek letters that were entered in a textbox in MarvinSketch.

ChemAxon cfb2ce1d3d

04-07-2016 08:45:08










bobgr wrote:

I wanted to check in on this problem again. It's pretty serious that the image generator cannot properly render Greek letters that were entered in a textbox in MarvinSketch.


Hi Bob,


My apologies for not being able to get back to this report much earlier.


I confirm that there exists a problem with greek letter handling (probably unicode in general) during SVG export. As other formats have no problem whatsoever the culprit is likely the 3rd party library we use. I'll try to dig into that.


Kind regards


Zsolt

ChemAxon 5693b0ec15

02-08-2016 08:55:56

Dear Bob,


we are happy to inform you that the issue has been fixed, and will be available with
this week's release.


Best regards,


Nikolett Mihala