copy-paste problem

With this structure loaded into Marvin JS, both 15.12.7 and 15.6.29:

<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-10.842002547225016" y2="2.461683662856709"/><atom id="a2" elementType="C" x2="-10.842002547225016" y2="0.921649781738628"/><atom id="a3" elementType="C" x2="-9.508333206176758" y2="0.15163284117958753"/><atom id="a4" elementType="C" x2="-8.1746638651285" y2="0.921649781738628"/><atom id="a5" elementType="O" x2="-8.1746638651285" y2="4.001683662856709" lonePair="2"/><atom id="a6" elementType="H" x2="-4.841666638851166" y2="2.5083333253860474" formalCharge="1"/><atom id="a7" elementType="C" x2="-2.282526858012629" y2="2.423347869707083"/><atom id="a8" elementType="C" x2="-2.282526858012629" y2="0.883313988589002"/><atom id="a9" elementType="C" x2="-0.9488575169643703" y2="0.11329704802996154"/><atom id="a10" elementType="C" x2="0.38481182408388825" y2="0.883313988589002"/><atom id="a11" elementType="C" x2="-9.508333206176758" y2="3.2317006034157494"/><atom id="a12" elementType="C" x2="-8.1746638651285" y2="2.461683662856709"/><atom id="a13" elementType="C" x2="-0.9488575169643703" y2="3.1933648102661234"/><atom id="a14" elementType="C" x2="0.38481182408388825" y2="2.423347869707083"/><atom id="a15" elementType="R" x2="-6.840984743300464" y2="3.231683662856709" sgroupRef="sg1"/><atom id="a16" elementType="R" x2="1.718490945911924" y2="3.193347869707083" sgroupRef="sg2"/></atomArray><bondArray><bond atomRefs2="a11 a1" order="1"/><bond atomRefs2="a1 a2" order="1"/><bond atomRefs2="a2 a3" order="1"/><bond atomRefs2="a3 a4" order="1"/><bond atomRefs2="a4 a12" order="1"/><bond atomRefs2="a11 a12" order="1"/><bond atomRefs2="a12 a5" order="1"/><bond atomRefs2="a13 a7" order="1"/><bond atomRefs2="a7 a8" order="1"/><bond atomRefs2="a8 a9" order="1"/><bond atomRefs2="a9 a10" order="1"/><bond atomRefs2="a10 a14" order="2"/><bond atomRefs2="a13 a14" order="1"/><bond atomRefs2="a14 a16" order="1"/><bond atomRefs2="a12 a15" order="1"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a17" elementType="C" x2="-6.840984743300464" y2="3.231683662856709"/><atom id="a18" elementType="C" x2="-5.507305621472426" y2="4.00168366285671"/><atom id="a19" elementType="C" x2="-5.507305621472426" y2="5.541683662856709"/><atom id="a20" elementType="C" x2="-6.840984743300462" y2="6.311683662856709"/><atom id="a21" elementType="C" x2="-8.174663865128498" y2="5.541683662856711"/><atom id="a22" elementType="C" x2="-8.174663865128498" y2="4.00168366285671"/></atomArray><bondArray><bond atomRefs2="a17 a18" order="2"/><bond atomRefs2="a17 a22" order="1"/><bond atomRefs2="a18 a19" order="1"/><bond atomRefs2="a19 a20" order="2"/><bond atomRefs2="a20 a21" order="1"/><bond atomRefs2="a21 a22" order="2"/></bondArray></molecule><molecule id="sg2" molID="m3" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a23" elementType="C" x2="1.718490945911924" y2="3.193347869707083"/><atom id="a24" elementType="C" x2="3.0521700677399615" y2="3.9633478697070843"/><atom id="a25" elementType="C" x2="3.0521700677399615" y2="5.503347869707083"/><atom id="a26" elementType="C" x2="1.7184909459119257" y2="6.273347869707083"/><atom id="a27" elementType="C" x2="0.38481182408389003" y2="5.503347869707085"/><atom id="a28" elementType="C" x2="0.38481182408388914" y2="3.9633478697070843"/></atomArray><bondArray><bond atomRefs2="a23 a24" order="2"/><bond atomRefs2="a23 a28" order="1"/><bond atomRefs2="a24 a25" order="1"/><bond atomRefs2="a25 a26" order="2"/><bond atomRefs2="a26 a27" order="1"/><bond atomRefs2="a27 a28" order="2"/></bondArray></molecule></molecule></MChemicalStruct><MElectronContainer occupation="0 0" radical="0" id="o1"><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="o2"><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/></MElectronContainer><MPolyline headLength="0.6" headWidth="0.4" id="o3"><MPoint x="-5.600000321865082" y="1.750000238418579"/><MPoint x="-3.73333340883255" y="1.750000238418579"/></MPolyline></MDocument></cml>

Using Safari 9.0.2 on MacOS 10.11.2: if I want to copy the structure on the left, either by double-clicking on the right structure, then command-click-holding and dragging, or by typing command-C and then command-V, I don't get a clean copy; bonds to Ph disappear, or the copied structure retains highlighting.

Hi Bob,

The mrv file, you attached, is invalid, because it is missing the  sgroupAttachmentPoint attribute of the certain atom tag in the sgroup definition.

This means, that in the mrv there is no declared attachment point to the "Ph" abbreviated group, that is why Marvin JS breaks the bond between the root structure and the group.  (Marvin JS do not let you create a bond between a structure and an abbreviated group without attachment point.)

If you redraw this structure in Marvin JS or if your source contains sgroupAttachmentPoint attribute, the copy-paste should work.

Could you confirm, that this solved your problem?

Best regards,
Eszter 

Here's the original MRV of the drawing, which would have been drawn in MarvinSketch a long time ago:

<?xml version="1.0" ?>

<MDocument>

  <MPolyline headLength="0.8" headWidth="0.5">

    <MPoint x="-5.600000321865082" y="1.750000238418579" />

    <MPoint x="-3.73333340883255" y="1.750000238418579" />

  </MPolyline>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16"

          elementType="C C C C O H C C C C C C C C R R"

          formalCharge="0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0"

          sgroupRef="0 0 0 0 0 0 0 0 0 0 0 0 0 0 sg1 sg2"

          x2="-10.842002547225016 -10.842002547225016 -9.508333206176758 -8.1746638651285 -8.1746638651285 -4.841666638851166 -2.282526858012629 -2.282526858012629 -0.9488575169643703 0.38481182408388825 -9.508333206176758 -8.1746638651285 -0.9488575169643703 0.38481182408388825 -6.840984743300464 1.718490945911924"

          y2="2.461683662856709 0.921649781738628 0.15163284117958753 0.921649781738628 4.001683662856709 2.5083333253860474 2.423347869707083 0.883313988589002 0.11329704802996154 0.883313988589002 3.2317006034157494 2.461683662856709 3.1933648102661234 2.423347869707083 3.231683662856709 3.193347869707083"

          />

      <bondArray>

        <bond atomRefs2="a11 a1" order="1" />

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

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a4 a12" order="1" />

        <bond atomRefs2="a11 a12" order="1" />

        <bond atomRefs2="a12 a5" order="1" />

        <bond atomRefs2="a13 a7" order="1" />

        <bond atomRefs2="a7 a8" order="1" />

        <bond atomRefs2="a8 a9" order="1" />

        <bond atomRefs2="a9 a10" order="1" />

        <bond atomRefs2="a10 a14" order="2" />

        <bond atomRefs2="a13 a14" order="1" />

        <bond atomRefs2="a14 a16" order="1" />

        <bond atomRefs2="a12 a15" order="1" />

      </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"

            x2="-6.300000190734864 -4.966321068906827 -4.966321068906827 -6.300000190734862 -7.633679312562898 -7.633679312562899"

            y2="1.6683332538604727 2.438333253860474 3.978333253860473 4.748333253860473 3.978333253860475 2.438333253860474"

            />

        <bondArray>

          <bond atomRefs2="a17 a18" order="2" />

          <bond atomRefs2="a17 a22" order="1" />

          <bond atomRefs2="a18 a19" order="1" />

          <bond atomRefs2="a19 a20" order="2" />

          <bond atomRefs2="a20 a21" order="1" />

          <bond atomRefs2="a21 a22" order="2" />

        </bondArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">

        <atomArray

            atomID="a23 a24 a25 a26 a27 a28"

            elementType="C C C C C C"

            attachmentPoint="1 0 0 0 0 0"

            x2="1.925000011920928 3.2586791337489656 3.2586791337489656 1.9250000119209298 0.5913208900928941 0.5913208900928932"

            y2="1.6683332538604727 2.438333253860474 3.978333253860473 4.748333253860473 3.978333253860475 2.438333253860474"

            />

        <bondArray>

          <bond atomRefs2="a23 a24" order="2" />

          <bond atomRefs2="a23 a28" order="1" />

          <bond atomRefs2="a24 a25" order="1" />

          <bond atomRefs2="a25 a26" order="2" />

          <bond atomRefs2="a26 a27" order="1" />

          <bond atomRefs2="a27 a28" order="2" />

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

Looks to me like both shortcut groups have attachment points defined.

If I load this structure into Marvin JS, it looks like the figure that I have attached to this post. If I then press the Export button, the MRV that is generated (return characters added by me) is:

<cml>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray>

<atom id="a1" elementType="C" x2="-10.842002547225016" y2="2.461683662856709"/>

<atom id="a2" elementType="C" x2="-10.842002547225016" y2="0.921649781738628"/>

<atom id="a3" elementType="C" x2="-9.508333206176758" y2="0.15163284117958753"/>

<atom id="a4" elementType="C" x2="-8.1746638651285" y2="0.921649781738628"/>

<atom id="a5" elementType="O" x2="-8.1746638651285" y2="4.001683662856709" lonePair="2"/>

<atom id="a6" elementType="H" x2="-4.841666638851166" y2="2.5083333253860474" formalCharge="1"/>

<atom id="a7" elementType="C" x2="-2.282526858012629" y2="2.423347869707083"/>

<atom id="a8" elementType="C" x2="-2.282526858012629" y2="0.883313988589002"/>

<atom id="a9" elementType="C" x2="-0.9488575169643703" y2="0.11329704802996154"/>

<atom id="a10" elementType="C" x2="0.38481182408388825" y2="0.883313988589002"/>

<atom id="a11" elementType="C" x2="-9.508333206176758" y2="3.2317006034157494"/>

<atom id="a12" elementType="C" x2="-8.1746638651285" y2="2.461683662856709"/>

<atom id="a13" elementType="C" x2="-0.9488575169643703" y2="3.1933648102661234"/>

<atom id="a14" elementType="C" x2="0.38481182408388825" y2="2.423347869707083"/>

<atom id="a15" elementType="R" x2="-6.840984743300464" y2="3.231683662856709" sgroupRef="sg1"/>

<atom id="a16" elementType="R" x2="1.718490945911924" y2="3.193347869707083" sgroupRef="sg2"/>

</atomArray>

<bondArray>

<bond atomRefs2="a11 a1" order="1"/>

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

<bond atomRefs2="a2 a3" order="1"/>

<bond atomRefs2="a3 a4" order="1"/>

<bond atomRefs2="a4 a12" order="1"/>

<bond atomRefs2="a11 a12" order="1"/>

<bond atomRefs2="a12 a5" order="1"/>

<bond atomRefs2="a13 a7" order="1"/>

<bond atomRefs2="a7 a8" order="1"/>

<bond atomRefs2="a8 a9" order="1"/>

<bond atomRefs2="a9 a10" order="1"/>

<bond atomRefs2="a10 a14" order="2"/>

<bond atomRefs2="a13 a14" order="1"/>

<bond atomRefs2="a14 a16" order="1"/>

<bond atomRefs2="a12 a15" order="1"/>

</bondArray>

<molecule id="sg1" molID="m2" role="SuperatomSgroup" title="Ph">

<atomArray>

<atom id="a17" elementType="C" x2="-6.840984743300464" y2="3.231683662856709"/>

<atom id="a18" elementType="C" x2="-5.507305621472426" y2="4.00168366285671"/>

<atom id="a19" elementType="C" x2="-5.507305621472426" y2="5.541683662856709"/>

<atom id="a20" elementType="C" x2="-6.840984743300462" y2="6.311683662856709"/>

<atom id="a21" elementType="C" x2="-8.174663865128498" y2="5.541683662856711"/>

<atom id="a22" elementType="C" x2="-8.174663865128498" y2="4.00168366285671"/>

</atomArray>

<bondArray>

<bond atomRefs2="a17 a18" order="2"/>

<bond atomRefs2="a17 a22" order="1"/>

<bond atomRefs2="a18 a19" order="1"/>

<bond atomRefs2="a19 a20" order="2"/>

<bond atomRefs2="a20 a21" order="1"/>

<bond atomRefs2="a21 a22" order="2"/>

</bondArray>

</molecule>

<molecule id="sg2" molID="m3" role="SuperatomSgroup" title="Ph">

<atomArray>

<atom id="a23" elementType="C" x2="1.718490945911924" y2="3.193347869707083"/>

<atom id="a24" elementType="C" x2="3.0521700677399615" y2="3.9633478697070843"/>

<atom id="a25" elementType="C" x2="3.0521700677399615" y2="5.503347869707083"/>

<atom id="a26" elementType="C" x2="1.7184909459119257" y2="6.273347869707083"/>

<atom id="a27" elementType="C" x2="0.38481182408389003" y2="5.503347869707085"/>

<atom id="a28" elementType="C" x2="0.38481182408388914" y2="3.9633478697070843"/>

</atomArray>

<bondArray>

<bond atomRefs2="a23 a24" order="2"/>

<bond atomRefs2="a23 a28" order="1"/>

<bond atomRefs2="a24 a25" order="1"/>

<bond atomRefs2="a25 a26" order="2"/>

<bond atomRefs2="a26 a27" order="1"/>

<bond atomRefs2="a27 a28" order="2"/>

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

<MElectronContainer occupation="0 0" radical="0" id="o1">

<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="o2">

<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>

<MElectron atomRefs="m1.a5" difLoc="0.0 0.0 0.0"/>

</MElectronContainer>

<MPolyline headLength="0.6" headWidth="0.4" id="o3">

<MPoint x="-5.600000321865082" y="1.750000238418579"/>

<MPoint x="-3.73333340883255" y="1.750000238418579"/>

</MPolyline>

</MDocument>

</cml>

This MRV lacks the attachment point information that the original MRV had. So the attachment group problem was created by Marvin JS, when it failed to import the original attachment group information.

Thank you for reporting this problem. We have fixed the original issue (not exporting the attachment points) in version 15.12.14. (https://docs.chemaxon.com/display/docs/.History+of+Changes+-+Marvin+JS+v15.12.14.0). So, if you use the original MRV file, you will not see this problem anymore.

Best regards,

Efi

Thank you. We are currently using MarvinJS 15.6.29 with JChem Web Services 14.10.13. If we upgrade MarvinJS, will we also need to upgrade JChem Web Services? (Once previously we upgraded MarvinJS and found that JChem Web Services stopped working until we upgraded it as well.) If not, is there any other reason we should upgrade JChem Web Services?

P.S. Happy New Year.

Happy New Year!

 

I apologize for the late answer. We recommend to upgrade JChem Web Services together with Marvin JS. It has some chance that the Marvin JS will work with the older version of Webservice, but we have also had some clean and import/export bug fixes in the Webservice functions, so it worth and safer to upgrade.  

Best regards,

Efi

I knew I would regret upgrading JChem Web Services. I downloaded v. 16.1.4 and modified the webservices.war file to make it compatible with Tomcat 6. [We remove the filter definitions for continuation and gzip and the filter mapping for gzip.] I downloaded webservices.war to my desktop, pointed my browser to /manager/html, and undeployed the currently running version of Web services. Then I deployed the new version by uploading webservices.war and pressing Deploy. After some time, the page refreshed and showed that /webservices had been deployed, but it was not running. When I pressed Start, I was told, FAIL - Application at context path /webservices could not be started. I undeployed and repeated -- same problem. Please help.

Edit: Well, after some the manager page refreshed itself and said that /webservices was running after all, and Marvin JS is now communicating with it. So I guess it just took some time for /webservices to start.

We are glad that it works. Thank you for the update.

Efi