incipient bond to shortcut group

User 870ab5b546

17-01-2007 02:38:16

In Marvin 4.1.5, it does not appear to be possible to draw a incipient bond to a shortcut group. For example, try to draw an incipient bond from one of the B-H bonds to the Bu3Sn group in the following structure:





Code:
<?xml version="1.0" ?>


<MDocument>


  <MChemicalStruct>


    <molecule molID="m1">


      <atomArray


          atomID="a1 a2 a3 a4 a5 a6 a7"


          elementType="R I B H H H H"


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


          sgroupRef="sg1 0 0 0 0 0 0"


          x2="-5.538343128610549 -4.379374961853027 -1.8768752217292786 -1.8768752217292786 -0.33687522172927853 -1.8768752217292786 -3.4168752217292786"


          y2="10.247152511157593 11.261249542236328 7.8924994468688965 9.432499446868896 7.8924994468688965 6.352499446868897 7.8924994468688965"


          />


      <bondArray>


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


        <bond atomRefs2="a3 a5" order="1" />


        <bond atomRefs2="a3 a6" order="1" />


        <bond atomRefs2="a3 a7" order="1" />


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


      </bondArray>


      <molecule id="sg1" role="SuperatomSgroup" title="SnBu3"


                leftName="Bu3Sn" molID="m2">


        <atomArray


            atomID="a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20"


            elementType="Sn C C C C C C C C C C C C"


            attachmentPoint="1 0 0 0 0 0 0 0 0 0 0 0 0"


            x2="-5.160480921818661 -8.24048092181866 -7.470480921818661 -5.930480921818661 -9.780480921818661 -5.930480921818662 -7.4704809218186625 -8.240480921818662 -9.780480921818661 -3.620480921818661 -2.8504809218186615 -1.3104809218186615 -0.5404809218186619"


            y2="9.695887002548817 12.363245246204889 11.029566124376853 11.029566124376853 12.363245246204889 8.362207880720781 8.362207880720781 7.028528758892747 7.028528758892747 9.695887002548817 11.029566124376853 11.029566124376853 12.363245246204889"


            />


        <bondArray>


          <bond atomRefs2="a11 a8" order="1" />


          <bond atomRefs2="a8 a13" order="1" />


          <bond atomRefs2="a8 a17" order="1" />


          <bond atomRefs2="a12 a9" order="1" />


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


          <bond atomRefs2="a10 a11" order="1" />


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


          <bond atomRefs2="a14 a15" order="1" />


          <bond atomRefs2="a15 a16" order="1" />


          <bond atomRefs2="a17 a18" order="1" />


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


          <bond atomRefs2="a19 a20" order="1" />


        </bondArray>


      </molecule>


    </molecule>


  </MChemicalStruct>


  <MEFlow id="o2" color="#000000" arcAngle="248.39738999999997"


          headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.15">


    <MAtomSetPoint atomRefs="m1.a1 m1.a2" />


    <MAtomSetPoint atomRefs="m1.a2" />


  </MEFlow>


</MDocument>






As usual, the atom in the shortcut group that should be involved in the incipient bond is the attachment point.

User f359e526a1

17-01-2007 18:57:07

You can do it if you expand the group first - apparently that is the behaviour in 4.1.4 also . I will check the previous versions.

User 870ab5b546

17-01-2007 20:13:16

Yes, I know I can do it if I expand the group, but it should be possible to do without expanding the group.

User f359e526a1

17-01-2007 20:44:46

OK, you mean by default the attachemnt point should be the target but if an other atom is to be selected from the group, one should expand it first?

User 870ab5b546

17-01-2007 21:11:06

Yes, exactly. If one does not expand the group, the attachment point is the target. If one draws the arrow, then expands or ungroups the group, the attachment point remains the target.

User f359e526a1

18-01-2007 11:17:22

OK, that is clear, will have a check how to do it.