User 870ab5b546
24-10-2006 20:22:48
In the following compound, the terminal N atom should be underlined to indicate a valence error, but it is not. (Marvin 4.1.2.)
| Code: |
<?xml version="1.0" ?>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10"
elementType="C N C C C O C C C N"
formalCharge="0 1 0 0 0 -1 0 0 0 -1"
x2="-3.898124575614929 -2.1656245505809784 -6.655081593552572 -6.655081593552572 -5.321397581415341 -6.139522352533505 -3.987718459587305 -5.321412252504313 -3.9877429114560545 -0.6256245505809783"
y2="5.582500457763672 4.908751010894775 2.4543580689777027 3.9943919500957836 4.764383479769675 6.015633308108298 3.9943834797696756 1.6843411284186622 2.4543580689777027 4.908751010894775"
/>
<bondArray>
<bond atomRefs2="a5 a6" order="1" />
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a3 a8" order="1" />
<bond atomRefs2="a4 a3" order="1" />
<bond atomRefs2="a5 a4" order="1" />
<bond atomRefs2="a5 a7" order="1" />
<bond atomRefs2="a9 a7" order="1" />
<bond atomRefs2="a8 a9" order="1" />
<bond atomRefs2="a2 a10" order="3" />
<bond atomRefs2="a1 a5" order="1" />
</bondArray>
</molecule>
</MChemicalStruct>
</MDocument>
|
ChemAxon 43e6884a7a
25-10-2006 08:17:00
It will be fixed in the next release. Thanks.
User 870ab5b546
14-11-2006 14:48:29
Here's another, similar example:
| Code: |
<?xml version="1.0" ?>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31"
elementType="C N C N C C N N C O O O N C R C R N C C N N C C N C N O O O H"
formalCharge="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0"
mrvMap="0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 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 0 sg2 0 0 0 0 0 0 0 0 0 0 0 0 0 0"
x3="-1.4460707902908325 -2.779740131339091 -2.779740131339091 -1.4460707902908325 -0.112401449242574 -0.112401449242574 1.3522157735582905 1.3522324066241591 2.257376129549801 -1.4460707902908325 -4.0181564587508385 3.6873761295498007 1.727520022022814 3.1975200220228146 3.8675200220228145 1.732679769858997 3.2726797698589962 5.764261874480287 4.430592533432028 4.430592533432028 5.764261874480287 7.097931215528545 7.097931215528545 3.0969231923837697 1.7632538513355112 1.7632538513355112 3.0969231923837697 3.0969231923837697 0.5248375239237646 8.336347542940292 7.812109064526958"
y3="-12.256983931610801 -13.02700087216984 -14.567034753287922 -15.337051693846963 -14.567034753287922 -13.02700087216984 -12.551201423757597 -15.042925249042732 -13.797108615301704 -10.826983931610801 -15.282034753287924 -13.797108615301704 -16.44351769716188 -16.44351769716188 -17.603991738233027 -11.131290459112666 -11.131290459112666 13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 11.38131604521925 12.921349926337333 13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 15.121366866896372 10.666316045219249 13.636349926337333 10.667138196220838"
z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="1" />
<bond atomRefs2="a3 a4" order="1" />
<bond atomRefs2="a4 a5" order="1" />
<bond atomRefs2="a1 a6" order="1" />
<bond atomRefs2="a5 a8" order="1" />
<bond atomRefs2="a6 a5" order="2" />
<bond atomRefs2="a7 a6" order="1" />
<bond atomRefs2="a8 a9" order="1" />
<bond atomRefs2="a7 a9" order="1" />
<bond atomRefs2="a1 a10" order="2" />
<bond atomRefs2="a3 a11" order="2" />
<bond atomRefs2="a9 a12" order="2" />
<bond atomRefs2="a8 a13" order="1" />
<bond atomRefs2="a13 a14" order="2" />
<bond atomRefs2="a7 a16" order="1" />
<bond atomRefs2="a16 a17" order="1" />
<bond atomRefs2="a14 a15" order="1" />
<bond atomRefs2="a18 a19" order="2" />
<bond atomRefs2="a20 a21" order="2" />
<bond atomRefs2="a21 a22" order="1" />
<bond atomRefs2="a22 a23" order="1" />
<bond atomRefs2="a18 a23" order="1" />
<bond atomRefs2="a27 a20" order="1" />
<bond atomRefs2="a20 a19" order="1" />
<bond atomRefs2="a24 a19" order="1" />
<bond atomRefs2="a24 a25" order="1" />
<bond atomRefs2="a25 a26" order="1" />
<bond atomRefs2="a26 a27" order="1" />
<bond atomRefs2="a24 a28" order="2" />
<bond atomRefs2="a26 a29" order="2" />
<bond atomRefs2="a23 a30" order="2" />
<bond atomRefs2="a22 a31" order="1" />
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="CO2tBu"
leftName="tBuO2C" molID="m2">
<atomArray
atomID="a32 a33 a34 a35 a36 a37 a38"
elementType="C C C C O C O"
attachmentPoint="1 0 0 0 0 0 0"
x3="2.8695719869362097 3.1003654181975158 4.661932997080937 2.5482234434305884 2.6518124347451533 2.559683615992956 2.4101224979554328"
y3="-13.977833586223413 -15.797372992526396 -15.854278606297788 -17.256952119602964 -15.15493846257359 -15.112599789543562 -13.503704831298212"
z3="-1.914258616160573 -0.48727113997918875 -0.47662598591726224 -0.5479686845831234 -1.591314476785143 0.8091187534796863 -2.9392314405275055"
/>
<bondArray>
<bond atomRefs2="a36 a32" order="1" />
<bond atomRefs2="a32 a38" order="2" />
<bond atomRefs2="a37 a33" order="1" />
<bond atomRefs2="a33 a34" order="1" />
<bond atomRefs2="a33 a35" order="1" />
<bond atomRefs2="a33 a36" order="1" />
</bondArray>
</molecule>
<molecule id="sg2" role="SuperatomSgroup" title="CO2tBu"
leftName="tBuO2C" molID="m3">
<atomArray
atomID="a39 a40 a41 a42 a43 a44 a45"
elementType="C C C C O C O"
attachmentPoint="1 0 0 0 0 0 0"
x3="1.9551966817604285 2.1859901130217363 3.747557691905156 1.6338481382548071 1.737437129569372 1.6453083108171747 1.4957471927796515"
y3="-8.587833421714594 -10.407372828017577 -10.464278441788968 -11.866951955094144 -9.76493829806477 -9.722599625034743 -8.113704666789392"
z3="-1.914258616160573 -0.48727113997918875 -0.47662598591726224 -0.5479686845831234 -1.591314476785143 0.8091187534796863 -2.9392314405275055"
/>
<bondArray>
<bond atomRefs2="a43 a39" order="1" />
<bond atomRefs2="a39 a45" order="2" />
<bond atomRefs2="a44 a40" order="1" />
<bond atomRefs2="a40 a41" order="1" />
<bond atomRefs2="a40 a42" order="1" />
<bond atomRefs2="a40 a43" order="1" />
</bondArray>
</molecule>
</molecule>
</MChemicalStruct>
</MDocument>
|
ChemAxon 7c2d26e5cf
14-11-2006 15:00:08
Thanks for the new example.
ChemAxon 43e6884a7a
14-11-2006 20:36:01
Bob,
Relax, this bug was fixed right after you reported it :-)
The new release should come out in a few days.
Cheers,
Ferenc