User 870ab5b546
01-10-2007 19:43:59
When I make a link node such as X-(L1-4)-Y, the bonds between the link atoms are assumed to be single bonds. Only if I make the X-(L1-4) and (L1-4)-Y bonds into Any bonds are the bonds within the link consider to be Any bonds. I would like to be able to specify that the lnk bonds are Any bonds while keeping the X-(L1-4) and (L1-4)-Y bonds as single bonds.
ChemAxon a3d59b832c
01-10-2007 20:28:26
Hi Bob,
The rule with link nodes is that the linking bond is the same type as the bonds going out from the link node. (Outer bonds.) Additional conditions could be added to the outer atoms by, for example, recursive smarts.
Your example with X=O and Y=N and C in between:
| Code: |
<?xml version="1.0" ?>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3"
elementType="C N O"
mrvQueryProps="0 a2;str:[$([#7]-[#6])] a2;str:[$([#8]-[#6])]"
mrvLinkNodeRep="4 1 1"
mrvLinkNodeOut="a3,a2 - -"
x2="-2.9166667461395264 -1.5829876243114909 -4.250345867967562"
y2="0.8166666626930237 1.5866666626930237 1.5866666626930237"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" queryType="Any" />
<bond atomRefs2="a1 a3" order="1" queryType="Any" />
</bondArray>
</molecule>
</MChemicalStruct>
</MDocument>
|
I hope this helps,
Szabolcs