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#203 adjustBondOrdersToValency does not give correct double bonds

closed
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5
2012-10-08
2004-04-21
No

In running a large number (ca 1000) molecules through
CDK to generate bond orders we found that most did
not have the required number of double bonds and
some were misplaced.

We start from molecules with an exact number of
explicit hydrogen atoms (in CML) and bond orders set to
1(or S). We then convert to CDK, adjust bond orders
and return. The result for allopurinol is attached.

(I can't say exactly what version of CDK bbut it's before
2004-03-07).

Discussion

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    Which CDK class and which atom type list is used?

     
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    One solution is to use the ValencyChecker from CVS instead
    of SaturationChecker. Please file problems for that
    separaely, or email me directly.