Rajarshi Guha wrote:
> I took the source code from your Sourceforge bug report and tried
> running it. However I cannot get the 3D structure in the first place
> (it reports that not all ring atoms were placed).
>
> So I converted the SMILES to 3D using smi23d and tested it directly
> with the LengthOverBreadth descriptor and it works fine in that it
> does not report any typing error.
>
> Furthermore if run your code using CCCCC as the input SMILES it works
> fine. So I'm guessing that the problem is with the 3D structure
> generation code.
>
Couple of months ago I was told 3D generation code does not work well
currently - are there any changes of this status recently?
> > Also I'd appreciate any help on how to
> > use this better... I think what I've done with iterators and sets is a
> > messy solution.
>
> One problem I see in your code is the way you get the values from the
> DescriptorValue object. Since a descriptor can return a scalar or
> vector (also it could be Integer or Double), you need to coerce it to
> the appropriate descriptor result object:
>
> IDescriptorResult result = ((DescriptorValue)nextVal).getValue()
> if (result instanceof DoubleArrayResult) {
> // process
> } else if (resut instanceof DoubleResult) {
> // process
> }
>
> etc.
>
While this is correct for the current state of affairs, I am wondering
if it would be more convenient to introduce some class hierarchy that
will allow to avoid this kind of "instance of" checks, for example in
the manner java.lang.Number derived classes can all use methods like
"doubleValue()", "intValue()", exploiting the class inheritance. May not
be that straightforward to integrate array classes, but not impossible.
Regards,
Nina
> Of course, if you just want to print out the result as a string, your
> code works for scalar return values but I don't think it will work
> with vector return values. The above code will let you get the actual
> numerical values.
>
> > Also, for the descriptors which require parameters, what is the most
> > efficient way to set all the parameters for all the descriptors?
>
> There is no way to set parameters uniformly across all descriptors -
> mainly because different descriptors can have different (in terms of
> type and name) parameters.
>
> -------------------------------------------------------------------
> Rajarshi Guha <[EMAIL PROTECTED]>
> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
> -------------------------------------------------------------------
> All seems condemned in the long run to approximate a state akin to
> Gaussian noise.
> -- James Martin
>
>
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