Sorry meant to be on-list. Have you got the contents of examples.sdf,
specifically the one that causes the problem?
Not all atoms are represented by MMFF94 (of note is boron - OpenEye have
added support) - if the molecule has an atom not typed (by MMFF94) the
method will fail. However, there are known problems with the current MMFF
in CDK, in particular atom typing is baddddd. I've reimplemented the atom
types using SMARTS and tested on the CCL validation
<http://www.ccl.net/cca/data/MMFF94/> but have not integrated these in to
the partial charge descriptor yet. It is on my list of things to fix.
Regards,
John W May
john.wilkinson...@gmail.com
On 13 July 2015 at 22:28, John M <john.wilkinson...@gmail.com> wrote:
> Do you have a molecule it fails for?
>
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 13 July 2015 at 21:21, Zheng Shi <zs...@ualberta.ca> wrote:
>
>> Hi,
>>
>> I'm calculating partial charge with cdk using the code below. But for
>> some molecule, it throws some exceptions. I don't know what goes wrong. Can
>> anyone help? A example molecule is attached. Thanks.
>> String path = "example.sdf";
>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>> IteratingSDFReader sdfr = new IteratingSDFReader(new FileReader(path),
>> bldr);
>> while (sdfr.hasNext())
>> {
>> IAtomContainer mol= sdfr.next();
>> PartialTChargeMMFF94Descriptor ptc= new
>> PartialTChargeMMFF94Descriptor();
>> PiElectronegativityDescriptor pen=new PiElectronegativityDescriptor();
>> SigmaElectronegativityDescriptor sen=new
>> SigmaElectronegativityDescriptor();
>> DescriptorValue pt=ptc.calculate(a, mol);
>> IDescriptorResult v_1=pt.getValue();
>> DescriptorValue pe=pen.calculate(a, mol);
>> IDescriptorResult v_2=pe.getValue();
>> DescriptorValue se=sen.calculate(a, mol);
>>
>> IDescriptorResult v_3=se.getValue();
>> }
>>
>>
>>
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