In fact even better please submit a PR since you've identified and fixed
the problem.
On 6 August 2017 at 16:43, John Mayfield <[email protected]>
wrote:
> Please post an issue: github.com/cdk/cdk
>
>
> On 5 August 2017 at 01:50, Andrei Kazakov <[email protected]> wrote:
>
>> Hello,
>>
>> The "bugs" list seems to be deserted so I am posting it here. It appears
>> to be an overflow issue in MDEDescriptor.java that produces zero values for
>> long chains (the code is unchanged across 1.4, 1.5, and 2.0 series).
>> Specifically, MDEC-22 becomes zero starting from C23 (tricosane). It is
>> caused by geometric mean evaluation via direct product; replacing product
>> with the sum of logs fixes the issue:
>>
>> private double evalCValue(int[][] distmat, int[][] codemat, int
>> type1, int type2) {
>> /* double lambda = 1; */
>> double lambda = 0;
>> double n = 0;
>>
>> List<Integer> v1 = new ArrayList<Integer>();
>> List<Integer> v2 = new ArrayList<Integer>();
>> for (int i = 0; i < codemat.length; i++) {
>> if (codemat[i][0] == type1) v1.add(codemat[i][1]);
>> if (codemat[i][0] == type2) v2.add(codemat[i][1]);
>> }
>>
>> for (int i = 0; i < v1.size(); i++) {
>> for (int j = 0; j < v2.size(); j++) {
>> int a = v1.get(i);
>> int b = v2.get(j);
>> if (a == b) continue;
>> double distance = distmat[a][b];
>> /* lambda = lambda * distance; */
>> lambda += Math.log(distance);
>> n++;
>> }
>> }
>>
>> if (type1 == type2) {
>> /* lambda = Math.sqrt(lambda); */
>> lambda /= 2;
>> n = n / 2;
>> }
>> if (n == 0) return 0.0;
>> else
>> /* return n / Math.pow(Math.pow(lambda, 1.0 / (2.0 * n)), 2);
>> */
>> return n / Math.exp(lambda / n);
>> }
>>
>>
>> --Andrei
>>
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>>
>>
>
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