Hi Yannick,
Thanks for your email.
1: Do you mean, you expect to see the pattern in the list or you expected
it to match? The pattern is present:
System.err.println(sf.getSubstructure(32));
// [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
However the SMARTS doesn't match your structure:
[NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
The problem is: [N]*~[#7,#8,#15,#16], here's the match
<http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?sma=%5BN%5D*~%5B%237%2C%238%2C%2315%2C%2316%5D&smi=CN(C)c1cc(OS(O)(O)%3DO)nc(n1)-c1cncc(c1)C(O)%3DO&zoom=1.3&annotate=none>
visualized.
2: The cardinality of a fingerprint is the number of 'on' bits, the size of
fingerprint is the number of possible bits. There are 320 bits (addressed 0
to 319) in the fingerprint, so i < fingerprint.cardinality() will only show
the first 14.
for(int k = 0; k < fingerprint.size(); k++) {
> System.out.println(k + " " + fingerprint.get(k));
> }
Actually really not a fan of the API so I normally just get the underlying
JDK bitset and throw away the CDK object:
BitSet bitset = fingerprint.asBitSet();
Hope that helps,
John
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