On a side note, they structure looks wrong. Where did you get it from?
You're structure would be fine if the S were a P but the S as it is should
have another double bond. Notice how the abbreviations kick in when I
change it.
[image: Inline images 1]
Charge separated would also make sense.
[image: Inline images 2]
Regards,
John W May
john.wilkinson...@gmail.com
On 27 April 2016 at 11:36, John M <john.wilkinson...@gmail.com> wrote:
> 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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