Hi Jing,
Most fingerprints are binary, thus can be stored as np.bool_, which
compared to double should be 64 times more memory efficient.
Best,
Maciej
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-08-27 16:15 GMT+02:00 Jing Lu <ajin...@gmail.com>:
> Hi Greg,
>
> Thanks! It works! But, is that possible to fold the fingerprint to smaller
> size? np.zeros((1000000,2048)) still takes a lot of memory...
>
>
> Best,
> Jing
>
> On Wed, Aug 26, 2015 at 11:02 PM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>>
>> On Thu, Aug 27, 2015 at 3:00 AM, Jing Lu <ajin...@gmail.com> wrote:
>>
>>>
>>> So, I wonder is there any way to convert fingerprint to a numpy vector?
>>>
>>
>> Indeed there is:
>>
>> In [11]: from rdkit import Chem
>>
>> In [12]: from rdkit import DataStructs
>>
>> In [13]: import numpy
>>
>> In [14]: m =Chem.MolFromSmiles('C1CCC1')
>>
>> In [15]: fp = Chem.RDKFingerprint(m)
>>
>> In [16]: fpa = numpy.zeros((len(fp),),numpy.double)
>>
>> In [17]: DataStructs.ConvertToNumpyArray(fp,fpa)
>>
>>
>> Best,
>> -greg
>>
>>
>
>
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