OK, thanks for this – I’ll have a go and see it works for me.
Cheers,
Steve.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 13 June 2014 13:23
To: Stephen O'hagan
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints
hmm, this got lost in my mailbox. Sorry.
You can do what I think you want to do using the information theory machinery
that the rdkit has available. Here's a short snippet that finds the bits that
are not redundant in a data set (redundancy here calculated using information
entropy):
In [48]: ms = [Chem.MolFromSmiles(x.split()[1]) for x in
file('./Target_no_107_58879.txt')]
In [49]: nbits = 2048
In [50]: fps = [rdMolDescriptors.GetHashedAtomPairFingerprintAsBitVect(x,nbits)
for x in ms]
In [58]: entropies = []
In [59]: for i in range(nbits):
arr = numpy.array([x[i] for x in fps])
e = InfoTheory.InfoEntropy(arr)
entropies.append(e)
....:
In [60]: entropies = numpy.array(entropies)
In [61]: goodbits = numpy.array(range(nbits))[entropies>0.0]
In [62]: len(goodbits)
Out[62]: 891
your case is pretty big, so this may take a bit, but it shouldn't be too slow.
-greg
On Wed, Jun 4, 2014 at 5:08 AM, Stephen O'hagan
<soha...@manchester.ac.uk<mailto:soha...@manchester.ac.uk>> wrote:
Hi,
I have a set of say 1000 generated fingerprints each of length 39972; across
all 1000 fingerprints many bits are the same – they contain no information
about the differences between the 1000 molecules.
e.g. for list
010100001
010110100
010101110
010100010
The first four bits are redundant, I could just record them as:
00001
10100
01110
00010
In reality, the redundant bits are distributed through the bit string, so I
need a method to determine which bits are redundant, and then remove them from
each fingerprint.
Cheers,
Steve.
From: Greg Landrum
[mailto:greg.land...@gmail.com<mailto:greg.land...@gmail.com>]
Sent: 04 June 2014 04:40
To: Stephen O'hagan
Cc:
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints
Hi Steve,
On Tue, Jun 3, 2014 at 2:08 PM, Stephen O'hagan
<soha...@manchester.ac.uk<mailto:soha...@manchester.ac.uk>> wrote:
I have a fragment of code generating fingerprints for a long list of molecules
(length ~ 1000)
for index in range(0,len(smi)):
smiles=smi[index]
mol=Chem.MolFromSmiles(smiles)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
dm = Chem.Get3DDistanceMatrix(mol)
fp = Generate.Gen2DFingerprint(mol,factory, dMat=dm)
fp = fp.ToBitString()
bs[index]=fp
The length of each bitvectors generated is 39972, and the list has a lot of
redundant ‘1’s and ‘0’s.
Is there an easy method to filter out these redundant bits?
What do you mean by redundant bits?
The length of the bit vectors is determined by the parameters you provide for
building the pharmacophore fingerprints (number of points, number of features,
and number of distance bins). The length of the strings that you get from
fp.ToBitString() should be equal to this number of bits.
-greg
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