Hi Greg,
That's great , thanks a lot for your help.
Regards,
George
On 30 September 2011 07:01, Greg Landrum <[email protected]> wrote:
> Hi George,
>
> On Thu, Sep 29, 2011 at 1:11 PM, George Papadatos <[email protected]>
> wrote:
> > I'd like to calculate the *rooted* Morgan fingerprint for a set of
> > molecules. By rooted I mean the subset of the whole-molecule fingerprint
> > which contains just the bits which correspond to circular atom layers (up
> to
> > N bond lengths) that include a specific atom.
> > So let's say that there is a single Uranium atom in each molecule. What I
> > want to calculate is the subset of the Morgan fingerprint (let's say with
> a
> > radius of 3) which contains the bits set on by layers including my U
> atom.
> > This should include not only the bits where U was the root of the layer,
> but
> > also the bits where U was in the layer of neighboring atoms, up to 3
> bonds
> > away.
>
> A minor point: I wouldn't call this the rooted fingerprint since it
> includes bits that are set by layers that are not centered at your U
> atom.
>
> > After checking the super-helpful "Getting Started with the RDKit in
> Python"
> > (Q2 2011) tutorial, section 5.4.1, I can see one way of doing this:
> > calculating the Morgan fp and then enumerating all the sub-molecules (or
> > layers) that set the corresponding bits on and then checking if U is in
> any
> > one of these submolecules. If it is then the corresponding bit is part of
> > the root Morgan fp.
> > Is there any other more efficient way???
>
> If you only want the bits that are set by a particular atom (i.e.
> those that are centered at that atom), you can use the fromAtoms
> argument:
> >>> from rdkit import Chem
> >>> from rdkit.Chem import rdMolDescriptors
> >>> m1 = Chem.MolFromSmiles('Cc1ccccc1')
> >>> m2 = Chem.MolFromSmiles('Cc1c(C)cccc1')
> >>>
> rdMolDescriptors.GetMorganFingerprint(m1,1,fromAtoms=[0]).GetNonzeroElements()
> {2246728737: 1, 422715066: 1}
> >>>
> rdMolDescriptors.GetMorganFingerprint(m1,2,fromAtoms=[0]).GetNonzeroElements()
> {2246728737: 1, 422715066: 1, 2218109011: 1}
> >>>
> rdMolDescriptors.GetMorganFingerprint(m2,1,fromAtoms=[0]).GetNonzeroElements()
> {2246728737: 1, 422715066: 1}
> >>>
> rdMolDescriptors.GetMorganFingerprint(m2,2,fromAtoms=[0]).GetNonzeroElements()
> {2246728737: 1, 422715066: 1, 2368203427: 1}
>
> Note that I just fixed a bug that was leading to missing bits in the
> morgan fingerprints generated with a fromAtoms argument.
>
> If you want all bits that the atom is involved in, I would suggest
> using the fromAtoms argument, but also including all the atoms that
> are within the appropriate radius of your atom. You can find these
> atoms using the molecule's distance matrix:
> >>> m1 = Chem.MolFromSmiles('Cc1ccccc1')
> >>> dm=Chem.GetDistanceMatrix(m1)
> >>> dm
> array([[ 0., 1., 2., 3., 4., 3., 2.],
> [ 1., 0., 1., 2., 3., 2., 1.],
> [ 2., 1., 0., 1., 2., 3., 2.],
> [ 3., 2., 1., 0., 1., 2., 3.],
> [ 4., 3., 2., 1., 0., 1., 2.],
> [ 3., 2., 3., 2., 1., 0., 1.],
> [ 2., 1., 2., 3., 2., 1., 0.]])
>
>
> I hope this helps,
> -greg
>
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