Re: [Rdkit-discuss] reaction fingerprint as bitstring

2017-03-24 Thread Ambrish 
Thanks Greg.
I am trying to pre-calculate reaction fingerprints of all my database
reactions and store it in database, so that for any new reaction I can run
Tanimoto similarity or similar calculation and pick similar reactions. So I
decided to convert it to a BitString of fixed length, but I get your point
I am loosing information in this way. Any suggestion on how it can be done
?






On Fri, Mar 24, 2017 at 3:08 AM Greg Landrum  wrote:

> Hi Ambrish,
>
> Assuming that I understand correctly what you want to do, here's an
> example using built-in RDKit functionality that generates a reaction
> fingerprint (using default parameters, you can change these) and then
> converts it into a bit vector using a simple: "if the bit is set in the
> original fingerprint set it in the bit vector":
>
> In [3]: from rdkit.Chem import rdChemReactions
>
> In [4]: fp = rdChemReactions.CreateDifferenceFingerprintForReaction(rxn)
>
> In [5]: fp
> Out[5]: 
>
> In [6]: from rdkit import DataStructs
>
> In [7]: ebv = DataStructs.ExplicitBitVect(2048)
>
> In [8]: for bit in fp:
>...: ebv.SetBit(bit%ebv.GetNumBits())
>...:
>
> In [9]: ebv.GetNumOnBits()
> Out[9]: 5
>
>
> I don't think this is the best strategy since it treats positive and
> negative values the same, but without more information on what you want to
> do it's the best I can do.
>
> Best,
> -greg
>
>
>
> Best,
> -greg
>
>
> On Thu, Mar 23, 2017 at 6:10 PM, Ambrish  wrote:
>
> Hi RDKitters,
>
>   I am trying to calculate reaction fingerprints and store it in database.
> The transformation fingerprint created using the routine below is a
> IntSparseIntVect and I would like to convert it to a BitString of a
> particular length. How do we do that .
>
> def create_transformation_FP(rxn, fp_size, fp_type):
> rkfp = None
> rfp = None
> pfp = None
> for react in range(rxn.GetNumReactantTemplates()):
> mol = rxn.GetReactantTemplate(react)
> mol.UpdatePropertyCache(strict=False)
> Chem.GetSSSR(mol)
>
> try:
> if fp_type == 'AP':
> fp = AllChem.GetAtomPairFingerprint(mol=mol, 
> maxLength=fp_size)
> elif fp_type == 'Morgan':
> fp = AllChem.GetMorganFingerprint(mol=mol, radius=fp_size)
> elif fp_type == 'Topological':
> fp = AllChem.GetTopologicalTorsionFingerprint(mol=mol)
> else:
> print "Unsupported fingerprint type"
> except:
> print "Cannot build reactant fingerprint"
> if rfp is None:
> rfp = fp
> else:
> rfp += fp
>
> for product in range(rxn.GetNumProductTemplates()):
> mol = rxn.GetProductTemplate(product)
> mol.UpdatePropertyCache(strict=False)
> Chem.GetSSSR(mol)
> try:
> if fp_type == 'AP':
> fp = AllChem.GetAtomPairFingerprint(mol=mol, 
> maxLength=fp_size)
> elif fp_type == 'Morgan':
> fp = AllChem.GetMorganFingerprint(mol=mol, radius=fp_size)
> elif fp_type == 'Topological':
> fp = AllChem.GetTopologicalTorsionFingerprint(mol=mol)
> else:
> print "Unsupported fingerprint type"
> except:
> print "Cannot build product fingerprint"
> if pfp is None:
> pfp = fp
> else:
> pfp += fp
> if pfp is not None and rfp is not None:
> rkfp = pfp - rfp
>
>
> return rkfp
>
> Thanks.
>
>
> 
> --
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Re: [Rdkit-discuss] reaction fingerprint as bitstring

2017-03-24 Thread Greg Landrum 
Hi Ambrish,

Assuming that I understand correctly what you want to do, here's an example
using built-in RDKit functionality that generates a reaction fingerprint
(using default parameters, you can change these) and then converts it into
a bit vector using a simple: "if the bit is set in the original fingerprint
set it in the bit vector":

In [3]: from rdkit.Chem import rdChemReactions

In [4]: fp = rdChemReactions.CreateDifferenceFingerprintForReaction(rxn)

In [5]: fp
Out[5]: 

In [6]: from rdkit import DataStructs

In [7]: ebv = DataStructs.ExplicitBitVect(2048)

In [8]: for bit in fp:
   ...: ebv.SetBit(bit%ebv.GetNumBits())
   ...:

In [9]: ebv.GetNumOnBits()
Out[9]: 5


I don't think this is the best strategy since it treats positive and
negative values the same, but without more information on what you want to
do it's the best I can do.

Best,
-greg



Best,
-greg


On Thu, Mar 23, 2017 at 6:10 PM, Ambrish  wrote:

> Hi RDKitters,
>
>   I am trying to calculate reaction fingerprints and store it in database.
> The transformation fingerprint created using the routine below is a
> IntSparseIntVect and I would like to convert it to a BitString of a
> particular length. How do we do that .
>
> def create_transformation_FP(rxn, fp_size, fp_type):
> rkfp = None
> rfp = None
> pfp = None
> for react in range(rxn.GetNumReactantTemplates()):
> mol = rxn.GetReactantTemplate(react)
> mol.UpdatePropertyCache(strict=False)
> Chem.GetSSSR(mol)
>
> try:
> if fp_type == 'AP':
> fp = AllChem.GetAtomPairFingerprint(mol=mol, 
> maxLength=fp_size)
> elif fp_type == 'Morgan':
> fp = AllChem.GetMorganFingerprint(mol=mol, radius=fp_size)
> elif fp_type == 'Topological':
> fp = AllChem.GetTopologicalTorsionFingerprint(mol=mol)
> else:
> print "Unsupported fingerprint type"
> except:
> print "Cannot build reactant fingerprint"
> if rfp is None:
> rfp = fp
> else:
> rfp += fp
>
> for product in range(rxn.GetNumProductTemplates()):
> mol = rxn.GetProductTemplate(product)
> mol.UpdatePropertyCache(strict=False)
> Chem.GetSSSR(mol)
> try:
> if fp_type == 'AP':
> fp = AllChem.GetAtomPairFingerprint(mol=mol, 
> maxLength=fp_size)
> elif fp_type == 'Morgan':
> fp = AllChem.GetMorganFingerprint(mol=mol, radius=fp_size)
> elif fp_type == 'Topological':
> fp = AllChem.GetTopologicalTorsionFingerprint(mol=mol)
> else:
> print "Unsupported fingerprint type"
> except:
> print "Cannot build product fingerprint"
> if pfp is None:
> pfp = fp
> else:
> pfp += fp
> if pfp is not None and rfp is not None:
> rkfp = pfp - rfp
>
>
> return rkfp
>
> Thanks.
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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