rdkit.Chem.Fraggle.FraggleSim

Package rdkit :: Package Chem :: Package Fraggle :: Module FraggleSim |
[hide private]
[frames] | no frames]

# Module FraggleSim

source code

Functions | [hide private]
delete_bonds(mol, bonds, ftype, hac) | source code
is_ring_cut_valid(smi) | source code
select_fragments(f_smi, ftype, hac) | source code
generate_fraggle_fragmentation(mol) >>> q = Chem.MolFromSmiles('COc1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12')... | source code
atomContrib(subs, mol, tverskyThresh=0.8) | source code
compute_fraggle_similarity_for_subs(inMol, qMol, qSmi, qSubs, tverskyThresh=0.8) | source code
GetFraggleSimilarity(queryMol, refMol, tverskyThresh=0.8) return the Fraggle similarity between two molecules | source code
_test() | source code

Variables | [hide private]
| rdkitFpParams = ``{``'``fpSize``'``:` 1024`,` `'``maxPath``'``:` 5`,` `'``nBitsPerHash``'``:` 2`}``
| acyc_smarts = `<rdkit.Chem.rdchem.Mol object>`
| cyc_smarts = `<rdkit.Chem.rdchem.Mol object>`
| cSma1 = `<rdkit.Chem.rdchem.Mol object>`
| cSma2 = `<rdkit.Chem.rdchem.Mol object>`
| modified_query_fps = ``{``}``
| __package__ = ``'``rdkit.Chem.Fraggle``'``

Imports: sys, Chem, DataStructs

Function Details | [hide private]

### generate_fraggle_fragmentation(mol) | source code
    >>> q = Chem.MolFromSmiles('COc1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12')
    >>> list(generate_fraggle_fragmentation(q))
     ['[*]C(=O)NC1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1', '[*]C(=O)c1cncc(C)c1.[*]C1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1', '[*]C(=O)c1cncc(C)c1.[*]Cc1cc(OC)c2ccccc2c1OC', '[*]C(=O)c1cncc(C)c1.[*]c1cc(OC)c2ccccc2c1OC', '[*]C1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1', '[*]C1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1.[*]c1cncc(C)c1', '[*]Cc1cc(OC)c2ccccc2c1OC.[*]NC(=O)c1cncc(C)c1', '[*]Cc1cc(OC)c2ccccc2c1OC.[*]c1cncc(C)c1', '[*]N1CCC(NC(=O)c2cncc(C)c2)CC1.[*]c1cc(OC)c2ccccc2c1OC', '[*]NC(=O)c1cncc(C)c1.[*]c1cc(OC)c2ccccc2c1OC', '[*]NC1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1', '[*]NC1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1.[*]c1cncc(C)c1', '[*]c1c(CN2CCC(NC(=O)c3cncc(C)c3)CC2)cc(OC)c2ccccc12', '[*]c1c(OC)cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c1[*]', '[*]c1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12', '[*]c1cc(OC)c2ccccc2c1OC.[*]c1cncc(C)c1']

### GetFraggleSimilarity(queryMol, refMol, tverskyThresh=0.8) | source code
    return the Fraggle similarity between two molecules

    >>> q = Chem.MolFromSmiles('COc1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12')
    >>> m = Chem.MolFromSmiles('COc1cc(CN2CCC(NC(=O)c3ccccc3)CC2)c(OC)c2ccccc12')
    >>> sim,match = GetFraggleSimilarity(q,m)
    >>> sim
    0.980...
    >>> match
    '[*]C1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1'

    >>> m = Chem.MolFromSmiles('COc1cc(CN2CCC(Nc3nc4ccccc4s3)CC2)c(OC)c2ccccc12')
    >>> sim,match = GetFraggleSimilarity(q,m)
    >>> sim
    0.794...
    >>> match
    '[*]C1CCN(Cc2cc(OC)c3ccccc3c2OC)CC1'

    >>> q = Chem.MolFromSmiles('COc1ccccc1')
    >>> sim,match = GetFraggleSimilarity(q,m)
    >>> sim
    0.347...
    >>> match
    '[*]c1ccccc1'