rdkit.Chem.Fraggle.FraggleSim module

Fragmentation algorithm

identify acyclic bonds enumerate all single cuts make sure you chop off more that 1 atom keeps bits which are >60% query mol enumerate all double cuts keeps bits with 1 attachment point (i.e throw middle bit away) need to be >60% query mol

identify exocyclic bonds enumerate all single “ring” cuts Check if it results in more that one component keep correct bit if >40% query mol

enumerate successful “rings” cuts with an acyclic cut Check if it results in more that one component keep correct if >60% query mol

rdkit.Chem.Fraggle.FraggleSim.GetFraggleSimilarity(queryMol, refMol, tverskyThresh=0.8)

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'

rdkit.Chem.Fraggle.FraggleSim.atomContrib(subs, mol, tverskyThresh=0.8)

atomContrib algorithm generate fp of query_substructs (qfp)

loop through atoms of smiles

For each atom Generate partial fp of the atom (pfp) Find Tversky sim of pfp in qfp If Tversky < 0.8, mark atom in smiles

Loop through marked atoms

If marked atom in ring - turn all atoms in that ring to * (aromatic) or Sc (aliphatic) For each marked atom

If aromatic turn to a * If aliphatic turn to a Sc

Return modified smiles

rdkit.Chem.Fraggle.FraggleSim.compute_fraggle_similarity_for_subs(inMol, qMol, qSmi, qSubs, tverskyThresh=0.8)

rdkit.Chem.Fraggle.FraggleSim.delete_bonds(mol, bonds, ftype, hac)

Fragment molecule on bonds and reduce to fraggle fragmentation SMILES. If none exists, returns None

rdkit.Chem.Fraggle.FraggleSim.generate_fraggle_fragmentation(mol, verbose=False)

Create all possible fragmentations for molecule >>> q = Chem.MolFromSmiles(‘COc1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12’) >>> fragments = generate_fraggle_fragmentation(q) >>> fragments = sorted([‘.’.join(sorted(s.split(‘.’))) for s in fragments]) >>> fragments

[’*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’]

rdkit.Chem.Fraggle.FraggleSim.isValidRingCut(mol)

to check is a fragment is a valid ring cut, it needs to match the SMARTS: [$([#0][r].[r][#0]),$([#0][r][#0])]

rdkit.Chem.Fraggle.FraggleSim.select_fragments(fragments, ftype, hac)