rdkit.Chem.Recap module — The RDKit 2016.09.1 documentation

# rdkit.Chem.Recap module

Implementation of the RECAP algorithm from Lewell et al. JCICS 38 511-522 (1998)

The published algorithm is implemented more or less without modification. The results are returned as a hierarchy of nodes instead of just as a set of fragments. The hope is that this will allow a bit more flexibility in working with the results.

For example: >>> from rdkit import Chem >>> from rdkit.Chem import Recap >>> m = Chem.MolFromSmiles(‘C1CC1Oc1ccccc1-c1ncc(OC)cc1’) >>> res = Recap.RecapDecompose(m) >>> res <...Chem.Recap.RecapHierarchyNode object at ...> >>> sorted(res.children.keys()) [‘[*]C1CC1’, ‘[*]c1ccc(OC)cn1’, ‘[*]c1ccccc1-c1...cc(OC)c...1’, ‘[*]c1ccccc1OC1CC1’] >>> sorted(res.GetAllChildren().keys()) [‘[*]C1CC1’, ‘[*]c1ccc(OC)cn1’, ‘[*]c1ccccc1-c1...cc(OC)c...1’, ‘[*]c1ccccc1OC1CC1’, ‘[*]c1ccccc1[*]’]

To get the standard set of RECAP results, use GetLeaves(): >>> leaves=res.GetLeaves() >>> sorted(leaves.keys()) [‘[*]C1CC1’, ‘[*]c1ccc(OC)cn1’, ‘[*]c1ccccc1[*]’] >>> leaf = leaves[‘[*]C1CC1’] >>> leaf.mol <...Chem.rdchem.Mol object at ...>

`rdkit.Chem.Recap.` `RecapDecompose`(mol, allNodes=None, minFragmentSize=0, onlyUseReactions=None)

  returns the recap decomposition for a molecule

class `rdkit.Chem.Recap.` `RecapHierarchyNode`(mol)

  Bases: `object`

  This class is used to hold the Recap hiearchy

  `GetAllChildren`()

    returns a dictionary, keyed by SMILES, of children

  `GetLeaves`()

    returns a dictionary, keyed by SMILES, of leaf (terminal) nodes

  `children` = None
  `getUltimateParents`()

    returns all the nodes in the hierarchy tree that contain this node as a child

  `mol` = None
  `parents` = None
  `smiles` = None