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-c1ccc(OC)cn1’, ‘*c1ccccc1OC1CC1’] >>> sorted(res.GetAllChildren().keys()) [‘*C1CC1’, ‘*c1ccc(OC)cn1’, ‘*c1ccccc1’, ‘*c1ccccc1-c1ccc(OC)cn1’, ‘*c1ccccc1OC1CC1’]

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

class rdkit.Chem.Recap.TestCase(methodName='runTest')

Bases: TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test1()

test2()

test3()

testAmideRxn()

testAmineRxn()

testAromCAromCRxn()

testAromNAliphCRxn()

testAromNAromCRxn()

testEsterRxn()

testEtherRxn()

testLactamNAliphCRxn()

testMinFragmentSize()

testOlefinRxn()

testSFNetIssue1801871()

testSFNetIssue1804418()

testSFNetIssue1881803()

testSulfonamideRxn()

testUreaRxn()