rdkit.Chem.Recap

Module Recap

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: >>> m = Chem.MolFromSmiles('C1CC1Oc1ccccc1-c1ncc(OC)cc1') >>> res = Recap.RecapDecompose(m) >>> res <Chem.Recap.RecapHierarchyNode object at 0x00CDB5D0> >>> res.children.keys() ['[*]C1CC1', '[*]c1ccccc1-c1ncc(OC)cc1', '[*]c1ccc(OC)cn1', '[*]c1ccccc1OC1CC1'] >>> res.GetAllChildren().keys() ['[*]c1ccccc1[*]', '[*]C1CC1', '[*]c1ccccc1-c1ncc(OC)cc1', '[*]c1ccc(OC)cn1', '[*]c1ccccc1OC1CC1'] To get the standard set of RECAP results, use GetLeaves(): >>> leaves=res.GetLeaves() >>> leaves.keys() ['[*]c1ccccc1[*]', '[*]c1ccc(OC)cn1', '[*]C1CC1'] >>> leaf = leaves['[*]C1CC1'] >>> leaf.mol <Chem.rdchem.Mol object at 0x00CBE0F0>

Classes

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RecapHierarchyNode
This class is used to hold the Recap hiearchy...

Functions

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RecapDecompose(mol, allNodes=None, minFragmentSize=0, onlyUseReactions=None)
returns the recap decomposition for a molecule

source code

Variables

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reactionDefs = "[#7;+0;D2,D3:1]!@C(!@=O)!@[#7;+0;D2,D3:2]>>[*]...

reactions = tuple([Reactions.ReactionFromSmarts(x) for x in re...

Imports: sys, weakref, Chem, Reactions, iterkeys, iteritems, next

Variables Details

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reactionDefs

Value:

"[#7;+0;D2,D3:1]!@C(!@=O)!@[#7;+0;D2,D3:2]>>[*][#7:1].[#7:2][*]", "[C;
!$(C([#7])[#7]):1](=!@[O:2])!@[#7;+0;!D1:3]>>[*][C:1]=[O:2].[*][#7:3]"
, "[C:1](=!@[O:2])!@[O;+0:3]>>[*][C:1]=[O:2].[O:3][*]", "[N;!D1;+0;!$(
N-C=[#7,#8,#15,#16])](-!@[*:1])-!@[*:2]>>[*][*:1].[*:2][*]", "[#7;R;D3
;+0:1]-!@[*:2]>>[*][#7:1].[*:2][*]", "[#6:1]-!@[O;+0]-!@[#6:2]>>[#6:1]
[*].[*][#6:2]", "[C:1]=!@[C:2]>>[C:1][*].[*][C:2]", "[n;+0:1]-!@[C:2]>
>[n:1][*].[C:2][*]", "[O:3]=[C:4]-@[N;+0:1]-!@[C:2]>>[O:3]=[C:4]-[N:1]
[*].[C:2][*]", "[c:1]-!@[c:2]>>[c:1][*].[*][c:2]", "[n;+0:1]-!@[c:2]>>
...

reactions

Value:

tuple([Reactions.ReactionFromSmarts(x) for x in reactionDefs])