rdkit.Chem.Scaffolds.rdScaffoldNetwork module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Scaffolds.rdScaffoldNetwork module

Module containing functions for creating a Scaffold Network

rdkit.Chem.Scaffolds.rdScaffoldNetwork.BRICSScaffoldParams() → ScaffoldNetworkParams :

  Returns parameters for generating scaffolds using BRICS fragmentation rules

  C++ signature :

    RDKit::ScaffoldNetwork::ScaffoldNetworkParams* BRICSScaffoldParams()

rdkit.Chem.Scaffolds.rdScaffoldNetwork.CreateScaffoldNetwork((object)mols, (ScaffoldNetworkParams)params) → ScaffoldNetwork :

  create (and return) a new network from a sequence of molecules

  C++ signature :

    RDKit::ScaffoldNetwork::ScaffoldNetwork* CreateScaffoldNetwork(boost::python::api::object,RDKit::ScaffoldNetwork::ScaffoldNetworkParams)

class rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType

  Bases: `enum`

  Fragment = rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Fragment
  Generic = rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Generic
  GenericBond = rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.GenericBond
  Initialize = rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Initialize
  RemoveAttachment = rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.RemoveAttachment
  names = {'Fragment': rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Fragment, 'Generic': rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Generic, 'GenericBond': rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.GenericBond, 'Initialize': rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Initialize, 'RemoveAttachment': rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.RemoveAttachment}
  values = {1: rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Fragment, 2: rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Generic, 3: rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.GenericBond, 4: rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.RemoveAttachment, 5: rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType.Initialize}

class rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge

  Bases: `instance`

  A scaffold network edge

  Raises an exception This class cannot be instantiated from Python

  property beginIdx

    index of the begin node in node list

  property endIdx

    index of the end node in node list

  property type

    type of the edge

class rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge_VECT((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  append((NetworkEdge_VECT)arg1, (object)arg2) → None :
    C++ signature :

      void append(std::vector<RDKit::ScaffoldNetwork::NetworkEdge, std::allocator<RDKit::ScaffoldNetwork::NetworkEdge> > {lvalue},boost::python::api::object)

  extend((NetworkEdge_VECT)arg1, (object)arg2) → None :
    C++ signature :

      void extend(std::vector<RDKit::ScaffoldNetwork::NetworkEdge, std::allocator<RDKit::ScaffoldNetwork::NetworkEdge> > {lvalue},boost::python::api::object)

class rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetwork((object)self) → None :

  Bases: `instance`

  A scaffold network

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (str)pkl) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  property counts

    the number of times each node was encountered while building the network.

  property edges

    the sequence of network edges

  property molCounts

    the number of moleclues each node was found in.

  property nodes

    the sequence of SMILES defining the nodes

class rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams((object)self) → None :

  Bases: `instance`

  Scaffold network parameters

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE)bondBreakerSmartsList) -> None :

    Constructor taking a list of Reaction SMARTS for the fragmentation reactions

    C++ signature :

      void __init__(_object*,std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)

  property collectMolCounts

    keep track of the number of molecules each scaffold was found in

  property flattenChirality

    remove chirality and bond stereo when flattening

  property flattenIsotopes

    remove isotopes when flattening

  property flattenKeepLargest

    keep only the largest fragment when doing flattening

  property includeGenericBondScaffolds

    include scaffolds with all bonds replaced by single bonds

  property includeGenericScaffolds

    include scaffolds with all atoms replaced by dummies

  property includeNames

    Include molecules names of the input molecules

  property includeScaffoldsWithAttachments

    Include the version of the scaffold with attachment points

  property includeScaffoldsWithoutAttachments

    remove attachment points from scaffolds and include the result

  property keepOnlyFirstFragment

    keep only the first fragment from the bond breaking rule

  property pruneBeforeFragmenting

    Do a pruning/flattening step before starting fragmenting

rdkit.Chem.Scaffolds.rdScaffoldNetwork.UpdateScaffoldNetwork((object)mols, (ScaffoldNetwork)network, (ScaffoldNetworkParams)params) → None :

  update an existing network by adding molecules

  C++ signature :

    void UpdateScaffoldNetwork(boost::python::api::object,RDKit::ScaffoldNetwork::ScaffoldNetwork {lvalue},RDKit::ScaffoldNetwork::ScaffoldNetworkParams)