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((AtomPairsParameters)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)

Bases: instance

C++ signature :

void __init__(_object*)

append((NetworkEdge_VECT)arg1, (AtomPairsParameters)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, (AtomPairsParameters)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)

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)

Bases: instance

Scaffold network parameters

C++ signature :

void __init__(_object*)

__init__( (object)self, (_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 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((AtomPairsParameters)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)