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GenericGroups.h
Go to the documentation of this file.
//
// Copyright (C) 2021-2023 Greg Landrum and RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/MolOps.h>
#ifndef RD_GENERICGROUPS_H
#define RD_GENERICGROUPS_H
#include <vector>
#include <functional>
#include <map>
#include <boost/dynamic_bitset.hpp>
namespace RDKit {
class ROMol;
class Atom;
class Bond;
namespace GenericGroups {
// We'd like to be able to correctly interpret what's written by Marvin and
// MarvinJS, so the conditions for these are adapted from the ChemAxon
// documentation for homology groups
// (https://docs.chemaxon.com/display/docs/homology-groups.md)
//
// If I had questions about what the queries should do, I ran example in Reaxys
// with MarvinJS as the sketcher to see what that returns.
//
// I've tried to document deviations or surprises
namespace Matchers {
//! Matches any group as a side chain
/*!
Note: this is Reaxys query type G and matches any sidechain
Conditions:
- at least one non-hydrogen atom is in the sidechain
*/
RDKIT_GENERICGROUPS_EXPORT bool GroupAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches any group as a side chain including just an H atom
/*!
Note: this is Reaxys query type GH and matches any sidechain
Conditions:
- none
*/
RDKIT_GENERICGROUPS_EXPORT bool GroupHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches any group as a side chain
/*!
Note: this is Reaxys query type G* and matches any sidechain that has a ring
closure
Conditions:
- at least one non-hydrogen atom is in the sidechain
- at least one ring closure
*/
RDKIT_GENERICGROUPS_EXPORT bool GroupStarAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches any group as a side chain that has a ring closure or just an H atom
/*!
Note: this is Reaxys query type GH* and matches any sidechains
Conditions:
- at least one ring closure
- OR
- the entire group is just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool GroupStarHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkyl side chains
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- at least one carbon is present
- all bonds are single
- no ring bonds
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkyl side chains or an H atom
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- all bonds are single
- no ring bonds
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkenyl side chains
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- contains at least one C=C
- no ring bonds
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkenylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkenyl side chains or an H
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- contains at least one C=C
- no ring bonds
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkenylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkynyl side chains
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- contains at least one C#C
- no ring bonds
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkynylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches alkynyl side chains or an H
/*!
Conditions:
- side chain consists entirely of carbon or hydrogen
- contains at least one C#C
- no ring bonds
- OR
- the whole group is an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkynylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches carbocyclic side chains
/*!
Note: this is Reaxys query type CBC and matches carbocycles
Conditions:
- atom is in at least one ring composed entirely of carbon
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches carbocyclic side chains or an H atom
/*!
Note: this is Reaxys query type CBC and matches carbocycles
Conditions:
- atom is in at least one ring composed entirely of carbon
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules
- OR the entire group is just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cycloalkyl side chains
/*!
Note: this is Reaxys query type CAL and is directly equivalent to alkyl,
except the immediate atom needs to be in a ring.
Conditions:
- atom is in at least one ring composed entirely of carbon and connected
with single bonds
- atoms in the ring do not have unsaturations (including exocyclic)
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules (i.e. all
single bonds)
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cycloalkyl side chains or an H atom
/*!
Note: this is Reaxys query type CAL and is directly equivalent to alkyl,
except the immediate atom needs to be in a ring.
Conditions:
- atom is in at least one ring composed entirely of carbon and connected
with single bonds
- atoms in the ring do not have unsaturations (including exocyclic)
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules (i.e. all
single bonds)
- OR
- the whole group is an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cycloalkenyl side chains
/*!
Note: this is Reaxys query type CEL and matches carbocycles which have at
least one double or aromatic bond.
Conditions:
- atom is in at least one ring composed entirely of carbon and with at least
one double or aromatic bond
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules (including
that each ring must have at least one double or aromatic bond)
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cycloalkenyl side chains or an H atom
/*!
Note: this is Reaxys query type CEL and matches carbocycles which have at
least one double or aromatic bond.
Conditions:
- atom is in at least one ring composed entirely of carbon and with at least
one double or aromatic bond
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules (including
that each ring must have at least one double or aromatic bond)
*/
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches heterocyclic side chains
/*!
Note: this is Reaxys query type CHC and matches heterocycles
Conditions:
- atom is in at least one fused ring with a heteroatom
*/
RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches heterocyclic side chains or an H atom
/*!
Note: this is Reaxys query type CHH and matches heterocycles or an H atom
Conditions:
- atom is in at least one fused ring with a heteroatom
- or the entire group is a single H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches aryl side chains
/*!
Note: this is Reaxys query type ARY and matches carbocycles which are aromatic
Conditions:
- atom is in at least one aromatic ring composed entirely of carbon
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules
*/
RDKIT_GENERICGROUPS_EXPORT bool CarboarylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches aryl side chains or an H atom
/*!
Note: this is Reaxys query type ARH and matches carbocycles which are aromatic
or an H atom
Conditions:
- atom is in at least one aromatic ring composed entirely of carbon
- atom is not in any rings not compatible with the above conditions
- additional fused rings in the system must obey the same rules
*/
RDKIT_GENERICGROUPS_EXPORT bool CarboarylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches heteroaryl side chains
/*!
Note: this is Reaxys query type HAR and matches aromatic heterocycles
Conditions:
- atom is in at least one fused aromatic sytem with a heteroatom
*/
RDKIT_GENERICGROUPS_EXPORT bool HeteroarylAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches heteroaryl side chains or an H atom
/*!
Note: this is Reaxys query type HAR and matches aromatic heterocycles
Conditions:
- atom is in at least one fused aromatic sytem with a heteroatom
- or the entire group is an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool HeteroarylHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cyclic side chains
/*!
Note: this is Reaxys query type CYC and matches cycles
Conditions:
- atom is in at least one ring
*/
RDKIT_GENERICGROUPS_EXPORT bool CyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches cyclic side chains or an H atom
/*!
Note: this is Reaxys query type CYH and matches cycles
Conditions:
- atom is in at least one ring
- or the entire group is just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool CyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches acyclic side chains
/*!
Note: this is Reaxys query type ACY and matches sidechains with no cycles
Conditions:
- no atom in the sidechain is in a ring and the group is NOT just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool AcyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches acyclic side chains or an H atom
/*!
Note: this is Reaxys query type ACY and matches sidechains with no cycles
Conditions:
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool AcyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches all-carbon acyclic side chains
/*!
Note: this is Reaxys query type ABC and matches all-carbon sidechains with no
cycles
Conditions:
- all atoms in the sidechain are carbon
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches all-carbon acyclic side chainsor or an H atom
/*!
Note: this is Reaxys query type ABH and matches all-carbon sidechains with no
cycles or just a H atom
Conditions:
- all atoms in the sidechain are carbon or H
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches acyclic side chains with at least one heteroatom
/*!
Note: this is Reaxys query type AHC and matches sidechains with no cycles and
at least one heteroatom
Conditions:
- at least one non-carbon, non-hydrogen atom is in the sidechain
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches acyclic side chains with at least one heteroatom or an H atom
/*!
Note: this is Reaxys query type AHC and matches sidechains with no cycles and
at least one heteroatom
Conditions:
- at least one non-carbon, non-hydrogen atom is in the sidechain
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches acyclic alkoxy side chains
/*!
Note: this is Reaxys query type AOX and matches alkoxy sidechains
Conditions:
- first atom is an O
- all other atoms are C
- all single bonds
- no atom in the sidechain is in a ring
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
/*!
Note: this is Reaxys query type AOH and matches alkoxy sidechains or a hydrogen
Conditions:
- first atom is an O
- all other atoms are C
- all single bonds
- no atom in the sidechain is in a ring
- OR
- the whole group is just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches rings without carbon
/*!
Note: this is Reaxys query type CXX and matches rings which contain no carbon
Conditions:
- a ring is present
- none of the atoms in the fused ring system are carbon
*/
RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
//! Matches rings without carbon or just an H
/*!
Note: this is Reaxys query type CXH and matches rings which contain no carbon
Conditions:
- a ring is present
- none of the atoms in the fused ring system are carbon
- OR
- the entire group is just an H atom
*/
RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingHAtomMatcher(
const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore);
} // namespace Matchers
const static std::map<
std::string,
std::function<bool(const ROMol &, const Atom &, boost::dynamic_bitset<>)>>
genericMatchers = {
{"Group", Matchers::GroupAtomMatcher},
{"G", Matchers::GroupAtomMatcher},
{"GroupH", Matchers::GroupHAtomMatcher},
{"GH", Matchers::GroupHAtomMatcher},
{"Group*", Matchers::GroupStarAtomMatcher},
{"G*", Matchers::GroupStarAtomMatcher},
{"GroupH*", Matchers::GroupStarHAtomMatcher},
{"GH*", Matchers::GroupStarHAtomMatcher},
{"Alkyl", Matchers::AlkylAtomMatcher},
{"ALK", Matchers::AlkylAtomMatcher},
{"AlkylH", Matchers::AlkylHAtomMatcher},
{"ALH", Matchers::AlkylHAtomMatcher},
{"Alkenyl", Matchers::AlkenylAtomMatcher},
{"AEL", Matchers::AlkenylAtomMatcher},
{"AlkenylH", Matchers::AlkenylHAtomMatcher},
{"AEH", Matchers::AlkenylHAtomMatcher},
{"Alkynyl", Matchers::AlkynylAtomMatcher},
{"AYL", Matchers::AlkynylAtomMatcher},
{"AlkynylH", Matchers::AlkynylHAtomMatcher},
{"AYH", Matchers::AlkynylHAtomMatcher},
{"Carbocyclic", Matchers::CarbocyclicAtomMatcher},
{"CBC", Matchers::CarbocyclicAtomMatcher},
{"CarbocyclicH", Matchers::CarbocyclicHAtomMatcher},
{"CBH", Matchers::CarbocyclicHAtomMatcher},
{"Carbocycloalkyl", Matchers::CarbocycloalkylAtomMatcher},
{"CAL", Matchers::CarbocycloalkylAtomMatcher},
{"CarbocycloalkylH", Matchers::CarbocycloalkylHAtomMatcher},
{"CAH", Matchers::CarbocycloalkylHAtomMatcher},
{"Carbocycloalkenyl", Matchers::CarbocycloalkenylAtomMatcher},
{"CEL", Matchers::CarbocycloalkenylAtomMatcher},
{"CarbocycloalkenylH", Matchers::CarbocycloalkenylHAtomMatcher},
{"CEH", Matchers::CarbocycloalkenylHAtomMatcher},
{"Carboaryl", Matchers::CarboarylAtomMatcher},
{"ARY", Matchers::CarboarylAtomMatcher},
{"CarboarylH", Matchers::CarboarylHAtomMatcher},
{"ARH", Matchers::CarboarylHAtomMatcher},
{"Cyclic", Matchers::CyclicAtomMatcher},
{"CYC", Matchers::CyclicAtomMatcher},
{"CyclicH", Matchers::CyclicHAtomMatcher},
{"CYH", Matchers::CyclicHAtomMatcher},
{"Acyclic", Matchers::AcyclicAtomMatcher},
{"ACY", Matchers::AcyclicAtomMatcher},
{"AcyclicH", Matchers::AcyclicHAtomMatcher},
{"ACH", Matchers::AcyclicHAtomMatcher},
{"Carboacyclic", Matchers::CarboacyclicAtomMatcher},
{"ABC", Matchers::CarboacyclicAtomMatcher},
{"CarboacyclicH", Matchers::CarboacyclicHAtomMatcher},
{"ABH", Matchers::CarboacyclicHAtomMatcher},
{"Heteroacyclic", Matchers::HeteroacyclicAtomMatcher},
{"AHC", Matchers::HeteroacyclicAtomMatcher},
{"HeteroacyclicH", Matchers::HeteroacyclicHAtomMatcher},
{"AHH", Matchers::HeteroacyclicHAtomMatcher},
{"Alkoxy", Matchers::AlkoxyacyclicAtomMatcher},
{"AOX", Matchers::AlkoxyacyclicAtomMatcher},
{"AlkoxyH", Matchers::AlkoxyacyclicHAtomMatcher},
{"AOH", Matchers::AlkoxyacyclicHAtomMatcher},
{"Heterocyclic", Matchers::HeterocyclicAtomMatcher},
{"CHC", Matchers::HeterocyclicAtomMatcher},
{"HeterocyclicH", Matchers::HeterocyclicHAtomMatcher},
{"CHH", Matchers::HeterocyclicHAtomMatcher},
{"Heteroaryl", Matchers::HeteroarylAtomMatcher},
{"HAR", Matchers::HeteroarylAtomMatcher},
{"HeteroarylH", Matchers::HeteroarylHAtomMatcher},
{"HAH", Matchers::HeteroarylHAtomMatcher},
{"NoCarbonRing", Matchers::NoCarbonRingAtomMatcher},
{"CXX", Matchers::NoCarbonRingAtomMatcher},
{"NoCarbonRingH", Matchers::NoCarbonRingHAtomMatcher},
{"CXH", Matchers::NoCarbonRingHAtomMatcher}
};
// This is an extension of adjustQueryProperties from GraphMol that allows the search of generic groups
RDKIT_GENERICGROUPS_EXPORT ROMol *adjustQueryPropertiesWithGenericGroups(
const ROMol &mol,
const MolOps::AdjustQueryParameters *inParams=nullptr);
//! returns false if any of the molecule's generic atoms are not satisfied in
/// the current match
RDKIT_GENERICGROUPS_EXPORT bool genericAtomMatcher(
const ROMol &mol, const ROMol &query,
const std::vector<unsigned int> &match);
//! sets the apropriate generic query tags based on atom labels and/or SGroups
/*
- Generic query tags found in the atom labels/SGroups will be overwrite existing
generic query tags (if there are any present).
- only SUP SGroups are considered
- Any atom labels or SGroups which are converted will be removed
- If both atom labels and SGroups are being used and an atom has generic
query tags in both, the one from the SGroup will be used.
- Generic query tags not found in GenericGroups::genericMatchers will be ignored
*/
RDKIT_GENERICGROUPS_EXPORT void setGenericQueriesFromProperties(
ROMol &mol, bool useAtomLabels = true, bool useSGroups = true);
RDKIT_GENERICGROUPS_EXPORT void convertGenericQueriesToSubstanceGroups(
ROMol &mol);
} // namespace GenericGroups
} // namespace RDKit
#endif
MolOps.h
RWMol.h
Defines the editable molecule class RWMol.
RDKit::Atom
The class for representing atoms.
Definition Atom.h:68
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_GENERICGROUPS_EXPORT
#define RDKIT_GENERICGROUPS_EXPORT
Definition export.h:225
RDKit::GenericGroups::Matchers::CarboacyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches all-carbon acyclic side chainsor or an H atom.
RDKit::GenericGroups::Matchers::CyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cyclic side chains.
RDKit::GenericGroups::Matchers::GroupStarHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool GroupStarHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches any group as a side chain that has a ring closure or just an H atom.
RDKit::GenericGroups::Matchers::AlkylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkyl side chains.
RDKit::GenericGroups::Matchers::AcyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AcyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches acyclic side chains or an H atom.
RDKit::GenericGroups::Matchers::AlkenylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkenylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkenyl side chains or an H.
RDKit::GenericGroups::Matchers::NoCarbonRingHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches rings without carbon or just an H.
RDKit::GenericGroups::Matchers::HeteroarylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeteroarylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches heteroaryl side chains or an H atom.
RDKit::GenericGroups::Matchers::GroupHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool GroupHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches any group as a side chain including just an H atom.
RDKit::GenericGroups::Matchers::CarbocycloalkylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cycloalkyl side chains or an H atom.
RDKit::GenericGroups::Matchers::CarbocycloalkylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cycloalkyl side chains.
RDKit::GenericGroups::Matchers::HeteroacyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches acyclic side chains with at least one heteroatom.
RDKit::GenericGroups::Matchers::GroupStarAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool GroupStarAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches any group as a side chain.
RDKit::GenericGroups::Matchers::CyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cyclic side chains or an H atom.
RDKit::GenericGroups::Matchers::HeterocyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches heterocyclic side chains.
RDKit::GenericGroups::Matchers::CarbocyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches carbocyclic side chains.
RDKit::GenericGroups::Matchers::HeteroacyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeteroacyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches acyclic side chains with at least one heteroatom or an H atom.
RDKit::GenericGroups::Matchers::CarbocycloalkenylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cycloalkenyl side chains or an H atom.
RDKit::GenericGroups::Matchers::AcyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AcyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches acyclic side chains.
RDKit::GenericGroups::Matchers::HeterocyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches heterocyclic side chains or an H atom.
RDKit::GenericGroups::Matchers::AlkynylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkynylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkynyl side chains.
RDKit::GenericGroups::Matchers::AlkoxyacyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
RDKit::GenericGroups::Matchers::CarbocycloalkenylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches cycloalkenyl side chains.
RDKit::GenericGroups::Matchers::AlkynylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkynylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkynyl side chains or an H.
RDKit::GenericGroups::Matchers::CarboarylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarboarylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches aryl side chains or an H atom.
RDKit::GenericGroups::Matchers::NoCarbonRingAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches rings without carbon.
RDKit::GenericGroups::Matchers::CarboacyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarboacyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches all-carbon acyclic side chains.
RDKit::GenericGroups::Matchers::GroupAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool GroupAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches any group as a side chain.
RDKit::GenericGroups::Matchers::HeteroarylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool HeteroarylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches heteroaryl side chains.
RDKit::GenericGroups::Matchers::CarbocyclicHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches carbocyclic side chains or an H atom.
RDKit::GenericGroups::Matchers::AlkoxyacyclicAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches acyclic alkoxy side chains.
RDKit::GenericGroups::Matchers::AlkenylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkenylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkenyl side chains.
RDKit::GenericGroups::Matchers::AlkylHAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool AlkylHAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches alkyl side chains or an H atom.
RDKit::GenericGroups::Matchers::CarboarylAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool CarboarylAtomMatcher(const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
Matches aryl side chains.
RDKit::GenericGroups::adjustQueryPropertiesWithGenericGroups
RDKIT_GENERICGROUPS_EXPORT ROMol * adjustQueryPropertiesWithGenericGroups(const ROMol &mol, const MolOps::AdjustQueryParameters *inParams=nullptr)
RDKit::GenericGroups::genericAtomMatcher
RDKIT_GENERICGROUPS_EXPORT bool genericAtomMatcher(const ROMol &mol, const ROMol &query, const std::vector< unsigned int > &match)
RDKit::GenericGroups::setGenericQueriesFromProperties
RDKIT_GENERICGROUPS_EXPORT void setGenericQueriesFromProperties(ROMol &mol, bool useAtomLabels=true, bool useSGroups=true)
sets the apropriate generic query tags based on atom labels and/or SGroups
RDKit::GenericGroups::genericMatchers
static const std::map< std::string, std::function< bool(const ROMol &, const Atom &, boost::dynamic_bitset<>)> > genericMatchers
Definition GenericGroups.h:527
RDKit::GenericGroups::convertGenericQueriesToSubstanceGroups
RDKIT_GENERICGROUPS_EXPORT void convertGenericQueriesToSubstanceGroups(ROMol &mol)
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372
RDKit::MolOps::AdjustQueryParameters
Parameters controlling the behavior of MolOps::adjustQueryProperties.
Definition MolOps.h:343