RDKit::GenericGroups::Matchers Namespace Reference

Functions
RDKIT_GENERICGROUPS_EXPORT bool	GroupAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches any group as a side chain.
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_EXPORT bool	GroupStarAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches any group as a side chain.
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_EXPORT bool	AlkylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches alkyl side chains.
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_EXPORT bool	AlkenylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches alkenyl side chains.
RDKIT_GENERICGROUPS_EXPORT bool	AlkenylHAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches alkenyl side chains or an H.
RDKIT_GENERICGROUPS_EXPORT bool	AlkynylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches alkynyl side chains.
RDKIT_GENERICGROUPS_EXPORT bool	AlkynylHAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches alkynyl side chains or an H.
RDKIT_GENERICGROUPS_EXPORT bool	CarbocyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches carbocyclic side chains.
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_EXPORT bool	CarbocycloalkylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches cycloalkyl side chains.
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_EXPORT bool	CarbocycloalkenylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches cycloalkenyl side chains.
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_EXPORT bool	HeterocyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches heterocyclic side chains.
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_EXPORT bool	CarboarylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches aryl side chains.
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_EXPORT bool	HeteroarylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches heteroaryl side chains.
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_EXPORT bool	CyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches cyclic side chains.
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_EXPORT bool	AcyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches acyclic side chains.
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_EXPORT bool	CarboacyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches all-carbon acyclic side chains.
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_EXPORT bool	HeteroacyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches acyclic side chains with at least one heteroatom.
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_EXPORT bool	AlkoxyacyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches acyclic alkoxy side chains.
RDKIT_GENERICGROUPS_EXPORT bool	AlkoxyacyclicHAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
RDKIT_GENERICGROUPS_EXPORT bool	NoCarbonRingAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches rings without carbon.
RDKIT_GENERICGROUPS_EXPORT bool	NoCarbonRingHAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
	Matches rings without carbon or just an H.

Function Documentation

AcyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AcyclicAtomMatcher	(	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

AcyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AcyclicHAtomMatcher	(	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

AlkenylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkenylAtomMatcher	(	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

AlkenylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkenylHAtomMatcher	(	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

AlkoxyacyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkoxyacyclicAtomMatcher	(	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

AlkoxyacyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkoxyacyclicHAtomMatcher	(	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

AlkylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkylAtomMatcher	(	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

AlkylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkylHAtomMatcher	(	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

AlkynylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkynylAtomMatcher	(	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

AlkynylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::AlkynylHAtomMatcher	(	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

CarboacyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarboacyclicAtomMatcher	(	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

CarboacyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarboacyclicHAtomMatcher	(	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

CarboarylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarboarylAtomMatcher	(	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

CarboarylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarboarylHAtomMatcher	(	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

CarbocyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocyclicAtomMatcher	(	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

CarbocyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocyclicHAtomMatcher	(	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

CarbocycloalkenylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocycloalkenylAtomMatcher	(	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)

CarbocycloalkenylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocycloalkenylHAtomMatcher	(	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)

CarbocycloalkylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocycloalkylAtomMatcher	(	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)

CarbocycloalkylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CarbocycloalkylHAtomMatcher	(	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

CyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CyclicAtomMatcher	(	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

CyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::CyclicHAtomMatcher	(	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

GroupAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::GroupAtomMatcher	(	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

Conditions:

• at least one non-hydrogen atom is in the sidechain

GroupHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::GroupHAtomMatcher	(	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

GroupStarAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::GroupStarAtomMatcher	(	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

GroupStarHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::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.

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

HeteroacyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeteroacyclicAtomMatcher	(	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

HeteroacyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeteroacyclicHAtomMatcher	(	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

HeteroarylAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeteroarylAtomMatcher	(	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

HeteroarylHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeteroarylHAtomMatcher	(	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

HeterocyclicAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeterocyclicAtomMatcher	(	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

HeterocyclicHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::HeterocyclicHAtomMatcher	(	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

NoCarbonRingAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::NoCarbonRingAtomMatcher	(	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

NoCarbonRingHAtomMatcher()

RDKIT_GENERICGROUPS_EXPORT bool RDKit::GenericGroups::Matchers::NoCarbonRingHAtomMatcher	(	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