RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
RDKit::GenericGroups::Matchers Namespace Reference

Functions

RDKIT_GENERICGROUPS_EXPORT bool AlkylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches alkyl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool AlkenylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches alkenyl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool AlkynylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches alkynyl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool CarbocyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches carbocyclic side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches cycloalkyl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool CarbocycloalkenylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches cycloalkenyl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool HeterocyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches heterocyclic side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool CarboarylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches aryl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool HeteroarylAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches heteroaryl side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool CyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches cyclic side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool AcyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches acyclic side chains.
 
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 HeteroacyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches acyclic side chains with at least one heteroatom.
 
RDKIT_GENERICGROUPS_EXPORT bool AlkoxyacyclicAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches acyclic alkoxy side chains.
 
RDKIT_GENERICGROUPS_EXPORT bool NoCarbonRingAtomMatcher (const ROMol &mol, const Atom &atom, boost::dynamic_bitset<> ignore)
 Matches rings without carbon.
 

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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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)

◆ 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)

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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