OEFPAtomType

This namespace contains atom typing options that can be used when generating Circular, Path of Tree fingerprints. Atom type options control how the atoms of the enumerated circular, path or tree fragments are encoded during the fingerprint generation.

The OEFPAtomType namespace contains the following constants:

Constant name	Combination of
OEFPAtomType_Aromaticity
OEFPAtomType_AtomicNumber
OEFPAtomType_Chiral
OEFPAtomType_DefaultAtom	DefaultPathAtom
DefaultCircularAtom	AtomicNumber | Aromaticity | Chiral | FormalCharge | HCount | EqHalogen
OEFPAtomType_DefaultCircularVSAtom	AtomicNumber | Aromaticity | Chiral | HCount | EqHalogen
DefaultPathAtom	AtomicNumber | Aromaticity | Chiral | FormalCharge | HvyDegree | Hybridization | EqHalogen
OEFPAtomType_DefaultPathVSAtom	AtomicNumber | Aromaticity | Chiral | HvyDegree | EqHalogen
DefaultTreeAtom	AtomicNumber | Aromaticity | Chiral | FormalCharge | HvyDegree | Hybridization
OEFPAtomType_DefaultTreeVSAtom	AtomicNumber | Aromaticity | Chiral | HvyDegree
OEFPAtomType_EqAromatic
OEFPAtomType_EqHalogen
OEFPAtomType_EqHBondAcceptor
OEFPAtomType_EqHBondDonor
OEFPAtomType_FormalCharge
OEFPAtomType_HCount
OEFPAtomType_HvyDegree
OEFPAtomType_Hybridization
OEFPAtomType_InRing
OEFPAtomType_None

Note

The constants of the OEFPAtomType namespace can be combined using the bitwise OR operation.

Note

The images in this sections visualize the effect of the various atom typing options.

See also

• Visualizing Molecule Similarity section

See also

• OEFPBondType namespace

• OEMakeCircularFP function

• OEMakePathFP function

• OEMakeTreeFP function

• Atom and Bond Typing section

Note

All explicit hydrogens are suppressed of the molecule before generating any fingerprints. (See example in Example of molecules that are considered to be equivalent due to suppressing their explicit hydrogens).

Example of molecules that are considered to be equivalent due to suppressing their explicit hydrogens

AtomicNumber

This flag indicates that atomic number (the value returned by the OEAtomBase.GetAtomicNum method) is encoded into the generated fingerprint, i.e., if two fragments (either circular, paths or tree) are composed of atoms with different atomic numbers, then the two fragments will be mapped to different bits of the fingerprint. Table: Example of using the AtomicNumber option demonstrates the effect of using the OEFPAtomType_AtomicNumber flag.

Example of using the OEFPAtomType_AtomicNumber option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

Aromaticity

This flag indicates that aromaticity (the value returned by the OEAtomBase.IsAromatic method) is encoded into the generated fingerprint, i.e., an aromatic and an aliphatic fragment will be mapped to different bits of the fingerprint. Table: Example of using the Aromatic option demonstrates the effect of using the OEFPAtomType_Aromaticity flag.

Example of using the OEFPAtomType_Aromaticity option (Path, numbits=4096, bonds=0-5, bond typing = InRing).

Note

Prior to generating a fingerprint, the aromaticity of the molecule is re-perceived using the OEAroModel_OpenEye aromaticity model.

Chiral

This flag indicates that chiral and non-chiral atoms (the value returned by the OEAtomBase.IsChiral method) are distinguished during the fingerprint generation. Table: Example of using the Chiral option demonstrates the effect of using the OEFPAtomType_Chiral flag.

Example of using the OEFPAtomType_Chiral option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

Note

Different stereoisomers of molecules can not be distinguished when the OEFPAtomType_Chiral flag is set. (See example in Figure: Example of molecule similarity of stereoisomers).

Example of molecule similarity of stereoisomers

FormalCharge

This flag indicates that formal charge (the value returned by the OEAtomBase.GetFormalCharge method) is encoded into the generated fingerprint. Table: Example of using the FormalCharge option demonstrates the effect of using the OEFPAtomType_FormalCharge flag.

Example of using the OEFPAtomType_FormalCharge option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

HvyDegree

This flag indicates that heavy degree information (the value returned by the OEAtomBase.GetHvyDegree method) is encoded into the generated fingerprint. Table: Example of using the HvyDegree option demonstrates the effect of using the OEFPAtomType_HvyDegree flag.

Example of using the OEFPAtomType_FormalCharge option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

HCount

This flag indicates that number of hydrogens (the value returned by the OEAtomBase.GetTotalHCount method) is encoded into the generated fingerprint. Table: Example of using the HCount option demonstrates the effect of using the OEFPAtomType_HCount flag.

Example of using the OEFPAtomType_HCount option (Path, numbits=4096, bonds=0-5, bond typing = InRing).

Hybridization

This flag indicates that hybridization (the value returned by the OEAtomBase.GetHyb method) is encoded into the generated fingerprint. Table: Example of using the Hybridization option demonstrates the effect of using the OEFPAtomType_Hybridization flag.

Example of using the OEFPAtomType_Hybridization option (Path, numbits=4096, bonds=0-5, bond typing = InRing).

InRing

This flag indicates that atom topology (the value returned by the OEAtomBase.IsInRing method) is encoded into the generated fingerprint, i.e., if two fragments (either circular, path or tree) are composed of atoms with different atom topology, then the two fragments will be mapped to different bits of the fingerprint. Table: Example of using the InRing option demonstrates the effect of using the OEFPAtomType_InRing flag.

Example of using the OEFPAtomType_InRing option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

EqAromatic

This flag modifies the meaning of the OEFPAtomType_AtomicNumber flag. If the OEFPAtomType_EqAromatic flag is set then aromatic atoms are considered equivalent during the fingerprint generation. Table: Example of using the EqAromatic option demonstrates the effect of using the OEFPAtomType_EqAromatic flag.

Example of using the OEFPAtomType_EqAromatic option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

EqHalogen

This flag modifies the meaning of OEFPAtomType_AtomicNumber flag. If the OEFPAtomType_EqHalogen flag is set then halide atoms (OEElemNo_F, OEElemNo_Cl, OEElemNo_Br, and OEElemNo_I) are considered equivalent during the fingerprint generation. Table: Example of using the EqHalogen option demonstrates the effect of using the OEFPAtomType_EqHalogen flag.

Example of using the OEFPAtomType_EqHalogen option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

EqHBondAcceptor

This flag modifies the meaning of the OEFPAtomType_AtomicNumber flag. If the OEFPAtomType_EqHBondAcceptor flag is set then atoms that are perceived as hydrogen bonding acceptors are considered equivalent during the fingerprint generation. The GraphSim TK uses the same definition as the MolProp TK to identify hydrogen bond acceptors. See examples in Figure: Molecules with hydrogen bond acceptor annotation. Table: Example of using the EqHBondAcceptor option demonstrates the effect of using the OEFPAtomType_EqHBondAcceptor flag.

Example of molecules with hydrogen bond acceptor annotation

Example of using the OEFPAtomType_EqHBondAcceptor option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

EqHBondDonor

This flag modifies the meaning of the OEFPAtomType_AtomicNumber flag. If the OEFPAtomType_EqHBondDonor flag is set then atoms that are perceived as hydrogen bonding donors are considered equivalent during the fingerprint generation. The GraphSim TK uses the same definition as the MolProp TK to identify hydrogen bond donors. See examples in Figure: Molecules with hydrogen bond donor annotation. Table: Example of using the EqHBondDonor option demonstrates the effect of using the OEFPAtomType_EqHBondDonor flag.

Molecules with hydrogen bond donor annotation

Example of using the OEFPAtomType_EqHBondDonor option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).

DefaultAtom

Same as DefaultPathAtom constant.

DefaultCircularAtom

The bitwise OR’d value of the following atom typing options:

• OEFPAtomType_AtomicNumber

• OEFPAtomType_Aromaticity

• OEFPAtomType_Chiral

• OEFPAtomType_FormalCharge

• OEFPAtomType_HCount

• OEFPAtomType_EqHalogen

See example in Figure: Circular fingerprint similarity with default circular atom and bond typing. This constant is used as atom typing parameter when a default Circular fingerprint is generated by the following functions:

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType_Circular)

• OEMakeCircularFP (OEFingerPrint &, const OEMolBase &)

See also

• OEFPBondType_DefaultCircularBond constant

Circular fingerprint similarity with default circular atom and bond typing

DefaultCircularVSAtom

The default atom typing for the circular fingerprint that is designed for virtual screening. It is the same as DefaultCircularAtom without OEFPAtomType_FormalCharge.

DefaultPathAtom

The bitwise OR’d value of the following atom typing options:

• OEFPAtomType_AtomicNumber

• OEFPAtomType_Aromaticity

• OEFPAtomType_Chiral

• OEFPAtomType_FormalCharge

• OEFPAtomType_HvyDegree

• OEFPAtomType_Hybridization

• OEFPAtomType_EqHalogen

See example in Figure: Path fingerprint similarity with default path atom and bond typing. This constant is used as atom typing parameter when a default Path fingerprint is generated by the following functions:

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType_Path)

• OEMakePathFP (OEFingerPrint &, const OEMolBase &)

See also

• OEFPBondType_DefaultPathBond constant

Path fingerprint similarity with default path atom and bond typing

DefaultPathVSAtom

The default atom typing for the path fingerprint that is designed for virtual screening. It is the same as DefaultPathAtom without OEFPAtomType_FormalCharge and OEFPAtomType_Hybridization.

DefaultTreeAtom

The bitwise OR’d value of the following atom typing options:

• OEFPAtomType_AtomicNumber

• OEFPAtomType_Aromaticity

• OEFPAtomType_Chiral

• OEFPAtomType_FormalCharge

• OEFPAtomType_HvyDegree

• OEFPAtomType_Hybridization

See example in Figure: Tree fingerprint similarity with default tree atom and bond typing. This constant is used as atom typing parameter when a default Tree fingerprint is generated by the following functions:

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType_Tree)

• OEMakeTreeFP (OEFingerPrint &, const OEMolBase &)

See also

• OEFPBondType_DefaultTreeBond constant

Tree fingerprint similarity with default tree atom and bond typing

DefaultTreeVSAtom

The default atom typing for the tree fingerprint that is designed for virtual screening. It is the same as DefaultTreeAtom without OEFPAtomType_FormalCharge and OEFPAtomType_Hybridization.

None

No atom properties are encoded when generating a fingerprint.