OEFPAtomTypeΒΆ

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 OEFPBondType namespace contains the following constants:

Constant name Combination of
OEFPAtomType.Aromaticity  
OEFPAtomType.AtomicNumber  
OEFPAtomType.Chiral  
OEFPAtomType.DefaultAtom DefaultPathAtom
OEFPAtomType.DefaultCircularAtom AtomicNumber | Aromaticity | Chiral | FormalCharge | HCount | EqHalogen
OEFPAtomType.DefaultPathAtom AtomicNumber | Aromaticity | Chiral | FormalCharge | HvyDegree | Hybridization | EqHalogen
OEFPAtomType.DefaultTreeAtom AtomicNumber | Aromaticity | Chiral | FormalCharge | HvyDegree | Hybridization
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

See also

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).

../../_images/OEFPAtomTypeHydrogenHandling.png

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).
../../_images/OEFPAtomTypeNotAtomicNumber.png ../../_images/OEFPAtomTypeAtomicNumber.png

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).
../../_images/OEFPAtomTypeNotAromaticity.png ../../_images/OEFPAtomTypeAromaticity.png

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).
../../_images/OEFPAtomTypeNotChiral.png ../../_images/OEFPAtomTypeChiral.png

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).

../../_images/OEFPAtomTypeAtomStereoHandling.png

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).
../../_images/OEFPAtomTypeNotFormalCharge.png ../../_images/OEFPAtomTypeFormalCharge.png

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).
../../_images/OEFPAtomTypeNotHvyDegree.png ../../_images/OEFPAtomTypeHvyDegree.png

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).
../../_images/OEFPAtomTypeNotHCount.png ../../_images/OEFPAtomTypeHCount.png

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).
../../_images/OEFPAtomTypeNotHybridization.png ../../_images/OEFPAtomTypeHybridization.png

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).
../../_images/OEFPAtomTypeNotInRing.png ../../_images/OEFPAtomTypeInRing.png

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).
../../_images/OEFPAtomTypeNotEqAromatic.png ../../_images/OEFPAtomTypeEqAromatic.png

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).
../../_images/OEFPAtomTypeNotEqHalogen.png ../../_images/OEFPAtomTypeEqHalogen.png

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.

../../_images/OEFPAtomTypeAnnotateHBAcceptors.png

Example of molecules with hydrogen bond acceptor annotation

Example of using the OEFPAtomType.EqHBondAcceptor option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).
../../_images/OEFPAtomTypeNotEqHBondAcceptor.png ../../_images/OEFPAtomTypeEqHBondAcceptor.png

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.

../../_images/OEFPAtomTypeAnnotateHBDonor.png

Molecules with hydrogen bond donor annotation

Example of using the OEFPAtomType.EqHBondDonor option (Path, numbits=4096, bonds=0-5, bond typing = BondOrder).
../../_images/OEFPAtomTypeNotEqHBondDonor.png ../../_images/OEFPAtomTypeEqHBondDonor.png

DefaultAtom

Same as OEFPAtomType.DefaultPathAtom constant.

DefaultCircularAtom

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

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:

See also

../../_images/DefaultCircular.png

Circular fingerprint similarity with default circular atom and bond typing

DefaultPathAtom

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

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:

See also

../../_images/DefaultPath.png

Path fingerprint similarity with default path atom and bond typing

DefaultTreeAtom

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

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:

See also

../../_images/DefaultTree.png

Tree fingerprint similarity with default tree atom and bond typing

None

No atom properties are encoded when generating a fingerprint.