OEFPBondType

This namespace contains bond typing options that can be used when generating Circular, Path of Tree fingerprints. Bond type options control how the bonds 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
OEFPBondType.BondOrder
OEFPBondType.Chiral
OEFPBondType.DefaultBond	DefaultPathBond
OEFPBondType.DefaultCircularBond	BondOrder
OEFPBondType.DefaultCircularVSBond	BondOrder
OEFPBondType.DefaultPathBond	BondOrder | Chiral
OEFPBondType.DefaultPathVSBond	BondOrder | Chiral
OEFPBondType.DefaultTreeBond	BondOrder
OEFPBondType.DefaultTreeVSBond	BondOrder
OEFPBondType.InRing
OEFPBondType.None

Note

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

See also

• Visualizing Molecule Similarity section

See also

• OEFPAtomType namespace

• OEMakeCircularFP function

• OEMakePathFP function

• OEMakeTreeFP function

• Atom and Bond Typing section

BondOrder

This flag indicates that bond order information is encoded into the generated fingerprint, i.e., if two fragments (either circular, path or tree) are composed of bonds with different bond orders (the value returned by the GetOrder method) then the two fragments will be mapped to different bits of the fingerprint. Table: Example of using the BondOrder option demonstrates the effect of using the OEFPBondType.BondOrder flag.

Example of using the OEFPBondType.BondOrder option (Path, numbits=4096, bonds=0-5, atom typing = AtomicNumber).

Chiral

This flag indicates that chiral and non-chiral bonds (the value returned by the OEBondBase.IsChiral method) are distinguished during the circular, path, the tree fingerprint generation. Table: Example of using the Chiral option demonstrates the effect of using the OEFPBondType.Chiral flag.

Example of using the OEFPBondType.Chiral option (Path, numbits=4096, bonds=0-5, atom typing = AtomicNumber).

Note

Cis and trans chiral bonds can not be distinguished when the OEFPBondType.Chiral flag is set. Fingerprints generated for molecules C\C=C/C and C/C=C/C will always be identical. (See example in Figure: Example of molecule similarity of stereoisomers).

Example of molecule similarity of cis-trans stereoisomers

InRing

This flag indicates that bond topology information is encoded into the generated fingerprint, i.e., if two fragments (either circular, path or tree) are composed of bonds with different bond topology (the value returned by the OEBondBase.IsInRing method) 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 OEFPBondType.InRing flag.

Example of using the OEFPBondType.InRing option (Path, numbits=4096, bonds=0-5, atom typing = AtomicNumber).

DefaultBond

Same as OEFPBondType.DefaultPathBond constant.

DefaultCircularBond

Same as the OEFPBondType.BondOrder constant.

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

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType.Circular)

• OEMakeCircularFP

See also

• OEFPAtomType.DefaultCircularAtom constant

DefaultCircularVSBond

The default bond typing for the circular fingerprint that is designed for virtual screening. Currently it’s the same as OEFPBondType.DefaultCircularBond.

DefaultPathBond

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

• OEFPBondType.BondOrder

• OEFPBondType.Chiral

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

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType.Path)

• OEMakePathFP

See also

• OEFPAtomType.DefaultPathAtom constant

Path fingerprint similarity with default tree atom and bond typing

DefaultPathVSBond

The default bond typing for the tree fingerprint that is designed for virtual screening. Currently it’s the same as OEFPBondType.DefaultPathBond.

DefaultTreeBond

Same as the OEFPBondType.BondOrder constant.

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

• OEMakeFP (OEFingerPrint &, const OEMolBase &, OEFPType.Tree)

• OEMakeTreeFP

See also

• OEFPAtomType.DefaultTreeAtom constant

Tree fingerprint similarity with default tree atom and bond typing

DefaultTreeVSBond

The default bond typing for the tree fingerprint that is designed for virtual screening. Currently it’s the same as OEFPBondType.DefaultTreeBond.

None

No bond properties are encoded when generating a fingerprint.