OEFPBondTypeΒΆ

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_DefaultPathBond BondOrder | Chiral
OEFPBondType_DefaultTreeBond BondOrder
OEFPBondType_InRing  
OEFPBondType_None  

Note

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

See also

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).
../../_images/OEFPBondTypeNotBondOrder.png ../../_images/OEFPBondTypeBondOrder.png

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).
../../_images/OEFPBondTypeNotChiral.png ../../_images/OEFPBondTypeChiral.png

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).

../../_images/OEFPBondTypeBondStereoHandling.png

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).
../../_images/OEFPBondTypeNotInRing.png ../../_images/OEFPBondTypeInRing.png

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:

../../_images/DefaultCircular.png

DefaultPathBond

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

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:

See also

../../_images/DefaultPath.png

Path fingerprint similarity with default tree atom and bond typing

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:

See also

../../_images/DefaultTree.png

Tree fingerprint similarity with default tree atom and bond typing

None

No bond properties are encoded when generating a fingerprint.