OEExprOpts¶
Pattern matching in OEChem TK is always done using query molecules or query graphs (OEQMolBase). Non-query molecules, i.e. those that are defined by OEMolBase abstract base-class must be converted into a query molecule before using them in pattern matching algorithms (OESubSearch, OEMCSSearch or OECliqueSearch).
The OEExprOpts namespace contains expression options
that control the conversion into query molecules.
See also
OESubSearch.InitmethodOEMCSSearch.InitmethodOEQMolBase.BuildExpressionsmethod
The OEExprOpts namespace contains both atom and bond
expressions options.
Some options such as OEExprOpts.Aromaticity can be used
both as an atom or a bond expression.
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Atom expression |
Bond expression |
Should be used with |
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The OEExprOpts namespace also contains some predefined atom and bonds
expression combinations listed in the table below.
Constant name |
Combination of expression flags |
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Aromaticity
The OEExprOpts.Aromaticity flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, atoms are considered equivalent if the
OEAtomBase.IsAromaticmethod returns the same value for them.When using this option as a bond expression option, bonds are considered equivalent if the
OEBondBase.IsAromaticmethod returns the same value for them.
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AtomicNumber
The OEExprOpts.AtomicNumber flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetAtomicNum method returns the
same value for them.
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AutomorphAtoms
This constant along with OEExprOpts.AutomorphBonds
is used when determining automorphism related graphs
OEExprOpts.AutomorphAtoms is the combination of the
following atom expression constants:
AutomorphBonds
This constant along with OEExprOpts.AutomorphAtoms
is used when determining automorphism related graphs.
OEExprOpts.AutomorphBonds is equivalent to the
OEExprOpts.Aromaticity constant.
BondOrder
The OEExprOpts.BondOrder flag can be used
as a bond expression option.
When using this option, bonds are considered equivalent if the
OEBondBase.GetOrder method returns the
same value for them.
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DefaultAtoms
This constant along with OEExprOpts.DefaultBonds
is used when a moderate degree of discrimination is required
of the graph equivalence.
OEExprOpts.DefaultAtoms is the combination of
the following atom expression constants:
This combination of flags is intended to give a moderate degree of discrimination of the graph equivalence of atoms. Accordingly, two atoms are considered equivalent if they have the same element, aromaticity value and formal charge.
DefaultBonds
OEExprOpts.DefaultBonds is the combination of the
following bond expression constants:
This combination of flags is intended to give a moderate degree of discrimination of the graph equivalence of bonds. Accordingly, two bonds are considered equivalent if they have the same bond order and aromaticity value.
Chiral
The OEExprOpts.Chiral flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, if the query atom has specified tetrahedral configuration, than it can only be mapped to an atom with the same stereo configuration.
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Warning
The OEExprOpts.Chiral is not available
as an atom expression option in maximum common substructure
search (OEMCSSearch) and clique search
(OECliqueSearch).
When using this option as a bond expression option, if the query bond has specified cis/trans configuration, than it can only be mapped to a bond with the same stereo configuration.
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Warning
The OEExprOpts.Chiral is not available
as a bond expression option in maximum common substructure
search (OEMCSSearch) and clique search
(OECliqueSearch).
Degree
The OEExprOpts.Degree flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetDegree method returns the
same value for them.
Hint
The OEAtomBase.GetDegree method returns the total
degree including the contribution from implicit hydrogens.
EqAromatic
The OEExprOpts.EqAromatic flag can be used
as an atom expression option.
When using this option, aromatic atoms are considered equivalent
regardless of their atomic number.
Warning
The OEExprOpts.EqAromatic should always be used
with the OEExprOpts.AtomicNumber flag.
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EqCAliphaticONS
The OEExprOpts.EqCAliphaticONS flag can be used
as an atom expression option.
When using this option, aliphatic query carbon atoms are considered equivalent
with aliphatic oxygen, nitrogen, or sulfur atoms.
Warning
The OEExprOpts.EqCAliphaticONS should always be used
with the OEExprOpts.AtomicNumber flag.
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EqCHalogen
The OEExprOpts.EqCHalogen flag can be used
as an atom expression option.
When using this option, carbons are considered equivalent
with halogen atoms.
Warning
The OEExprOpts.EqCHalogen should always be used
with the OEExprOpts.AtomicNumber flag.
EqCPSAcidRoot
The OEExprOpts.EqCPSAcidRoot flag can be used
as an atom expression option.
When using this option, query atoms which are the central atom of a carboxylic,
phosphonic, or sulfonic acid moiety are equivalent to a
potential match atom which is also the central atom of a
carboxylic, phosphonic, or sulfonic moiety.
Warning
The OEExprOpts.EqCPSAcidRoot should always be used
with the OEExprOpts.AtomicNumber flag.
EqDoubleTriple
The OEExprOpts.EqDoubleTriple flag can be used
as a bond expression option.
When using this option, double and triple bonds are considered equivalent.
Warning
The OEExprOpts.EqDoubleTriple should always be used
with the OEExprOpts.BondOrder flag.
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EqHalogen
The OEExprOpts.EqHalogen flag can be used
as an atom expression option.
When using this option, halide atoms (OEElemNo.F,
OEElemNo.Cl, OEElemNo.Br,
and OEElemNo.I) are considered equivalent.
Warning
The OEExprOpts.EqHalogen should always be used
with the OEExprOpts.AtomicNumber flag.
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EqKetoneSulfoneRoot
The OEExprOpts.EqKetoneSulfoneRoot flag can be used
as an atom expression option.
When using this option, query atoms
which are the central atom of a ketone or sulfone moiety are
equivalent to a potential match atom which is also the central
atom of a ketone or sulfone moiety.
Warning
The OEExprOpts.EqKetoneSulfoneRoot should always be used
with the OEExprOpts.AtomicNumber flag.
EqMetal
The OEExprOpts.EqMetal flag can be used
as an atom expression option.
When using this option, metal atoms are considered equivalent.
Warning
The OEExprOpts.EqMetal should always be used
with the OEExprOpts.AtomicNumber flag.
EqNotAromatic
The OEExprOpts.EqNotAromatic flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, aliphatic atoms are considered equivalent regardless of their atomic number.
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When using this option as a bond expression option, aliphatic bonds are considered equivalent regardless of their bond order.
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Warning
The OEExprOpts.EqNotAromatic should always be used
with either the OEExprOpts.AtomicNumber or
the OEExprOpts.BondOrder flag.
EqON
The OEExprOpts.EqON flag can be used
as an atom expression option.
When using this option, nitrogen and oxygen atoms are considered equivalent.
Warning
The OEExprOpts.EqON should always be used
with the OEExprOpts.AtomicNumber flag.
EqONS
The OEExprOpts.EqONS flag can be used
as an atom expression option.
When using this option, nitrogen, oxygen and sulfur atoms
are considered equivalent.
Warning
The OEExprOpts.EqONS should always be used
with the OEExprOpts.AtomicNumber flag.
EqPS
The OEExprOpts.EqPS flag can be used
as an atom expression option.
When using this option, phosphorus and sulfur atoms
are considered equivalent.
Warning
The OEExprOpts.EqPS should always be used
with the OEExprOpts.AtomicNumber flag.
EqSingleDouble
The OEExprOpts.EqSingleDouble flag can be used
as a bond expression option.
When using this option, single and double bonds and are considered equivalent.
Warning
The OEExprOpts.EqSingleDouble should always be used
with the OEExprOpts.BondOrder flag.
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ExactAtoms
OEExprOpts.ExactAtoms is the combination of the
following bond expression constants:
This combination of flags is intended to give a high degree of discrimination of the graph equivalence of atoms.
ExactBonds
OEExprOpts.ExactBonds is the combination of the
following bond expression constants:
This combination of flags is intended to give a high degree of discrimination of the graph equivalence of bonds.
ExplicitDegree
The OEExprOpts.ExplicitDegree flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetHvyDegree method returns the
same value for them.
FormalCharge
The OEExprOpts.FormalCharge flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetFormalCharge method returns the
same value for them and the query atom has a non-zero charge.
If you want to consider zero charges see option
OEExprOpts.StrictFormalCharge.
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See also
OEExprOpts.StrictFormalChargeconstants
HCount
The OEExprOpts.HCount flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetTotalHCount method returns the
same value for them.
Hint
The OEAtomBase.GetTotalHCount method returns
the number of explicit and implicit hydrogens i.e.
the expression built when the OEExprOpts.HCount
flag is set will therefore not discriminate between implicit and
explicit hydrogen counts.
HvyDegree
The OEExprOpts.HvyDegree flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetHvyDegree method returns the
same value for them.
Hybridization
The OEExprOpts.Hybridization flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetHyb method returns the
same value for them.
Warning
Hybridization of the molecules must be perceived by calling
the OEAssignHybridization function.
ImplicitHCount
The OEExprOpts.ImplicitHCount flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetImplicitHCount method returns the
same value for them.
IntType
The OEExprOpts.IntType flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, atoms are considered equivalent if the
OEAtomBase.GetIntTypemethod returns the same value for them.When using this option as a bond expression option, bonds are considered equivalent if the
OEBondBase.GetIntTypemethod returns the same value for them.
Mass
The OEExprOpts.Mass flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetIsotope method returns the
same value for them.
RingMember
The OEExprOpts.RingMember flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, atoms are considered equivalent if the
OEAtomBase.IsInRingmethod returns the same value for them.
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When using this option as a bond expression option, bonds are considered equivalent if the
OEBondBase.IsInRingmethod returns the same value for them.
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StrictFormalCharge
The OEExprOpts.StrictFormalCharge flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetFormalCharge method returns the
same value for them.
The formal charges must be equivalent even if the formal charge
of the query atom is zero.
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See also
OEExprOpts.FormalChargeconstant
StringType
The OEExprOpts.StringType flag can be used both
as atom and bond expression option.
When using this option as an atom expression option, atoms are considered equivalent if the
OEAtomBase.GetTypemethod returns the same value for them.When using this option as a bond expression option, bonds are considered equivalent if the
OEBondBase.GetTypemethod returns the same value for them.
SymmetryClass
The OEExprOpts.SymmetryClass flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetSymmetryClass method returns the
same value for them.
Warning
Symmetry of the molecules must be perceived by calling
the OEPerceiveSymmetry function.
Valence
The OEExprOpts.Valence flag can be used
as an atom expression option.
When using this option, atoms are considered equivalent if the
OEAtomBase.GetValence method returns the
same value for them.
Hint
The OEAtomBase.GetValence method
includes the valence contribution from implicit hydrogens,
therefore, the expression test may return successfully even when
the explicit valence of two corresponding atoms differ.