OEPerceiveInteractionOptions¶

class OEPerceiveInteractionOptions


This class is a container for all the parameters that control interaction perception when invoking the OEPerceiveInteractionHints function.

The current list of interactions include:

Each interaction type has one or more parameters that control its perception. In addition, hydrogen-bonding clashes, intramolecular hydrogen-bonds, unpaired hydrogen-bonds and unpaired salt-bridges are also perceived. Unpaired interactions are those that are near the protein-ligand interface, but do not form an apparent bond.

 Get method Set method Interaction type(s) GetExtendedSaltBridgeDistance salt bridge GetMaxAcceptorAngle SetMaxAcceptorAngle hbond GetMaxAtomPairDistance GetMaxCationPiAngle SetMaxCationPiAngle cation-Pi GetMaxCationPiDistance SetMaxCationPiDistance cation-Pi GetMaxChargeAidedHBondDistance SetMaxChargeAidedHBondDistance hbond GetMaxContactFraction SetMaxContactFraction contact GetMaxCovalentFraction SetMaxCovalentFraction covalent GetMaxDonorAngle SetMaxDonorAngle hbond GetMaxHBondDistance SetMaxHBondDistance hbond GetMaxHalogenAngle SetMaxHalogenAngle halogen bond GetMaxHalogenBondDistance SetMaxHalogenBondDistance halogen bond GetMaxMetalBondDistance SetMaxMetalBondDistance chelator GetMaxPiStackAngle SetMaxPiStackAngle Pi-stacking GetMaxPiStackDistance SetMaxPiStackDistance Pi-stacking GetMaxSaltBridgeDistance SetMaxSaltBridgeDistance salt bridge GetMaxTStackAngle SetMaxTStackAngle T-stacking GetMaxTStackDistance SetMaxTStackDistance T-stacking GetMaxUnpairedAngle SetMaxUnpairedAngle hbond GetMaxUnpairedDistance SetMaxUnpairedDistance hbond GetMinContactFraction SetMinContactFraction contact, clash GetMinCovalentFraction SetMinCovalentFraction covalent GetMinHBondContactFraction SetMinHBondContactFraction hbond

Constructors¶

OEPerceiveInteractionOptions()


The default constructor for perception of interaction options. It sets all of the interaction parameters to their default value.

GetExtendedSaltBridgeDistance¶

double GetExtendedSaltBridgeDistance() const


Actual salt bridge interaction distance is calculated from the geometric centers of the two interacting charge groups, which may or may not be comprised of a single atom. The distance returned by this function is the maximum distance between two formally charged atoms for subsequent identification of charge groups. This is a simple increment larger than the value associated with OEPerceiveInteractionOptions.GetMaxSaltBridgeDistance and OEPerceiveInteractionOptions.SetMaxSaltBridgeDistance.

GetMaxAcceptorAngle¶

double GetMaxAcceptorAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxAcceptorAngle.

GetMaxAtomPairDistance¶

double GetMaxAtomPairDistance() const


Returns the maximum value of

GetMaxCationPiAngle¶

double GetMaxCationPiAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxCationPiAngle.

GetMaxCationPiDistance¶

double GetMaxCationPiDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxCationPiDistance.

GetMaxChargeAidedHBondDistance¶

double GetMaxChargeAidedHBondDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxChargeAidedHBondDistance.

GetMaxContactFraction¶

double GetMaxContactFraction() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxContactFraction.

GetMaxCovalentFraction¶

double GetMaxCovalentFraction() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxCovalentFraction.

GetMaxDonorAngle¶

double GetMaxDonorAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxDonorAngle.

GetMaxHBondDistance¶

double GetMaxHBondDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxHBondDistance.

GetMaxHalogenAngle¶

double GetMaxHalogenAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxHalogenAngle.

GetMaxHalogenBondDistance¶

double GetMaxHalogenBondDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxHalogenBondDistance.

GetMaxMetalBondDistance¶

double GetMaxMetalBondDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxMetalBondDistance.

GetMaxPiStackAngle¶

double GetMaxPiStackAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxPiStackAngle.

GetMaxPiStackDistance¶

double GetMaxPiStackDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxPiStackDistance.

GetMaxSaltBridgeDistance¶

double GetMaxSaltBridgeDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxSaltBridgeDistance.

GetMaxTStackAngle¶

double GetMaxTStackAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxTStackAngle.

GetMaxTStackDistance¶

double GetMaxTStackDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxTStackDistance.

GetMaxUnpairedAngle¶

double GetMaxUnpairedAngle() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxUnpairedAngle.

GetMaxUnpairedDistance¶

double GetMaxUnpairedDistance() const


Returns the value set by OEPerceiveInteractionOptions.SetMaxUnpairedDistance.

GetMinContactFraction¶

double GetMinContactFraction() const


Returns the value set by OEPerceiveInteractionOptions.SetMinContactFraction.

GetMinCovalentFraction¶

double GetMinCovalentFraction() const


Returns the value set by OEPerceiveInteractionOptions.SetMinCovalentFraction.

GetMinHBondContactFraction¶

double GetMinHBondContactFraction() const


Returns the value set by OEPerceiveInteractionOptions.SetMinHBondContactFraction.

SetMaxAcceptorAngle¶

void SetMaxAcceptorAngle(double radians)


In perception of a hydrogen bond, we define the angle $$X-A...D$$, where A and D are the acceptor and donor respectively, and X is one or more points in space that are located so that an idealized hydrogen-bond would give an angle of $$\pi$$. The maximum acceptor angle is the maximum allowed deviation (in radians) from the idealized angle (or the minimum deviation from multiple angles when more than one X position is possible).

Default= $$(\pi * \frac{10.0}{36.0})$$ = 50 degrees

SetMaxCationPiAngle¶

void SetMaxCationPiAngle(double radians)


This option sets the maximum allowed angle defined by a point on the vector normal from the pi ring system, the geometric center of the ring system and the geometric center of the charged system. For the purposes of Cation Pi interaction hints, only Lysine, N-methyl Lysine and Arginine are recognized cations. For Lysine and N-methyl Lysine, the charge center is the charged Nitrogen atom, while for the Arginine residue, the charge center will be the geometric center of the Carbon and three Nitrogen atoms that share the resonant charge. Each smallest aromatic ring (independent of ring fusions) is considered separately and a cation can interact with more than one pi system simultaneously.

Default= $$(\pi * \frac{10.0}{36.0})$$ = 50 degrees

SetMaxCationPiDistance¶

void SetMaxCationPiDistance(double dist)


This is the maximum allowed distance between the center of a cation system and the center of an aromatic pi system. For the purposes of Cation Pi interaction hints, only Lysine, N-methyl Lysine and Arginine are recognized cations. Each smallest aromatic ring (independent of ring fusions) is considered separately and a cation can interact with more than one pi system simultaneously.

Default= 5.5 Ångströms

SetMaxChargeAidedHBondDistance¶

void SetMaxChargeAidedHBondDistance(double dist)


For the purpose of hydrogen bond perception, charge assisted hydrogen bonds, are identified when one of the two bonding partners is part of a functional group with a net formal charge. These interactions include dipole - charge interactions and are perceived at slightly longer range than simple hydrogen- bonds by default.

Default= 3.5 Ångströms

SetMaxContactFraction¶

void SetMaxContactFraction(double frac)


Van der Waals interactions are perceived as non-interacting, in attractive contact, or clashing. The three classes are determined by comparing the atom - atom distance Daa to the sum of the van der Waals radii of the two atoms VDWtot. The distance Daa is represented as a fraction of VDWtot which we will call Faa. If the value of Faa is greater than the value stored in OEPerceiveInteractionOptions.SetMaxContactFraction, then the two atoms are non-interacting. If the value of Faa is between the values set by OEPerceiveInteractionOptions.SetMaxContactFraction and OEPerceiveInteractionOptions.SetMinContactFraction then the atoms are in attractive contact. If the value of Faa is less than OEPerceiveInteractionOptions.SetMinContactFraction then the atoms are clashing.

Any two atoms that are forming a hydrogen bond can be in attractive contact at shorter distances than generic atom pairs because of the balance of forces. To handle this, when two atoms are forming a hydrogen bond, the value of Faa is compared to OEPerceiveInteractionOptions.SetMinHBondContactFraction to determine clashing rather than OEPerceiveInteractionOptions.SetMinContactFraction.

Default = 1.2

SetMaxCovalentFraction¶

void SetMaxCovalentFraction(double frac)


This function sets the maximum ratio of the distance between to atoms to the sum of their covalent radii allowed for perception of a covalent bond.

Covalent interactions are perceived based on comparing the distance between two atoms D to the sum of the covalent radii SumRc. If D is > SumRc times the value set by OEPerceiveInteractionOptions.SetMinCovalentFraction and D is < SumRc times the value set by OEPerceiveInteractionOptions.SetMaxCovalentFraction, then a covalent interaction will be perceived. Currently no angle constraint is used in perceiving covalent interactions.

Hydrogen and Halide atoms as well as water molecules are excluded from covalent interaction hint perception. Metal atom interactions are preceived as OEChelatorInteractionHint rather than as covalent interactions.

When a covalent interaction exists between atom P of the protein and atom L of the ligand, then no other interactions will be perceived for atoms P and L. Further, atoms bonded to atoms L and P will be excluded from perceiption of clash or contact interactions. Bonded atoms will be able to participate in other interactions such as hydrogen bonding.

Default = 1.1

SetMaxDonorAngle¶

void SetMaxDonorAngle(double radians)


In the perception of a hydrogen bond with the interaction $$A...H-D$$, the angle $$A-D-H$$ is ideally zero in most cases. This function determines the maximum allowed value of this angle in a perceived hydrogen-bond.

Default = $$(\pi * \frac{7.0}{36.0})$$ = 35 degrees

SetMaxHBondDistance¶

void SetMaxHBondDistance(double dist)


This function sets the maximum distance between the donor and acceptor heavy atoms for a hydrogen-bond to be perceived.

Default = 3.2 Ångströms

SetMaxHalogenAngle¶

void SetMaxHalogenAngle(double radians)


In the perception of halogen bonds, there is an angle formed between $$R-X...E/N$$ where X is a univalent halogen, E/N are the electrophile or nucleophile, and R is the attachment of the halogen. For nucleophiles, the ideal interaction angle is $$\pi$$, for electrophiles, the ideal interaction angle $$\frac{\pi}{2}$$. This function determines the maximum allowed deviation (in radian) from these ideal angles, respectively, for perception of a halogen bond.

Default = $$(\pi * \frac{7.0}{36.0})$$ = 35 degrees

SetMaxHalogenBondDistance¶

void SetMaxHalogenBondDistance(double dist)


This is the maximum distance between the halogen atom and the electrophile or nucleophile atom for perception of a halogen bond.

Default = 3.2 Ångströms

SetMaxMetalBondDistance¶

void SetMaxMetalBondDistance(double dist)


This is the maximum distance allowed for an interaction to be perceived between a metal atom and a chelating non-metal atom.

Default = 3.5 Ångströms

SetMaxPiStackAngle¶

void SetMaxPiStackAngle(double radians)


Sets the maximum angle deviation (in radian) from the ideal angle calculated between the two aromatic ring normals to be considered for Pi-stacking interaction.

Default = $$\frac{\pi}{9.0}$$

SetMaxPiStackDistance¶

void SetMaxPiStackDistance(double dist)


Sets the maximum distance (in Ångström) allowed between the geometric center of two aromatic rings in order to being considered for Pi-stacking interaction.

Default = 5.0 Ångströms

SetMaxSaltBridgeDistance¶

void SetMaxSaltBridgeDistance(double dist)


Sets the maximum distance (in Ångströms) allowed between the geometric centers of the two formally charged groups in a perceived salt bridge interaction.

Default = 5.0 Ångströms

SetMaxTStackAngle¶

void SetMaxTStackAngle(double radians)


Sets the maximum angle deviation (in radian) from the ideal angle ($$\frac{\pi}{2}$$) calculated between the two aromatic ring normals to be considered for T-stacking interaction.

Default = $$\frac{\pi}{9.0}$$

SetMaxTStackDistance¶

void SetMaxTStackDistance(double dist)


Sets the maximum distance (in Ångström) allowed between the geometric center of two aromatic rings in order to being considered for T-stacking interaction.

Default = 5.35 Ångströms

SetMaxUnpairedAngle¶

void SetMaxUnpairedAngle(double radians)


In perception of unpaired interactions, the unpaired potential interaction group should be oriented toward the ligand or protein where it could make an interaction. This is the maximum deviation (in radian) allowed between the potential interaction group and the nearest potential partner atom.

Default = $$\frac{\pi}{2}$$

SetMaxUnpairedDistance¶

void SetMaxUnpairedDistance(double dist)


In perception of unpaired interactions, the unpaired potential interaction group should be within a minimum distance of the nearest potential paired atom. This function sets the maximum distance (in Ångströms) for perception of an unpaired potential.

Default = 5.0 Ångströms

SetMinContactFraction¶

void SetMinContactFraction(double frac)


der Waals interactions are perceived as non-interacting, in attractive contact, or clashing. The three classes are determined by comparing the atom - atom distance Daa to the sum of the van der Waals radii of the two atoms VDWtot. The distance Daa is represented as a fraction of VDWtot which we will call Faa. If the value of Faa is greater than the value stored in OEPerceiveInteractionOptions.SetMaxContactFraction, then the two atoms are non-interacting. If the value of Faa is between the values set by OEPerceiveInteractionOptions.SetMaxContactFraction and OEPerceiveInteractionOptions.SetMinContactFraction then the atoms are in attractive contact. If the value of Faa is less than OEPerceiveInteractionOptions.SetMinContactFraction then the atoms are clashing.

Any two atoms that are forming a hydrogen bond can be in attractive contact at shorter distances than generic atom pairs because of the balance of forces. To handle this, when two atoms are forming a hydrogen bond, the value of Faa is compared to OEPerceiveInteractionOptions.SetMinHBondContactFraction to determine clashing rather than OEPerceiveInteractionOptions.SetMinContactFraction.

Default = 0.8

SetMinCovalentFraction¶

void SetMinCovalentFraction(double frac)


This function sets the minimum ratio of the distance between to atoms to the sum of their covalent radii allowed for perception of a covalent bond.

Covalent interactions are perceived based on comparing the distance between two atoms D to the sum of the covalent radii SumRc. If D is > SumRc times the value set by OEPerceiveInteractionOptions.SetMinCovalentFraction and D is < SumRc times the value set by OEPerceiveInteractionOptions.SetMaxCovalentFraction, then a covalent interaction will be perceived. Currently no angle constraint is used in perceiving covalent interactions.

Hydrogen and Halide atoms as well as water molecules are excluded from covalent interaction hint perception. Metal atom interactions are preceived as OEChelatorInteractionHint rather than as covalent interactions.

When a covalent interaction exists between atom P of the protein and atom L of the ligand, then no other interactions will be perceived for atoms P and L. Further, atoms bonded to atoms L and P will be excluded from perceiption of clash or contact interactions. Bonded atoms will be able to participate in other interactions such as hydrogen bonding.

Default = 0.9

void SetMinHBondContactFraction(double frac)