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: contacts (OEContactInteractionHint), clashes ( OEClashInteractionHint), salt bridges( OESaltBridgeInteractionHint), hydrogen bonds (OEHBondInteractionHint), metal interaction (OEChelatorInteractionHint), PI and T stacking (OEStackingInteractionHint), and halogen bonds (OEHalogenBondInteractionHint).

Each interaction type has one or more parameters that control its perception. In addition, hydrogen-bonding clashes, intra-molecular 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.

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.

GetMaxChargeAidedHBondDistance

double GetMaxChargeAidedHBondDistance() const

Returns the value set by OEPerceiveInteractionOptions::SetMaxChargeAidedHBondDistance.

GetMaxContactFraction

double GetMaxContactFraction() const

Returns the value set by OEPerceiveInteractionOptions::SetMaxContactFraction.

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.

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

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

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

SetMinHBondContactFraction

void SetMinHBondContactFraction(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 = 0.5