Subsections

7.3 OEBestOverlayScore

class OEBestOverlayScore

This small class is used to contain all the results from a single optimization of a fit molecule conformer with a reference molecule conformer. The user will not normally construct an instance of OEBestOverlayScore, but will instead iterate over a set of instances as contained in an instance of OEBestOverlayresults (see section ) .

Much of the data is contained in public member variables:

unsigned int refconfidx: Index of the reference conformer. You can get the actual OEConfBase via refMol.GetConf(OEHasConfIdx(refconfidx)).
unsigned int fitconfidx: Index of the fit conformer. You can get the actual OEConfBase via fitMol.GetConf(OEHasConfIdx(fitconfidx)).
float tanimoto: Shape tanimoto score for this alignment.
float overlap: Overlap score for this alignment.
float refSelfOverlap: Self overlap of reference conformer.
float fitSelfOverlap: Self overlap of fit conformer.
float refSelfColor: Self color score of reference conformer.
float fitSelfColor: Self color score of fit conformer.
float colorscore: Absolute color score of this alignment.
float scaledcolor: Color scaled to ref self color score.
float rmat[9]: Rotation matrix to move fit conformer into this alignment. Use with OERotate to manipulate the conformer. Note that OpenEye standard is to perform rotation then translation.
float trans[3]: Translation matrix to move fit conformer into this alignment.

OEBestOverlay also has a few member methods to access data calculable from the contained data.

7.3.1 Constructors

OEBestOverlayScore()

Default and copy constructors.

7.3.2 GetColorTanimoto

float GetColorTanimoto() const

7.3.3 GetColorTversky

float GetColorTversky(float alpha=0.95f, float beta=0.05f) const

7.3.4 GetComboScore

float GetComboScore() const

Return combo score, defined as the sum of Shape Tanimoto and scaled color score. Value ranges from 0.0 to 2.0.

7.3.5 GetTanimotoCombo

float GetTanimotoCombo() const

Return TanimotoCombo score, defined as the sum of Shape Tanimoto and Color Tanimoto. Value ranges from 0.0 to 2.0.

7.3.6 GetFitColorTversky

float GetFitColorTversky() const

7.3.7 GetFitTversky

float GetFitTversky() const

Return the Tversky score using an alpha of 0.05 and beta of 0.95, where alpha is the prefactor for the ref molecule self overlap.

7.3.8 GetFitTverskyCombo

float GetFitTverskyCombo() const

Return FitTverskyCombo score, defined as the sum of Shape FitTversky and Color FitTversky. Value ranges from 0.0 to 2.0.

7.3.9 GetRefColorTversky

float GetRefColorTversky() const

Return RefTverskyCombo score, defined as the sum of Shape RefTversky and Color RefTversky. Value ranges from 0.0 to 2.0.

7.3.10 GetRefTversky

float GetRefTversky() const

Return the Tversky score using an alpha of 0.95 and beta of 0.05, where alpha is the prefactor for the ref molecule self overlap.

7.3.11 GetRefTverskyCombo

float GetRefTverskyCombo() const

7.3.12 GetTversky

float GetTversky(float alpha=0.95f, float beta=0.05f) const

Return the Tversky score for user-defined values of alpha and beta, where alpha is the prefactor for the ref molecule self overlap. Note that calling GetTversky with the default arguments returns the same value as GetRefTversky.

7.3.13 Transform

bool Transform(OEChem::OEMolBase &mol) const
bool Transform(OEChem::OEConfBase &mol) const

Perform the proper rotation and translation to move the passed-in molecule or conformer into the final orientation as calculated in the best overlay optimization. This provides the same feature as manually calling OERotate then OETranslate using the rmat and trans, but to lessen the chance of doing them in the improper order.

				Shape Toolkit Java Programming Manual

				Shape Toolkit Java Programming Manual