#include <SingleConformerAlignment.h>

Public Member Functions
	SingleConformerAlignment ()=delete
	SingleConformerAlignment (const std::vector< double > &ref, const int refTypes, const boost::dynamic_bitset<> refCarbonRadii, int nRefShape, int nRefColor, double refShapeVol, double refColorVol, const std::vector< double > &fit, const int fitTypes, const boost::dynamic_bitset<> fitCarbonRadii, int nFitShape, int nFitColor, double fitShapeVol, double fitColorVol, const std::array< double, 7 > &initQuatTrans, OptimMode optimMode, double simAlpha, double simBeta, double mixingParam, bool useCutoff, double distCutoff, double shapeConvergenceCriterion, unsigned int maxIts)
	Do the overlay for a single conformer of fit against a single conformer of ref. The output in scores is the rotation and translation that moves fit to optimise its score with ref.
	SingleConformerAlignment (const SingleConformerAlignment &other)=delete
	SingleConformerAlignment (SingleConformerAlignment &&other)=delete
SingleConformerAlignment &	operator= (const SingleConformerAlignment &other)=delete
SingleConformerAlignment &	operator= (SingleConformerAlignment &&other)=delete
	~SingleConformerAlignment ()=default
void	setQuatTrans (const std::array< double, 7 > &quatTrans)
void	getFinalQuatTrans (RDGeom::Transform3D &xform) const
std::array< double, 5 >	calcScores (const double ref, const double fit, bool includeColor=false)
std::array< double, 5 >	calcScores (bool includeColor=false)
std::array< double, 5 >	calcScores (const double shapeOvVol, const double colorOvVol, bool includeColor=true) const
void	applyQuatTrans (const std::array< double, 7 > &quatTrans)
void	calcVolumeAndGradients (const std::array< double, 7 > &quatTrans, double &shapeOvlpVol, double &colorOvlpVol, std::array< double, 7 > &gradients)
bool	doOverlay (std::array< double, 20 > &scores, unsigned int cycle)
	Do the overlay, feeding the results into scores.
bool	optimise (unsigned int maxIters)

Public Attributes
std::vector< double >	d_ref
std::vector< double >	d_refTemp
const int *	d_refTypes
const boost::dynamic_bitset *	d_refCarbonRadii
const int	d_nRefShape
const int	d_nRefColor
const double	d_refShapeVol
const double	d_refColorVol
std::vector< double >	d_fit
std::vector< double >	d_fitTemp
const int *	d_fitTypes
const boost::dynamic_bitset *	d_fitCarbonRadii
const int	d_nFitShape
const int	d_nFitColor
double	d_fitShapeVol
double	d_fitColorVol
std::array< double, 7 >	d_initQuatTrans
const OptimMode	d_optimMode
const double	d_simAlpha
const double	d_simBeta
const double	d_mixingParam
const bool	d_useCutoff
const double	d_distCutoff2
const double	d_shapeConvergenceCriterion
const unsigned int	d_maxIts
std::array< double, 7 >	d_quatTrans {1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0}
double	d_qStepSize {-0.001}
double	d_tStepSize {-0.01}
std::vector< double >	d_gradConverters

Detailed Description

Definition at line 32 of file SingleConformerAlignment.h.

Constructor & Destructor Documentation

◆ SingleConformerAlignment() [1/4]

RDKit::GaussianShape::SingleConformerAlignment::SingleConformerAlignment ( )

delete

Referenced by operator=(), operator=(), SingleConformerAlignment(), and SingleConformerAlignment().

◆ SingleConformerAlignment() [2/4]

RDKit::GaussianShape::SingleConformerAlignment::SingleConformerAlignment	(	const std::vector< double > &	ref,
		const int *	refTypes,
		const boost::dynamic_bitset<> *	refCarbonRadii,
		int	nRefShape,
		int	nRefColor,
		double	refShapeVol,
		double	refColorVol,
		const std::vector< double > &	fit,
		const int *	fitTypes,
		const boost::dynamic_bitset<> *	fitCarbonRadii,
		int	nFitShape,
		int	nFitColor,
		double	fitShapeVol,
		double	fitColorVol,
		const std::array< double, 7 > &	initQuatTrans,
		OptimMode	optimMode,
		double	simAlpha,
		double	simBeta,
		double	mixingParam,
		bool	useCutoff,
		double	distCutoff,
		double	shapeConvergenceCriterion,
		unsigned int	maxIts )

Do the overlay for a single conformer of fit against a single conformer of ref. The output in scores is the rotation and translation that moves fit to optimise its score with ref.

Parameters

ref	- the query molecule as 1D array of 4 * N entries. Each block of 4 is the coords and atom radius
refTypes	- the feature types for molecule ref
refCarbonRadii	- whether each atom has a carbon radius
nRefShape	- the number of atoms in ref
nRefColor	- the number of features in ref
refShapeVol	- overlap volume of ref with itself
refColorVol	- color overlap of ref with itself
fit	- the fit molecule as 1D array of 4 * N entries. Each block of 4 is the coords and atom radius.
fitTypes	- the feature types for fit molecule
fitCarbonRadii	- whether each atom has a carbon radius
nFitShape	- the number of atoms in fit
nFitColor	- the number of features in fit
fitShapeVol	- overlap volume of fit with itself
fitColorVol	- color overlap of fit with itself
optimMode	- optimisation mode
simAlpha	- for the Tversky similarity, the alpha value
simBeta	- for the Tversky similarity, the beta value
mixingParam	- how to mix the 2 Tversky values
useCutoff	- whether to use a distance cutoff in the volume calculation
distCutoff	- the cutoff to use if we're doing it.
maxIts	- maximum number of iterations for optimiser of optimiser

◆ SingleConformerAlignment() [3/4]

RDKit::GaussianShape::SingleConformerAlignment::SingleConformerAlignment ( const SingleConformerAlignment & other )

delete

References SingleConformerAlignment().

◆ SingleConformerAlignment() [4/4]

RDKit::GaussianShape::SingleConformerAlignment::SingleConformerAlignment ( SingleConformerAlignment && other )

delete

References SingleConformerAlignment().

◆ ~SingleConformerAlignment()

RDKit::GaussianShape::SingleConformerAlignment::~SingleConformerAlignment ( )

default

Member Function Documentation

◆ applyQuatTrans()

void RDKit::GaussianShape::SingleConformerAlignment::applyQuatTrans ( const std::array< double, 7 > & quatTrans )

◆ calcScores() [1/3]

std::array< double, 5 > RDKit::GaussianShape::SingleConformerAlignment::calcScores ( bool includeColor = false )

◆ calcScores() [2/3]

std::array< double, 5 > RDKit::GaussianShape::SingleConformerAlignment::calcScores	(	const double *	ref,
		const double *	fit,
		bool	includeColor = false )

◆ calcScores() [3/3]

std::array< double, 5 > RDKit::GaussianShape::SingleConformerAlignment::calcScores	(	const double	shapeOvVol,
		const double	colorOvVol,
		bool	includeColor = true ) const

◆ calcVolumeAndGradients()

void RDKit::GaussianShape::SingleConformerAlignment::calcVolumeAndGradients	(	const std::array< double, 7 > &	quatTrans,
		double &	shapeOvlpVol,
		double &	colorOvlpVol,
		std::array< double, 7 > &	gradients )

◆ doOverlay()

bool RDKit::GaussianShape::SingleConformerAlignment::doOverlay	(	std::array< double, 20 > &	scores,
		unsigned int	cycle )

Do the overlay, feeding the results into scores.

Returns: scores - the output scores and transformation to reproduce the overlay - an array of size 20. Only the first 16 are used here. They are: 0 - the combo score 1 - the shape Tversky score 2 - the color Tversky score 3 - the shape overlap volume 4 - the color overlap volume 5 - the shape volume of fit 6 - the shape volume of ref 7 - the color volume of fit 8 - the color volume of ref 9-12 - the quaternion to rotate fit onto ref. Applied first. 13-15 - the translation to move fit onto ref. Applied second. 16-19 - not used at present, returned as zeros. Returns false if it didn't finish with the allowed maximum number of iterations.

◆ getFinalQuatTrans()

void RDKit::GaussianShape::SingleConformerAlignment::getFinalQuatTrans ( RDGeom::Transform3D & xform ) const

◆ operator=() [1/2]

SingleConformerAlignment & RDKit::GaussianShape::SingleConformerAlignment::operator= ( const SingleConformerAlignment & other )

delete

References SingleConformerAlignment().

◆ operator=() [2/2]

SingleConformerAlignment & RDKit::GaussianShape::SingleConformerAlignment::operator= ( SingleConformerAlignment && other )

delete

References SingleConformerAlignment().

◆ optimise()

bool RDKit::GaussianShape::SingleConformerAlignment::optimise ( unsigned int maxIters )

◆ setQuatTrans()

void RDKit::GaussianShape::SingleConformerAlignment::setQuatTrans ( const std::array< double, 7 > & quatTrans )

inline

Definition at line 81 of file SingleConformerAlignment.h.

References d_quatTrans.

Member Data Documentation

◆ d_distCutoff2

const double RDKit::GaussianShape::SingleConformerAlignment::d_distCutoff2

Definition at line 165 of file SingleConformerAlignment.h.

◆ d_fit

std::vector<double> RDKit::GaussianShape::SingleConformerAlignment::d_fit

Definition at line 151 of file SingleConformerAlignment.h.

◆ d_fitCarbonRadii

const boost::dynamic_bitset* RDKit::GaussianShape::SingleConformerAlignment::d_fitCarbonRadii

Definition at line 154 of file SingleConformerAlignment.h.

◆ d_fitColorVol

double RDKit::GaussianShape::SingleConformerAlignment::d_fitColorVol

Definition at line 158 of file SingleConformerAlignment.h.

◆ d_fitShapeVol

double RDKit::GaussianShape::SingleConformerAlignment::d_fitShapeVol

Definition at line 157 of file SingleConformerAlignment.h.

◆ d_fitTemp

std::vector<double> RDKit::GaussianShape::SingleConformerAlignment::d_fitTemp

Definition at line 152 of file SingleConformerAlignment.h.

◆ d_fitTypes

const int* RDKit::GaussianShape::SingleConformerAlignment::d_fitTypes

Definition at line 153 of file SingleConformerAlignment.h.

◆ d_gradConverters

std::vector<double> RDKit::GaussianShape::SingleConformerAlignment::d_gradConverters

Definition at line 175 of file SingleConformerAlignment.h.

◆ d_initQuatTrans

std::array<double, 7> RDKit::GaussianShape::SingleConformerAlignment::d_initQuatTrans

Definition at line 159 of file SingleConformerAlignment.h.

◆ d_maxIts

const unsigned int RDKit::GaussianShape::SingleConformerAlignment::d_maxIts

Definition at line 167 of file SingleConformerAlignment.h.

◆ d_mixingParam

const double RDKit::GaussianShape::SingleConformerAlignment::d_mixingParam

Definition at line 163 of file SingleConformerAlignment.h.

◆ d_nFitColor

const int RDKit::GaussianShape::SingleConformerAlignment::d_nFitColor

Definition at line 156 of file SingleConformerAlignment.h.

◆ d_nFitShape

const int RDKit::GaussianShape::SingleConformerAlignment::d_nFitShape

Definition at line 155 of file SingleConformerAlignment.h.

◆ d_nRefColor

const int RDKit::GaussianShape::SingleConformerAlignment::d_nRefColor

Definition at line 148 of file SingleConformerAlignment.h.

◆ d_nRefShape

const int RDKit::GaussianShape::SingleConformerAlignment::d_nRefShape

Definition at line 147 of file SingleConformerAlignment.h.

◆ d_optimMode

const OptimMode RDKit::GaussianShape::SingleConformerAlignment::d_optimMode

Definition at line 160 of file SingleConformerAlignment.h.

◆ d_qStepSize

double RDKit::GaussianShape::SingleConformerAlignment::d_qStepSize {-0.001}

Definition at line 172 of file SingleConformerAlignment.h.

◆ d_quatTrans

std::array<double, 7> RDKit::GaussianShape::SingleConformerAlignment::d_quatTrans {1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0}

Definition at line 169 of file SingleConformerAlignment.h.

Referenced by setQuatTrans().

◆ d_ref

std::vector<double> RDKit::GaussianShape::SingleConformerAlignment::d_ref

Definition at line 143 of file SingleConformerAlignment.h.

◆ d_refCarbonRadii

const boost::dynamic_bitset* RDKit::GaussianShape::SingleConformerAlignment::d_refCarbonRadii

Definition at line 146 of file SingleConformerAlignment.h.

◆ d_refColorVol

const double RDKit::GaussianShape::SingleConformerAlignment::d_refColorVol

Definition at line 150 of file SingleConformerAlignment.h.

◆ d_refShapeVol

const double RDKit::GaussianShape::SingleConformerAlignment::d_refShapeVol

Definition at line 149 of file SingleConformerAlignment.h.

◆ d_refTemp

std::vector<double> RDKit::GaussianShape::SingleConformerAlignment::d_refTemp

Definition at line 144 of file SingleConformerAlignment.h.

◆ d_refTypes

const int* RDKit::GaussianShape::SingleConformerAlignment::d_refTypes

Definition at line 145 of file SingleConformerAlignment.h.

◆ d_shapeConvergenceCriterion

const double RDKit::GaussianShape::SingleConformerAlignment::d_shapeConvergenceCriterion

Definition at line 166 of file SingleConformerAlignment.h.

◆ d_simAlpha

const double RDKit::GaussianShape::SingleConformerAlignment::d_simAlpha

Definition at line 161 of file SingleConformerAlignment.h.

◆ d_simBeta

const double RDKit::GaussianShape::SingleConformerAlignment::d_simBeta

Definition at line 162 of file SingleConformerAlignment.h.

◆ d_tStepSize

double RDKit::GaussianShape::SingleConformerAlignment::d_tStepSize {-0.01}

Definition at line 173 of file SingleConformerAlignment.h.

◆ d_useCutoff

const bool RDKit::GaussianShape::SingleConformerAlignment::d_useCutoff

Definition at line 164 of file SingleConformerAlignment.h.

The documentation for this struct was generated from the following file:

SingleConformerAlignment.h

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SingleConformerAlignment() [1/4]

◆ SingleConformerAlignment() [2/4]

◆ SingleConformerAlignment() [3/4]

◆ SingleConformerAlignment() [4/4]

◆ ~SingleConformerAlignment()

Member Function Documentation

◆ applyQuatTrans()

◆ calcScores() [1/3]

◆ calcScores() [2/3]

◆ calcScores() [3/3]

◆ calcVolumeAndGradients()

◆ doOverlay()

◆ getFinalQuatTrans()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ optimise()

◆ setQuatTrans()

Member Data Documentation

◆ d_distCutoff2

◆ d_fit

◆ d_fitCarbonRadii

◆ d_fitColorVol

◆ d_fitShapeVol

◆ d_fitTemp

◆ d_fitTypes

◆ d_gradConverters

◆ d_initQuatTrans

◆ d_maxIts

◆ d_mixingParam

◆ d_nFitColor

◆ d_nFitShape

◆ d_nRefColor

◆ d_nRefShape

◆ d_optimMode

◆ d_qStepSize

◆ d_quatTrans

◆ d_ref

◆ d_refCarbonRadii

◆ d_refColorVol

◆ d_refShapeVol

◆ d_refTemp

◆ d_refTypes

◆ d_shapeConvergenceCriterion

◆ d_simAlpha

◆ d_simBeta

◆ d_tStepSize

◆ d_useCutoff