RDPickers::MaxMinPicker Class Reference

Implements the MaxMin algorithm for picking a subset of item from a pool. More...

#include <MaxMinPicker.h>

Inheritance diagram for RDPickers::MaxMinPicker:

Public Member Functions
	MaxMinPicker ()
	Default Constructor.
template<typename T >
RDKit::INT_VECT	lazyPick (T &func, unsigned int poolSize, unsigned int pickSize) const
	Contains the implementation for a lazy MaxMin diversity picker.
template<typename T >
RDKit::INT_VECT	lazyPick (T &func, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, int seed=-1) const
template<typename T >
RDKit::INT_VECT	lazyPick (T &func, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, int seed, double &threshold) const
RDKit::INT_VECT	pick (const double *distMat, unsigned int poolSize, unsigned int pickSize, RDKit::INT_VECT firstPicks, int seed=-1) const
	Contains the implementation for the MaxMin diversity picker.
RDKit::INT_VECT	pick (const double *distMat, unsigned int poolSize, unsigned int pickSize) const override
Public Member Functions inherited from RDPickers::DistPicker
	DistPicker ()
	Default constructor.
virtual	~DistPicker ()

Detailed Description

Implements the MaxMin algorithm for picking a subset of item from a pool.

This class inherits from the DistPicker and implements a specific picking strategy aimed at diversity. See documentation for "pick()" member function for the algorithm details

Definition at line 35 of file MaxMinPicker.h.

Constructor & Destructor Documentation

MaxMinPicker()

RDPickers::MaxMinPicker::MaxMinPicker ( )

inline

Default Constructor.

Definition at line 40 of file MaxMinPicker.h.

Member Function Documentation

lazyPick() [1/3]

template<typename T >

RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick	(	T &	func,
		unsigned int	poolSize,
		unsigned int	pickSize
	)		const

Contains the implementation for a lazy MaxMin diversity picker.

See the documentation for the pick() method for details about the algorithm

Parameters

func	- a function (or functor) taking two unsigned ints as arguments and returning the distance (as a double) between those two elements.
poolSize	- the size of the pool to pick the items from. It is assumed that the distance matrix above contains the right number of elements; i.e. poolSize*(poolSize-1)
pickSize	- the number items to pick from pool (<= poolSize)
firstPicks	- (optional)the first items in the pick list
seed	- (optional) seed for the random number generator. If this is <0 the generator will be seeded with a random number.

Definition at line 293 of file MaxMinPicker.h.

References lazyPick().

Referenced by lazyPick(), and lazyPick().

lazyPick() [2/3]

template<typename T >

RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick	(	T &	func,
		unsigned int	poolSize,
		unsigned int	pickSize,
		const RDKit::INT_VECT &	firstPicks,
		int	seed,
		double &	threshold
	)		const

Definition at line 144 of file MaxMinPicker.h.

References CHECK_INVARIANT, RDPickers::MaxMinPickInfo::dist_bound, RDPickers::MaxMinPickInfo::next, pick(), and RDPickers::MaxMinPickInfo::picks.

lazyPick() [3/3]

template<typename T >

RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick	(	T &	func,
		unsigned int	poolSize,
		unsigned int	pickSize,
		const RDKit::INT_VECT &	firstPicks,
		int	seed = -1
	)		const

Definition at line 283 of file MaxMinPicker.h.

References lazyPick().

pick() [1/2]

RDKit::INT_VECT RDPickers::MaxMinPicker::pick ( const double *  distMat, unsigned int  poolSize, unsigned int  pickSize  ) const

inlineoverridevirtual

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Implements RDPickers::DistPicker.

Definition at line 128 of file MaxMinPicker.h.

pick() [2/2]

RDKit::INT_VECT RDPickers::MaxMinPicker::pick ( const double *  distMat, unsigned int  poolSize, unsigned int  pickSize, RDKit::INT_VECT  firstPicks, int  seed = -1  ) const

inline

Contains the implementation for the MaxMin diversity picker.

Here is how the picking algorithm works, refer to Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604 for more detail:

A subset of k items is to be selected from a pool containing N molecules. Then the MaxMin method is as follows:

1. Initialise Subset with some appropriately chosen seed compound and set x = 1.
2. For each of the N-x remaining compounds in Dataset calculate its dissimilarity with each of the x compounds in Subset and retain the smallest of these x dissimilarities for each compound in Dataset.
3. Select the molecule from Dataset with the largest value for the smallest dissimilarity calculated in Step 2 and transfer it to Subset.
4. Set x = x + 1 and return to Step 2 if x < k.

Parameters

distMat	- distance matrix - a vector of double. It is assumed that only the lower triangle element of the matrix are supplied in a 1D array
poolSize	- the size of the pool to pick the items from. It is assumed that the distance matrix above contains the right number of elements; i.e. poolSize*(poolSize-1)
pickSize	- the number items to pick from pool (<= poolSize)
firstPicks	- indices of the items used to seed the pick set.
seed	- (optional) seed for the random number generator If this is <0 the generator will be seeded with a random number.

Definition at line 113 of file MaxMinPicker.h.

References CHECK_INVARIANT.

Referenced by lazyPick().

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

• MaxMinPicker.h