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199 lines
7.1 KiB
C++
199 lines
7.1 KiB
C++
//
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// Copyright (C) 2003-2007 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#ifndef __RD_MAXMINPICKER_H__
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#define __RD_MAXMINPICKER_H__
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#include <RDGeneral/types.h>
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#include <RDGeneral/utils.h>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <RDBoost/Exceptions.h>
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#include <cstdlib>
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#include "DistPicker.h"
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#include <boost/random.hpp>
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namespace RDPickers {
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namespace {
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class distmatFunctor{
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public:
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distmatFunctor(const double *distMat) : dp_distMat(distMat) {};
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double operator()(unsigned int i,unsigned int j) {
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return getDistFromLTM(this->dp_distMat,i,j);
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}
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private:
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const double *dp_distMat;
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};
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}
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/*! \brief Implements the MaxMin algorithm for picking a subset of item from a pool
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*
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* This class inherits from the DistPicker and implements a specific picking strategy
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* aimed at diversity. See documentation for "pick()" member function for the algorithm details
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*/
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class MaxMinPicker : public DistPicker {
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public:
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/*! \brief Default Constructor
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*
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*/
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MaxMinPicker() {};
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/*! \brief Contains the implementation for a lazy MaxMin diversity picker
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*
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* See the documentation for the pick() method for details about the algorithm
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*
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* \param func - a function (or functor) taking two unsigned ints as arguments
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* and returning the distance (as a double) between those two elements.
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* \param poolSize - the size of the pool to pick the items from. It is assumed that the
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* distance matrix above contains the right number of elements; i.e.
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* poolSize*(poolSize-1) \n
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* \param pickSize - the number items to pick from pool (<= poolSize)
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* \param firstPicks - (optional)the first items in the pick list
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*/
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template <typename T>
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RDKit::INT_VECT lazyPick(T &func,
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unsigned int poolSize, unsigned int pickSize,
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RDKit::INT_VECT firstpicks=RDKit::INT_VECT(),
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int seed=-1) const;
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/*! \brief Contains the implementation for the MaxMin diversity picker
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*
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* Here is how the picking algorithm works, refer to
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* Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604
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* for more detail:
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*
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* A subset of k items is to be selected from a pool containing N molecules.
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* Then the MaxMin method is as follows:
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* -# Initialise Subset with some appropriately chosen seed
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* compound and set x = 1.
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* -# For each of the N-x remaining compounds in Dataset
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* calculate its dissimilarity with each of the x compounds in
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* Subset and retain the smallest of these x dissimilarities for
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* each compound in Dataset.
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* -# Select the molecule from Dataset with the largest value
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* for the smallest dissimilarity calculated in Step 2 and
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* transfer it to Subset.
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* -# Set x = x + 1 and return to Step 2 if x < k.
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*
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*
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*
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* \param distMat - distance matrix - a vector of double. It is assumed that only the
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* lower triangle element of the matrix are supplied in a 1D array\n
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* \param poolSize - the size of the pool to pick the items from. It is assumed that the
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* distance matrix above contains the right number of elements; i.e.
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* poolSize*(poolSize-1) \n
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* \param pickSize - the number items to pick from pool (<= poolSize)
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* \param firstPicks - indices of the items used to seed the pick set.
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*/
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RDKit::INT_VECT pick(const double *distMat,
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unsigned int poolSize, unsigned int pickSize,
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RDKit::INT_VECT firstPicks,
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int seed=-1) const {
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CHECK_INVARIANT(distMat, "Invalid Distance Matrix");
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if(poolSize<pickSize)
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throw ValueErrorException("pickSize cannot be larger than the poolSize");
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distmatFunctor functor(distMat);
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return this->lazyPick(functor,poolSize,pickSize,firstPicks,seed);
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}
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/*! \overload */
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RDKit::INT_VECT pick(const double *distMat,
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unsigned int poolSize, unsigned int pickSize) const {
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RDKit::INT_VECT iv;
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return pick(distMat,poolSize,pickSize,iv);
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}
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};
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// we implement this here in order to allow arbitrary functors without link errors
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template <typename T>
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RDKit::INT_VECT MaxMinPicker::lazyPick(T &func,
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unsigned int poolSize, unsigned int pickSize,
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RDKit::INT_VECT firstPicks,
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int seed) const {
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if(poolSize<pickSize)
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throw ValueErrorException("pickSize cannot be larger than the poolSize");
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RDKit::INT_LIST pool;
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RDKit::INT_VECT picks;
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picks.reserve(pickSize);
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unsigned int pick=0;
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// enter the pool into a list so that we can pick out of it easily
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for (unsigned int i = 0; i < poolSize; i++) {
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pool.push_back(i);
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}
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// get a seeded random number generator:
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typedef boost::mt19937 rng_type;
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typedef boost::uniform_int<> distrib_type;
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typedef boost::variate_generator<rng_type &,distrib_type> source_type;
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rng_type generator(42u);
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distrib_type dist(0,poolSize);
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source_type randomSource(generator,dist);
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if(seed>0) generator.seed(static_cast<rng_type::result_type>(seed));
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// pick the first entry
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if(!firstPicks.size()){
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pick = randomSource();
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// add the pick to the picks
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picks.push_back(pick);
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// and remove it from the pool
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pool.remove(pick);
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} else{
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for(RDKit::INT_VECT::const_iterator pIdx=firstPicks.begin();
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pIdx!=firstPicks.end();++pIdx){
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pick = static_cast<unsigned int>(*pIdx);
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if(pick>=poolSize)
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throw ValueErrorException("pick index was larger than the poolSize");
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picks.push_back(pick);
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pool.remove(pick);
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}
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}
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// now pick 1 compound at a time
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while (picks.size() < pickSize) {
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double maxOFmin = -1.0;
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RDKit::INT_LIST_I plri=pool.end();
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for(RDKit::INT_LIST_I pli=pool.begin();
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pli!=pool.end(); ++pli){
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unsigned int poolIdx = (*pli);
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double minTOi = RDKit::MAX_DOUBLE;
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for (RDKit::INT_VECT_CI pi = picks.begin();
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pi != picks.end(); ++pi) {
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unsigned int pickIdx = (*pi);
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CHECK_INVARIANT(poolIdx!=pickIdx,"");
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double dist = func(poolIdx,pickIdx);
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if (dist <= minTOi) {
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minTOi = dist;
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}
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}
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if (minTOi > maxOFmin || (RDKit::feq(minTOi,maxOFmin) && poolIdx<pick) ) {
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maxOFmin = minTOi;
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pick = poolIdx;
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plri = pli;
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}
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}
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// now add the new pick to picks and remove it from the pool
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picks.push_back(pick);
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CHECK_INVARIANT(plri!=pool.end(),"");
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pool.erase(plri);
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}
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return picks;
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}
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};
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#endif
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