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//
// Copyright (C) David Cosgrove 2023
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
// This file contains an implementation of Butina clustering
// (Butina JCICS 39 747-750 (1999)) using the RascalMCES
// Johnson similarity metric. It is largely a transliteration
// of $RDBASE/rdkit/ML/Cluster/Butina.py.
#include <algorithm>
#include <iterator>
#include <vector>
#include <set>
#include <GraphMol/ROMol.h>
#include <GraphMol/RascalMCES/RascalMCES.h>
#include <GraphMol/RascalMCES/RascalClusterOptions.h>
#include <GraphMol/RascalMCES/RascalDetails.h>
namespace RDKit {
namespace RascalMCES {
namespace details {
std::vector<std::vector<unsigned int>> buildNborLists(
const std::vector<std::vector<ClusNode>> &proxGraph) {
std::vector<std::vector<unsigned int>> nborLists;
for (size_t i = 0; i < proxGraph.size(); ++i) {
std::vector<std::pair<unsigned int, double>> tmpList;
for (const auto &cn : proxGraph[i]) {
if (cn.d_res) {
if (i == cn.d_mol1Num) {
tmpList.push_back({cn.d_mol2Num, cn.d_sim});
} else {
tmpList.push_back({cn.d_mol1Num, cn.d_sim});
}
}
}
std::sort(tmpList.begin(), tmpList.end(),
[](const std::pair<unsigned int, double> &p1,
const std::pair<unsigned int, double> &p2) -> bool {
return p1.second > p2.second;
});
std::vector<unsigned int> nborList(tmpList.size() + 1, 0);
nborList[0] = i;
std::transform(
tmpList.begin(), tmpList.end(), nborList.begin() + 1,
[](const std::pair<unsigned int, double> &p) -> unsigned int {
return p.first;
});
nborLists.push_back(nborList);
}
std::sort(nborLists.begin(), nborLists.end(),
[](const std::vector<unsigned int> &nl1,
const std::vector<unsigned int> &nl2) -> bool {
if (nl1.size() == nl2.size()) {
return nl1 > nl2;
} else {
return nl1.size() > nl2.size();
}
});
return nborLists;
}
// This function destroys nborLists.
std::vector<std::vector<unsigned int>> formClusters(
std::vector<std::vector<unsigned int>> &nborLists) {
std::vector<std::vector<unsigned int>> clusters;
while (!nborLists.empty()) {
clusters.push_back(nborLists.front());
std::set<unsigned int> inNborList(nborLists.front().begin(),
nborLists.front().end());
nborLists.front().clear();
for (auto &nborList : nborLists) {
for (auto &n : nborList) {
if (inNborList.find(n) != inNborList.end()) {
n = std::numeric_limits<unsigned int>::max();
}
}
nborList.erase(std::remove(nborList.begin(), nborList.end(),
std::numeric_limits<unsigned int>::max()),
nborList.end());
}
nborLists.erase(
std::remove_if(nborLists.begin(), nborLists.end(),
[](const std::vector<unsigned int> &nl) -> bool {
return nl.empty();
}),
nborLists.end());
std::sort(nborLists.begin(), nborLists.end(),
[](const std::vector<unsigned int> &nl1,
const std::vector<unsigned int> &nl2) -> bool {
if (nl1.size() == nl2.size()) {
return nl1 > nl2;
} else {
return nl1.size() > nl2.size();
}
});
}
return clusters;
}
} // namespace details
std::vector<std::vector<unsigned int>> rascalButinaCluster(
const std::vector<std::shared_ptr<ROMol>> &mols,
const RascalClusterOptions &clusOpts) {
auto proxGraph = details::buildProximityGraph(mols, clusOpts);
auto nborLists = details::buildNborLists(proxGraph);
auto clusters = details::formClusters(nborLists);
return clusters;
}
} // namespace RascalMCES
} // namespace RDKit
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