mirror of
https://github.com/rdkit/rdkit.git
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6cfc8f36a7
* initial commit of Roger's contrib * add the new file to the headers list * clang-format * stub of the python wrapper * code added for testing * code added for testing * add LeaderPicker.seq.h * default pickSize value * first crude python wrapper * Add C++ tests for the LeaderPicker combine the thread and non-thread versions * that was not really a test * support providing a functor from Python * no longer need the .seq header * temporarily disable the threaded version to allow CI runs to pass * some refactoring and cleanup
89 lines
2.5 KiB
C++
89 lines
2.5 KiB
C++
//
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// Copyright (C) 2019
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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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#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
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// this in one cpp file
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#include "catch.hpp"
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#include <RDGeneral/types.h>
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#include <RDGeneral/test.h>
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#include <DataStructs/ExplicitBitVect.h>
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#include <DataStructs/BitOps.h>
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#include <SimDivPickers/LeaderPicker.h>
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#include <iostream>
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#include <fstream>
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template <typename T>
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class BVFunctor {
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public:
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BVFunctor(const T &obj) : d_obj(obj) {}
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~BVFunctor() {}
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double operator()(unsigned int i, unsigned int j) {
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double res = 1. - TanimotoSimilarity(*d_obj[i], *d_obj[j]);
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return res;
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}
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const T &d_obj;
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};
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TEST_CASE(
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"Leader Picker basics"
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"[LeaderPicker]") {
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std::string rdbase = getenv("RDBASE");
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std::string fName =
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rdbase + "/Code/SimDivPickers/Wrap/test_data/chembl_cyps.head.fps";
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std::ifstream inf(fName);
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std::string fpsText;
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std::getline(inf, fpsText);
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std::vector<std::unique_ptr<ExplicitBitVect>> fps;
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while (!inf.eof() && !fpsText.empty()) {
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fps.emplace_back(new ExplicitBitVect(fpsText.size() * 4));
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UpdateBitVectFromFPSText(*fps.back(), fpsText);
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std::getline(inf, fpsText);
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};
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REQUIRE(fps.size() == 1000);
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BVFunctor<std::vector<std::unique_ptr<ExplicitBitVect>>> bvf(fps);
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RDPickers::LeaderPicker pkr;
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SECTION("basics1") {
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double threshold = 0.8;
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auto res = pkr.lazyPick(bvf, fps.size(), 0, threshold);
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CHECK(res.size() == 146);
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for (unsigned i = 0; i < res.size(); ++i) {
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for (unsigned j = 0; j < i; ++j) {
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CHECK(bvf(res[i], res[j]) >= threshold);
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}
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}
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}
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SECTION("basics2") {
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double threshold = 0.9;
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auto res = pkr.lazyPick(bvf, fps.size(), 0, threshold);
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CHECK(res.size() == 14);
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for (unsigned i = 0; i < res.size(); ++i) {
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for (unsigned j = 0; j < i; ++j) {
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CHECK(bvf(res[i], res[j]) >= threshold);
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}
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}
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}
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#ifdef RDK_THREADSAFE_SSS
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SECTION("basics multithreaded") {
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double threshold = 0.8;
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RDKit::INT_VECT firstPicks;
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int nThreads = 0; // use max available
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auto res =
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pkr.lazyPick(bvf, fps.size(), 0, firstPicks, threshold, nThreads);
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CHECK(res.size() == 146);
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for (unsigned i = 0; i < res.size(); ++i) {
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for (unsigned j = 0; j < i; ++j) {
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CHECK(bvf(res[i], res[j]) >= threshold);
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}
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}
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}
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#endif
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}
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