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https://github.com/rdkit/rdkit.git
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20a0759590
* Update `testMHFP.py` to check distance to self is zero * Fix `MHFPEncoder::Distance` to compute a distance instead of a similarity * Fix distance used for testing `MHFPEncoder::Distance` in `testMHFP.py` * Fix expected distance values in `testMHFPFingerprint.cpp` * Fix undeclared variable in `testMHFP.py` * Fix C++ documentation of `MHFPEncoder::Distance` to mention Hamming instead of Jaccard distance
162 lines
4.4 KiB
C++
162 lines
4.4 KiB
C++
//
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// 2019, Daniel Probst, Reymond Group @ University of Bern
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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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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/test.h>
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#include <RDGeneral/utils.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Fingerprints/MHFP.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/Fingerprints/MHFP.h>
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using namespace RDKit;
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void testMHFPInit() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test MHFP fingerprint encoder initialization"
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<< std::endl;
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std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
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std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
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ROMol *mol_s = SmilesToMol(s);
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ROMol *mol_t = SmilesToMol(t);
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MHFPFingerprints::MHFPEncoder enc(128, 42);
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auto fp_s = enc.Encode(s);
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auto fp_t = enc.Encode(t);
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auto fp_mol_s = enc.Encode(*mol_s);
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auto fp_mol_t = enc.Encode(*mol_t);
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TEST_ASSERT(fp_s.size() == 128);
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TEST_ASSERT(fp_s[0] == fp_mol_s[0]);
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TEST_ASSERT(fp_t[127] == fp_mol_t[127]);
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delete mol_s;
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delete mol_t;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testMHFPHashing() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test MHFP hashing of string and uint arrays"
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<< std::endl;
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MHFPFingerprints::MHFPEncoder enc(8);
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std::vector<uint32_t> input_a = {1, 2, 4, 5, 6, 7, 8, 9};
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std::vector<uint32_t> output_a = {188049437, 364485576, 737251017,
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810894466, 300249621, 154369992,
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2221926165, 283729444};
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TEST_ASSERT(enc.FromArray(input_a) == output_a);
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std::vector<std::string> input_b = {"a", "b", "c", "d", "e", "f"};
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std::vector<uint32_t> output_b = {631555539, 835857365, 445245415, 4162827301,
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955545975, 943207071, 712975995, 363547692};
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TEST_ASSERT(enc.FromStringArray(input_b) == output_b);
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testMHFPShingling() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test MHFP shingling creation" << std::endl;
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std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
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std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
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ROMol *mol_s = SmilesToMol(s);
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MHFPFingerprints::MHFPEncoder enc;
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auto fp_s = enc.Encode(s);
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auto fp_t = enc.Encode(t);
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auto sh_a = enc.CreateShingling(s);
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auto sh_b = enc.CreateShingling(*mol_s);
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TEST_ASSERT(sh_a.size() == 44);
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TEST_ASSERT(sh_b.size() == 44);
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TEST_ASSERT(enc.CreateShingling(s, 3, false).size() == 42);
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TEST_ASSERT(enc.CreateShingling(s, 3, true, false, true, 0).size() == 58);
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delete mol_s;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testMHFPSECFP() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test SECFP fingerprint functionality" << std::endl;
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std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
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ROMol *mol_s = SmilesToMol(s);
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MHFPFingerprints::MHFPEncoder enc;
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auto fp_s = enc.EncodeSECFP(s, 3, true, false, true, 1, 16);
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auto fp_mol_s = enc.EncodeSECFP(*mol_s, 3, true, false, true, 1, 16);
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TEST_ASSERT(fp_s.size() == 16);
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TEST_ASSERT(fp_s[10]);
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TEST_ASSERT(fp_s[15]);
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delete mol_s;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testMHFPDistance() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test MHFP shingling creation" << std::endl;
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std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
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std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
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MHFPFingerprints::MHFPEncoder enc;
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auto fp_s = enc.Encode(s);
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auto fp_t = enc.Encode(t);
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TEST_ASSERT(
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feq(MHFPFingerprints::MHFPEncoder::Distance(fp_s, fp_s), 0.0));
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TEST_ASSERT(
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feq(MHFPFingerprints::MHFPEncoder::Distance(fp_s, fp_t), 0.7109375));
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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int main(int argc, char *argv[]) {
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(void)argc;
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(void)argv;
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RDLog::InitLogs();
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testMHFPInit();
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testMHFPShingling();
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testMHFPHashing();
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testMHFPSECFP();
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return 0;
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}
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