mirror of
https://github.com/rdkit/rdkit.git
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21b3c4e6f1
* Add MolTransforms library. * Transform to inertial frame of reference before overlay. * Vital fix of typo in comment. * Tidy up debugging cruft. * Comment in CMakeLists.txt. * Fix python wrappers. * Extra tidy. * Response to review. * Tidy includes. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
666 lines
30 KiB
C++
666 lines
30 KiB
C++
#include <catch2/catch_test_macros.hpp>
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#include <catch2/matchers/catch_matchers_floating_point.hpp>
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#include <iostream>
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#include <sstream>
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#include <stdexcept>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/RWMol.h>
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#include "PubChemShape.hpp"
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#include "GraphMol/SmilesParse/SmilesWrite.h"
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using namespace RDKit;
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constexpr double test_opt_param = 0.5;
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constexpr unsigned int test_max_preiters = 3;
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constexpr unsigned int test_max_postiters = 16;
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constexpr bool test_use_colors = true;
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TEST_CASE("basic alignment") {
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std::string dirName = getenv("RDBASE");
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dirName += "/External/pubchem_shape/test_data";
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auto suppl = v2::FileParsers::SDMolSupplier(dirName + "/test1.sdf");
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auto ref = suppl[0];
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REQUIRE(ref);
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auto probe = suppl[1];
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REQUIRE(probe);
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SECTION("basics") {
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RWMol cp(*probe);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, cp, matrix, -1, -1, test_use_colors, test_opt_param,
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test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.773, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.303, 0.005));
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for (auto i = 0u; i < probe->getNumAtoms(); ++i) {
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CHECK(probe->getConformer().getAtomPos(i).x !=
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cp.getConformer().getAtomPos(i).x);
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}
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}
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SECTION("from shape") {
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auto ref_shape = PrepareConformer(*ref);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(ref_shape, *probe, matrix, -1, test_use_colors,
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test_opt_param, test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.773, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.303, 0.005));
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}
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SECTION("RDKit features") {
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ref->clearProp("PUBCHEM_PHARMACOPHORE_FEATURES");
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probe->clearProp("PUBCHEM_PHARMACOPHORE_FEATURES");
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, *probe, matrix, -1, -1, test_use_colors,
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test_opt_param, test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.773, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.231, 0.005));
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}
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SECTION("no colors") {
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std::vector<float> matrix(12, 0.0);
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int refConfId = -1;
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int prbConfId = -1;
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bool useColors = false;
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, *probe, matrix, refConfId, prbConfId, useColors,
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test_opt_param, test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.773, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.000, 0.005));
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}
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SECTION("we are re-entrant") {
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RWMol cp(*probe);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, cp, matrix, -1, -1, test_use_colors, test_opt_param,
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test_max_preiters, test_max_postiters);
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RWMol cp2(cp);
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auto [nbr_st2, nbr_ct2] =
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AlignMolecule(*ref, cp2, matrix, -1, -1, test_use_colors,
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test_opt_param, test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(nbr_st2, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(nbr_ct2, 0.005));
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for (auto i = 0u; i < probe->getNumAtoms(); ++i) {
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CHECK_THAT(
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cp.getConformer().getAtomPos(i).x,
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Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).x, 0.05));
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CHECK_THAT(
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cp.getConformer().getAtomPos(i).y,
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Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).y, 0.05));
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CHECK_THAT(
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cp.getConformer().getAtomPos(i).z,
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Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).z, 0.05));
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}
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}
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}
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TEST_CASE("bulk") {
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std::string dirName = getenv("RDBASE");
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dirName += "/External/pubchem_shape/test_data";
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auto suppl = v2::FileParsers::SDMolSupplier(dirName + "/bulk.pubchem.sdf");
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auto ref = suppl[0];
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REQUIRE(ref);
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for (auto i = 1u; i < suppl.length(); ++i) {
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auto probe = suppl[1];
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REQUIRE(probe);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, *probe, matrix, -1, -1, test_use_colors,
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test_opt_param, test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st,
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Catch::Matchers::WithinAbs(
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probe->getProp<float>("shape_align_shape_tanimoto"), 0.005));
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CHECK_THAT(nbr_ct,
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Catch::Matchers::WithinAbs(
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probe->getProp<float>("shape_align_color_tanimoto"), 0.005));
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}
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}
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TEST_CASE("handling molecules with Hs") {
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std::string dirName = getenv("RDBASE");
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dirName += "/External/pubchem_shape/test_data";
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v2::FileParsers::MolFileParserParams params;
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params.removeHs = false;
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auto suppl =
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v2::FileParsers::SDMolSupplier(dirName + "/align_with_hs.sdf", params);
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auto ref = suppl[0];
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REQUIRE(ref);
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auto probe = suppl[1];
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REQUIRE(probe);
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ShapeInputOptions mol1Opts, mol2Opts;
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SECTION("basics") {
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RWMol cp(*probe);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, cp, matrix, -1, -1, test_use_colors, test_opt_param,
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test_max_preiters, test_max_postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.840, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.753, 0.005));
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for (auto i = 0u; i < cp.getNumAtoms(); ++i) {
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// the failure mode here was that Hs had HUGE coordinates
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auto pos = cp.getConformer().getAtomPos(i);
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CHECK((pos.x > -10 && pos.x < 10));
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}
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}
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}
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TEST_CASE("re-entrant") {
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SECTION("basics") {
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auto ref = R"CTAB(
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RDKit 3D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 5 5 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -4.333279 6.212121 0.00000 0
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M V30 2 C -5.393939 5.151461 0.100000 0
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M V30 3 C -6.454600 6.212121 0.000000 0
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M V30 4 C -5.393939 7.272781 0.100000 0
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M V30 5 C -2.833279 6.212121 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 3 4
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M V30 4 1 4 1
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M V30 5 1 5 1
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M V30 END BOND
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M V30 END CTAB
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M END
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$$$$
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)CTAB"_ctab;
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auto probe = R"CTAB(
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RDKit 3D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 6 6 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -4.333279 8.212121 0.000000 0
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M V30 2 C -5.393939 7.151461 0.100000 0
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M V30 3 C -6.454600 8.212121 0.000000 0
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M V30 4 C -5.393939 9.272781 0.100000 0
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M V30 5 C -2.833279 8.212121 0.000000 0
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M V30 6 C -1.333279 8.212121 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 3 4
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M V30 4 1 4 1
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M V30 5 1 5 1
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M V30 6 1 5 6
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M V30 END BOND
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M V30 END CTAB
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M END
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$$$$
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)CTAB"_ctab;
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MolOps::removeAllHs(*ref);
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MolOps::removeAllHs(*probe);
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RWMol cp(*probe);
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std::vector<float> matrix(12, 0.0);
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bool useColors = true;
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int refConfId = -1;
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int prbConfId = -1;
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double opt_param = 1.0;
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unsigned int preiters = 100u;
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unsigned int postiters = 100u;
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, cp, matrix, refConfId, prbConfId, useColors,
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opt_param, preiters, postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.923, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.882, 0.005));
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auto rmsd = MolAlign::CalcRMS(*ref, cp);
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CHECK_THAT(rmsd, Catch::Matchers::WithinAbs(0.255, 0.005));
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RWMol cp2(cp);
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auto [nbr_st2, nbr_ct2] =
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AlignMolecule(*ref, cp2, matrix, refConfId, prbConfId, useColors,
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opt_param, preiters, postiters);
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CHECK_THAT(nbr_st2, Catch::Matchers::WithinAbs(nbr_st2, 0.005));
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CHECK_THAT(nbr_ct2, Catch::Matchers::WithinAbs(nbr_ct2, 0.005));
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auto rmsd2 = MolAlign::CalcRMS(cp, cp2);
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CHECK_THAT(rmsd2, Catch::Matchers::WithinAbs(0.0, 0.005));
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}
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SECTION("real example") {
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std::string dirName = getenv("RDBASE");
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dirName += "/External/pubchem_shape/test_data";
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v2::FileParsers::MolFileParserParams params;
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params.removeHs = false;
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auto suppl =
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v2::FileParsers::SDMolSupplier(dirName + "/P17612.sdf", params);
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auto ref = suppl[0];
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REQUIRE(ref);
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auto probe = suppl[1];
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REQUIRE(probe);
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MolOps::removeAllHs(*ref);
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MolOps::removeAllHs(*probe);
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RWMol cp(*probe);
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std::vector<float> matrix(12, 0.0);
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bool useColors = true;
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int refConfId = -1;
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int prbConfId = -1;
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double opt_param = 1.0;
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unsigned int preiters = 100u;
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unsigned int postiters = 100u;
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auto [nbr_st, nbr_ct] =
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AlignMolecule(*ref, cp, matrix, refConfId, prbConfId, useColors,
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opt_param, preiters, postiters);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.483, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.046, 0.005));
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RWMol cp2(cp);
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auto [nbr_st2, nbr_ct2] =
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AlignMolecule(*ref, cp2, matrix, refConfId, prbConfId, useColors,
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opt_param, preiters, postiters);
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CHECK_THAT(nbr_st2, Catch::Matchers::WithinAbs(nbr_st, 0.005));
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CHECK_THAT(nbr_ct2, Catch::Matchers::WithinAbs(nbr_ct, 0.005));
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auto rmsd = MolAlign::CalcRMS(cp, cp2);
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CHECK_THAT(rmsd, Catch::Matchers::WithinAbs(0.007, 0.005));
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}
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}
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TEST_CASE("Github #8096") {
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SECTION("as reported") {
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auto m1 =
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"[H]c1c([H])c([H])c([2H])c([H])c1[H] |(1.55967,1.91617,0.0546381;0.885536,1.07172,0.030849;1.38172,-0.23747,0.0274262;2.44539,-0.439501,0.0483424;0.470206,-1.27516,-0.00361916;0.856925,-2.30002,-0.00633525;-0.896665,-1.07227,-0.0310991;-1.60071,-1.87642,-0.0551085;-1.36315,0.22877,-0.0271173;-2.43593,0.379132,-0.0487835;-0.479018,1.29083,0.00359778;-0.823965,2.31421,0.00720933)|"_smiles;
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REQUIRE(m1);
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auto m2 =
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"[H]c1c([H])c([H])c([H])c([H])c1[H] |(-2.06264,-0.844763,-0.0261403;-1.04035,-0.481453,-0.0114878;-0.00743655,-1.41861,-0.0137121;-0.215455,-2.47997,-0.0295909;1.29853,-0.949412,0.00507497;2.12524,-1.65277,0.00390664;1.58501,0.395878,0.0254188;2.61997,0.704365,0.0394811;0.550242,1.31385,0.0273741;0.783172,2.37039,0.0434262;-0.763786,0.88847,0.00908113;-1.60557,1.58532,0.0100194)|"_smiles;
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REQUIRE(m2);
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std::vector<float> matrix(12, 0.0);
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auto [nbr_st, nbr_ct] = AlignMolecule(*m1, *m2, matrix);
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CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(1.0, 0.005));
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CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(1.0, 0.005));
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}
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}
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#ifdef RDK_USE_BOOST_SERIALIZATION
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TEST_CASE("Serialization") {
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auto m1 =
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"[H]c1c([H])c([H])c([H])c([H])c1[H] |(-2.06264,-0.844763,-0.0261403;-1.04035,-0.481453,-0.0114878;-0.00743655,-1.41861,-0.0137121;-0.215455,-2.47997,-0.0295909;1.29853,-0.949412,0.00507497;2.12524,-1.65277,0.00390664;1.58501,0.395878,0.0254188;2.61997,0.704365,0.0394811;0.550242,1.31385,0.0273741;0.783172,2.37039,0.0434262;-0.763786,0.88847,0.00908113;-1.60557,1.58532,0.0100194)|"_smiles;
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REQUIRE(m1);
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auto shape = PrepareConformer(*m1);
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auto istr = shape.toString();
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ShapeInput shape2(istr);
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CHECK(shape2.coord == shape.coord);
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CHECK(shape2.alpha_vector == shape.alpha_vector);
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CHECK(shape2.atom_type_vector == shape.atom_type_vector);
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CHECK(shape2.volumeAtomIndexVector == shape.volumeAtomIndexVector);
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CHECK(shape2.colorAtomType2IndexVectorMap ==
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shape.colorAtomType2IndexVectorMap);
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CHECK(shape2.shift == shape.shift);
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CHECK_THAT(shape2.sov, Catch::Matchers::WithinAbs(253.764, 0.005));
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CHECK_THAT(shape2.sof, Catch::Matchers::WithinAbs(5.074, 0.005));
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}
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#endif
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TEST_CASE("d2CutOff set") {
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// Previously, shape1.sov and shape2.sov were slightly different because
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// useCutOff was only being set in AlignMolecule, not PrepareConformer.
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// Thus aligning a different molecule meant that PrepareConformer gave
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// different results before and after the alignment.
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auto m1 =
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"c1ccc(-c2ccccc2)cc1 |(-3.26053,-0.0841607,-0.741909;-2.93383,0.123873,0.593407;-1.60713,0.377277,0.917966;-0.644758,0.654885,-0.0378428;0.743308,0.219134,0.168663;1.82376,1.0395,-0.0112769;3.01462,0.695405,0.613858;3.18783,-0.589771,1.09649;2.15761,-1.50458,1.01949;0.988307,-1.1313,0.385783;-1.1048,0.797771,-1.34022;-2.39754,0.435801,-1.69921)|"_smiles;
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REQUIRE(m1);
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auto shape1 = PrepareConformer(*m1, -1);
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std::vector<float> matrix(12, 0.0);
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auto m2 =
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"c1ccc(-c2ccccc2)cc1 |(-3.26053,-0.0841607,-0.741909;-2.93383,0.123873,0.593407;-1.60713,0.377277,0.917966;-0.644758,0.654885,-0.0378428;0.743308,0.219134,0.168663;1.82376,1.0395,-0.0112769;3.01462,0.695405,0.613858;3.18783,-0.589771,1.09649;2.15761,-1.50458,1.01949;0.988307,-1.1313,0.385783;-1.1048,0.797771,-1.34022;-2.39754,0.435801,-1.69921)|"_smiles;
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REQUIRE(m2);
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AlignMolecule(*m2, *m2, matrix);
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auto shape2 = PrepareConformer(*m1, -1);
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CHECK(shape1.sov == shape2.sov);
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}
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TEST_CASE("Overlay onto shape bug (Github8462)") {
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auto m1 =
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"c1ccc(-c2ccccc2)cc1 |(-3.26053,-0.0841607,-0.741909;-2.93383,0.123873,0.593407;-1.60713,0.377277,0.917966;-0.644758,0.654885,-0.0378428;0.743308,0.219134,0.168663;1.82376,1.0395,-0.0112769;3.01462,0.695405,0.613858;3.18783,-0.589771,1.09649;2.15761,-1.50458,1.01949;0.988307,-1.1313,0.385783;-1.1048,0.797771,-1.34022;-2.39754,0.435801,-1.69921)|"_smiles;
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REQUIRE(m1);
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ROMol m2(*m1);
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for (auto a : m2.atoms()) {
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auto &pos = m2.getConformer().getAtomPos(a->getIdx());
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pos.x += 3.0;
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pos.y += 2.0;
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}
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ROMol m3(m2);
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std::vector<float> matrix(12, 0.0);
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auto [st, ct] = AlignMolecule(*m1, m2, matrix);
|
|
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.0, 0.005));
|
|
CHECK_THAT(ct, Catch::Matchers::WithinAbs(1.0, 0.005));
|
|
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
|
|
auto pos1 = m1->getConformer().getAtomPos(i);
|
|
auto pos2 = m2.getConformer().getAtomPos(i);
|
|
CHECK_THAT((pos1 - pos2).length(), Catch::Matchers::WithinAbs(0.0, 0.005));
|
|
}
|
|
|
|
auto s1 = PrepareConformer(*m1, -1);
|
|
auto [st1, ct1] = AlignMolecule(s1, m3, matrix);
|
|
CHECK_THAT(st1, Catch::Matchers::WithinAbs(1.0, 0.005));
|
|
CHECK_THAT(ct1, Catch::Matchers::WithinAbs(1.0, 0.005));
|
|
for (unsigned int i = 0; i < m3.getNumAtoms(); ++i) {
|
|
RDGeom::Point3D pos1(s1.coord[3 * i], s1.coord[3 * i + 1],
|
|
s1.coord[3 * i + 2]);
|
|
auto pos2 = m3.getConformer().getAtomPos(i);
|
|
CHECK_THAT((pos1 - pos2).length(), Catch::Matchers::WithinAbs(0.0, 0.005));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Shape subset") {
|
|
auto m1 =
|
|
"c1ccc(-c2ccccc2)cc1 |(-3.26053,-0.0841607,-0.741909;-2.93383,0.123873,0.593407;-1.60713,0.377277,0.917966;-0.644758,0.654885,-0.0378428;0.743308,0.219134,0.168663;1.82376,1.0395,-0.0112769;3.01462,0.695405,0.613858;3.18783,-0.589771,1.09649;2.15761,-1.50458,1.01949;0.988307,-1.1313,0.385783;-1.1048,0.797771,-1.34022;-2.39754,0.435801,-1.69921)|"_smiles;
|
|
REQUIRE(m1);
|
|
ShapeInputOptions shapeOpts;
|
|
shapeOpts.atomSubset = std::vector<unsigned int>{0, 1, 2, 3, 10, 11};
|
|
auto partShape = PrepareConformer(*m1, -1, shapeOpts);
|
|
CHECK(partShape.coord.size() == 21);
|
|
CHECK_THAT(partShape.sov, Catch::Matchers::WithinAbs(253.929, 0.005));
|
|
CHECK_THAT(partShape.sof, Catch::Matchers::WithinAbs(5.074, 0.005));
|
|
|
|
shapeOpts.atomSubset.clear();
|
|
auto wholeShape = PrepareConformer(*m1, -1, shapeOpts);
|
|
CHECK(wholeShape.coord.size() == 42);
|
|
CHECK_THAT(wholeShape.sov, Catch::Matchers::WithinAbs(542.04, 0.005));
|
|
CHECK_THAT(wholeShape.sof, Catch::Matchers::WithinAbs(10.148, 0.005));
|
|
}
|
|
|
|
TEST_CASE("Dummy radii") {
|
|
auto m1 =
|
|
"[Xe]c1ccccc1 |(0.392086,-2.22477,0.190651;0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097),atomProp:0.dummyLabel.*|"_smiles;
|
|
auto shape1 = PrepareConformer(*m1, -1);
|
|
CHECK(shape1.coord.size() == 24);
|
|
|
|
// The dummy radius defaults to 2.16, the same as Xe, so these shapes should
|
|
// come out the same.
|
|
auto m2 =
|
|
"*c1ccccc1 |(0.392086,-2.22477,0.190651;0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097),atomProp:0.dummyLabel.*|"_smiles;
|
|
ShapeInputOptions shapeOpts;
|
|
shapeOpts.includeDummies = true;
|
|
auto shape2 = PrepareConformer(*m2, -1, shapeOpts);
|
|
CHECK(shape2.coord.size() == 24);
|
|
CHECK(shape1.sov == shape2.sov);
|
|
|
|
shapeOpts.dummyRadius = 2.5;
|
|
auto shape3 = PrepareConformer(*m2, -1, shapeOpts);
|
|
CHECK_THAT(shape3.sov, Catch::Matchers::WithinAbs(427.925, 0.005));
|
|
|
|
shapeOpts.includeDummies = false;
|
|
auto shape4 = PrepareConformer(*m2, -1, shapeOpts);
|
|
CHECK(shape4.coord.size() == 21);
|
|
CHECK(shape4.sov < shape2.sov);
|
|
CHECK_THAT(shape4.sov, Catch::Matchers::WithinAbs(254.578, 0.005));
|
|
}
|
|
|
|
TEST_CASE("Non-standard radii") {
|
|
auto m1 =
|
|
"[Xe]c1ccccc1 |(0.392086,-2.22477,0.190651;0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097),atomProp:0.dummyLabel.*|"_smiles;
|
|
auto shape1 = PrepareConformer(*m1, -1);
|
|
CHECK(shape1.coord.size() == 24);
|
|
CHECK_THAT(shape1.sov, Catch::Matchers::WithinAbs(376.434, 0.005));
|
|
|
|
ShapeInputOptions shapeOpts;
|
|
// Benzene derivative with atom 4 with an N radius.
|
|
shapeOpts.atomRadii =
|
|
std::vector<std::pair<unsigned int, double>>{{0, 2.5}, {4, 1.55}};
|
|
auto shape2 = PrepareConformer(*m1, -1, shapeOpts);
|
|
CHECK_THAT(shape2.sov, Catch::Matchers::WithinAbs(412.666, 0.005));
|
|
|
|
// Corresponding pyridine derivative.
|
|
auto m2 =
|
|
"[Xe]c1ccncc1 |(0.392086,-2.22477,0.190651;0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097),atomProp:0.dummyLabel.*|"_smiles;
|
|
auto shape3 = PrepareConformer(*m2, -1, shapeOpts);
|
|
CHECK(shape3.sov == shape2.sov);
|
|
}
|
|
|
|
TEST_CASE("Shape-Shape alignment") {
|
|
std::string dirName = getenv("RDBASE");
|
|
dirName += "/External/pubchem_shape/test_data";
|
|
|
|
auto suppl = v2::FileParsers::SDMolSupplier(dirName + "/test1.sdf");
|
|
auto ref = suppl[0];
|
|
REQUIRE(ref);
|
|
auto probe = suppl[1];
|
|
REQUIRE(probe);
|
|
RWMol probeCP(*probe);
|
|
|
|
auto refShape = PrepareConformer(*ref, -1);
|
|
auto probeShape = PrepareConformer(*probe, -1);
|
|
|
|
std::vector<float> matrix(12, 0.0);
|
|
auto [mol_st, mol_ct] = AlignMolecule(*ref, *probe, matrix, -1, -1);
|
|
auto [shape_st, shape_ct] = AlignShape(refShape, probeShape, matrix);
|
|
|
|
// Check that the same results are achieved when overlaying the probe
|
|
// molecule onto the reference molecule and the probe shape onto the reference
|
|
// shape. The shapes are transformed to their centroid and principal axes, so
|
|
// the final coords will not match. Just check the tanimotos.
|
|
CHECK_THAT(shape_st, Catch::Matchers::WithinAbs(mol_st, 0.001));
|
|
CHECK_THAT(shape_ct, Catch::Matchers::WithinAbs(mol_ct, 0.001));
|
|
}
|
|
|
|
TEST_CASE("Atoms excluded from Color features") {
|
|
auto m1 =
|
|
"Nc1ccccc1 |(0.392086,-2.22477,0.190651;0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097),atomProp:0.dummyLabel.*|"_smiles;
|
|
auto shape1 = PrepareConformer(*m1, -1);
|
|
// The aniline N comes out as a donor, acceptor and basic so gets 3
|
|
// features.
|
|
CHECK(shape1.coord.size() == 33);
|
|
ShapeInputOptions opts;
|
|
opts.notColorAtoms = std::vector<unsigned int>{0};
|
|
auto shape2 = PrepareConformer(*m1, -1, opts);
|
|
CHECK(shape2.coord.size() == 24);
|
|
}
|
|
|
|
TEST_CASE("Hs not properly transformed when hcount = feature count") {
|
|
std::string dirName = getenv("RDBASE");
|
|
dirName += "/External/pubchem_shape/test_data";
|
|
|
|
SECTION("as reported") {
|
|
v2::FileParsers::MolFileParserParams ps;
|
|
ps.removeHs = false;
|
|
auto mol1 =
|
|
v2::FileParsers::MolFromMolFile(dirName + "/hcount_ex1_1.mol", ps);
|
|
REQUIRE(mol1);
|
|
auto mol2 =
|
|
v2::FileParsers::MolFromMolFile(dirName + "/hcount_ex1_2.mol", ps);
|
|
REQUIRE(mol2);
|
|
|
|
{
|
|
RWMol cp(*mol2);
|
|
std::vector<float> matrix(12, 0.0);
|
|
auto [nbr_st, nbr_ct] =
|
|
AlignMolecule(*mol1, cp, matrix, -1, -1, true, 1.0, 30, 30);
|
|
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.911, 0.005));
|
|
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.555, 0.005));
|
|
|
|
// the bug led to H atoms in stupid positions, so we can detect it by just
|
|
// looking at bond lengths to Hs:
|
|
for (auto i = cp.getNumHeavyAtoms(); i < cp.getNumAtoms(); ++i) {
|
|
INFO("checking atom " << i);
|
|
auto at = cp.getAtomWithIdx(i);
|
|
for (auto nbr : cp.atomNeighbors(at)) {
|
|
auto dist = (cp.getConformer().getAtomPos(i) -
|
|
cp.getConformer().getAtomPos(nbr->getIdx()))
|
|
.length();
|
|
CHECK(dist < 1.2); // should be a bond to H
|
|
}
|
|
}
|
|
|
|
MolToMolFile(*mol1, "m1_out.mol");
|
|
MolToMolFile(cp, "m2_out.mol");
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("custom feature points") {
|
|
auto m1 =
|
|
"O=CC=O |(-1.75978,0.148897,0;-0.621382,-0.394324,0;0.624061,0.3656,.1;1.7571,-0.120174,.1)|"_smiles;
|
|
SECTION("using shapes") {
|
|
auto shape1 = PrepareConformer(*m1, -1);
|
|
// each carbonyl O gets one feature:
|
|
CHECK(shape1.coord.size() == 18);
|
|
ShapeInputOptions opts2;
|
|
opts2.customFeatures = {{1, RDGeom::Point3D(-1.75978, 0.148897, 0), 1.0},
|
|
{2, RDGeom::Point3D(1.7571, -0.120174, 0.1), 1.0}};
|
|
auto shape2 = PrepareConformer(*m1, -1, opts2);
|
|
CHECK(shape2.coord.size() == 18);
|
|
|
|
{
|
|
// confirm that we don't add the features if useColors is false
|
|
ShapeInputOptions topts;
|
|
topts.customFeatures = {
|
|
{1, RDGeom::Point3D(-1.75978, 0.148897, 0), 1.0},
|
|
{2, RDGeom::Point3D(1.7571, -0.120174, 0.1), 1.0}};
|
|
topts.useColors = false;
|
|
auto tshape = PrepareConformer(*m1, -1, topts);
|
|
CHECK(tshape.coord.size() == 12);
|
|
}
|
|
|
|
// we'll swap the features on the second shape so that the alignment has to
|
|
// be inverted
|
|
ShapeInputOptions opts3;
|
|
opts3.customFeatures = {{2, RDGeom::Point3D(-1.75978, 0.148897, 0), 1.0},
|
|
{1, RDGeom::Point3D(1.7571, -0.120174, 0.1), 1.0}};
|
|
|
|
auto m2 = ROMol(*m1);
|
|
auto shape3 = PrepareConformer(m2, -1, opts3);
|
|
CHECK(shape3.coord.size() == 18);
|
|
double opt_param = 0.5;
|
|
std::vector<float> matrix(12, 0.0);
|
|
auto [st, ct] = AlignShape(shape2, shape3, matrix, opt_param);
|
|
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.000, 0.001));
|
|
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.997, 0.001));
|
|
CHECK(shape3.coord[0] > 0); // x coord of first atom
|
|
CHECK(shape3.coord[3 * 3] < 0); // x coord of fourth atom
|
|
|
|
auto conf = m2.getConformer(-1);
|
|
TransformConformer(shape2.shift, shape2.inertialRot, matrix, shape3, conf);
|
|
CHECK(conf.getAtomPos(0).x > 0);
|
|
CHECK(conf.getAtomPos(3).x < 0);
|
|
}
|
|
SECTION("using molecules") {
|
|
ShapeInputOptions opts2;
|
|
opts2.customFeatures = {{1, RDGeom::Point3D(-1.75978, 0.148897, 0), 1.0},
|
|
{2, RDGeom::Point3D(1.7571, -0.120174, 0.1), 1.0}};
|
|
|
|
auto m2 = ROMol(*m1);
|
|
// we'll swap the features on the second shape so that the alignment has to
|
|
// be inverted
|
|
ShapeInputOptions opts3;
|
|
opts3.customFeatures = {{2, RDGeom::Point3D(-1.75978, 0.148897, 0), 1.0},
|
|
{1, RDGeom::Point3D(1.7571, -0.120174, 0.1), 1.0}};
|
|
|
|
double opt_param = 0.5;
|
|
std::vector<float> matrix(12, 0.0);
|
|
auto [st, ct] =
|
|
AlignMolecule(*m1, m2, matrix, opts2, opts3, -2, -2, opt_param);
|
|
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.000, 0.001));
|
|
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.997, 0.001));
|
|
auto conf = m2.getConformer(-1);
|
|
CHECK(conf.getAtomPos(0).x > 0);
|
|
CHECK(conf.getAtomPos(3).x < 0);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Score No Overlay") {
|
|
// These are 2 ligands used by Andy Grant and Co in their original paper
|
|
// https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19961115)17:14%3C1653::AID-JCC7%3E3.0.CO;2-K
|
|
// Ligands as extracted from PDB, with a bit of munging to get them as
|
|
// SMILES strings (downloaded the Ideal ligand structures from RCSB
|
|
// as SDFs and transferred the corresponding atom coords from 3tmn and 1tmn).
|
|
auto pdb_trp_3tmn =
|
|
R"(N[C@H](C(=O)O)Cc1c[nH]c2c1cccc2 |(37.935,40.394,-3.825;39.119,39.593,-4.13;38.758,38.486,-5.101;37.526,38.337,-5.395;39.716,37.852,-5.605;39.883,39.108,-2.906;39.086,38.098,-2.209;38.093,38.363,-1.34;37.565,37.179,-0.881;38.201,36.136,-1.471;39.193,36.684,-2.308;40.015,35.812,-3.036;39.846,34.441,-2.913;38.844,33.933,-2.075;38.015,34.752,-1.333),wU:1.0|)"_smiles;
|
|
REQUIRE(pdb_trp_3tmn);
|
|
auto pdb_0zn_1tmn =
|
|
R"([C@H](CCc1ccccc1)(C(=O)O)N[C@H](C(=O)N[C@H](C(=O)O)Cc1c[nH]c2c1cccc2)CC(C)C |(35.672,41.482,-5.722;34.516,40.842,-6.512;34.843,39.355,-6.7;33.819,38.475,-7.45;33.825,38.414,-8.838;32.951,37.553,-9.53;32.064,36.747,-8.81;32.096,36.799,-7.402;32.985,37.656,-6.73;35.934,42.778,-6.452;36.833,42.858,-7.316;35.175,43.735,-6.275;35.516,41.561,-4.218;36.707,42.096,-3.513;38.055,41.449,-3.859;39.11,42.138,-3.959;37.975,40.129,-3.983;39.134,39.277,-4.298;38.825,38.04,-5.133;37.649,37.934,-5.605;39.788,37.369,-5.652;39.985,38.945,-3.037;39.221,37.953,-2.164;37.934,37.961,-1.823;37.579,36.695,-1.314;38.63,35.975,-1.286;39.736,36.771,-1.642;41.052,36.341,-1.48;41.213,35.042,-0.964;40.095,34.215,-0.69;38.765,34.665,-0.855;36.506,41.966,-2.002;37.6,42.757,-1.31;37.546,44.225,-1.728;37.408,42.58,0.19),wD:0.0,wU:17.21,13.33|)"_smiles;
|
|
REQUIRE(pdb_0zn_1tmn);
|
|
ShapeInputOptions mol1Opts, mol2Opts;
|
|
{
|
|
auto [singleShape, singleColor] =
|
|
ScoreMolecule(*pdb_trp_3tmn, *pdb_trp_3tmn, mol1Opts, mol2Opts);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(1.0, 0.001));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(1.0, 0.001));
|
|
}
|
|
{
|
|
auto pdb_trp_3tmn_cp =
|
|
R"(N[C@H](C(=O)O)Cc1c[nH]c2c1cccc2 |(37.935,40.394,-3.825;39.119,39.593,-4.13;38.758,38.486,-5.101;37.526,38.337,-5.395;39.716,37.852,-5.605;39.883,39.108,-2.906;39.086,38.098,-2.209;38.093,38.363,-1.34;37.565,37.179,-0.881;38.201,36.136,-1.471;39.193,36.684,-2.308;40.015,35.812,-3.036;39.846,34.441,-2.913;38.844,33.933,-2.075;38.015,34.752,-1.333),wU:1.0|)"_smiles;
|
|
RDGeom::Point3D trans{100.0, 100.0, 100.0};
|
|
RDGeom::Transform3D transform_3d;
|
|
transform_3d.SetTranslation(trans);
|
|
MolTransforms::transformConformer(pdb_trp_3tmn_cp->getConformer(),
|
|
transform_3d);
|
|
|
|
auto [singleShape, singleColor] =
|
|
ScoreMolecule(*pdb_trp_3tmn, *pdb_trp_3tmn_cp, mol1Opts, mol2Opts);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(0.0, 0.001));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(0.0, 0.001));
|
|
}
|
|
{
|
|
auto [singleShape, singleColor] =
|
|
ScoreMolecule(*pdb_0zn_1tmn, *pdb_0zn_1tmn, mol1Opts, mol2Opts);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(1.0, 0.001));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(1.0, 0.001));
|
|
}
|
|
{
|
|
auto [singleShape, singleColor] =
|
|
ScoreMolecule(*pdb_trp_3tmn, *pdb_0zn_1tmn, mol1Opts, mol2Opts);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(0.3376, 0.0005));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(0.2674, 0.0005));
|
|
}
|
|
{
|
|
ShapeInputOptions opts;
|
|
opts.normalize = false;
|
|
auto shape = PrepareConformer(*pdb_trp_3tmn, -1, opts);
|
|
auto [singleShape, singleColor] =
|
|
ScoreMolecule(shape, *pdb_0zn_1tmn, mol1Opts);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(0.3376, 0.0005));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(0.2674, 0.0005));
|
|
}
|
|
{
|
|
ShapeInputOptions opts;
|
|
opts.normalize = false;
|
|
auto shape1 = PrepareConformer(*pdb_trp_3tmn, -1, opts);
|
|
auto shape2 = PrepareConformer(*pdb_0zn_1tmn, -1, opts);
|
|
auto [singleShape, singleColor] = ScoreShape(shape1, shape2, true);
|
|
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(0.3376, 0.0005));
|
|
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(0.2674, 0.0005));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Iressa onto Tagrisso") {
|
|
// Conformations from PubChem produced by Omega. Iressa rotated and translated
|
|
// by a random amount. PubChem puts them both in their inertial frame which
|
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// makes things too easy.
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auto tagrisso =
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"C=CC(=O)Nc1cc(Nc2nccc(-c3cn(C)c4ccccc34)n2)c(OC)cc1N(C)CCN(C)C |(-0.9161,3.8415,-2.9811;0.1848,3.1933,-2.588;0.1064,1.7789,-2.12;-0.9619,1.1797,-2.0847;1.3654,1.2872,-1.7553;1.6841,0.0144,-1.273;0.6638,-0.9235,-1.1146;0.9578,-2.1997,-0.6343;-0.0813,-3.1358,-0.4783;-1.4556,-2.9979,-0.1847;-2.1716,-4.1359,-0.1085;-3.4803,-3.9673,0.173;-4.0689,-2.7353,0.3728;-3.2269,-1.647,0.2676;-3.7311,-0.317,0.4568;-5.0275,0.0291,0.153;-5.1887,1.3569,0.4454;-6.4231,2.0889,0.2595;-4.0141,1.8811,0.9361;-3.7121,3.1796,1.3615;-2.4139,3.4249,1.8179;-1.4588,2.4106,1.8467;-1.7752,1.1164,1.4181;-3.0776,0.8453,0.9537;-1.9103,-1.7423,-0.011;2.2723,-2.5382,-0.3127;2.58,-3.7798,0.1575;2.539,-3.9651,1.571;3.2927,-1.6003,-0.4713;2.9986,-0.324,-0.9514;4.0475,0.61,-1.1047;4.7738,0.6956,-2.3546;4.4021,1.497,-0.0162;5.4401,0.8254,0.8736;5.8294,1.7155,1.9601;4.8213,1.7057,3.0218;7.1361,1.3324,2.4981)|"_smiles;
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REQUIRE(tagrisso);
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auto iressa =
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"COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN1CCOCC1 |(11.4672,-0.467948,5.63989;12.0133,0.532631,6.49693;11.2039,1.5801,6.81985;11.2014,2.71958,6.00975;10.3926,3.81652,6.29699;10.4038,4.90395,5.50623;9.58889,5.91871,5.85946;8.76443,5.96486,6.91838;8.77814,4.86059,7.68868;7.92337,4.86224,8.81914;7.44878,5.8925,9.64622;8.22182,7.03851,9.85619;7.75051,8.06265,10.6777;6.50441,7.94546,11.2936;6.06567,8.93802,12.0809;5.72932,6.80403,11.0875;4.19056,6.65372,11.8447;6.20047,5.78015,10.2656;9.57161,3.74547,7.43436;9.56851,2.60328,8.25407;10.3868,1.52933,7.93769;10.3797,0.419365,8.74203;11.3064,0.402096,9.81907;10.7104,-0.399165,10.9685;9.40938,0.22121,11.4678;9.64205,1.59049,11.9223;8.38006,2.22985,12.3199;8.64991,3.65266,12.8011;9.56883,3.64192,13.8942;10.8103,3.05101,13.5078;10.5931,1.61394,13.0425)|"_smiles;
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REQUIRE(iressa);
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std::vector<float> matrix(12, 0.0);
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auto sims =
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AlignMolecule(*tagrisso, *iressa, matrix, -1, -1, true, 0.5, 10, 30);
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CHECK_THAT(sims.first, Catch::Matchers::WithinAbs(0.582, 0.005));
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CHECK_THAT(sims.second, Catch::Matchers::WithinAbs(0.092, 0.005));
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}
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