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5a79190261
We leave the names of the bit connected with Mol files as SGroups, since that is appropriate there, but the more generic pieces are renamed
291 lines
8.9 KiB
C++
291 lines
8.9 KiB
C++
//
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//
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// Copyright (C) 2018 Greg Landrum and T5 Informatics GmbH
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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 <GraphMol/RDKitBase.h>
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#include <GraphMol/SubstanceGroup.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include "GraphMol/FileParsers/FileParsers.h"
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using namespace RDKit;
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/* Auxiliary functions */
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void testIdxVector(const std::vector<unsigned int> &groupVector,
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const std::vector<unsigned int> &reference) {
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size_t vecSize = reference.size();
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CHECK(groupVector.size() == vecSize);
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auto sgItr = groupVector.begin();
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for (auto refItr = reference.begin(); refItr != reference.end();
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++sgItr, ++refItr) {
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CHECK(1 + *sgItr == *refItr);
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}
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}
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void testBrackets(
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const std::vector<SubstanceGroup::Bracket> &brackets,
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const std::vector<std::array<std::array<double, 3>, 3>> &reference) {
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CHECK(brackets.size() == 2);
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for (int i = 0; i < 2; ++i) {
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for (int j = 0; j < 3; ++j) {
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for (int k = 0; k < 3; ++k) {
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CHECK(std::abs(brackets[i][j][k] - reference[i][j][k]) < 1.e-6);
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}
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}
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}
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}
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RWMol buildSampleMolecule() {
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// This builds a RDKit::RWMol with all implemented SubstanceGroup features in
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// order to test them. SubstanceGroups and features probably do not make any
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// sense.
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//// Initialize Molecule ////
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RWMol mol;
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// Add some atoms and bonds
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for (unsigned i = 0; i < 6; ++i) {
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mol.addAtom(new Atom(6), false, true);
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if (i > 0) {
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mol.addBond(i - 1, i, Bond::SINGLE);
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}
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}
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//// First SubstanceGroup ////
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{
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SubstanceGroup sg(&mol, "MUL");
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sg.setProp("SUBTYPE", "BLO");
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sg.setProp("MULT", "n");
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sg.setProp("CONNECT", "HH");
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// Add some atoms and bonds
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for (unsigned i = 0; i < 3; ++i) {
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sg.addAtomWithIdx(i);
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sg.addParentAtomWithIdx(i);
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sg.addBondWithIdx(i); // add 2 CBONDs + 1 XBOND
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}
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sg.setProp("COMPNO", 7u);
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sg.setProp("ESTATE", "E");
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SubstanceGroup::Bracket bracket1 = {{RDGeom::Point3D(1., 3., 0.),
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RDGeom::Point3D(5., 7., 0.),
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RDGeom::Point3D(0., 0., 0.)}};
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sg.addBracket(bracket1);
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SubstanceGroup::Bracket bracket2 = {{RDGeom::Point3D(2., 4., 0.),
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RDGeom::Point3D(6., 8., 0.),
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RDGeom::Point3D(0., 0., 0.)}};
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sg.addBracket(bracket2);
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// Vector should not be parsed (not a SUP group)
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sg.addCState(2, RDGeom::Point3D());
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sg.setProp("CLASS", "TEST CLASS");
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sg.addAttachPoint(0, 0, "XX");
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sg.setProp("BRKTYP", "PAREN");
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addSubstanceGroup(mol, sg);
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}
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//// Second SubstanceGroup ////
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{
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SubstanceGroup sg(&mol, "SUP");
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// Add some atoms and bonds
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for (unsigned i = 3; i < 6; ++i) {
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sg.addAtomWithIdx(i);
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sg.addParentAtomWithIdx(i);
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sg.addBondWithIdx(i - 1); // add 1 XBOND + 2 CBONDs
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}
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sg.setProp("LABEL", "TEST LABEL");
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// V2000 has only x and y coords; z value restricted to 0.
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RDGeom::Point3D vector(3., 4., 0.);
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sg.addCState(2, vector); // Vector should be parsed now!
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sg.addAttachPoint(3, -1, "YY");
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addSubstanceGroup(mol, sg);
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}
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//// Third SubstanceGroup ////
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{
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SubstanceGroup sg(&mol, "DAT");
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sg.setProp("FIELDNAME", "SAMPLE FIELD NAME"); // 30 char max
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// Field Type is ignored in V3000
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sg.setProp("FIELDINFO", "SAMPLE FIELD INFO"); // 20 char max
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sg.setProp("QUERYTYPE", "PQ"); // 2 char max
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sg.setProp("QUERYOP", "SAMPLE QUERY OP"); // 15 char max (rest of line)
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// This should be properly formatted, but format is not checked
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sg.setProp("FIELDDISP", "SAMPLE FIELD DISP");
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STR_VECT dataFields = {"SAMPLE DATA FIELD 1", "SAMPLE DATA FIELD 2",
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"SAMPLE DATA FIELD 3"};
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sg.setProp("DATAFIELDS", dataFields);
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addSubstanceGroup(mol, sg);
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}
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// Set a parent with higher index
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const auto &sgroups = getSubstanceGroups(mol);
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sgroups.at(0).setProp<unsigned int>("PARENT", 2);
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return mol;
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}
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/* End Auxiliary functions */
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TEST_CASE("Basic Sgroup creation", "[Sgroups]") {
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// Create two SubstanceGroups and add them to a molecule
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RWMol mol;
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{
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SubstanceGroup sg0(&mol, "DAT");
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SubstanceGroup sg1(&mol, "SUP");
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addSubstanceGroup(mol, sg0);
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addSubstanceGroup(mol, sg1);
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}
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const auto &sgroups = getSubstanceGroups(mol);
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REQUIRE(sgroups.size() == 2);
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CHECK(sgroups.at(0).getProp<std::string>("TYPE") == "DAT");
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CHECK(sgroups.at(1).getProp<std::string>("TYPE") == "SUP");
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}
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TEST_CASE("Build and test sample molecule", "[Sgroups]") {
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auto mol = buildSampleMolecule();
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const auto &sgroups = getSubstanceGroups(mol);
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CHECK(sgroups.size() == 3);
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SECTION("first sgroup") {
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const auto &sg = sgroups.at(0);
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CHECK(sg.getProp<std::string>("TYPE") == "MUL");
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CHECK(sg.getProp<std::string>("SUBTYPE") == "BLO");
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CHECK(sg.getProp<std::string>("MULT") == "n");
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CHECK(sg.getProp<std::string>("CONNECT") == "HH");
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std::vector<unsigned int> atoms_reference = {1, 2, 3};
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auto atoms = sg.getAtoms();
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testIdxVector(atoms, atoms_reference);
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std::vector<unsigned int> patoms_reference = {1, 2, 3};
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testIdxVector(sg.getParentAtoms(), patoms_reference);
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std::vector<unsigned int> bonds_reference = {1, 2, 3};
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auto bonds = sg.getBonds();
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// bonds are not sorted in V3000; sort them here
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std::sort(bonds.begin(), bonds.end());
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testIdxVector(bonds, bonds_reference);
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CHECK(sg.getBondType(bonds[0]) == SubstanceGroup::BondType::CBOND);
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CHECK(sg.getBondType(bonds[1]) == SubstanceGroup::BondType::CBOND);
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CHECK(sg.getBondType(bonds[2]) == SubstanceGroup::BondType::XBOND);
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CHECK(sg.getProp<unsigned int>("COMPNO") == 7u);
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CHECK(sg.getProp<std::string>("ESTATE") == "E");
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std::vector<std::array<std::array<double, 3>, 3>> brackets_reference = {{
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{{{{1., 3., 0.}}, {{5., 7., 0.}}, {{0., 0., 0.}}}},
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{{{{2., 4., 0.}}, {{6., 8., 0.}}, {{0., 0., 0.}}}},
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}};
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testBrackets(sg.getBrackets(), brackets_reference);
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auto cstates = sg.getCStates();
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CHECK(cstates.size() == 1);
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CHECK(cstates[0].bondIdx == bonds[2]);
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CHECK(cstates[0].vector.x == 0.);
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CHECK(cstates[0].vector.y == 0.);
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CHECK(cstates[0].vector.z == 0.);
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CHECK(sg.getProp<std::string>("CLASS") == "TEST CLASS");
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auto ap = sg.getAttachPoints();
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CHECK(ap.size() == 1);
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CHECK(ap[0].aIdx == atoms[0]);
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CHECK(ap[0].lvIdx == static_cast<int>(atoms[0]));
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CHECK(ap[0].id == "XX");
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CHECK(sg.getProp<std::string>("BRKTYP") == "PAREN");
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CHECK(sg.getProp<unsigned int>("PARENT") == 2u);
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}
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SECTION("second sgroup") {
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const auto &sg = sgroups.at(1);
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CHECK(sg.getProp<std::string>("TYPE") == "SUP");
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std::vector<unsigned int> atoms_reference = {4, 5, 6};
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auto atoms = sg.getAtoms();
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testIdxVector(atoms, atoms_reference);
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std::vector<unsigned int> patoms_reference = {4, 5, 6};
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testIdxVector(sg.getParentAtoms(), patoms_reference);
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std::vector<unsigned int> bonds_reference = {3, 4, 5};
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auto bonds = sg.getBonds();
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// bonds are not sorted in V3000; sort them here
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std::sort(bonds.begin(), bonds.end());
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testIdxVector(bonds, bonds_reference);
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CHECK(sg.getBondType(bonds[0]) == SubstanceGroup::BondType::XBOND);
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CHECK(sg.getBondType(bonds[1]) == SubstanceGroup::BondType::CBOND);
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CHECK(sg.getBondType(bonds[2]) == SubstanceGroup::BondType::CBOND);
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CHECK(sg.getProp<std::string>("LABEL") == "TEST LABEL");
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auto cstates = sg.getCStates();
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CHECK(cstates.size() == 1);
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CHECK(cstates[0].bondIdx == bonds[0]);
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CHECK(cstates[0].vector.x == 3.);
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CHECK(cstates[0].vector.y == 4.);
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CHECK(cstates[0].vector.z == 0.);
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auto ap = sg.getAttachPoints();
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CHECK(ap.size() == 1);
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CHECK(ap[0].aIdx == atoms[0]);
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CHECK(ap[0].lvIdx == -1);
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CHECK(ap[0].id == "YY");
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}
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SECTION("third sgroup") {
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const auto &sg = sgroups.at(2);
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CHECK(sg.getProp<std::string>("TYPE") == "DAT");
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CHECK(sg.getProp<std::string>("FIELDNAME") == "SAMPLE FIELD NAME");
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CHECK(sg.getProp<std::string>("FIELDINFO") == "SAMPLE FIELD INFO");
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CHECK(sg.getProp<std::string>("QUERYTYPE") == "PQ");
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CHECK(sg.getProp<std::string>("QUERYOP") == "SAMPLE QUERY OP");
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CHECK(sg.getProp<std::string>("FIELDDISP") == "SAMPLE FIELD DISP");
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auto dataFields = sg.getProp<STR_VECT>("DATAFIELDS");
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CHECK(dataFields.size() == 3);
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CHECK(dataFields[0] == "SAMPLE DATA FIELD 1");
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CHECK(dataFields[1] == "SAMPLE DATA FIELD 2");
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CHECK(dataFields[2] == "SAMPLE DATA FIELD 3");
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}
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}
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