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74fc77f959
* normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter * Update Code/GraphMol/Depictor/catch_tests.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * fix catch test --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2340 lines
92 KiB
C++
2340 lines
92 KiB
C++
//
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// Copyright (C) 2021 Greg Landrum and other RDKit contributors
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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 <catch2/catch_all.hpp>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Chirality.h>
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#include "RDDepictor.h"
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#include "DepictUtils.h"
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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using namespace RDKit;
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TEST_CASE(
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"github #4504: overlapping coordinates with 1,1-disubstituted "
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"cyclobutanes") {
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SECTION("basics") {
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auto m = "CCC1(CCC1)CC1CCCCC1"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
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CHECK(v.length() > 0.1);
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v = conf.getAtomPos(1) - conf.getAtomPos(5);
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CHECK(v.length() > 0.1);
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}
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SECTION("this one was ok") {
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auto m = "CCC1(CCC1)C1CCCCC1"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
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CHECK(v.length() > 0.1);
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v = conf.getAtomPos(1) - conf.getAtomPos(5);
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CHECK(v.length() > 0.1);
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}
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}
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TEST_CASE("square planar", "[nontetrahedral]") {
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SECTION("cis-platin") {
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auto m = "Cl[Pt@SP1](Cl)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
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CHECK(v1.length() < v2.length());
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}
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SECTION("trans-platin") {
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auto m = "Cl[Pt@SP2](Cl)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
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CHECK(v1.length() > v2.length());
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}
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SECTION("trans-metal in a ring") {
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auto m = "C1[Pt@SP2](CCC1)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
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CHECK(v1.length() > v2.length());
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}
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SECTION("cis-metal in a ring") {
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auto m = "C1[Pt@SP1](CCC1)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
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CHECK(v1.length() < v2.length());
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}
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}
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TEST_CASE("trigonal bipyramidal", "[nontetrahedral]") {
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SECTION("TB1") {
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auto m = "S[As@TB1](F)(Cl)(Br)N"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - ax
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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SECTION("TB3") {
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auto m = "S[As@TB3](F)(Cl)(N)Br"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - ax
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(5); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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SECTION("TB1 missing ax") {
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// // S[As@TB1](F)(Cl)(Br)* => S[As@TB7](*)(F)(Cl)Br
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auto m = "S[As@TB7](F)(Cl)Br"_smiles;
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REQUIRE(m);
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(120, 0.001));
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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}
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TEST_CASE("octahedral", "[nontetrahedral]") {
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SECTION("OH1") {
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auto m = "O[Co@OH1](Cl)(C)(N)(F)P"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
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auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
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auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
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auto v5 = conf.getAtomPos(0) - conf.getAtomPos(6); // eq - eq cross
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auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v1.length() > v4.length());
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CHECK(v1.length() > v6.length());
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CHECK(v5.length() > v4.length());
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CHECK(v5.length() > v6.length());
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}
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SECTION("OH3") {
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auto m = "O[Co@OH3](Cl)(C)(N)(P)F"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(3) - conf.getAtomPos(6); // ax - ax
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auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
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auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
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auto v5 = conf.getAtomPos(0) - conf.getAtomPos(5); // eq - eq cross
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auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v1.length() > v4.length());
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CHECK(v1.length() > v6.length());
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CHECK(v5.length() > v4.length());
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CHECK(v5.length() > v6.length());
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}
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SECTION("OH1 missing one ligand") {
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// O[Co@OH1](Cl)(C)(N)(F)* => O[Co@OH25](*)(Cl)(C)(N)F
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auto m = "O[Co@OH25](Cl)(C)(N)F"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
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auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
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auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
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auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v1.length() > v4.length());
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CHECK(v1.length() > v6.length());
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}
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}
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TEST_CASE("use ring system templates") {
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auto mol = "C1CCC2C(C1)C1CCN2NN1"_smiles;
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RDDepict::Compute2DCoordParameters params;
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RDDepict::compute2DCoords(*mol, params);
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auto diff =
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mol->getConformer().getAtomPos(10) - mol->getConformer().getAtomPos(11);
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// when templates are not used, bond from 10-11 is very short
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TEST_ASSERT(RDKit::feq(diff.length(), 0.116, .1));
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params.useRingTemplates = true;
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RDDepict::compute2DCoords(*mol, params);
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diff =
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mol->getConformer().getAtomPos(10) - mol->getConformer().getAtomPos(11);
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TEST_ASSERT(RDKit::feq(diff.length(), 1.0, .1))
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}
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TEST_CASE("find core rings") {
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// perhydroanthracene and perhydrophenalene, and their
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// expected number of core rings
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std::map<std::string, unsigned int> examples = {
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{"C1CCC2CC3CCCCC3CC2C1", 1u}, {"C1CC2CCCC3C2C(C1)CCC3", 3u}};
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for (auto example : examples) {
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auto mol = v2::SmilesParse::MolFromSmiles(example.first);
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RDKit::VECT_INT_VECT arings;
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bool includeDativeBonds = true;
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RDKit::MolOps::symmetrizeSSSR(*mol, arings, includeDativeBonds);
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CHECK(arings.size() == 3);
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RDKit::INT_VECT coreRingsIds;
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auto coreRings = RDDepict::findCoreRings(arings, coreRingsIds, *mol);
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CHECK(coreRings.size() == example.second);
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}
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}
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TEST_CASE("match template with added rings") {
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// this is a molecule we have a template for
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auto mol1 = "C1C2CC3CC1CC3C2"_smiles;
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// and this is the same molecule with an extra ring added
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auto mol2 = "C1C2CC3C1CC1(C2)NC31"_smiles;
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// generate coordinates
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RDDepict::Compute2DCoordParameters params;
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params.useRingTemplates = true;
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RDDepict::compute2DCoords(*mol1, params);
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RDDepict::compute2DCoords(*mol2, params);
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// align the two molecules
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auto rmsd = MolAlign::getBestRMS(*mol1, *mol2);
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CHECK(rmsd < 0.2);
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}
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TEST_CASE("templates are aware of E/Z stereochemistry") {
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// this is a molecule we have a template for
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auto mol1 =
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"CCC1C2=N[C@@](C)(C3N/C(=C(/C)C4=N/C(=C\\C5=N/C(=C\\2C)[C@@](C)(CC(N)=O)C5CCC(N)=O)C(C)(C)C4CCC(N)=O)[C@](C)(CCC(=O)NC)C3C)C1(C)C"_smiles;
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// and this is the same molecule with different stereochemistry on double
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// bonds
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auto mol2 =
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"CCC1C2=N[C@@](C)(C3N/C(=C(\\C)C4=N/C(=C/C5=N/C(=C/2C)[C@@](C)(CC(N)=O)C5CCC(N)=O)C(C)(C)C4CCC(N)=O)[C@](C)(CCC(=O)NC)C3C)C1(C)C"_smiles;
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// generate coordinates for the two molecules, they should be different
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// because only the first one matches the template
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RDDepict::Compute2DCoordParameters params;
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params.useRingTemplates = true;
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RDDepict::compute2DCoords(*mol1, params);
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RDDepict::compute2DCoords(*mol2, params);
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auto rmsd = MolAlign::getBestRMS(*mol1, *mol2);
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CHECK(rmsd > 1.);
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}
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TEST_CASE("dative bonds and rings") {
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auto mol = "O->[Pt]1(<-O)<-NC2CCC2N->1"_smiles;
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REQUIRE(mol);
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auto rings = mol->getRingInfo();
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CHECK(rings->numRings() == 1); // the dative bonds are ignored
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RDDepict::compute2DCoords(*mol);
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CHECK(rings->numRings() == 1); // ensure the ring count hasn't changed
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auto conf = mol->getConformer();
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auto v1 = conf.getAtomPos(1) - conf.getAtomPos(3);
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auto v2 = conf.getAtomPos(1) - conf.getAtomPos(8);
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CHECK_THAT(v1.length(), Catch::Matchers::WithinAbs(v2.length(), 0.01));
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}
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TEST_CASE("vicinal R groups can match an aromatic ring") {
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auto benzene = R"CTAB(
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MJ201100
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8 8 0 0 0 0 0 0 0 0999 V2000
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-1.0263 -0.3133 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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-2.4553 0.5116 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7408 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7408 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.4553 -1.9633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.1698 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.1698 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.4553 -0.3133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3 1 1 0 0 0 0
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8 2 1 0 0 0 0
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4 3 2 0 0 0 0
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5 4 1 0 0 0 0
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6 5 2 0 0 0 0
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7 6 1 0 0 0 0
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8 3 1 0 0 0 0
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8 7 2 0 0 0 0
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M RGP 2 1 2 2 1
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M END)CTAB"_ctab;
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REQUIRE(benzene);
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auto biphenyl = R"CTAB(
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MJ201100
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14 15 0 0 0 0 0 0 0 0999 V2000
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-0.6027 2.4098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3171 1.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3171 1.1722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6027 0.7597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1117 1.1722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1117 1.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6027 -0.0652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3171 -0.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3171 -1.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6028 -1.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1117 -1.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1117 -0.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.0316 0.7597 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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-2.0316 -0.0652 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 6 2 0 0 0 0
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6 1 1 0 0 0 0
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4 7 1 0 0 0 0
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8 9 1 0 0 0 0
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9 10 2 0 0 0 0
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10 11 1 0 0 0 0
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11 12 2 0 0 0 0
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7 8 2 0 0 0 0
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12 7 1 0 0 0 0
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3 13 1 0 0 0 0
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8 14 1 0 0 0 0
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M RGP 2 13 1 14 2
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M END)CTAB"_ctab;
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REQUIRE(biphenyl);
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SECTION("R groups on benzene match quinoxaline") {
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auto quinoxaline = "c1ccc2nccnc2c1"_smiles;
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REQUIRE(quinoxaline);
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auto match = RDDepict::generateDepictionMatching2DStructure(
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*quinoxaline, *benzene, -1, nullptr, false, false, true);
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CHECK(match.size() == 8);
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}
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SECTION("R groups on benzene match tetralin") {
|
|
auto tetralin = "c1cccc2CCCCc12"_smiles;
|
|
REQUIRE(tetralin);
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*tetralin, *benzene, -1, nullptr, false, false, true);
|
|
CHECK(match.size() == 8);
|
|
}
|
|
SECTION("R groups on biphenyl match phenantridine") {
|
|
auto phenantridine = "c1cccc2ncc3ccccc3c12"_smiles;
|
|
REQUIRE(phenantridine);
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*phenantridine, *biphenyl, -1, nullptr, false, false, true);
|
|
CHECK(match.size() == 14);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("trans bonds in large rings") {
|
|
// In large rings, we need to retain a trans geometry for double bonds.
|
|
// This simulates the case where we write to SDF and read again.
|
|
auto mol = "C1=C/CCCCCCCCCCCCC/1"_smiles;
|
|
RDDepict::compute2DCoords(*mol);
|
|
// simulate writing to SDF and reading again:
|
|
RDKit::MolOps::removeStereochemistry(*mol);
|
|
mol->getConformer().set3D(true);
|
|
RDKit::MolOps::assignStereochemistryFrom3D(*mol);
|
|
CHECK(RDKit::MolToSmiles(*mol) == "C1=C/CCCCCCCCCCCCC/1");
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords accept failure") {
|
|
auto template_ref_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 9 0 0 0 0 0 0 0 0999 V2000
|
|
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0
|
|
2 3 1 0
|
|
3 4 2 0
|
|
4 5 1 0
|
|
5 6 2 0
|
|
6 1 1 0
|
|
6 8 1 0
|
|
3 9 1 0
|
|
2 7 1 0
|
|
M RGP 3 7 1 8 2 9 3
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> template_ref(MolBlockToMol(template_ref_molblock));
|
|
REQUIRE(template_ref);
|
|
auto mol_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 9 0 0 0 0 0 0 0 0999 V2000
|
|
-0.8929 1.0942 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 1.0942 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7051 1.0942 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 -1.9059 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0
|
|
2 3 1 0
|
|
3 4 2 0
|
|
4 5 1 0
|
|
5 6 2 0
|
|
6 1 1 0
|
|
6 8 1 0
|
|
3 9 1 0
|
|
2 7 1 0
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
SECTION("acceptFailure false, existing coords preserved") {
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, false, false, true),
|
|
RDDepict::DepictException);
|
|
CHECK(MolToMolBlock(*mol) == mol_molblock);
|
|
}
|
|
SECTION("acceptFailure true, existing coords overwritten") {
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, true, false, true)
|
|
.empty());
|
|
CHECK(MolToMolBlock(*mol) != mol_molblock);
|
|
}
|
|
SECTION("acceptFailure false, no existing coords") {
|
|
mol->removeConformer(0);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.acceptFailure = false;
|
|
CHECK(mol->getNumConformers() == 0);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, p),
|
|
RDDepict::DepictException);
|
|
CHECK(mol->getNumConformers() == 0);
|
|
}
|
|
SECTION("acceptFailure true, no existing coords") {
|
|
mol->removeConformer(0);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.acceptFailure = true;
|
|
CHECK(mol->getNumConformers() == 0);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *template_ref,
|
|
-1, nullptr, p)
|
|
.empty());
|
|
CHECK(mol->getNumConformers() == 1);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords alignOnly") {
|
|
auto template_ref_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
6 6 0 0 0 0 0 0 0 0999 V2000
|
|
-13.7477 6.3036 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-13.7477 4.7567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-12.6540 3.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-13.7477 2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-14.8414 3.6628 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-11.1071 3.6628 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
2 5 1 0
|
|
3 6 1 0
|
|
M RGP 2 1 1 6 2
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> template_ref(MolBlockToMol(template_ref_molblock));
|
|
REQUIRE(template_ref);
|
|
auto mol_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
18 22 0 0 0 0 0 0 0 0999 V2000
|
|
4.3922 -1.5699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9211 -2.0479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.5995 -0.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.3731 0.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.8441 1.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0704 -0.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.8666 0.7748 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7736 -0.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7749 -1.8666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7718 -1.8679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7731 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.8679 0.7718 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0718 -0.0598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.3933 -1.5729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.9222 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6008 -0.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.3744 0.8016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.8454 1.2795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9 10 1 0
|
|
11 10 1 0
|
|
11 8 1 0
|
|
8 9 1 0
|
|
4 5 1 0
|
|
6 5 1 0
|
|
7 6 1 0
|
|
3 4 1 0
|
|
3 7 1 0
|
|
1 6 1 0
|
|
2 3 1 0
|
|
2 1 1 0
|
|
17 18 1 0
|
|
13 18 1 0
|
|
12 13 1 0
|
|
16 17 1 0
|
|
16 12 1 0
|
|
14 13 1 0
|
|
15 16 1 0
|
|
15 14 1 0
|
|
12 11 1 0
|
|
8 7 1 0
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
auto bondLength11_12 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 11, 12);
|
|
auto bondLength5_6 = MolTransforms::getBondLength(mol->getConformer(), 5, 6);
|
|
REQUIRE(fabs(bondLength11_12 - bondLength5_6) < 1.e-4);
|
|
REQUIRE(bondLength11_12 > 2.3);
|
|
SECTION("alignOnly false/true") {
|
|
for (auto alignOnly : {false, true}) {
|
|
mol.reset(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.alignOnly = alignOnly;
|
|
auto res = RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, p);
|
|
std::vector<int> expectedMolIndices{11, 10, 7, 8, 9, 6};
|
|
auto sameIndices = std::all_of(
|
|
res.begin(), res.end(), [&expectedMolIndices](const auto &pair) {
|
|
return pair.second == expectedMolIndices.at(pair.first);
|
|
});
|
|
CHECK(sameIndices);
|
|
CHECK(MolToSmiles(*mol) == "C1CC2CCC1N2C1CNC1N1C2CCC1CC2");
|
|
auto samePositions = std::all_of(
|
|
res.begin(), res.end(), [&mol, &template_ref](const auto &pair) {
|
|
return (mol->getConformer().getAtomPos(pair.second) -
|
|
template_ref->getConformer().getAtomPos(pair.first))
|
|
.lengthSq() < 1.e-4;
|
|
});
|
|
CHECK(samePositions);
|
|
auto bondLengthAli11_12 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 11, 12);
|
|
auto bondLengthAli5_6 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 5, 6);
|
|
CHECK(fabs(bondLengthAli11_12 - bondLengthAli5_6) < 1.e-4);
|
|
if (alignOnly) {
|
|
CHECK(bondLengthAli11_12 > 2.3);
|
|
} else {
|
|
CHECK(bondLengthAli11_12 < 1.6);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords and wedging") {
|
|
auto wedgedMol = R"CTAB(
|
|
RDKit 2D
|
|
|
|
29 34 0 0 1 0 0 0 0 0999 V2000
|
|
1.3719 5.1304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5985 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9482 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7216 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2685 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.8994 3.5835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5597 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5597 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.8994 6.6771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.2389 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.5784 6.6771 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.2389 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3719 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5985 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3719 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9188 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6921 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9188 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2389 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.0124 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2389 -1.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6921 -1.5673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.8996 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2391 -4.2467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.5777 -6.5331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9909 -5.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.0124 -2.9070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.3306 -6.6772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5784 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 6
|
|
5 6 1 0
|
|
6 7 1 0
|
|
7 8 1 0
|
|
9 8 1 1
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 1
|
|
10 12 1 0
|
|
6 12 1 1
|
|
2 13 1 0
|
|
13 14 2 0
|
|
14 15 1 0
|
|
15 16 2 0
|
|
16 17 1 0
|
|
17 18 2 0
|
|
13 18 1 0
|
|
17 19 1 0
|
|
19 20 1 0
|
|
20 21 1 0
|
|
21 22 1 0
|
|
16 22 1 0
|
|
23 24 1 0
|
|
23 25 1 0
|
|
25 26 1 0
|
|
24 27 1 0
|
|
27 26 1 0
|
|
26 28 1 0
|
|
24 29 1 0
|
|
28 29 1 0
|
|
21 27 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(wedgedMol);
|
|
auto originalWedges = R"CTAB( 2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 6
|
|
5 6 1 0
|
|
6 7 1 0
|
|
7 8 1 0
|
|
9 8 1 1
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 1
|
|
10 12 1 0
|
|
6 12 1 1
|
|
2 13 1 0
|
|
13 14 2 0
|
|
14 15 1 0
|
|
15 16 2 0
|
|
16 17 1 0
|
|
17 18 2 0
|
|
13 18 1 0
|
|
17 19 1 0
|
|
19 20 1 0
|
|
20 21 1 0
|
|
21 22 1 0
|
|
16 22 1 0
|
|
23 24 1 0
|
|
23 25 1 0
|
|
25 26 1 0
|
|
24 27 1 0
|
|
27 26 1 0
|
|
26 28 1 0
|
|
24 29 1 0
|
|
28 29 1 0
|
|
21 27 1 0
|
|
M END
|
|
)CTAB";
|
|
auto invertedWedges = R"CTAB( 2 1 1 6
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 0
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 6
|
|
2 13 1 0
|
|
13 14 2 0
|
|
14 15 1 0
|
|
15 16 2 0
|
|
16 17 1 0
|
|
17 18 2 0
|
|
13 18 1 0
|
|
17 19 1 0
|
|
19 20 1 0
|
|
20 21 1 0
|
|
21 22 1 0
|
|
16 22 1 0
|
|
23 24 1 0
|
|
23 25 1 0
|
|
25 26 1 0
|
|
24 27 1 0
|
|
27 26 1 0
|
|
26 28 1 0
|
|
24 29 1 0
|
|
28 29 1 0
|
|
21 27 1 0
|
|
)CTAB";
|
|
SECTION("wedging all within scaffold") {
|
|
auto scaffold = R"CTAB(
|
|
RDKit 2D
|
|
|
|
13 14 0 0 1 0 0 0 0 0999 V2000
|
|
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.2953 4.1222 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 6
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 0
|
|
2 13 1 6
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffold);
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(invertedWedges) != std::string::npos);
|
|
}
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (same as original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(invertedWedges) != std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (same as the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should succeed and clear original wedging
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system. Additionally, CoordGen
|
|
// also rebuilds the scaffold, therefore original wedging should be cleared
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(invertedWedges) == std::string::npos);
|
|
CHECK(mbAlignOnly.find(originalWedges) == std::string::npos);
|
|
}
|
|
// the "rebuildCoordGen" alignment should succeed and keep original wedging
|
|
// unaltered.
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system.
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
SECTION("wedging outside scaffold") {
|
|
auto scaffold = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 10 0 0 1 0 0 0 0 0999 V2000
|
|
-0.8816 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6651 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2958 -0.9804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0435 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0435 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2958 2.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6355 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9750 2.1129 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6355 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 6
|
|
4 5 1 0
|
|
6 5 1 6
|
|
2 6 1 0
|
|
6 7 1 0
|
|
7 8 1 6
|
|
7 9 1 0
|
|
3 9 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffold);
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(invertedWedges) != std::string::npos);
|
|
}
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (same as original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should succeed and clear original wedging
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) == std::string::npos);
|
|
CHECK(mbAlignOnly.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (same as the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should succeed and clear original wedging
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system. Additionally, CoordGen
|
|
// also rebuilds the scaffold, therefore original wedging should be cleared
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(invertedWedges) == std::string::npos);
|
|
CHECK(mbAlignOnly.find(originalWedges) == std::string::npos);
|
|
}
|
|
// the "rebuildCoordGen" alignment should succeed and keep original wedging
|
|
// unaltered.
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system.
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
auto mbAlignOnly = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(mbAlignOnly.find(originalWedges) != std::string::npos);
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
SECTION("wedging no match") {
|
|
auto scaffoldNoMatch = R"CTAB(
|
|
RDKit 2D
|
|
|
|
13 14 0 0 1 0 0 0 0 0999 V2000
|
|
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.2953 4.1222 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 6
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 0
|
|
2 13 1 6
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffoldNoMatch);
|
|
std::string origMolBlock;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
origMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
}
|
|
REQUIRE(!origMolBlock.empty());
|
|
// the "alignOnly" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "alignOnly" alignment should return an empty MatchVect if
|
|
// acceptFailure is true and generate new coordinates, hence wedging should
|
|
// be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should return an empty MatchVect if acceptFailure
|
|
// is true and generate new coordinates, hence wedging should be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuildCoordGen" alignment should return an empty MatchVect if
|
|
// acceptFailure is true and generate new coordinates, hence wedging should
|
|
// be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords R group match") {
|
|
auto templateRef = R"CTAB(
|
|
MJ201100
|
|
|
|
7 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.5804 1.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2948 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2948 -0.0330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.5804 -0.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1340 -0.0330 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1340 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8485 -0.4455 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
3 4 2 0 0 0 0
|
|
6 1 1 0 0 0 0
|
|
4 5 1 0 0 0 0
|
|
5 6 2 0 0 0 0
|
|
5 7 1 0 0 0 0
|
|
M RGP 1 7 1
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(templateRef);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
SECTION("heavy") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "Cc1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
SECTION("implicit hydrogen") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "c1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 6);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 6);
|
|
}
|
|
}
|
|
SECTION("explicit hydrogen") {
|
|
auto smi = "[H]c1ccccc1";
|
|
SmilesParserParams smilesParams;
|
|
smilesParams.removeHs = false;
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
std::unique_ptr<RWMol> mol(SmilesToMol(smi, smilesParams));
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
SECTION("no atom") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "n1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 6);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 6);
|
|
}
|
|
}
|
|
SECTION("charged") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "C[n+]1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("test GitHub6816") {
|
|
SECTION("double-2000") {
|
|
auto mol = R"CTAB(double-2000.mol
|
|
ChemDraw10192311132D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.7145 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 0.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7145 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7145 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0
|
|
2 3 1 4 0
|
|
1 4 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-3000") {
|
|
auto mol = R"CTAB(double-3000.mol
|
|
ChemDraw10232310312D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.714435 0.206182 0.000000 0
|
|
M V30 2 C 0.000000 0.618744 0.000000 0
|
|
M V30 3 F 0.714435 0.206182 0.000000 0
|
|
M V30 4 O -0.714435 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(double-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.7144 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7144 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7144 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 3
|
|
2 3 1 4
|
|
1 4 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(double-explicit-crossed-3000.mol
|
|
ChemDraw10232310422D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.714435 0.206182 0.000000 0
|
|
M V30 2 C 0.000000 0.618744 0.000000 0
|
|
M V30 3 F 0.714435 0.206182 0.000000 0
|
|
M V30 4 O -0.714435 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2 CFG=2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-2000") {
|
|
auto mol = R"CTAB(double-2-2000.mol
|
|
ChemDraw10192311332D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0717 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.0717 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0
|
|
2 3 1 4 0
|
|
1 4 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-3000") {
|
|
auto mol = R"CTAB(double-2-3000.mol
|
|
ChemDraw10232310312D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.357168 -0.206181 0.000000 0
|
|
M V30 2 C 0.357167 0.206182 0.000000 0
|
|
M V30 3 F 1.071603 0.618744 0.000000 0
|
|
M V30 4 O -1.071603 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(double-2-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0716 0.6187 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.0716 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 3
|
|
2 3 1 4
|
|
1 4 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(double-2-explicit-crossed-3000.mol
|
|
ChemDraw10232310422D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.357168 -0.206181 0.000000 0
|
|
M V30 2 C 0.357167 0.206182 0.000000 0
|
|
M V30 3 F 1.071603 0.618744 0.000000 0
|
|
M V30 4 O -1.071603 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2 CFG=2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-2000") {
|
|
auto mol = R"CTAB(di-imine-2-2000.mol
|
|
ChemDraw10192311522D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0 0
|
|
2 3 1 0 0
|
|
3 4 1 0 0
|
|
2 5 2 0 0
|
|
5 6 1 4 0
|
|
3 7 2 0 0
|
|
7 8 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-3000") {
|
|
auto mol = R"CTAB(di-imine-2-3000.mol
|
|
ChemDraw10232310302D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.995922 -1.060024 0.000000 0
|
|
M V30 2 C -0.412509 -0.476711 0.000000 0
|
|
M V30 3 C 0.412509 -0.476711 0.000000 0
|
|
M V30 4 C 0.995923 -1.060024 0.000000 0
|
|
M V30 5 N -0.728217 0.285506 0.000000 0
|
|
M V30 6 C -0.997122 1.060024 0.000000 0
|
|
M V30 7 N 0.728216 0.285506 0.000000 0
|
|
M V30 8 C 0.997122 1.027023 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5
|
|
M V30 5 1 5 6 CFG=2
|
|
M V30 6 2 3 7
|
|
M V30 7 1 7 8 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(di-imine-2-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
2 5 2 3
|
|
5 6 1 4
|
|
3 7 2 0
|
|
7 8 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(di-imine-2-explicit-crossed-3000.mol
|
|
ChemDraw10232310432D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.995922 -1.060024 0.000000 0
|
|
M V30 2 C -0.412509 -0.476711 0.000000 0
|
|
M V30 3 C 0.412509 -0.476711 0.000000 0
|
|
M V30 4 C 0.995923 -1.060024 0.000000 0
|
|
M V30 5 N -0.728217 0.285506 0.000000 0
|
|
M V30 6 C -0.997122 1.060024 0.000000 0
|
|
M V30 7 N 0.728216 0.285506 0.000000 0
|
|
M V30 8 C 0.997122 1.027023 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5 CFG=2
|
|
M V30 5 1 5 6 CFG=2
|
|
M V30 6 2 3 7
|
|
M V30 7 1 7 8 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
|
|
SECTION("di-imine-cross-2000") {
|
|
auto mol = R"CTAB(di-imine-cross-2000.mol
|
|
ChemDraw10192311582D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-1.0099 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.5974 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.2276 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6401 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8109 0.3984 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6401 0.3160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2234 1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2234 0.8994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0 0
|
|
2 3 1 0 0
|
|
3 4 1 0 0
|
|
2 5 2 3 0
|
|
3 6 2 3 0
|
|
5 7 1 0 0
|
|
6 8 1 0 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
}
|
|
SECTION("di-imine-cross-3000") {
|
|
auto mol = R"CTAB(di-imine-cross-3000.mol
|
|
ChemDraw10232310302D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -1.009900 -1.112900 0.000000 0
|
|
M V30 2 C -0.597400 -0.398400 0.000000 0
|
|
M V30 3 C 0.227600 -0.398400 0.000000 0
|
|
M V30 4 C 0.640100 -1.112900 0.000000 0
|
|
M V30 5 N -0.810900 0.398400 0.000000 0
|
|
M V30 6 N 0.640100 0.316000 0.000000 0
|
|
M V30 7 C -1.223400 1.112900 0.000000 0
|
|
M V30 8 C 1.223400 0.899400 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5 CFG=2
|
|
M V30 5 2 3 6 CFG=2
|
|
M V30 6 1 5 7
|
|
M V30 7 1 6 8
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
}
|
|
SECTION(
|
|
"roundtripping molblock with cis double bond should not change it into crosssed") {
|
|
auto molblockIn = R"CTAB(
|
|
RDKit 2D
|
|
|
|
5 4 0 0 0 0 0 0 0 0999 V2000
|
|
-2.4998 2.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2142 2.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.4998 3.3022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2142 3.7147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.9287 3.3022 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
1 3 2 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
M END
|
|
)CTAB";
|
|
{
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molblockIn, false));
|
|
auto molblockOut = MolToMolBlock(*mol);
|
|
CHECK(molblockIn == molblockOut);
|
|
}
|
|
{
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molblockIn, false));
|
|
RDKit::Chirality::reapplyMolBlockWedging(*mol);
|
|
auto molblockOut = MolToMolBlock(*mol);
|
|
CHECK(molblockIn == molblockOut);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("test GitHub6952") {
|
|
auto methotrexate = R"CTAB(
|
|
RDKit 2D
|
|
|
|
33 35 0 0 0 0 0 0 0 0999 V2000
|
|
9.6907 -4.0059 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.7594 -1.2647 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.3558 -2.5828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.1529 -1.2392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.1064 -3.9607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.5157 -2.6141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.7874 -2.5470 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.6071 0.3538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.4061 0.1262 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.3656 1.7364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.0321 -1.1768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.7519 0.4301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6721 0.2392 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.9466 1.7689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.0366 4.5624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.0167 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4339 -1.1557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0736 0.2603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.4076 -0.9769 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-10.9286 4.6884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.9966 -0.9397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.8226 0.1920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.2221 5.9171 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.3253 -5.3137 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2570 -1.0243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2450 1.6744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3066 -1.0682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3566 1.6406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12.1001 -2.6593 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6878 3.1631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.2654 3.1830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.3214 0.4451 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4912 1.6022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 6 2 0
|
|
3 5 1 0
|
|
4 2 1 0
|
|
5 1 2 0
|
|
6 1 1 0
|
|
7 3 2 0
|
|
8 16 1 0
|
|
9 4 2 0
|
|
10 8 1 0
|
|
11 7 1 0
|
|
14 12 1 0
|
|
13 17 1 0
|
|
14 10 1 0
|
|
15 31 1 0
|
|
16 26 2 0
|
|
17 11 1 0
|
|
18 13 1 0
|
|
19 8 2 0
|
|
20 15 1 0
|
|
21 12 2 0
|
|
22 9 1 0
|
|
23 15 2 0
|
|
24 5 1 0
|
|
25 27 2 0
|
|
26 28 1 0
|
|
27 18 1 0
|
|
28 18 2 0
|
|
29 6 1 0
|
|
14 30 1 6
|
|
31 30 1 0
|
|
32 12 1 0
|
|
33 13 1 0
|
|
4 3 1 0
|
|
22 11 2 0
|
|
16 25 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(methotrexate);
|
|
auto methotrexateAnalog = R"CTAB(
|
|
RDKit 2D
|
|
|
|
33 35 0 0 1 0 0 0 0 0999 V2000
|
|
-4.0189 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6792 -0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6792 -1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0189 -2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0189 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.3584 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6981 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.3773 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-10.7169 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.3773 -2.7069 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -0.3866 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6981 -2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.3584 -1.9335 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3395 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3395 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3395 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6792 2.7069 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.3584 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.6981 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.0378 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.3773 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.7169 2.7069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.3773 0.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.3584 4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.6981 5.0273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 5.0273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3395 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 0.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 2 0
|
|
5 6 1 0
|
|
6 7 2 0
|
|
7 8 1 0
|
|
8 9 2 0
|
|
9 10 1 0
|
|
9 11 1 0
|
|
11 12 2 0
|
|
12 13 1 0
|
|
12 14 1 0
|
|
7 14 1 0
|
|
14 15 2 0
|
|
4 15 1 0
|
|
2 16 1 0
|
|
16 17 2 0
|
|
17 18 1 0
|
|
18 19 2 0
|
|
22 23 1 0
|
|
23 24 1 0
|
|
24 25 1 0
|
|
25 26 2 0
|
|
25 27 1 0
|
|
22 28 1 0
|
|
28 29 2 0
|
|
28 30 1 0
|
|
19 31 1 0
|
|
31 32 2 0
|
|
16 32 1 0
|
|
19 20 1 0
|
|
22 21 1 0
|
|
20 21 1 0
|
|
21 33 2 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(methotrexateAnalog);
|
|
auto refPatt =
|
|
"[#7]1:[#6](:[#7]:[#6](:[#6]2:[#6]:1:[#7]:[#6]:[#6](:[#7]:2)-[#6])-[#7])-[#7]"_smarts;
|
|
REQUIRE(refPatt);
|
|
MatchVectType expected{{1, 7}, {5, 8}, {0, 10}, {4, 11}, {2, 13},
|
|
{3, 6}, {8, 5}, {21, 4}, {10, 3}, {6, 14},
|
|
{16, 2}, {23, 12}, {28, 9}};
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*methotrexateAnalog, *methotrexate, -1, refPatt.get(), p);
|
|
CHECK(match == expected);
|
|
}
|
|
|
|
TEST_CASE("Normalize should always center in centroid, irrespective of canonicalize parameter") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
25 27 0 0 0 0 0 0 0 0999 V2000
|
|
18.2425 6.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.8948 6.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.3808 7.4101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
14.8817 7.3567 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
14.4692 5.9146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
15.7134 5.0766 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
|
|
13.0271 6.3270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
13.4395 7.7692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12.7114 9.0806 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.7156 5.5989 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.4294 6.3705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.4545 7.8703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.1179 5.6424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.8316 6.4141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.8568 7.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5705 8.6855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2591 7.9574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2339 6.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5202 5.6860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9728 8.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.0928 4.1426 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
17.2187 8.6543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.5602 10.0020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
18.7151 8.5507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
17.6905 4.7294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
5 6 1 6
|
|
5 7 1 0
|
|
7 8 1 0
|
|
8 9 2 0
|
|
7 10 1 6
|
|
10 11 1 0
|
|
11 12 2 0
|
|
11 13 1 0
|
|
13 14 1 0
|
|
14 15 2 0
|
|
15 16 1 0
|
|
16 17 2 0
|
|
17 18 1 0
|
|
18 19 2 0
|
|
17 20 1 0
|
|
13 21 1 6
|
|
3 22 1 1
|
|
22 23 2 0
|
|
22 24 1 0
|
|
2 25 1 0
|
|
6 2 1 0
|
|
8 4 1 0
|
|
19 14 1 0
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
RDDepict::normalizeDepiction(*m, -1, 0);
|
|
auto ctd = MolTransforms::computeCentroid(m->getConformer());
|
|
CHECK_THAT(ctd.x, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
|
|
CHECK_THAT(ctd.y, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
|
|
}
|