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//
// Copyright (C) 2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Chirality.h>
#include "RDDepictor.h"
#include "DepictUtils.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
using namespace RDKit;
TEST_CASE(
"github #4504: overlapping coordinates with 1,1-disubstituted "
"cyclobutanes") {
SECTION("basics") {
auto m = "CCC1(CCC1)CC1CCCCC1"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
CHECK(v.length() > 0.1);
v = conf.getAtomPos(1) - conf.getAtomPos(5);
CHECK(v.length() > 0.1);
}
SECTION("this one was ok") {
auto m = "CCC1(CCC1)C1CCCCC1"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
CHECK(v.length() > 0.1);
v = conf.getAtomPos(1) - conf.getAtomPos(5);
CHECK(v.length() > 0.1);
}
}
TEST_CASE("square planar", "[nontetrahedral]") {
SECTION("cis-platin") {
auto m = "Cl[Pt@SP1](Cl)(<-[NH3])<-[NH3]"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
CHECK(v1.length() < v2.length());
}
SECTION("trans-platin") {
auto m = "Cl[Pt@SP2](Cl)(<-[NH3])<-[NH3]"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
CHECK(v1.length() > v2.length());
}
SECTION("trans-metal in a ring") {
auto m = "C1[Pt@SP2](CCC1)(<-[NH3])<-[NH3]"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
// std::cerr << MolToV3KMolBlock(*m) << std::endl;
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
CHECK(v1.length() > v2.length());
}
SECTION("cis-metal in a ring") {
auto m = "C1[Pt@SP1](CCC1)(<-[NH3])<-[NH3]"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
// std::cerr << MolToV3KMolBlock(*m) << std::endl;
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
CHECK(v1.length() < v2.length());
}
}
TEST_CASE("trigonal bipyramidal", "[nontetrahedral]") {
SECTION("TB1") {
auto m = "S[As@TB1](F)(Cl)(Br)N"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - ax
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
CHECK(v1.length() > v2.length());
CHECK(v1.length() > v3.length());
CHECK(v3.length() > v2.length());
CHECK(v3.length() > v4.length());
CHECK(v2.length() > v4.length());
}
SECTION("TB3") {
auto m = "S[As@TB3](F)(Cl)(N)Br"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - ax
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - eq
auto v3 = conf.getAtomPos(2) - conf.getAtomPos(5); // eq - eq long
auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
CHECK(v1.length() > v2.length());
CHECK(v1.length() > v3.length());
CHECK(v3.length() > v2.length());
CHECK(v3.length() > v4.length());
CHECK(v2.length() > v4.length());
}
SECTION("TB1 missing ax") {
auto m = "S[As@TB1](F)(Cl)Br"_smiles;
REQUIRE(m);
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(120, 0.001));
CHECK(RDDepict::compute2DCoords(*m) == 0);
auto &conf = m->getConformer();
auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
CHECK(v3.length() > v2.length());
CHECK(v3.length() > v4.length());
CHECK(v2.length() > v4.length());
}
}
TEST_CASE("octahedral", "[nontetrahedral]") {
SECTION("OH1") {
auto m = "O[Co@OH1](Cl)(C)(N)(F)P"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
// std::cerr << MolToV3KMolBlock(*m) << std::endl;
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
auto v5 = conf.getAtomPos(0) - conf.getAtomPos(6); // eq - eq cross
auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
CHECK(v1.length() > v2.length());
CHECK(v1.length() > v3.length());
CHECK(v1.length() > v4.length());
CHECK(v1.length() > v6.length());
CHECK(v5.length() > v4.length());
CHECK(v5.length() > v6.length());
}
SECTION("OH3") {
auto m = "O[Co@OH3](Cl)(C)(N)(P)F"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
// std::cerr << MolToV3KMolBlock(*m) << std::endl;
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(3) - conf.getAtomPos(6); // ax - ax
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
auto v5 = conf.getAtomPos(0) - conf.getAtomPos(5); // eq - eq cross
auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
CHECK(v1.length() > v2.length());
CHECK(v1.length() > v3.length());
CHECK(v1.length() > v4.length());
CHECK(v1.length() > v6.length());
CHECK(v5.length() > v4.length());
CHECK(v5.length() > v6.length());
}
SECTION("OH1 missing one ligand") {
auto m = "O[Co@OH1](Cl)(C)(N)F"_smiles;
REQUIRE(m);
CHECK(RDDepict::compute2DCoords(*m) == 0);
// std::cerr << MolToV3KMolBlock(*m) << std::endl;
auto &conf = m->getConformer();
auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
CHECK(v1.length() > v2.length());
CHECK(v1.length() > v3.length());
CHECK(v1.length() > v4.length());
CHECK(v1.length() > v6.length());
}
}
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