mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
107 lines
3.2 KiB
C++
107 lines
3.2 KiB
C++
//
|
|
// Copyright (C) 2023 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 <algorithm>
|
|
#include <fstream>
|
|
#include <string>
|
|
#include <sstream>
|
|
#include <string_view>
|
|
#include <streambuf>
|
|
|
|
#include "RDGeneral/test.h"
|
|
#include <catch2/catch_all.hpp>
|
|
#include <RDGeneral/Invariant.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/FileParsers/FileParsers.h>
|
|
#include <GraphMol/SmilesParse/SmilesParse.h>
|
|
#include <GraphMol/FileParsers/ProximityBonds.h>
|
|
|
|
using namespace RDKit;
|
|
|
|
TEST_CASE(
|
|
"Github #6756: ConnectTheDots can segfault if atoms do not have residue info") {
|
|
SECTION("small molecule, was not a problem") {
|
|
std::string smiles =
|
|
"[H]C([H])=C([H])C([H])([H])[H] |(1.35283,-0.241953,-1.28693;1.35436,-0.216135,-0.201646;2.30673,-0.352635,0.30154;0.23076,-0.0239947,0.500064;0.281106,-0.00576639,1.58653;-1.11716,0.171588,-0.112486;-1.08265,0.139951,-1.20609;-1.52627,1.14083,0.188471;-1.79971,-0.611884,0.230548)|";
|
|
SmilesParserParams ps;
|
|
ps.removeHs = false;
|
|
std::unique_ptr<RWMol> m(SmilesToMol(smiles, ps));
|
|
REQUIRE(m);
|
|
CHECK(m->getNumBonds() == 8);
|
|
// start without bonds
|
|
m->beginBatchEdit();
|
|
for (auto bond : m->bonds()) {
|
|
m->removeBond(bond->getBeginAtomIdx(), bond->getEndAtomIdx());
|
|
}
|
|
m->commitBatchEdit();
|
|
CHECK(m->getNumBonds() == 0);
|
|
ConnectTheDots(m.get());
|
|
CHECK(m->getNumBonds() == 8);
|
|
}
|
|
SECTION("small molecule with bivalent H, this did crash") {
|
|
std::string smiles = "F[H]F |(1.1,0,0;0,0,0;-1.1,0,0)|";
|
|
SmilesParserParams ps;
|
|
ps.removeHs = false;
|
|
ps.sanitize = false;
|
|
std::unique_ptr<RWMol> m(SmilesToMol(smiles, ps));
|
|
REQUIRE(m);
|
|
m->updatePropertyCache(false);
|
|
CHECK(m->getNumBonds() == 2);
|
|
// start without bonds
|
|
m->beginBatchEdit();
|
|
for (auto bond : m->bonds()) {
|
|
m->removeBond(bond->getBeginAtomIdx(), bond->getEndAtomIdx());
|
|
}
|
|
m->commitBatchEdit();
|
|
CHECK(m->getNumBonds() == 0);
|
|
ConnectTheDots(m.get());
|
|
CHECK(m->getNumBonds() == 1);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("ctdQUICKREMOVE_H_H_CONTACTS mode") {
|
|
SECTION("H2, basics") {
|
|
auto m = "[H].[H] |(0.0,0.0,0.3;0.0,0.0,-0.3)|"_smiles;
|
|
REQUIRE(m);
|
|
// by default we get a bond:
|
|
{
|
|
RWMol m2(*m);
|
|
ConnectTheDots(&m2, 0);
|
|
CHECK(m2.getNumBonds() == 1);
|
|
}
|
|
{
|
|
RWMol m2(*m);
|
|
ConnectTheDots(&m2, ctdIGNORE_H_H_CONTACTS);
|
|
CHECK(m2.getNumBonds() == 0);
|
|
}
|
|
{
|
|
RWMol m2(*m);
|
|
ConnectTheDots(&m2, ctdQUICKREMOVE_H_H_CONTACTS);
|
|
CHECK(m2.getNumBonds() == 1);
|
|
}
|
|
}
|
|
SECTION("H2, basics") {
|
|
auto m = "[H].[H].[C] |(0.0,0.0,0.3;0.0,0.0,-0.3;0.0,0.0,-1.3)|"_smiles;
|
|
REQUIRE(m);
|
|
{
|
|
RWMol m2(*m);
|
|
ConnectTheDots(&m2, 0);
|
|
CHECK(m2.getNumBonds() == 1);
|
|
CHECK(m2.getBondBetweenAtoms(0, 1));
|
|
}
|
|
{
|
|
RWMol m2(*m);
|
|
ConnectTheDots(&m2, ctdQUICKREMOVE_H_H_CONTACTS);
|
|
CHECK(m2.getNumBonds() == 1);
|
|
CHECK(!m2.getBondBetweenAtoms(0, 1));
|
|
CHECK(m2.getBondBetweenAtoms(1, 2));
|
|
}
|
|
}
|
|
}
|