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fix a thread-safety bug in the UFF parameter acquisition (#4553)

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This commit is contained in:
Greg Landrum
2021-09-29 09:31:36 +02:00
committed by GitHub
parent 092552349c
commit 157df3c296
6 changed files with 42 additions and 35 deletions
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13
Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp
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@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2004-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -393,7 +392,7 @@ std::string getAtomLabel(const Atom *atom) {
std::pair<AtomicParamVect, bool> getAtomTypes(const ROMol &mol,
const std::string &) {
bool foundAll = true;
ParamCollection *params = ParamCollection::getParams();
auto params = ParamCollection::getParams();
AtomicParamVect paramVect;
paramVect.resize(mol.getNumAtoms());
@@ -420,7 +419,7 @@ std::pair<AtomicParamVect, bool> getAtomTypes(const ROMol &mol,
bool getUFFBondStretchParams(const ROMol &mol, unsigned int idx1,
unsigned int idx2, UFFBond &uffBondStretchParams) {
ParamCollection *params = ParamCollection::getParams();
auto params = ParamCollection::getParams();
unsigned int idx[2] = {idx1, idx2};
AtomicParamVect paramVect(2);
unsigned int i;
@@ -445,7 +444,7 @@ bool getUFFBondStretchParams(const ROMol &mol, unsigned int idx1,
bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
UFFAngle &uffAngleBendParams) {
ParamCollection *params = ParamCollection::getParams();
auto params = ParamCollection::getParams();
unsigned int idx[3] = {idx1, idx2, idx3};
AtomicParamVect paramVect(3);
unsigned int i;
@@ -477,7 +476,7 @@ bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1,
bool getUFFTorsionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4,
UFFTor &uffTorsionParams) {
ParamCollection *params = ParamCollection::getParams();
auto params = ParamCollection::getParams();
unsigned int idx[4] = {idx1, idx2, idx3, idx4};
AtomicParamVect paramVect(2);
unsigned int i;
@@ -599,7 +598,7 @@ bool getUFFInversionParams(const ROMol &mol, unsigned int idx1,
bool getUFFVdWParams(const ROMol &mol, unsigned int idx1, unsigned int idx2,
UFFVdW &uffVdWParams) {
bool res = true;
ParamCollection *params = ParamCollection::getParams();
auto params = ParamCollection::getParams();
unsigned int idx[2] = {idx1, idx2};
AtomicParamVect paramVect(2);
unsigned int i;

5
Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
View File

@@ -1,5 +1,5 @@
//
// Copyright (C) 2004-2018 Greg Landrum and Rational Discovery LLC
// Copyright (C) 2004-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -1387,8 +1387,7 @@ void testGitHubIssue613() {
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size() == mol->getNumAtoms());
ForceFields::UFF::ParamCollection *params =
ForceFields::UFF::ParamCollection::getParams();
auto params = ForceFields::UFF::ParamCollection::getParams();
const ForceFields::UFF::AtomicParams *ap = (*params)("Eu6+3");
TEST_ASSERT(ap);
TEST_ASSERT(ap->r1 == types[0]->r1);