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swap boost::tuple to std::tuple (#5851)

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This commit is contained in:
Greg Landrum
2022-12-16 16:01:19 +01:00
committed by GitHub
parent cba7ecf3a4
commit e322928028
30 changed files with 284 additions and 319 deletions
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12
Code/DataStructs/MultiFPBReader.cpp
View File

@@ -8,8 +8,6 @@
// of the RDKit source tree.
//
#include <boost/tuple/tuple_comparison.hpp>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDThreads.h>
#ifdef RDK_BUILD_THREADSAFE_SSS
@@ -29,14 +27,14 @@ std::uint8_t *bitsetToBytes(const boost::dynamic_bitset<> &bitset);
namespace {
auto tplSorter = [](const MultiFPBReader::ResultTuple &v1,
const MultiFPBReader::ResultTuple &v2) {
if (v1.get<0>() == v2.get<0>()) {
if (v1.get<2>() == v2.get<2>()) {
return v1.get<1>() < v2.get<1>();
if (std::get<0>(v1) == std::get<0>(v2)) {
if (std::get<2>(v1) == std::get<2>(v2)) {
return std::get<1>(v1) < std::get<1>(v2);
} else {
return v1.get<2>() < v2.get<2>();
return std::get<2>(v1) < std::get<2>(v2);
}
} else {
return v1.get<0>() > v2.get<0>();
return std::get<0>(v1) > std::get<0>(v2);
}
};

8
Code/DataStructs/MultiFPBReader.h
View File

@@ -1,5 +1,5 @@
//
// Copyright (c) 2016 Greg Landrum
// Copyright (c) 2016-2022 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -21,7 +21,7 @@
#include <RDGeneral/Exceptions.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/FPBReader.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
namespace RDKit {
@@ -36,7 +36,7 @@ namespace RDKit {
MultiFPBReader fpbs(readers);
fpbs.init();
boost::shared_ptr<ExplicitBitVect> ebv = fpbs.getReader(0)->getFP(95);
std::vector<boost::tuple<double,unsigned int, unsigned int> > nbrs =
std::vector<std::tuple<double,unsigned int, unsigned int> > nbrs =
fpbs.getTanimotoNeighbors(*ebv.get(), 0.70);
\endcode
@@ -52,7 +52,7 @@ namespace RDKit {
*/
class RDKIT_DATASTRUCTS_EXPORT MultiFPBReader {
public:
typedef boost::tuple<double, unsigned int, unsigned int> ResultTuple;
typedef std::tuple<double, unsigned int, unsigned int> ResultTuple;
MultiFPBReader() {}
/*!

6
Code/DataStructs/Wrap/wrap_FPB.cpp
View File

@@ -58,7 +58,8 @@ python::tuple multiTaniNbrHelper(const MultiFPBReader *self,
self->getTanimotoNeighbors(bv, threshold, numThreads);
python::list result;
for (auto &nbr : nbrs) {
result.append(python::make_tuple(nbr.get<0>(), nbr.get<1>(), nbr.get<2>()));
result.append(python::make_tuple(std::get<0>(nbr), std::get<1>(nbr),
std::get<2>(nbr)));
}
return python::tuple(result);
}
@@ -71,7 +72,8 @@ python::tuple multiTverskyNbrHelper(const MultiFPBReader *self,
self->getTverskyNeighbors(bv, ca, cb, threshold, numThreads);
python::list result;
for (auto &nbr : nbrs) {
result.append(python::make_tuple(nbr.get<0>(), nbr.get<1>(), nbr.get<2>()));
result.append(python::make_tuple(std::get<0>(nbr), std::get<1>(nbr),
std::get<2>(nbr)));
}
return python::tuple(result);
}

209
Code/DataStructs/testMultiFPB.cpp
View File

@@ -75,12 +75,12 @@ void test2MultiFPBReaderTanimoto() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTanimotoNeighbors(bytes);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 0);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 0);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
}
{ // with a threshold
boost::shared_array<std::uint8_t> bytes = mfps.getReader(0)->getBytes(0);
@@ -88,15 +88,15 @@ void test2MultiFPBReaderTanimoto() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 10);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 0);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.3703));
TEST_ASSERT(nbrs[2].get<1>() == 1);
TEST_ASSERT(nbrs[2].get<2>() == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 0);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.3703));
TEST_ASSERT(std::get<1>(nbrs[2]) == 1);
TEST_ASSERT(std::get<2>(nbrs[2]) == 0);
}
{ // with a threshold
boost::shared_array<std::uint8_t> bytes = mfps.getReader(0)->getBytes(95);
@@ -104,15 +104,15 @@ void test2MultiFPBReaderTanimoto() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTanimotoNeighbors(bytes, 0.30);
TEST_ASSERT(nbrs.size() == 4);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 95);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 95);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.4125));
TEST_ASSERT(nbrs[2].get<1>() == 89);
TEST_ASSERT(nbrs[2].get<2>() == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 95);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 95);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.4125));
TEST_ASSERT(std::get<1>(nbrs[2]) == 89);
TEST_ASSERT(std::get<2>(nbrs[2]) == 0);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
@@ -140,12 +140,12 @@ void test3MultiFPBReaderTversky() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTverskyNeighbors(bytes, 1., 1.);
TEST_ASSERT(nbrs.size() == 2);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 0);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 0);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
}
{ // with a threshold
boost::shared_array<std::uint8_t> bytes = mfps.getReader(0)->getBytes(0);
@@ -153,15 +153,15 @@ void test3MultiFPBReaderTversky() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTverskyNeighbors(bytes, 1., 1., 0.30);
TEST_ASSERT(nbrs.size() == 10);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 0);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.3703));
TEST_ASSERT(nbrs[2].get<1>() == 1);
TEST_ASSERT(nbrs[2].get<2>() == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 0);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.3703));
TEST_ASSERT(std::get<1>(nbrs[2]) == 1);
TEST_ASSERT(std::get<2>(nbrs[2]) == 0);
}
{ // with a threshold, asymmetric
boost::shared_array<std::uint8_t> bytes = mfps.getReader(0)->getBytes(0);
@@ -169,15 +169,15 @@ void test3MultiFPBReaderTversky() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTverskyNeighbors(bytes, 1., 0.5, 0.30);
TEST_ASSERT(nbrs.size() == 10);
TEST_ASSERT(feq(nbrs[0].get<0>(), 1.));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 0);
TEST_ASSERT(feq(nbrs[1].get<0>(), 1.));
TEST_ASSERT(nbrs[1].get<1>() == 0);
TEST_ASSERT(nbrs[1].get<2>() == 1);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.4255));
TEST_ASSERT(nbrs[2].get<1>() == 1);
TEST_ASSERT(nbrs[2].get<2>() == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 1.));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 1.));
TEST_ASSERT(std::get<1>(nbrs[1]) == 0);
TEST_ASSERT(std::get<2>(nbrs[1]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.4255));
TEST_ASSERT(std::get<1>(nbrs[2]) == 1);
TEST_ASSERT(std::get<2>(nbrs[2]) == 0);
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
@@ -263,27 +263,28 @@ void test5MultiFPBReaderThreaded() {
mfps.getTanimotoNeighbors(qbv, 0.6);
TEST_ASSERT(nbrs.size() == 6);
// for (unsigned int i = 0; i < nbrs.size(); ++i) {
// std::cerr << i << ": " << nbrs[i].get<0>() << " " << nbrs[i].get<1>()
// << " " << nbrs[i].get<2>() << " " << std::endl;
// std::cerr << i << ": " << std::get<0>(nbrs[i]) << " " <<
// std::get<1>(nbrs[i])
// << " " << std::get<2>(nbrs[i]) << " " << std::endl;
// }
TEST_ASSERT(feq(nbrs[0].get<0>(), 0.66412));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 3);
TEST_ASSERT(feq(nbrs[1].get<0>(), 0.65289));
TEST_ASSERT(nbrs[1].get<1>() == 1);
TEST_ASSERT(nbrs[1].get<2>() == 2);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.64341));
TEST_ASSERT(nbrs[2].get<1>() == 2);
TEST_ASSERT(nbrs[2].get<2>() == 1);
TEST_ASSERT(feq(nbrs[3].get<0>(), 0.61940));
TEST_ASSERT(nbrs[3].get<1>() == 1);
TEST_ASSERT(nbrs[3].get<2>() == 0);
TEST_ASSERT(feq(nbrs[4].get<0>(), 0.61905));
TEST_ASSERT(nbrs[4].get<1>() == 0);
TEST_ASSERT(nbrs[4].get<2>() == 0);
TEST_ASSERT(feq(nbrs[5].get<0>(), 0.61344));
TEST_ASSERT(nbrs[5].get<1>() == 0);
TEST_ASSERT(nbrs[5].get<2>() == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 0.66412));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 3);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 0.65289));
TEST_ASSERT(std::get<1>(nbrs[1]) == 1);
TEST_ASSERT(std::get<2>(nbrs[1]) == 2);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.64341));
TEST_ASSERT(std::get<1>(nbrs[2]) == 2);
TEST_ASSERT(std::get<2>(nbrs[2]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[3]), 0.61940));
TEST_ASSERT(std::get<1>(nbrs[3]) == 1);
TEST_ASSERT(std::get<2>(nbrs[3]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[4]), 0.61905));
TEST_ASSERT(std::get<1>(nbrs[4]) == 0);
TEST_ASSERT(std::get<2>(nbrs[4]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[5]), 0.61344));
TEST_ASSERT(std::get<1>(nbrs[5]) == 0);
TEST_ASSERT(std::get<2>(nbrs[5]) == 1);
}
#ifdef RDK_TEST_MULTITHREADED
@@ -291,47 +292,47 @@ void test5MultiFPBReaderThreaded() {
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTanimotoNeighbors(qbv, 0.6, 4);
TEST_ASSERT(nbrs.size() == 6);
TEST_ASSERT(feq(nbrs[0].get<0>(), 0.66412));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 3);
TEST_ASSERT(feq(nbrs[1].get<0>(), 0.65289));
TEST_ASSERT(nbrs[1].get<1>() == 1);
TEST_ASSERT(nbrs[1].get<2>() == 2);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.64341));
TEST_ASSERT(nbrs[2].get<1>() == 2);
TEST_ASSERT(nbrs[2].get<2>() == 1);
TEST_ASSERT(feq(nbrs[3].get<0>(), 0.61940));
TEST_ASSERT(nbrs[3].get<1>() == 1);
TEST_ASSERT(nbrs[3].get<2>() == 0);
TEST_ASSERT(feq(nbrs[4].get<0>(), 0.61905));
TEST_ASSERT(nbrs[4].get<1>() == 0);
TEST_ASSERT(nbrs[4].get<2>() == 0);
TEST_ASSERT(feq(nbrs[5].get<0>(), 0.61344));
TEST_ASSERT(nbrs[5].get<1>() == 0);
TEST_ASSERT(nbrs[5].get<2>() == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 0.66412));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 3);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 0.65289));
TEST_ASSERT(std::get<1>(nbrs[1]) == 1);
TEST_ASSERT(std::get<2>(nbrs[1]) == 2);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.64341));
TEST_ASSERT(std::get<1>(nbrs[2]) == 2);
TEST_ASSERT(std::get<2>(nbrs[2]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[3]), 0.61940));
TEST_ASSERT(std::get<1>(nbrs[3]) == 1);
TEST_ASSERT(std::get<2>(nbrs[3]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[4]), 0.61905));
TEST_ASSERT(std::get<1>(nbrs[4]) == 0);
TEST_ASSERT(std::get<2>(nbrs[4]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[5]), 0.61344));
TEST_ASSERT(std::get<1>(nbrs[5]) == 0);
TEST_ASSERT(std::get<2>(nbrs[5]) == 1);
}
{ // request more threads than we have readers, this shouldn't be a problem
std::vector<MultiFPBReader::ResultTuple> nbrs =
mfps.getTanimotoNeighbors(qbv, 0.6, 8);
TEST_ASSERT(nbrs.size() == 6);
TEST_ASSERT(feq(nbrs[0].get<0>(), 0.66412));
TEST_ASSERT(nbrs[0].get<1>() == 0);
TEST_ASSERT(nbrs[0].get<2>() == 3);
TEST_ASSERT(feq(nbrs[1].get<0>(), 0.65289));
TEST_ASSERT(nbrs[1].get<1>() == 1);
TEST_ASSERT(nbrs[1].get<2>() == 2);
TEST_ASSERT(feq(nbrs[2].get<0>(), 0.64341));
TEST_ASSERT(nbrs[2].get<1>() == 2);
TEST_ASSERT(nbrs[2].get<2>() == 1);
TEST_ASSERT(feq(nbrs[3].get<0>(), 0.61940));
TEST_ASSERT(nbrs[3].get<1>() == 1);
TEST_ASSERT(nbrs[3].get<2>() == 0);
TEST_ASSERT(feq(nbrs[4].get<0>(), 0.61905));
TEST_ASSERT(nbrs[4].get<1>() == 0);
TEST_ASSERT(nbrs[4].get<2>() == 0);
TEST_ASSERT(feq(nbrs[5].get<0>(), 0.61344));
TEST_ASSERT(nbrs[5].get<1>() == 0);
TEST_ASSERT(nbrs[5].get<2>() == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[0]), 0.66412));
TEST_ASSERT(std::get<1>(nbrs[0]) == 0);
TEST_ASSERT(std::get<2>(nbrs[0]) == 3);
TEST_ASSERT(feq(std::get<0>(nbrs[1]), 0.65289));
TEST_ASSERT(std::get<1>(nbrs[1]) == 1);
TEST_ASSERT(std::get<2>(nbrs[1]) == 2);
TEST_ASSERT(feq(std::get<0>(nbrs[2]), 0.64341));
TEST_ASSERT(std::get<1>(nbrs[2]) == 2);
TEST_ASSERT(std::get<2>(nbrs[2]) == 1);
TEST_ASSERT(feq(std::get<0>(nbrs[3]), 0.61940));
TEST_ASSERT(std::get<1>(nbrs[3]) == 1);
TEST_ASSERT(std::get<2>(nbrs[3]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[4]), 0.61905));
TEST_ASSERT(std::get<1>(nbrs[4]) == 0);
TEST_ASSERT(std::get<2>(nbrs[4]) == 0);
TEST_ASSERT(feq(std::get<0>(nbrs[5]), 0.61344));
TEST_ASSERT(std::get<1>(nbrs[5]) == 0);
TEST_ASSERT(std::get<2>(nbrs[5]) == 1);
}
#endif

11
Code/ForceField/MMFF/TorsionAngle.cpp
View File

@@ -1,8 +1,5 @@
// $Id$
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2013-2022 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -35,10 +32,10 @@ double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
return cosPhi;
}
boost::tuple<double, double, double> calcTorsionForceConstant(
std::tuple<double, double, double> calcTorsionForceConstant(
const MMFFTor *mmffTorParams) {
return boost::make_tuple(mmffTorParams->V1, mmffTorParams->V2,
mmffTorParams->V3);
return std::make_tuple(mmffTorParams->V1, mmffTorParams->V2,
mmffTorParams->V3);
}
double calcTorsionEnergy(const double V1, const double V2, const double V3,

12
Code/ForceField/MMFF/TorsionAngle.h
View File

@@ -1,7 +1,5 @@
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2013-2022 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -10,11 +8,11 @@
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_MMFFTORSIONANGLE_H__
#define __RD_MMFFTORSIONANGLE_H__
#ifndef RD_MMFFTORSIONANGLE_H
#define RD_MMFFTORSIONANGLE_H
#include <ForceField/Contrib.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
namespace RDGeom {
class Point3D;
@@ -62,7 +60,7 @@ RDKIT_FORCEFIELD_EXPORT double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint);
//! returns the 3-tuple of a torsion angle force constants
RDKIT_FORCEFIELD_EXPORT boost::tuple<double, double, double>
RDKIT_FORCEFIELD_EXPORT std::tuple<double, double, double>
calcTorsionForceConstant(const MMFFTor *mmffTorParams);
//! calculates and returns the torsional MMFF energy
RDKIT_FORCEFIELD_EXPORT double calcTorsionEnergy(const double V1,

23
Code/ForceField/UFF/Inversion.cpp
View File

@@ -1,8 +1,5 @@
// $Id$
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2013 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -38,7 +35,7 @@ double calculateCosY(const RDGeom::Point3D &iPoint,
return n.dotProduct(rJL);
}
boost::tuple<double, double, double, double>
std::tuple<double, double, double, double>
calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
double res = 0.0;
double C0 = 0.0;
@@ -82,7 +79,7 @@ calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO) {
}
res /= 3.0;
return boost::make_tuple(res, C0, C1, C2);
return std::make_tuple(res, C0, C1, C2);
}
} // end of namespace Utils
@@ -103,14 +100,12 @@ InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1,
d_at3Idx = idx3;
d_at4Idx = idx4;
boost::tuple<double, double, double, double> invCoeffForceCon =
Utils::calcInversionCoefficientsAndForceConstant(at2AtomicNum,
isCBoundToO);
d_forceConstant =
oobForceScalingFactor * boost::tuples::get<0>(invCoeffForceCon);
d_C0 = boost::tuples::get<1>(invCoeffForceCon);
d_C1 = boost::tuples::get<2>(invCoeffForceCon);
d_C2 = boost::tuples::get<3>(invCoeffForceCon);
auto invCoeffForceCon = Utils::calcInversionCoefficientsAndForceConstant(
at2AtomicNum, isCBoundToO);
d_forceConstant = oobForceScalingFactor * std::get<0>(invCoeffForceCon);
d_C0 = std::get<1>(invCoeffForceCon);
d_C1 = std::get<2>(invCoeffForceCon);
d_C2 = std::get<3>(invCoeffForceCon);
}
double InversionContrib::getEnergy(double *pos) const {

12
Code/ForceField/UFF/Inversion.h
View File

@@ -1,7 +1,5 @@
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2013 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -10,10 +8,10 @@
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_UFFINVERSION_H__
#define __RD_UFFINVERSION_H__
#ifndef RD_UFFINVERSION_H
#define RD_UFFINVERSION_H
#include <ForceField/Contrib.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <Geometry/point.h>
namespace ForceFields {
@@ -73,7 +71,7 @@ RDKIT_FORCEFIELD_EXPORT double calculateCosY(const RDGeom::Point3D &iPoint,
\return the force constant
*/
RDKIT_FORCEFIELD_EXPORT boost::tuple<double, double, double, double>
RDKIT_FORCEFIELD_EXPORT std::tuple<double, double, double, double>
calcInversionCoefficientsAndForceConstant(int at2AtomicNum, bool isCBoundToO);
} // namespace Utils
} // namespace UFF

18
Code/GraphMol/Canon.cpp
View File

@@ -80,7 +80,7 @@ bool chiralAtomNeedsTagInversion(const RDKit::ROMol &mol,
}
auto _possibleCompare = [](const PossibleType &arg1, const PossibleType &arg2) {
return (arg1.get<0>() < arg2.get<0>());
return (std::get<0>(arg1) < std::get<0>(arg2));
};
bool checkBondsInSameBranch(MolStack &molStack, Bond *dblBnd, Bond *dirBnd) {
@@ -654,16 +654,16 @@ void dfsFindCycles(ROMol &mol, int atomIdx, int inBondIdx,
std::sort(possibles.begin(), possibles.end(), _possibleCompare);
// if (possibles.size())
// std::cerr << " aIdx1: " << atomIdx
// << " first: " << possibles.front().get<0>() << " "
// << possibles.front().get<1>() << std::endl;
// << " first: " << possibles.front()std:std::get<0>() << " "
// << possibles.front()std:std::get<1>() << std::endl;
// // ---------------------
//
// Now work the children
//
// ---------------------
for (auto &possible : possibles) {
int possibleIdx = possible.get<1>();
Bond *bond = possible.get<2>();
int possibleIdx = std::get<1>(possible);
Bond *bond = std::get<2>(possible);
switch (colors[possibleIdx]) {
case WHITE_NODE:
// -----
@@ -825,8 +825,8 @@ void dfsBuildStack(ROMol &mol, int atomIdx, int inBondIdx,
std::sort(possibles.begin(), possibles.end(), _possibleCompare);
// if (possibles.size())
// std::cerr << " aIdx2: " << atomIdx
// << " first: " << possibles.front().get<0>() << " "
// << possibles.front().get<1>() << std::endl;
// << " first: " << possibles.front()std:std::get<0>() << " "
// << possibles.front()std:std::get<1>() << std::endl;
// ---------------------
//
@@ -835,14 +835,14 @@ void dfsBuildStack(ROMol &mol, int atomIdx, int inBondIdx,
// ---------------------
for (auto possiblesIt = possibles.begin(); possiblesIt != possibles.end();
possiblesIt++) {
int possibleIdx = possiblesIt->get<1>();
int possibleIdx = std::get<1>(*possiblesIt);
if (colors[possibleIdx] != WHITE_NODE) {
// we're either done or it's a ring-closure, which we already processed...
// this test isn't strictly required, because we only added WHITE notes to
// the possibles list, but it seems logical to document it
continue;
}
Bond *bond = possiblesIt->get<2>();
Bond *bond = std::get<2>(*possiblesIt);
Atom *otherAtom = mol.getAtomWithIdx(possibleIdx);
// ww might have some residual data from earlier calls, clean that up:
otherAtom->clearProp(common_properties::_TraversalBondIndexOrder);

10
Code/GraphMol/Canon.h
View File

@@ -1,5 +1,5 @@
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2004-2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -8,11 +8,11 @@
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_CANON_H_
#define _RD_CANON_H_
#ifndef RD_CANON_H
#define RD_CANON_H
#include <RDGeneral/BoostStartInclude.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
@@ -95,7 +95,7 @@ class RDKIT_GRAPHMOL_EXPORT MolStackElem {
typedef std::vector<MolStackElem> MolStack;
//! used to represent possible branches from an atom
typedef boost::tuple<int, int, Bond *> PossibleType;
typedef std::tuple<int, int, Bond *> PossibleType;
//! constructs the canonical traversal order for a molecular fragment
/*!

2
Code/GraphMol/Fingerprints/FingerprintUtil.cpp
View File

@@ -18,8 +18,6 @@
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <boost/dynamic_bitset.hpp>
#include <boost/tuple/tuple.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <algorithm>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/flyweight.hpp>

5
Code/GraphMol/Fingerprints/FingerprintUtil.h
View File

@@ -16,7 +16,7 @@
#include <DataStructs/SparseIntVect.h>
#include <DataStructs/BitVects.h>
#include <cstdint>
#include <tuple>
#include <vector>
#include <map>
#include <DataStructs/ExplicitBitVect.h>
@@ -95,8 +95,7 @@ class RDKIT_FINGERPRINTS_EXPORT ss_matcher {
RDKit::ROMOL_SPTR m_matcher;
};
typedef boost::tuple<boost::dynamic_bitset<>, uint32_t, unsigned int>
AccumTuple;
typedef std::tuple<boost::dynamic_bitset<>, uint32_t, unsigned int> AccumTuple;
RDKIT_FINGERPRINTS_EXPORT extern std::vector<std::string> defaultFeatureSmarts;

30
Code/GraphMol/Fingerprints/MorganFingerprints.cpp
View File

@@ -41,8 +41,6 @@
#include <RDGeneral/BoostStartInclude.h>
#include <boost/dynamic_bitset.hpp>
#include <boost/tuple/tuple.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <algorithm>
@@ -245,8 +243,8 @@ void calcFingerprint(const ROMol &mol, unsigned int radius,
}
roundInvariants[atomIdx] = static_cast<uint32_t>(invar);
neighborhoodsThisRound.push_back(
boost::make_tuple(roundAtomNeighborhoods[atomIdx],
static_cast<uint32_t>(invar), atomIdx));
std::make_tuple(roundAtomNeighborhoods[atomIdx],
static_cast<uint32_t>(invar), atomIdx));
if (!includeRedundantEnvironments &&
std::find(neighborhoods.begin(), neighborhoods.end(),
roundAtomNeighborhoods[atomIdx]) != neighborhoods.end()) {
@@ -265,28 +263,28 @@ void calcFingerprint(const ROMol &mol, unsigned int radius,
// fingerprint:
if (includeRedundantEnvironments ||
std::find(neighborhoods.begin(), neighborhoods.end(),
iter->get<0>()) == neighborhoods.end()) {
if (!onlyNonzeroInvariants || invariantCpy[iter->get<2>()]) {
if (includeAtoms[iter->get<2>()]) {
uint32_t bit = updateElement(res, iter->get<1>(), useCounts);
std::get<0>(*iter)) == neighborhoods.end()) {
if (!onlyNonzeroInvariants || invariantCpy[std::get<2>(*iter)]) {
if (includeAtoms[std::get<2>(*iter)]) {
uint32_t bit = updateElement(res, std::get<1>(*iter), useCounts);
if (atomsSettingBits) {
(*atomsSettingBits)[bit].push_back(
std::make_pair(iter->get<2>(), layer + 1));
std::make_pair(std::get<2>(*iter), layer + 1));
}
}
if (!fromAtoms || std::find(fromAtoms->begin(), fromAtoms->end(),
iter->get<2>()) != fromAtoms->end()) {
neighborhoods.push_back(iter->get<0>());
std::get<2>(*iter)) != fromAtoms->end()) {
neighborhoods.push_back(std::get<0>(*iter));
}
}
// std::cerr<<" layer: "<<layer<<" atom: "<<iter->get<2>()<<" "
// <<iter->get<0>()<< " " << iter->get<1>() << " " <<
// deadAtoms[iter->get<2>()]<<std::endl;
// std::cerr<<" layer: "<<layer<<" atom: "<<std::get<2>(*iter)<<" "
// <<std::get<0>(*iter)<< " " << std::get<1>(*iter) << " " <<
// deadAtoms[std::get<2>(*iter)]<<std::endl;
} else {
// we have seen this exact environment before, this atom
// is now out of consideration:
// std::cerr<<" atom: "<< iter->get<2>()<<" is dead."<<std::endl;
deadAtoms[iter->get<2>()] = 1;
// std::cerr<<" atom: "<< std::get<2>(*iter)<<" is dead."<<std::endl;
deadAtoms[std::get<2>(*iter)] = 1;
}
}

19
Code/GraphMol/Fingerprints/MorganGenerator.cpp
View File

@@ -17,8 +17,7 @@
#include <RDGeneral/BoostStartInclude.h>
#include <boost/dynamic_bitset.hpp>
#include <boost/tuple/tuple.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <tuple>
#include <RDGeneral/BoostEndInclude.h>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
@@ -320,8 +319,8 @@ MorganEnvGenerator<OutputType>::getEnvironments(
// store the environment that generated this bit id along with the bit
// id and the atom id
allNeighborhoodsThisRound.push_back(
boost::make_tuple(roundAtomNeighborhoods[atomIdx],
static_cast<OutputType>(invar), atomIdx));
std::make_tuple(roundAtomNeighborhoods[atomIdx],
static_cast<OutputType>(invar), atomIdx));
if (std::find(neighborhoods.begin(), neighborhoods.end(),
roundAtomNeighborhoods[atomIdx]) != neighborhoods.end()) {
// we have seen this exact environment before, this atom
@@ -340,19 +339,19 @@ MorganEnvGenerator<OutputType>::getEnvironments(
// result
if (morganArguments->df_includeRedundantEnvironments ||
std::find(neighborhoods.begin(), neighborhoods.end(),
iter->get<0>()) == neighborhoods.end()) {
std::get<0>(*iter)) == neighborhoods.end()) {
if (!morganArguments->df_onlyNonzeroInvariants ||
(*atomInvariants)[iter->get<2>()]) {
if (includeAtoms[iter->get<2>()]) {
(*atomInvariants)[std::get<2>(*iter)]) {
if (includeAtoms[std::get<2>(*iter)]) {
result.push_back(new MorganAtomEnv<OutputType>(
iter->get<1>(), iter->get<2>(), layer + 1));
neighborhoods.push_back(iter->get<0>());
std::get<1>(*iter), std::get<2>(*iter), layer + 1));
neighborhoods.push_back(std::get<0>(*iter));
}
}
} else {
// we have seen this exact environment before, this atom
// is now out of consideration:
deadAtoms[iter->get<2>()] = 1;
deadAtoms[std::get<2>(*iter)] = 1;
}
}

6
Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h
View File

@@ -1,7 +1,5 @@
//
// Copyright (C) 2015 Sereina Riniker
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2015 Sereina Riniker and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -14,7 +12,7 @@
#define RD_TORSIONANGLEM6_H
#include <ForceField/Contrib.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <vector>
namespace RDGeom {

6
Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h
View File

@@ -1,7 +1,5 @@
//
// Copyright (C) 2013-2018 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
// Copyright (C) 2013-2022 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -21,7 +19,7 @@
#include <mutex>
#endif
#include <boost/noncopyable.hpp>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <cstdint>
namespace ForceFields {

4
Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp
View File

@@ -703,10 +703,10 @@ bool getUFFInversionParams(const ROMol &mol, unsigned int idx1,
}
if (res) {
isBoundToSP2O = (isBoundToSP2O && (at2AtomicNum == 6));
boost::tuple<double, double, double, double> invCoeffForceCon =
auto invCoeffForceCon =
UFF::Utils::calcInversionCoefficientsAndForceConstant(at2AtomicNum,
isBoundToSP2O);
uffInversionParams.K = boost::tuples::get<0>(invCoeffForceCon);
uffInversionParams.K = std::get<0>(invCoeffForceCon);
}
return res;
}

21
Code/GraphMol/FragCatalog/FragCatalogEntry.cpp
View File

@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
// Copyright (C) 2003-2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -22,6 +21,7 @@
#include <fstream>
#include <cstdint>
#include <RDGeneral/hash/hash.hpp>
#include <tuple>
namespace RDKit {
@@ -127,23 +127,12 @@ bool FragCatalogEntry::match(const FragCatalogEntry *other, double tol) const {
Subgraphs::DiscrimTuple tdiscs, odiscs;
odiscs = other->getDiscrims();
// double x1 = boost::tuples::get<0>(odiscs);
// std::cout << x1 << "\n";
tdiscs = this->getDiscrims();
#if 0
std::cout << "DISCRIMS: " << d_descrip << " ";
std::cout << tdiscs.get<0>() << " " << tdiscs.get<1>() << " " << tdiscs.get<2>();
std::cout << " -- "<<odiscs.get<0>() << " " << odiscs.get<1>() << " " << odiscs.get<2>();
std::cout << std::endl;
#endif
// REVIEW: need an overload of feq that handles tuples in MolOps, or wherever
// DiscrimTuple is defined
if (!(feq(boost::tuples::get<0>(tdiscs), boost::tuples::get<0>(odiscs),
tol)) ||
!(feq(boost::tuples::get<1>(tdiscs), boost::tuples::get<1>(odiscs),
tol)) ||
!(feq(boost::tuples::get<2>(tdiscs), boost::tuples::get<2>(odiscs),
tol))) {
if (!(feq(std::get<0>(tdiscs), std::get<0>(odiscs), tol)) ||
!(feq(std::get<1>(tdiscs), std::get<1>(odiscs), tol)) ||
!(feq(std::get<2>(tdiscs), std::get<2>(odiscs), tol))) {
return false;
}

9
Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp
View File

@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (C) 2003-2006 Rational Discovery LLC
// Copyright (C) 2003-2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -104,9 +103,9 @@ DOUBLE_VECT GetBitDiscrims(const FragCatalog *self, unsigned int idx) {
DOUBLE_VECT res;
const FragCatalogEntry *entry = self->getEntryWithBitId(idx);
Subgraphs::DiscrimTuple tmp = entry->getDiscrims();
res.push_back(tmp.get<0>());
res.push_back(tmp.get<1>());
res.push_back(tmp.get<2>());
res.push_back(std::get<0>(tmp));
res.push_back(std::get<1>(tmp));
res.push_back(std::get<2>(tmp));
return res;
}

1
Code/GraphMol/MolDraw2D/MolDraw2D.cpp
View File

@@ -44,7 +44,6 @@
#include <memory>
#include <boost/lexical_cast.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <boost/assign/list_of.hpp>
#include <boost/format.hpp>

4
Code/GraphMol/MolDraw2D/MolDraw2DDetails.h
View File

@@ -1,5 +1,5 @@
//
// Copyright (C) 2015-2020 Greg Landrum
// Copyright (C) 2015-2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -18,7 +18,7 @@
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <boost/format.hpp>
// ****************************************************************************

2
Code/GraphMol/MolDraw2D/MolDraw2DUtils.h
View File

@@ -13,7 +13,7 @@
#define MOLDRAW2DUTILS_H
#include <GraphMol/RWMol.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
// ****************************************************************************

7
Code/GraphMol/StructChecker/Utilites.cpp
View File

@@ -1,5 +1,6 @@
//
// Copyright (C) 2016 Novartis Institutes for BioMedical Research
// Copyright (C) 2016-2022 Novartis Institutes for BioMedical Research and
// other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -11,6 +12,8 @@
#include "../../Geometry/point.h"
#include "Utilites.h"
#include <algorithm>
#include <tuple>
namespace RDKit {
namespace StructureCheck {
@@ -56,7 +59,7 @@ bool getMolAtomPoints(const ROMol &mol, std::vector<RDGeom::Point3D> &atomPoint,
return non_zero_z;
}
typedef boost::tuple<std::string, int, int, int> NbrData;
typedef std::tuple<std::string, int, int, int> NbrData;
bool lessTuple(const NbrData &left, const NbrData &right) {
if (left.get<0>() < right.get<0>()) return true;

3
Code/GraphMol/Subgraphs/SubgraphUtils.cpp
View File

@@ -17,7 +17,6 @@
#include <iostream>
#include <algorithm>
#include <map>
#include <boost/tuple/tuple_comparison.hpp>
#include <RDGeneral/hash/hash.hpp>
namespace RDKit {
@@ -218,7 +217,7 @@ DiscrimTuple calcPathDiscriminators(const ROMol &mol, const PATH_TYPE &path,
// also include the path size (bond count) and number of atoms
// in the discriminator
return boost::make_tuple(pathInvar, path.size(), nAtoms);
return std::make_tuple(pathInvar, path.size(), nAtoms);
}
//

11
Code/GraphMol/Subgraphs/SubgraphUtils.h
View File

@@ -1,5 +1,5 @@
//
// Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
// Copyright (C) 2003-2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -8,12 +8,12 @@
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_SUBGRAPHUTILS_H_
#define _RD_SUBGRAPHUTILS_H_
#ifndef RD_SUBGRAPHUTILS_H
#define RD_SUBGRAPHUTILS_H
#include "Subgraphs.h"
#include <RDGeneral/BoostStartInclude.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <RDGeneral/BoostEndInclude.h>
#include <cstdint>
@@ -23,8 +23,7 @@ class ROMol;
namespace Subgraphs {
//! used to return path discriminators (three unsigned ints):
typedef boost::tuples::tuple<std::uint32_t, std::uint32_t, std::uint32_t>
DiscrimTuple;
typedef std::tuple<std::uint32_t, std::uint32_t, std::uint32_t> DiscrimTuple;
RDKIT_SUBGRAPHS_EXPORT DiscrimTuple calcPathDiscriminators(
const ROMol &mol, const PATH_TYPE &path, bool useBO = true,

3
Code/JavaWrappers/MolDraw2D.i
View File

@@ -29,11 +29,10 @@
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%include "boost_tuple.i"
%include "std_vector.i"
%include "std_map.i"
%include "std_pair.i"
%include "boost_tuple.i"
%include "std_tuple.i"
%{
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolDraw2D/MolDraw2DHelpers.h>

6
Code/JavaWrappers/Subgraphs.i
View File

@@ -41,9 +41,9 @@
std::vector<int> calcPathDiscriminators(RDKit::ROMol &mol,RDKit::PATH_TYPE &path){
std::vector<int> res(3);
RDKit::Subgraphs::DiscrimTuple tpl=RDKit::Subgraphs::calcPathDiscriminators(mol,path);
res[0]=boost::get<0>(tpl);
res[1]=boost::get<1>(tpl);
res[2]=boost::get<2>(tpl);
res[0]=std::get<0>(tpl);
res[1]=std::get<1>(tpl);
res[2]=std::get<2>(tpl);
return res;
}
%}

64
Code/JavaWrappers/boost_tuple.i
View File

@@ -1,64 +0,0 @@
/*
*
*
* Copyright (c) 2015, Greg Landrum
* 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.
*
* taken from this stackexchange answer: http://stackoverflow.com/a/12768318
*/
%{
#include <boost/tuple/tuple.hpp>
%}
namespace boost {
template <typename T1=void, typename T2=void, typename T3=void>
struct tuple;
template <>
struct tuple<void,void,void> {
};
template <typename T1>
struct tuple<T1, void, void> {
tuple(T1);
%extend {
T1 first() const {
return boost::get<0>(*$self);
}
}
};
template <typename T1, typename T2>
struct tuple <T1, T2, void> {
tuple(T1,T2);
%extend {
T1 first() const {
return boost::get<0>(*$self);
}
T2 second() const {
return boost::get<1>(*$self);
}
}
};
template <typename T1, typename T2, typename T3>
struct tuple <T1,T2,T3> {
tuple(T1,T2,T3);
%extend {
T1 first() const {
return boost::get<0>(*$self);
}
T2 second() const {
return boost::get<1>(*$self);
}
T3 third() const {
return boost::get<2>(*$self);
}
}
};
}

63
Code/JavaWrappers/std_tuple.i Normal file
View File

@@ -0,0 +1,63 @@
/*
*
*
* Copyright (c) 2015-2022, Greg Landrum
* 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.
*
* adapted from this stackexchange answer: https://stackoverflow.com/a/72849351
*/
// [1]
%{
#include <tuple>
#include <utility>
%}
// [2]
#define make_getter(pos, type) const type& get##pos() const { return std::get<pos>(*$self); }
#define make_setter(pos, type) void set##pos(const type& val) { std::get<pos>(*$self) = val; }
#define make_ctorargN(pos, type) , type v##pos
#define make_ctorarg(first, ...) const first& v0 FOR_EACH(make_ctorargN, __VA_ARGS__)
// [3]
#define FE_0(...)
#define FE_1(action,a1) action(0,a1)
#define FE_2(action,a1,a2) action(0,a1) action(1,a2)
#define FE_3(action,a1,a2,a3) action(0,a1) action(1,a2) action(2,a3)
#define FE_4(action,a1,a2,a3,a4) action(0,a1) action(1,a2) action(2,a3) action(3,a4)
#define FE_5(action,a1,a2,a3,a4,a5) action(0,a1) action(1,a2) action(2,a3) action(3,a4) action(4,a5)
#define GET_MACRO(_1,_2,_3,_4,_5,NAME,...) NAME
%define FOR_EACH(action,...)
GET_MACRO(__VA_ARGS__, FE_5, FE_4, FE_3, FE_2, FE_1, FE_0)(action,__VA_ARGS__)
%enddef
// [4]
%define %std_tuple(Name, ...)
%rename(Name) std::tuple<__VA_ARGS__>;
namespace std {
struct tuple<__VA_ARGS__> {
// [5]
tuple(make_ctorarg(__VA_ARGS__));
%extend {
// [6]
FOR_EACH(make_getter, __VA_ARGS__)
FOR_EACH(make_setter, __VA_ARGS__)
size_t __len__() const { return std::tuple_size<std::decay_t<decltype(*$self)>>{}; }
%pythoncode %{
# [7]
def __getitem__(self, n):
if n >= len(self): raise IndexError()
return getattr(self, 'get%d' % n)()
def __setitem__(self, n, val):
if n >= len(self): raise IndexError()
getattr(self, 'set%d' % n)(val)
%}
}
};
}
%enddef

16
External/INCHI-API/inchi.cpp vendored
View File

@@ -1,5 +1,6 @@
//
// Copyright (c) 2011, Novartis Institutes for BioMedical Research Inc.
// Copyright (c) 2011-2022 Novartis Institutes for BioMedical Research Inc. and
// other RDkit contributors
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
@@ -70,7 +71,7 @@
#include <algorithm>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/tuple/tuple.hpp>
#include <tuple>
#include <RDGeneral/BoostEndInclude.h>
//#define DEBUG 1
@@ -1277,7 +1278,7 @@ RWMol* InchiToMol(const std::string& inchi, ExtraInchiReturnValues& rv,
}
// for isotopes of H
typedef std::vector<boost::tuple<unsigned int, unsigned int, unsigned int>>
typedef std::vector<std::tuple<unsigned int, unsigned int, unsigned int>>
ISOTOPES_t;
ISOTOPES_t isotopes;
if (retcode == inchi_Ret_OKAY || retcode == inchi_Ret_WARNING) {
@@ -1314,11 +1315,11 @@ RWMol* InchiToMol(const std::string& inchi, ExtraInchiReturnValues& rv,
// number of hydrogens
atom->setNumExplicitHs(inchiAtom->num_iso_H[0]);
if (inchiAtom->num_iso_H[1]) {
isotopes.push_back(boost::make_tuple(1, i, inchiAtom->num_iso_H[1]));
isotopes.push_back(std::make_tuple(1, i, inchiAtom->num_iso_H[1]));
} else if (inchiAtom->num_iso_H[2]) {
isotopes.push_back(boost::make_tuple(2, i, inchiAtom->num_iso_H[2]));
isotopes.push_back(std::make_tuple(2, i, inchiAtom->num_iso_H[2]));
} else if (inchiAtom->num_iso_H[3]) {
isotopes.push_back(boost::make_tuple(3, i, inchiAtom->num_iso_H[3]));
isotopes.push_back(std::make_tuple(3, i, inchiAtom->num_iso_H[3]));
}
// at this point the molecule has all Hs it should have. Set the
// noImplicit flag so
@@ -1397,8 +1398,7 @@ RWMol* InchiToMol(const std::string& inchi, ExtraInchiReturnValues& rv,
// adding isotopes at the end
for (auto& ii : isotopes) {
unsigned int isotope, aid, repeat;
boost::tie(isotope, aid, repeat) = ii;
auto [isotope, aid, repeat] = ii;
aid = indexToAtomIndexMapping[aid];
for (unsigned int i = 0; i < repeat; i++) {
// create atom