mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
8bed437c5f
* Address minor compilation warning messages
Addresses trivial compilation warning messages:
[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o
rdkit/Code/GraphMol/AddHs.cpp:497:9: warning: unused variable 'dblBond' [-Wunused-variable]
Bond *dblBond = nullptr;
^
1 warning generated.
[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o
rdkit/Code/GraphMol/Chirality.cpp:1738:62: warning: unused parameter 'mol' [-Wunused-parameter]
bool isBondCandidateForStereo(const Bond *bond, const ROMol &mol) {
^
1 warning generated.
[ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o
rdkit/Code/GraphMol/molopstest.cpp:4694:12: warning: unused variable 'nm' [-Wunused-variable]
ROMol *nm = MolOps::renumberAtoms(*m, nVect);
^
rdkit/Code/GraphMol/molopstest.cpp:6941:16: warning: unused variable 'm' [-Wunused-variable]
RWMol *m = SmilesToMol(smiles);
^
2 warnings generated.
[ 42%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o
rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:14: warning: unused parameter 'argc' [-Wunused-parameter]
int main(int argc, char *argv[]) {
^
rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:26: warning: unused parameter 'argv' [-Wunused-parameter]
int main(int argc, char *argv[]) {
^
2 warnings generated.
[ 55%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o
rdkit/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:176:20: warning: unused variable 'NUM_FUNCS' [-Wunused-const-variable]
const unsigned int NUM_FUNCS =
^
1 warning generated.
[ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o
rdkit/Code/GraphMol/StructChecker/ReCharge.cpp:405:17: warning: unused variable 'atom' [-Wunused-variable]
const Atom &atom = *Mol.getAtomWithIdx(i);
^
1 warning generated.
[ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o
rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:12: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (-1 == ti || -1 == tj) continue;
~~ ^ ~~
rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:24: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (-1 == ti || -1 == tj) continue;
~~ ^ ~~
2 warnings generated.
[ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o
rdkit/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:428:9: warning: unused variable 'res' [-Wunused-variable]
int res = decomp.add(*mol);
^
1 warning generated.
[ 96%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o
rdkit/Code/SimDivPickers/testPickers.cpp:19:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
return abs((double)i - (double)j);
^
rdkit/Code/SimDivPickers/testPickers.cpp:19:10: note: use function 'std::abs' instead
return abs((double)i - (double)j);
^~~
std::abs
1 warning generated.
* Close open file handles during build set-up
Under Python3, the update_pains.py file generated warning
messages like:
== Done updating pains files
/Code/GraphMol/FilterCatalog/update_pains.py:140: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/../../../Data/Pains/wehi_pains.csv'
mode='r' encoding='UTF-8'>
for smiles, name in csv.reader(open(PAINS_CSV)):
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_a.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_b.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_c.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
262 lines
8.7 KiB
C++
262 lines
8.7 KiB
C++
//
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// Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <RDBoost/test.h>
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#include <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/MonomerInfo.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <RDGeneral/RDLog.h>
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#include <stdlib.h>
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#include <ctime>
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#include <iostream>
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#include <fstream>
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#include <boost/algorithm/string.hpp>
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using namespace RDKit;
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void testGlobalPickleProps() {
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BOOST_LOG(rdInfoLog) << "-----------------------\n";
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BOOST_LOG(rdInfoLog) << "Testing pickling of properties"
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<< std::endl;
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std::vector<double> v;
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v.push_back(1234.);
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v.push_back(444.);
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v.push_back(1123.);
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ROMol *m = SmilesToMol("CC");
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m->setProp("double", 1.0);
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m->setProp("int", 100);
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m->setProp("bool", true);
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m->setProp("boolfalse", false);
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m->setProp("dvec", v);
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Atom *a = m->getAtomWithIdx(0);
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a->setProp("double", 1.0);
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a->setProp("int", 100);
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a->setProp("bool", true);
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a->setProp("boolfalse", false);
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a->setProp("dvec", v);
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a->setProp("_private", true);
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Bond *b = m->getBondWithIdx(0);
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b->setProp("double", 1.0);
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b->setProp("int", 100);
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b->setProp("bool", true);
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b->setProp("boolfalse", false);
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b->setProp("dvec", v);
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b->setProp("_private", true);
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std::string pkl;
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::AllProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(m2->getProp<double>("double") == 1.0);
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TEST_ASSERT(m2->getProp<int>("int") == 100);
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TEST_ASSERT(m2->getProp<bool>("bool") == true);
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TEST_ASSERT(m2->getProp<bool>("boolfalse") == false);
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(a->getProp<double>("double") == 1.0);
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TEST_ASSERT(a->getProp<int>("int") == 100);
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TEST_ASSERT(a->getProp<bool>("bool") == true);
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TEST_ASSERT(a->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(a->getProp<bool>("_private") == true);
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(b->getProp<double>("double") == 1.0);
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TEST_ASSERT(b->getProp<int>("int") == 100);
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TEST_ASSERT(b->getProp<bool>("bool") == true);
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TEST_ASSERT(b->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(b->getProp<bool>("_private") == true);
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//TEST_ASSERT(b->getProp<std::vector<double> >("dvec") == v);
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delete m2;
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}
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::MolProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(m2->getProp<double>("double") == 1.0);
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TEST_ASSERT(m2->getProp<int>("int") == 100);
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TEST_ASSERT(m2->getProp<bool>("bool") == true);
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TEST_ASSERT(m2->getProp<bool>("boolfalse") == false);
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(!a->hasProp("double"));
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TEST_ASSERT(!a->hasProp("int"));
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TEST_ASSERT(!a->hasProp("bool"));
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TEST_ASSERT(!a->hasProp("boolfalse"));
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TEST_ASSERT(!a->hasProp("_private"));
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(!b->hasProp("double"));
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TEST_ASSERT(!b->hasProp("int"));
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TEST_ASSERT(!b->hasProp("bool"));
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TEST_ASSERT(!b->hasProp("boolfalse"));
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TEST_ASSERT(!b->hasProp("_private"));
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delete m2;
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}
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::AtomProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m2->hasProp("double"));
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TEST_ASSERT(!m2->hasProp("int"));
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TEST_ASSERT(!m2->hasProp("bool"));
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TEST_ASSERT(!m2->hasProp("boolfalse"));
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(a->getProp<double>("double") == 1.0);
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TEST_ASSERT(a->getProp<int>("int") == 100);
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TEST_ASSERT(a->getProp<bool>("bool") == true);
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TEST_ASSERT(a->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(!a->hasProp("_private"));
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(!b->hasProp("double"));
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TEST_ASSERT(!b->hasProp("int"));
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TEST_ASSERT(!b->hasProp("bool"));
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TEST_ASSERT(!b->hasProp("boolfalse"));
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TEST_ASSERT(!b->hasProp("_private"));
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delete m2;
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}
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::AtomProps |
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PicklerOps::PrivateProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m2->hasProp("double"));
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TEST_ASSERT(!m2->hasProp("int"));
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TEST_ASSERT(!m2->hasProp("bool"));
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TEST_ASSERT(!m2->hasProp("boolfalse"));
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(a->getProp<double>("double") == 1.0);
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TEST_ASSERT(a->getProp<int>("int") == 100);
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TEST_ASSERT(a->getProp<bool>("bool") == true);
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TEST_ASSERT(a->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(a->getProp<bool>("_private") == true);
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(!b->hasProp("double"));
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TEST_ASSERT(!b->hasProp("int"));
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TEST_ASSERT(!b->hasProp("bool"));
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TEST_ASSERT(!b->hasProp("boolfalse"));
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TEST_ASSERT(!b->hasProp("_private"));
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delete m2;
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}
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::BondProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m2->hasProp("double"));
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TEST_ASSERT(!m2->hasProp("int"));
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TEST_ASSERT(!m2->hasProp("bool"));
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TEST_ASSERT(!m2->hasProp("boolfalse"));
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(!a->hasProp("double"));
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TEST_ASSERT(!a->hasProp("int"));
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TEST_ASSERT(!a->hasProp("bool"));
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TEST_ASSERT(!a->hasProp("boolfalse"));
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TEST_ASSERT(!a->hasProp("_private"));
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(b->getProp<double>("double") == 1.0);
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TEST_ASSERT(b->getProp<int>("int") == 100);
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TEST_ASSERT(b->getProp<bool>("bool") == true);
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TEST_ASSERT(b->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(!b->hasProp("_private"));
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delete m2;
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}
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{
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MolPickler::setDefaultPickleProperties(PicklerOps::BondProps |
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PicklerOps::PrivateProps);
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MolPickler::pickleMol(*m, pkl);
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RWMol *m2 = new RWMol(pkl);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m2->hasProp("double"));
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TEST_ASSERT(!m2->hasProp("int"));
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TEST_ASSERT(!m2->hasProp("bool"));
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TEST_ASSERT(!m2->hasProp("boolfalse"));
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a = m2->getAtomWithIdx(0);
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TEST_ASSERT(!a->hasProp("double"));
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TEST_ASSERT(!a->hasProp("int"));
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TEST_ASSERT(!a->hasProp("bool"));
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TEST_ASSERT(!a->hasProp("boolfalse"));
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TEST_ASSERT(!a->hasProp("_private"));
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b = m2->getBondWithIdx(0);
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TEST_ASSERT(b->getProp<double>("double") == 1.0);
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TEST_ASSERT(b->getProp<int>("int") == 100);
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TEST_ASSERT(b->getProp<bool>("bool") == true);
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TEST_ASSERT(b->getProp<bool>("boolfalse") == false);
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TEST_ASSERT(b->getProp<bool>("_private") == true);
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delete m2;
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}
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delete m;
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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int main(int, char**) {
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RDLog::InitLogs();
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testGlobalPickleProps();
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}
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