mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
e70599a12e
* Adds pickling of properties (optional) * Ignores RDKit::Dict::Pairs - previously private * Fixes AllProps definition * Fixes BondProps seperation * Fixes reaction pickling - Adds ability to pickle atom + QueryAtom * Bumps pickle version * Removes fugly post-increments * Changes Default to NoProps * Tests more options for pickling * Runs clang format * Adds get/setDefaultPropertyPickleOptions, exposes to python * turns tests back on. * Fixes enum (clang was allowing c++11 semantics) * Adds global settings test * Code/GraphMol/testPicklerGlobalSettings.cpp
261 lines
8.7 KiB
C++
261 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 <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 argc, char *argv[]) {
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RDLog::InitLogs();
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testGlobalPickleProps();
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}
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