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//
// 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 <catch2/catch_all.hpp>
#include <algorithm>
#include <limits>
#include <fstream>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
using namespace RDKit;
TEST_CASE("Github #6312: space overhead of serializing properties") {
SECTION("Bonds v2000") {
auto mol = R"CTAB(
Mrv1810 02111915042D
4 3 0 0 0 0 999 V2000
-1.5625 1.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8480 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2770 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5625 0.7821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 3 1 0 0 0 0
1 2 6 0 0 0 0
1 4 1 1 0 0 0
M END)CTAB"_ctab;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 6);
CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 1);
CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondStereo) == 1);
std::string basepkl;
MolPickler::pickleMol(*mol, basepkl);
std::string pkl;
MolPickler::pickleMol(*mol, pkl,
PicklerOps::PropertyPickleOptions::BondProps |
PicklerOps::PropertyPickleOptions::PrivateProps);
// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
RWMol mol2(pkl);
CHECK(mol2.getBondWithIdx(1)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 6);
CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 1);
CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondStereo) == 1);
}
SECTION("bonds-v3k") {
auto mol = R"CTAB(
Mrv1810 02111915102D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -2.9167 3 0 0
M V30 2 C -1.583 3.77 0 0
M V30 3 C -4.2503 3.77 0 0
M V30 4 C -2.9167 1.46 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 3
M V30 2 6 1 2
M V30 3 1 1 4 CFG=1
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 6);
CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 1);
CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondCfg) == 1);
std::string basepkl;
MolPickler::pickleMol(*mol, basepkl);
std::string pkl;
MolPickler::pickleMol(*mol, pkl,
PicklerOps::PropertyPickleOptions::BondProps |
PicklerOps::PropertyPickleOptions::PrivateProps);
CHECK(pkl.size() > basepkl.size());
// make sure the property names aren't in the pickle
CHECK(pkl.find(common_properties::_MolFileBondType) == std::string::npos);
CHECK(pkl.find(common_properties::_MolFileBondCfg) == std::string::npos);
// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
RWMol mol2(pkl);
CHECK(mol2.getBondWithIdx(1)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 6);
CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondType) == 1);
CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
common_properties::_MolFileBondCfg) == 1);
}
SECTION("atoms") {
auto mol = R"CTAB(
Mrv2211 04272306392D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.375 3.125 0 0 CFG=2
M V30 2 C -6.0413 3.895 0 0
M V30 3 O -8.7087 3.895 0 0
M V30 4 F -7.375 1.585 0 0
M V30 5 Cl -6.1532 2.1875 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 3
M V30 2 1 1 4
M V30 3 1 1 2 CFG=1
M V30 4 1 1 5 CFG=3
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(mol);
std::string basepkl;
MolPickler::pickleMol(*mol, basepkl);
CHECK(mol->getAtomWithIdx(0)->getProp<int>(common_properties::molParity) ==
2);
CHECK(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::_ChiralityPossible) == 1);
mol->getAtomWithIdx(0)->setProp(common_properties::_CIPCode,
std::string("S"));
mol->getAtomWithIdx(1)->setProp(common_properties::molAtomMapNumber, 1);
mol->getAtomWithIdx(2)->setAtomMapNum(2);
mol->getAtomWithIdx(3)->setProp(common_properties::dummyLabel,
std::string("foo"));
std::string pkl;
MolPickler::pickleMol(*mol, pkl,
PicklerOps::PropertyPickleOptions::AtomProps |
PicklerOps::PropertyPickleOptions::PrivateProps);
CHECK(pkl.size() > basepkl.size());
RWMol mol2(pkl);
CHECK(mol2.getAtomWithIdx(0)->getProp<int>(common_properties::molParity) ==
2);
CHECK(mol2.getAtomWithIdx(0)->getProp<int>(
common_properties::_ChiralityPossible) == 1);
CHECK(mol2.getAtomWithIdx(0)->getProp<std::string>(
common_properties::_CIPCode) == "S");
CHECK(mol2.getAtomWithIdx(1)->getProp<int>(
common_properties::molAtomMapNumber) == 1);
CHECK(mol2.getAtomWithIdx(2)->getProp<int>(
common_properties::molAtomMapNumber) == 2);
CHECK(mol2.getAtomWithIdx(3)->getProp<std::string>(
common_properties::dummyLabel) == "foo");
}
SECTION("attachment points") {
auto mol = R"CTAB(
Mrv2211 09062306242D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.7917 4.0833 0 0
M V30 2 C -6.458 4.8533 0 0
M V30 3 C -5.1243 4.0833 0 0
M V30 4 * -6.458 4.34 0 0
M V30 5 C -5.303 6.3405 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 4 5 ENDPTS=(3 1 2 3) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(2)->getProp<std::string>(
common_properties::_MolFileBondAttach) == "ANY");
CHECK(mol->getBondWithIdx(2)->getProp<std::string>(
common_properties::_MolFileBondEndPts) == "(3 1 2 3)");
std::string pkl;
MolPickler::pickleMol(*mol, pkl);
// make sure the property names aren't in the pickle
CHECK(pkl.find(common_properties::_MolFileBondAttach) == std::string::npos);
CHECK(pkl.find(common_properties::_MolFileBondEndPts) == std::string::npos);
// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
RWMol mol2(pkl);
CHECK(mol2.getBondWithIdx(2)->getProp<std::string>(
common_properties::_MolFileBondAttach) == "ANY");
CHECK(mol2.getBondWithIdx(2)->getProp<std::string>(
common_properties::_MolFileBondEndPts) == "(3 1 2 3)");
}
}
TEST_CASE("parsing old pickles with many features") {
std::string pklName = getenv("RDBASE");
pklName += "/Code/GraphMol/test_data/mol_with_sgroups_and_stereo.pkl";
auto m =
"C/C=C/C[C@H](O)[C@@H](C)F |a:6,o2:4,r,SgD:5:data_pt:4.5::::|"_smiles;
REQUIRE(m);
std::ifstream inStream(pklName.c_str(), std::ios_base::binary);
RWMol m2;
// if the mol can be read, the primary problem was addressed
MolPickler::molFromPickle(inStream, m2);
CHECK(m2.getNumAtoms() == m->getNumAtoms());
CHECK(MolToCXSmiles(*m) == MolToCXSmiles(m2));
}
TEST_CASE("github #7675 : pickling HasProp queries") {
SECTION("basics") {
auto mol = "CC"_smarts;
REQUIRE(mol);
mol->getAtomWithIdx(0)->expandQuery(makeHasPropQuery<Atom>("foo"));
mol->getBondWithIdx(0)->expandQuery(makeHasPropQuery<Bond>("foo"));
std::string pkl;
MolPickler::pickleMol(*mol, pkl);
RWMol mol2(pkl);
REQUIRE(mol2.getAtomWithIdx(0)->hasQuery());
}
}
TEST_CASE("pickling HasPropWithValue queries") {
SECTION("basics") {
if (0) {
auto mol = "CC"_smarts;
REQUIRE(mol);
mol->getAtomWithIdx(0)->expandQuery(
makePropQuery<Atom, int>("foo", 1, 2));
mol->getBondWithIdx(0)->expandQuery(
makePropQuery<Bond, int>("bar", 1, 0));
std::string pkl;
MolPickler::pickleMol(*mol, pkl);
RWMol mol2(pkl);
REQUIRE(mol2.getAtomWithIdx(0)->hasQuery());
REQUIRE(mol2.getAtomWithIdx(1)->hasQuery());
}
{
auto mol = "CC"_smarts;
REQUIRE(mol);
mol->getAtomWithIdx(0)->expandQuery(
makePropQuery<Atom, std::string>("foo", "asdfs"));
mol->getBondWithIdx(0)->expandQuery(
makePropQuery<Bond, std::string>("bar", "dsafasdf"));
std::string pkl;
MolPickler::pickleMol(*mol, pkl);
RWMol mol2(pkl);
REQUIRE(mol2.getAtomWithIdx(0)->hasQuery());
REQUIRE(mol2.getAtomWithIdx(1)->hasQuery());
}
{
auto mol = "CC"_smarts;
REQUIRE(mol);
ExplicitBitVect bv(10);
mol->getAtomWithIdx(0)->expandQuery(
makePropQuery<Atom, ExplicitBitVect>("foo", bv, 0.1));
mol->getBondWithIdx(0)->expandQuery(
makePropQuery<Bond, ExplicitBitVect>("bar", bv, 0.1));
std::string pkl;
MolPickler::pickleMol(*mol, pkl);
RWMol mol2(pkl);
REQUIRE(mol2.getAtomWithIdx(0)->hasQuery());
REQUIRE(mol2.getAtomWithIdx(1)->hasQuery());
}
}
}
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