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rdkit/Code/GraphMol/FileParsers/testPropertyLists.cpp
Brian Kelley 56903b0df6 Check for correctly sized propertylists to avoid dropping molecules (#8921) 
* Fixes #8918

* Use only the one check for compatible sizes

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
2026-01-30 05:00:55 +01:00

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//
// Copyright (C) 2019-2025 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 "RDGeneral/test.h"
#include <catch2/catch_all.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/FileParserUtils.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
using namespace RDKit;
TEST_CASE("Property list conversion") {
auto m = "COC"_smiles;
REQUIRE(m);
auto getter = [&m](size_t which) { return m->getAtomWithIdx(which); };
SECTION("basics: iprops") {
m->setProp("atom.iprop.foo1", "1 6 9");
m->setProp("atom.iprop.foo2", "3 n/a 9");
m->setProp("atom.iprop.foo3", "[?] 5 1 ?");
m->setProp("atom.iprop.foo4", "[foo] 3 foo 9");
FileParserUtils::applyMolListProps<int>(*m, "atom.iprop.", m->getNumAtoms(),
getter);
CHECK(m->getAtomWithIdx(0)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo2"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo3"));
CHECK(!m->getAtomWithIdx(2)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo4"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo4"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo4"));
CHECK(m->getAtomWithIdx(1)->getProp<int>("foo1") == 6);
CHECK(m->getAtomWithIdx(2)->getProp<int>("foo2") == 9);
CHECK(m->getAtomWithIdx(1)->getProp<int>("foo3") == 1);
CHECK(m->getAtomWithIdx(1)->getProp<std::string>("foo3") == "1");
}
SECTION("basics: dprops") {
m->setProp("atom.dprop.foo1", "1 6 9");
m->setProp("atom.dprop.foo2", "3 n/a 9");
m->setProp("atom.dprop.foo3", "[?] 5 1 ?");
FileParserUtils::applyMolListProps<double>(*m, "atom.dprop.",
m->getNumAtoms(), getter);
CHECK(m->getAtomWithIdx(0)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo2"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo3"));
CHECK(!m->getAtomWithIdx(2)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->getProp<double>("foo1") == 6);
CHECK(m->getAtomWithIdx(2)->getProp<double>("foo2") == 9);
CHECK(m->getAtomWithIdx(1)->getProp<double>("foo3") == 1);
}
SECTION("basics: props") {
m->setProp("atom.prop.foo1", "1 6 9");
m->setProp("atom.prop.foo2", "3 n/a 9");
m->setProp("atom.prop.foo3", "[?] 5 1 ?");
FileParserUtils::applyMolListProps<std::string>(*m, "atom.prop.",
m->getNumAtoms(), getter);
CHECK(m->getAtomWithIdx(0)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo2"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo3"));
CHECK(!m->getAtomWithIdx(2)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->getProp<std::string>("foo1") == "6");
CHECK(m->getAtomWithIdx(2)->getProp<std::string>("foo2") == "9");
CHECK(m->getAtomWithIdx(1)->getProp<std::string>("foo3") == "1");
}
SECTION("basics: bprops") {
m->setProp("atom.bprop.foo1", "1 0 0");
m->setProp("atom.bprop.foo2", "0 n/a 1");
m->setProp("atom.bprop.foo3", "[?] 0 1 ?");
FileParserUtils::applyMolListProps<bool>(*m, "atom.bprop.",
m->getNumAtoms(), getter);
CHECK(m->getAtomWithIdx(0)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo2"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo3"));
CHECK(!m->getAtomWithIdx(2)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->getProp<bool>("foo1") == false);
CHECK(m->getAtomWithIdx(2)->getProp<bool>("foo2") == true);
CHECK(m->getAtomWithIdx(1)->getProp<bool>("foo3") == true);
}
SECTION("basics: bond props") {
auto bgetter = [&m](size_t which) { return m->getBondWithIdx(which); };
m->setProp("bond.prop.foo1", "1 6");
m->setProp("bond.prop.foo2", "3 n/a");
m->setProp("bond.prop.foo3", "[?] ? 5");
FileParserUtils::applyMolListProps<std::string>(*m, "bond.prop.",
m->getNumBonds(), bgetter);
CHECK(m->getBondWithIdx(0)->hasProp("foo1"));
CHECK(m->getBondWithIdx(1)->hasProp("foo1"));
CHECK(m->getBondWithIdx(0)->hasProp("foo2"));
CHECK(!m->getBondWithIdx(1)->hasProp("foo2"));
CHECK(!m->getBondWithIdx(0)->hasProp("foo3"));
CHECK(m->getBondWithIdx(1)->hasProp("foo3"));
CHECK(m->getBondWithIdx(1)->getProp<std::string>("foo1") == "6");
CHECK(m->getBondWithIdx(1)->getProp<std::string>("foo3") == "5");
}
}
TEST_CASE("processMolPropertyLists") {
SECTION("basics") {
auto m = "COC"_smiles;
REQUIRE(m);
m->setProp("atom.iprop.foo1", "1 6 9");
m->setProp("atom.dprop.foo2", "3 n/a 9");
m->setProp("atom.prop.foo3", "[?] 5 1 ?");
m->setProp("atom.bprop.foo4", "1 0 0");
m->setProp("bond.prop.foo2", "3 7");
FileParserUtils::processMolPropertyLists(*m);
CHECK(m->getAtomWithIdx(0)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo1"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo2"));
CHECK(!m->getAtomWithIdx(1)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo2"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo3"));
CHECK(!m->getAtomWithIdx(2)->hasProp("foo3"));
CHECK(m->getAtomWithIdx(0)->hasProp("foo4"));
CHECK(m->getAtomWithIdx(1)->hasProp("foo4"));
CHECK(m->getAtomWithIdx(2)->hasProp("foo4"));
CHECK(m->getAtomWithIdx(1)->getProp<int>("foo1") == 6);
CHECK(m->getAtomWithIdx(2)->getProp<double>("foo2") == 9);
CHECK(m->getAtomWithIdx(1)->getProp<std::string>("foo3") == "1");
CHECK(m->getAtomWithIdx(1)->getProp<bool>("foo4") == false);
CHECK(m->getBondWithIdx(0)->hasProp("foo2"));
CHECK(m->getBondWithIdx(1)->hasProp("foo2"));
CHECK(m->getBondWithIdx(0)->getProp<int>("foo2"));
CHECK(m->getBondWithIdx(1)->getProp<int>("foo2"));
}
}
TEST_CASE("basic SDF handling") {
std::string sdf = R"SDF(
RDKit 2D
3 3 0 0 0 0 0 0 0 0999 V2000
0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4330 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4330 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 1 1 0
M END
> <atom.dprop.PartialCharge> (1)
0.008 -0.314 0.008
> <atom.iprop.NumHeavyNeighbors> (1)
2 2 2
> <atom.prop.AtomLabel> (1)
C1 N2 C3
> <atom.bprop.IsCarbon> (1)
1 0 1
> <atom.prop.PartiallyMissing> (1)
one n/a three
> <atom.iprop.PartiallyMissingInt> (1)
[?] 2 2 ?
> <bond.prop.foo> (1)
bar baz blah
> <atom.iprop.TooLong> (1)
0 1 2 3 4
$$$$
)SDF";
SECTION("no processing") {
RDKit::SDMolSupplier suppl;
suppl.setData(sdf);
suppl.setProcessPropertyLists(false);
std::unique_ptr<RDKit::ROMol> m(suppl[0]);
REQUIRE(m);
CHECK(m->hasProp("atom.prop.AtomLabel"));
CHECK(!m->getAtomWithIdx(0)->hasProp("AtomLabel"));
}
SECTION("with processing") {
RDKit::SDMolSupplier suppl;
suppl.setData(sdf);
std::unique_ptr<RDKit::ROMol> m(suppl[0]);
REQUIRE(m);
CHECK(m->hasProp("atom.prop.AtomLabel"));
CHECK(m->getAtomWithIdx(0)->hasProp("AtomLabel"));
CHECK(m->hasProp("bond.prop.foo"));
std::string val;
CHECK(m->getBondWithIdx(0)->getPropIfPresent("foo", val));
CHECK(val == "bar");
CHECK(m->hasProp("atom.iprop.TooLong"));
CHECK(!m->getAtomWithIdx(0)->hasProp("TooLong"));
}
}
TEST_CASE("createAtomPropertyLists") {
SECTION("basics") {
auto m = "COC"_smiles;
REQUIRE(m);
m->getAtomWithIdx(0)->setProp<int>("foo1", 1);
m->getAtomWithIdx(2)->setProp<int>("foo1", 9);
FileParserUtils::createAtomIntPropertyList(*m, "foo1");
REQUIRE(m->hasProp("atom.iprop.foo1"));
CHECK(m->getProp<std::string>("atom.iprop.foo1") == "1 n/a 9");
m->getAtomWithIdx(0)->setProp<double>("foo2", 1);
m->getAtomWithIdx(1)->setProp<double>("foo2", 4);
m->getAtomWithIdx(2)->setProp<double>("foo2", 9);
FileParserUtils::createAtomDoublePropertyList(*m, "foo2");
REQUIRE(m->hasProp("atom.dprop.foo2"));
CHECK(m->getProp<std::string>("atom.dprop.foo2") == "1 4 9");
m->getAtomWithIdx(0)->setProp<std::string>("foo3", "1");
m->getAtomWithIdx(1)->setProp<std::string>("foo3", "4");
FileParserUtils::createAtomStringPropertyList(*m, "foo3", "?");
REQUIRE(m->hasProp("atom.prop.foo3"));
CHECK(m->getProp<std::string>("atom.prop.foo3") == "[?] 1 4 ?");
m->getAtomWithIdx(0)->setProp<bool>("foo4", 1);
m->getAtomWithIdx(1)->setProp<bool>("foo4", 0);
m->getAtomWithIdx(2)->setProp<bool>("foo4", 0);
FileParserUtils::createAtomBoolPropertyList(*m, "foo4");
REQUIRE(m->hasProp("atom.bprop.foo4"));
CHECK(m->getProp<std::string>("atom.bprop.foo4") == "1 0 0");
m->getBondWithIdx(0)->setProp<bool>("foo5", 1);
m->getBondWithIdx(1)->setProp<bool>("foo5", 0);
FileParserUtils::createBondBoolPropertyList(*m, "foo5");
REQUIRE(m->hasProp("bond.bprop.foo5"));
CHECK(m->getProp<std::string>("bond.bprop.foo5") == "1 0");
}
SECTION("long lines") {
auto m = "COC"_smiles;
REQUIRE(m);
auto getter = [&m](size_t which) { return m->getAtomWithIdx(which); };
m->getAtomWithIdx(0)->setProp<std::string>("foo1", std::string(80, 'a'));
m->getAtomWithIdx(1)->setProp<std::string>("foo1", std::string(80, 'b'));
m->getAtomWithIdx(2)->setProp<std::string>("foo1", std::string(80, 'c'));
FileParserUtils::createAtomStringPropertyList(*m, "foo1");
REQUIRE(m->hasProp("atom.prop.foo1"));
std::string ps = m->getProp<std::string>("atom.prop.foo1");
CHECK(ps.length() > 240);
CHECK(ps.find("\n") != std::string::npos);
for (auto &atom : m->atoms()) {
atom->clearProp("foo1");
}
FileParserUtils::applyMolListProps<std::string>(*m, "atom.prop.",
m->getNumAtoms(), getter);
CHECK(m->getAtomWithIdx(0)->getProp<std::string>("foo1") ==
std::string(80, 'a'));
CHECK(m->getAtomWithIdx(1)->getProp<std::string>("foo1") ==
std::string(80, 'b'));
CHECK(m->getAtomWithIdx(2)->getProp<std::string>("foo1") ==
std::string(80, 'c'));
}
}
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