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dev/azure-windows-update
rdkit/Code/GraphMol/FileParsers/testPropertyLists.cpp
Greg Landrum 180c15fe0e support reading/writing atom props from SD files (#2297) 
* first crude pass

* fix a deprecation

* change naming scheme, support bools

* add standalone function

* add a default value for missings

* support long lines

* stupid typo

* make operator[] work

* revisit missing value handling

* modify missing value handling

* switch to an alternate scheme for specifying missing values

* clang-format

* First pass at property list parser
still needs more tests

* add test for processMolPropertyLists

* get this working as part of the ForwardSDMolSupplier

* first pass at python wrappers and tests

* clang-format run

* add creation of property lists at the mol level

* wrap long lines on output

* remove PoC implementation

* fix python wrappers

* remove out-of-date reference to the Python PoC

* changes in response to review
2019-03-03 13:17:13 -05:00

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//
// Copyright (C) 2019 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.
//
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
// this in one cpp file
#include "RDGeneral/test.h"
#include "catch.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", "[atom_list_properties]") {
SECTION("basics: iprops") {
auto m = "COC"_smiles;
REQUIRE(m);
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::applyMolListPropsToAtoms<std::int64_t>(*m,"atom.iprop.");
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<std::int64_t>("foo1")==6);
CHECK(m->getAtomWithIdx(2)->getProp<std::int64_t>("foo2")==9);
CHECK(m->getAtomWithIdx(1)->getProp<std::int64_t>("foo3")==1);
}
SECTION("basics: dprops") {
auto m = "COC"_smiles;
REQUIRE(m);
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::applyMolListPropsToAtoms<double>(*m,"atom.dprop.");
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") {
auto m = "COC"_smiles;
REQUIRE(m);
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::applyMolListPropsToAtoms<std::string>(*m,"atom.prop.");
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") {
auto m = "COC"_smiles;
REQUIRE(m);
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::applyMolListPropsToAtoms<bool>(*m,"atom.bprop.");
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);
}
}
TEST_CASE("processMolPropertyLists", "[atom_list_properties]") {
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");
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<std::int64_t>("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);
}
}
TEST_CASE("basic SDF handling", "[SDF,atom_list_properties]") {
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 ?
$$$$
)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"));
}
}
TEST_CASE("createAtomPropertyLists", "[atom_list_properties]") {
SECTION("basics") {
auto m = "COC"_smiles;
REQUIRE(m);
m->getAtomWithIdx(0)->setProp<std::int64_t>("foo1",1);
m->getAtomWithIdx(2)->setProp<std::int64_t>("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");
}
SECTION("long lines") {
auto m = "COC"_smiles;
REQUIRE(m);
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::applyMolListPropsToAtoms<std::string>(*m,"atom.prop.");
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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