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Release_2022_09
rdkit/Code/GraphMol/FileParsers/testPropertyLists.cpp
David Cosgrove f93016a77f Refactor mol draw2 d (#4948) 
* MolDraw2D refactoring
- rename setupMoleculeDraw->initMoleculeDraw
- track whether or not initDrawing() has been called
- centralize calls to initDrawing() and clearDrawing() into initMoleculeDraw()
- update svg hashes in tests

* update some expected test results

* support changing font scale and default scale
add reaction test

* does not work... this is hard

* all tests pass

* do something about legends

* docs

* more tests

* more docs

* cleanup

* going around in circles...
hopefully converging

* cleanup

* Single bond skeleton works.

* Simple bond drawing seems to be working.

* Initial addition of atom symbols.

* Stash of not-quite-working atom symbols prior to major surgery.

* Atom symbols seem to be working.  Major surgery not required, just inverted Y coords at the outset.

* Add classes to atom labels.

* Renamed AtomLabel AtomSymbol.

* Add highlights.

* Fix bug from PR4839.

* Molecule note.

* Added atom notes.

* Added bond notes.

* Extract radicals.

* Annotation via new DrawAnnotation class.

* Add brackets.

* Add linknodes.

* Add close contacts.

* Add attachment points.  Fix wavy lines.

* Draw molecules in grid.

* Tidy.

* Fix radicals when font has hit maxFontSize.
Make getDrawCoords work.

* Draw primitives take atom or draw coords.

* Fix legends.

* More fixing for tests.  DrawMol::setScale now takes font scale as well.

* tidy debug writes

* Variable fraction of panel for legend.

* Better legend positioning.

* Fix sub- and super-script spacing.
Added spaces to Freetype strings.

* Basic reaction drawing.

* Reaction highlighting.

* Minor tweak to reacctions.

* Tweaked reaction DrawMol widths.

* Fix atomTags.

* Fix catch tests except contours.

* Contouring working in catch_tests.cpp.

* Fix catch tests.

* AtomSymbol and DrawAnnotation into MolDraw2D_detail.

* DrawMol and DrawShape into MolDraw2D_detail.

* DrawText inot MolDraw2D_detail.

* Machete out.

* DrawText goes private.

* Move some stuff about, such as StringRect to its own header.

* Python wrapper compiles (but crashes when Draw imported).

* More tidying.  Python DrawArrow failing.

* Linux changes.

* Fixed error in DrawShapeArrow spotted by valgrind.
Fixed some warnings from gcc.

* Maybe fixed DrawArrow.

* Added basic argparse interface.

* Added newlines.

* Changes in response to review.
Non-const args in move constructors and operator=.
Added missing classes to MolDraw2D_detail.
Deleted move operator= where it had been forgotten.
Fixed copyright dates.

* Deleted all default c'tors in derived classes.

* Changes in response to review:
Wedge widths now a proportion of mean bond length in draw coords..
Add padding below legend when positioning it.

* Fix tests.

* Fix the private/protected mess of the new classes.

* Moved doesLineIntersect etc.

* Reinstate original alignString for non-FT drawings.

* More faffing about with reaction layouts.

* Fix font sizes in testGitHub3391.

* Fix atom notes fitting inside fat wedges.

* Fix molecule annotation font size.

* More fixes of rectangle/triangle collision detection.

* Test for highlight linewidth multiplier.

* Use push_back not emplace_back.

* Attempt at better Freetype char spacing.

* Option to turn off TEST_ASSERT. Currently off.

* Fixed embarrassing maths to do with wedge fatness.

* More tidying post-review.

* Document highlight_linewidth_multipliers.

* Expose baseFontSize to Python.

* Changes in response to review.

* Allow DrawMolecules molecules to be drawn to different scales.

* Fix bond sneaking between C:8 in, for example, reactions.

* Fix bad re-factoring.

* Fix globbing.

* Changes in response to review.

* Add invariant check.

* Add draw option to fix font size.

* suggested changes

* Update catch test results.

* Fix expected freetype results.

* Fix non-freetype drawers.

* Fin non-freetype test results.

* get the Qt drawer working too

* Fix disappearing reaction highlights.

* Changes as result of review.

* Fixed non-FreeType hash codes for reaction SVGs.  Extra comment in catch_tests.

* reactant highlighting was clearning properties

* Fix for failing contour python test.

* fix a non-freetype problem

* swig wrappers working

* Bump timeouts in test.

Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
2022-02-18 16:30:21 +01:00

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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.
//
#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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