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Fix offsets for DrawMoleculeWithHighlights. (#8680)

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* Fix offsets for DrawMoleculeWithHighlights.

* No Freetype test.

* Trigger Build

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
This commit is contained in:
David Cosgrove
2025-08-14 06:17:31 +01:00
committed by GitHub
parent db5378567b
commit b9666d93b8
2 changed files with 73 additions and 34 deletions
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1
Code/GraphMol/MolDraw2D/MolDraw2D.cpp
View File

@@ -163,6 +163,7 @@ void MolDraw2D::drawMoleculeWithHighlights(
break;
}
drawMols_.emplace_back(dm);
drawMols_.back()->setOffsets(x_offset_, y_offset_);
drawMols_.back()->createDrawObjects();
fixVariableDimensions(*drawMols_.back());
++activeMolIdx_;

106
Code/GraphMol/MolDraw2D/catch_tests.cpp
View File

@@ -369,6 +369,7 @@ const std::map<std::string, std::hash_result_t> SVG_HASHES = {
{"testStandardColoursHighlightedAtoms_1.svg", 4265528904U},
{"testStandardColoursHighlightedAtoms_2.svg", 2285000572U},
{"testArrowheads.svg", 3318006834U},
{"testOffsetHighlightedMols.svg", 3147614756U},
};
// These PNG hashes aren't completely reliable due to floating point cruft,
@@ -10754,7 +10755,7 @@ TEST_CASE("Solid arrowhead in wrong place (Github 8500)") {
}
TEST_CASE("Show all CIP codes (Github 8561)") {
auto m = R"CTAB(
auto m = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
@@ -10810,40 +10811,77 @@ M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
CIPLabeler::assignCIPLabels(*m);
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().showAllCIPCodes = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testShowAllCIPLabels.svg");
outs << text;
outs.close();
REQUIRE(m);
CIPLabeler::assignCIPLabels(*m);
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().showAllCIPCodes = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testShowAllCIPLabels.svg");
outs << text;
outs.close();
// Check for Blue (M) CIP label on Bond
TEST_ASSERT(
text.find("class='CIP_Code'") !=
std::string::npos);
// Check for Blue (M) CIP label on Bond
TEST_ASSERT(text.find("class='CIP_Code'") != std::string::npos);
//try again, this tiem using JSON to set options
const char *json =
"{\"addStereoAnnotation\":true, \"showAllCIPCodes\":true}";
MolDraw2DSVG drawer2(350, 300);
MolDrawOptions opts;
MolDraw2DUtils::updateMolDrawOptionsFromJSON(opts, json);
drawer2.drawOptions() = opts;
drawer2.drawMolecule(*m);
drawer2.finishDrawing();
auto text2 = drawer2.getDrawingText();
std::ofstream outs2("testShowAllCIPLabels2.svg");
outs2 << text2;
outs2.close();
// try again, this tiem using JSON to set options
const char *json = "{\"addStereoAnnotation\":true, \"showAllCIPCodes\":true}";
MolDraw2DSVG drawer2(350, 300);
MolDrawOptions opts;
MolDraw2DUtils::updateMolDrawOptionsFromJSON(opts, json);
drawer2.drawOptions() = opts;
drawer2.drawMolecule(*m);
drawer2.finishDrawing();
auto text2 = drawer2.getDrawingText();
std::ofstream outs2("testShowAllCIPLabels2.svg");
outs2 << text2;
outs2.close();
// Check for Blue (M) CIP label on Bond
TEST_ASSERT(
text2.find("class='CIP_Code'") !=
std::string::npos);
}
// Check for Blue (M) CIP label on Bond
TEST_ASSERT(text2.find("class='CIP_Code'") != std::string::npos);
}
TEST_CASE("Github 8679 - DrawMoleculesWithHighlights doesn't offset") {
auto mol1 = "c1ccccc1Cl"_smiles;
REQUIRE(mol1);
auto mol2 = "c1ccccc1Br"_smiles;
REQUIRE(mol2);
MolDraw2DSVG drawer(600, 300, 300, 300, true);
drawer.drawOptions().addAtomIndices = true;
std::map<int, std::vector<DrawColour>> atomCols;
std::map<int, double> atomRads;
std::map<int, int> bondMults;
std::map<int, std::vector<DrawColour>> bondCols;
drawer.drawMoleculeWithHighlights(*mol1, "", atomCols, bondCols, atomRads,
bondMults);
drawer.setOffset(300, 0);
drawer.drawMoleculeWithHighlights(*mol2, "", atomCols, bondCols, atomRads,
bondMults);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testOffsetHighlightedMols.svg");
outs << text;
outs.close();
const static std::regex atom6(
"<text x='(\\d+\\.\\d+)' y='(\\d+\\.\\d+)' class='atom-6'.*</text>");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), atom6),
std::sregex_iterator()));
// There are 4 characters for the 2 atom 6s. Check that the 1st and 3rd
// are in different panels, by x coord.
CHECK(match_count == 4);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), atom6);
std::smatch match = *match_begin;
double x1 = stod(match[1]);
CHECK(x1 < 300.0);
++match_begin;
++match_begin;
match = *match_begin;
double x2 = stod(match[1]);
CHECK((x2 > 300.0 && x2 < 600.0));
check_file_hash("testOffsetHighlightedMols.svg");
}