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- Expose multicolor highlights to MinimalLib (rdkit#7787)
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@ptosco
ptosco authored Sep 3, 2024
1 parent d8e3eab commit e4f4644
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Showing 6 changed files with 210 additions and 33 deletions.
1 change: 1 addition & 0 deletions Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,7 @@ void DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int atomIdx,
Point2D &centre,
double &xradius,
double &yradius) const {
PRECONDITION(atomIdx < atCds_.size() && atomIdx < atomLabels_.size(), "")
centre = atCds_[atomIdx];
getAtomRadius(atomIdx, xradius, yradius);
if (drawOptions_.atomHighlightsAreCircles || !atomLabels_[atomIdx] ||
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47 changes: 47 additions & 0 deletions Code/GraphMol/MolDraw2D/catch_tests.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9984,3 +9984,50 @@ TEST_CASE("Github 7739 - Bad multi-coloured wedge") {
check_file_hash(fileStem + "5.svg");
}
}

TEST_CASE("idx out of bounds should not cause a segfault") {
auto m = "C"_smiles;
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
std::map<int, std::vector<DrawColour>> atomCols{{2, {DrawColour(0, 0, 0)}}};
std::map<int, std::vector<DrawColour>> bondCols;
std::map<int, double> atomRads{{2, 1.0}};
std::map<int, int> bondMults;
REQUIRE_THROWS_AS(
drawer.drawMoleculeWithHighlights(*m, "nocrash", atomCols, bondCols,
atomRads, bondMults),
Invar::Invariant);
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
std::map<int, std::vector<DrawColour>> atomCols;
std::map<int, std::vector<DrawColour>> bondCols{{2, {DrawColour(0, 0, 0)}}};
std::map<int, double> atomRads;
std::map<int, int> bondMults;
REQUIRE_THROWS_AS(
drawer.drawMoleculeWithHighlights(*m, "nocrash", atomCols, bondCols,
atomRads, bondMults),
Invar::Invariant);
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
std::map<int, std::vector<DrawColour>> atomCols{{0, {DrawColour(0, 0, 0)}}};
std::map<int, std::vector<DrawColour>> bondCols;
std::map<int, double> atomRads{{2, 1.0}};
std::map<int, int> bondMults;
REQUIRE_NOTHROW(
drawer.drawMoleculeWithHighlights(*m, "nocrash", atomCols, bondCols,
atomRads, bondMults));
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
std::map<int, std::vector<DrawColour>> atomCols;
std::map<int, std::vector<DrawColour>> bondCols{{0, {DrawColour(0, 0, 0)}}};
std::map<int, double> atomRads;
std::map<int, int> bondMults{{2, 10}};
REQUIRE_THROWS_AS(
drawer.drawMoleculeWithHighlights(*m, "nocrash", atomCols, bondCols,
atomRads, bondMults),
Invar::Invariant);
}
}
47 changes: 41 additions & 6 deletions Code/MinimalLib/cffi_test.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2295,7 +2295,8 @@ void test_assign_chiral_tags_from_mol_parity() {
char *mpkl;
size_t mpkl_size;
char *smiles;
const char *artemisininCTAB = "68827\n\
const char *artemisininCTAB =
"68827\n\
-OEChem-03262404452D\n\
\n\
20 23 0 1 0 0 0 0 0999 V2000\n\
Expand Down Expand Up @@ -2350,10 +2351,13 @@ M END\n\
assert(!strcmp(smiles, "CC1CCC2C(C)C(=O)OC3OC4(C)CCC1C32OO4"));
free(smiles);
free(mpkl);
mpkl = get_mol(artemisininCTAB, &mpkl_size, "{\"assignChiralTypesFromMolParity\":true}");
mpkl = get_mol(artemisininCTAB, &mpkl_size,
"{\"assignChiralTypesFromMolParity\":true}");
assert(mpkl);
smiles = get_smiles(mpkl, mpkl_size, NULL);
assert(!strcmp(smiles, "C[C@@H]1CC[C@H]2[C@@H](C)C(=O)O[C@@H]3O[C@@]4(C)CC[C@@H]1[C@]32OO4"));
assert(!strcmp(
smiles,
"C[C@@H]1CC[C@H]2[C@@H](C)C(=O)O[C@@H]3O[C@@]4(C)CC[C@@H]1[C@]32OO4"));
free(smiles);
free(mpkl);
}
Expand Down Expand Up @@ -2663,9 +2667,9 @@ M END\n\
char *mpkl;
char *mpkl_copy;
size_t mpkl_size;
const char *mb_rdkit_wedging;
const char *mb_rdkit_wedging_post_orig;
const char *mb_orig_wedging;
char *mb_rdkit_wedging;
char *mb_rdkit_wedging_post_orig;
char *mb_orig_wedging;
mpkl = get_mol(mb, &mpkl_size, "");
assert(mpkl && mpkl_size);
mpkl_copy = malloc(mpkl_size);
Expand All @@ -2687,6 +2691,36 @@ M END\n\
free(mpkl_copy);
}

void test_multi_highlights() {
printf("--------------------------\n");
printf(" test_multi_highlights\n");
const char *smi =
"[H]c1cc2c(-c3ccnc(Nc4ccc(F)c(F)c4)n3)c(-c3cccc(C(F)(F)F)c3)nn2nc1C";
const char *details =
"{\"width\":250,\"height\":200,\"highlightAtomMultipleColors\":{\"15\":[[0.941,0.894,0.259]],\"17\":[[0,0.62,0.451]],\"21\":[[0.902,0.624,0]],\"22\":[[0.902,0.624,0]],\"23\":[[0.902,0.624,0]],\"24\":[[0.902,0.624,0]],\"25\":[[0.902,0.624,0]],\"26\":[[0.902,0.624,0]],\"27\":[[0.902,0.624,0]],\"28\":[[0.902,0.624,0]],\"29\":[[0.902,0.624,0]],\"30\":[[0.902,0.624,0]],\"35\":[[0.337,0.706,0.914]]},\"highlightBondMultipleColors\":{\"14\":[[0.941,0.894,0.259]],\"16\":[[0,0.62,0.451]],\"20\":[[0.902,0.624,0]],\"21\":[[0.902,0.624,0]],\"22\":[[0.902,0.624,0]],\"23\":[[0.902,0.624,0]],\"24\":[[0.902,0.624,0]],\"25\":[[0.902,0.624,0]],\"26\":[[0.902,0.624,0]],\"27\":[[0.902,0.624,0]],\"28\":[[0.902,0.624,0]],\"29\":[[0.902,0.624,0]],\"34\":[[0.337,0.706,0.914]],\"38\":[[0.902,0.624,0]]},\"highlightAtomRadii\":{\"15\":0.4,\"17\":0.4,\"21\":0.4,\"22\":0.4,\"23\":0.4,\"24\":0.4,\"25\":0.4,\"26\":0.4,\"27\":0.4,\"28\":0.4,\"29\":0.4,\"30\":0.4,\"35\":0.4},\"highlightLineWidthMultipliers\":{\"14\":2,\"16\":2,\"20\":2,\"21\":2,\"22\":2,\"23\":2,\"24\":2,\"25\":2,\"26\":2,\"27\":2,\"28\":2,\"29\":2,\"34\":2,\"38\":2}}";
const char *colors[] = {"#009E73", "#55B4E9", "#E69F00", "#EFE342", NULL};
char *mpkl;
char *svg_with_details;
char *svg_without_details;
size_t mpkl_size;
int i;
mpkl = get_mol(smi, &mpkl_size, "{\"removeHs\":false}");
assert(mpkl && mpkl_size);
svg_with_details = get_svg(mpkl, mpkl_size, details);
assert(strstr(svg_with_details, "ellipse"));
for (i = 0; colors[i]; ++i) {
assert(strstr(svg_with_details, colors[i]));
}
svg_without_details = get_svg(mpkl, mpkl_size, "");
assert(!strstr(svg_without_details, "ellipse"));
for (i = 0; colors[i]; ++i) {
assert(!strstr(svg_without_details, colors[i]));
}
free(svg_with_details);
free(svg_without_details);
free(mpkl);
}

int main() {
enable_logging();
char *vers = version();
Expand Down Expand Up @@ -2721,5 +2755,6 @@ int main() {
test_smiles_smarts_params();
test_wedged_bond_atropisomer();
test_get_molblock_use_molblock_wedging();
test_multi_highlights();
return 0;
}
78 changes: 71 additions & 7 deletions Code/MinimalLib/common.h
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Original file line number Diff line number Diff line change
Expand Up @@ -354,6 +354,41 @@ std::string parse_rgba_array(const rj::Value &val, DrawColour &color,
return "";
}

std::string parse_highlight_multi_colors(
const rj::Document &doc, std::map<int, std::vector<DrawColour>> &colorMap,
const std::string &keyName, bool &haveMultiColors) {
const auto it = doc.FindMember(keyName.c_str());
haveMultiColors = (it != doc.MemberEnd());
if (!haveMultiColors) {
return "";
}
if (!it->value.IsObject()) {
return "JSON contains '" + keyName + "' field, but it is not an object";
}
for (const auto &entry : it->value.GetObject()) {
int idx = std::atoi(entry.name.GetString());
auto &drawColorVect = colorMap[idx];
if (entry.value.IsArray()) {
const auto &arr = entry.value.GetArray();
if (std::all_of(arr.begin(), arr.end(),
[](const auto &item) { return item.IsArray(); })) {
for (const auto &item : arr) {
DrawColour color;
auto problems = parse_rgba_array(item, color, keyName);
if (!problems.empty()) {
return problems;
}
drawColorVect.push_back(std::move(color));
}
continue;
}
}
return "JSON contains '" + keyName +
"' field, but it is not an array of R,G,B[,A] arrays";
}
return "";
}

std::string parse_highlight_colors(const rj::Document &doc,
std::map<int, DrawColour> &colorMap,
const std::string &keyName) {
Expand Down Expand Up @@ -441,19 +476,48 @@ std::string process_mol_details(const std::string &details,
if (!problems.empty()) {
return problems;
}

problems = parse_highlight_colors(doc, molDrawingDetails.atomMap,
"highlightAtomColors");
bool haveAtomMultiColors;
problems = parse_highlight_multi_colors(doc, molDrawingDetails.atomMultiMap,
"highlightAtomMultipleColors",
haveAtomMultiColors);
if (!problems.empty()) {
return problems;
}

problems = parse_highlight_colors(doc, molDrawingDetails.bondMap,
"highlightBondColors");
bool haveBondMultiColors;
problems = parse_highlight_multi_colors(doc, molDrawingDetails.bondMultiMap,
"highlightBondMultipleColors",
haveBondMultiColors);
if (!problems.empty()) {
return problems;
}

if (haveAtomMultiColors || haveBondMultiColors) {
const auto lineWidthMultiplierMapit =
doc.FindMember("highlightLineWidthMultipliers");
if (lineWidthMultiplierMapit != doc.MemberEnd()) {
if (!lineWidthMultiplierMapit->value.IsObject()) {
return "JSON contains 'highlightLineWidthMultipliers' field, but it is not an object";
}
for (const auto &entry : lineWidthMultiplierMapit->value.GetObject()) {
if (!entry.value.IsInt()) {
return "JSON contains 'highlightLineWidthMultipliers' field, but the multipliers"
"are not ints";
}
int idx = std::atoi(entry.name.GetString());
molDrawingDetails.lineWidthMultiplierMap[idx] = entry.value.GetInt();
}
}
} else {
problems = parse_highlight_colors(doc, molDrawingDetails.atomMap,
"highlightAtomColors");
if (!problems.empty()) {
return problems;
}
problems = parse_highlight_colors(doc, molDrawingDetails.bondMap,
"highlightBondColors");
if (!problems.empty()) {
return problems;
}
}
const auto radiiMapit = doc.FindMember("highlightAtomRadii");
if (radiiMapit != doc.MemberEnd()) {
if (!radiiMapit->value.IsObject()) {
Expand Down
56 changes: 36 additions & 20 deletions Code/MinimalLib/common_defs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,10 @@ struct DrawingDetails {
struct MolDrawingDetails : public DrawingDetails {
std::map<int, DrawColour> atomMap;
std::map<int, DrawColour> bondMap;
std::map<int, std::vector<DrawColour>> atomMultiMap;
std::map<int, std::vector<DrawColour>> bondMultiMap;
std::map<int, double> radiiMap;
std::map<int, int> lineWidthMultiplierMap;
};

struct RxnDrawingDetails : public DrawingDetails {
Expand Down Expand Up @@ -87,28 +90,41 @@ class DrawerFromDetails {
}
initDrawer(molDrawingDetails);
const ROMol *molPtr = &mol;
std::unique_ptr<ROMol> origWedgingMol;
if (molDrawingDetails.useMolBlockWedging) {
origWedgingMol.reset(new ROMol(mol));
Chirality::reapplyMolBlockWedging(*origWedgingMol);
molPtr = origWedgingMol.get();
drawer().drawOptions().useMolBlockWedging = false;
std::unique_ptr<RWMol> drawnMol;
bool haveMultiMap = (!molDrawingDetails.atomMultiMap.empty() ||
!molDrawingDetails.bondMultiMap.empty());
if (molDrawingDetails.useMolBlockWedging || haveMultiMap) {
drawnMol.reset(new RWMol(mol));
molPtr = static_cast<ROMol *>(drawnMol.get());
if (molDrawingDetails.useMolBlockWedging) {
Chirality::reapplyMolBlockWedging(*drawnMol);
drawer().drawOptions().useMolBlockWedging = false;
}
}
drawer().setOffset(molDrawingDetails.offsetx, molDrawingDetails.offsety);

MolDraw2DUtils::prepareAndDrawMolecule(
drawer(), *molPtr, molDrawingDetails.legend, &molDrawingDetails.atomIds,
&molDrawingDetails.bondIds,
molDrawingDetails.atomMap.empty() ? nullptr
: &molDrawingDetails.atomMap,
molDrawingDetails.bondMap.empty() ? nullptr
: &molDrawingDetails.bondMap,
molDrawingDetails.radiiMap.empty() ? nullptr
: &molDrawingDetails.radiiMap,
-1, molDrawingDetails.kekulize, molDrawingDetails.addChiralHs,
molDrawingDetails.wedgeBonds, molDrawingDetails.forceCoords,
molDrawingDetails.wavyBonds);

if (!haveMultiMap) {
MolDraw2DUtils::prepareAndDrawMolecule(
drawer(), *molPtr, molDrawingDetails.legend,
&molDrawingDetails.atomIds, &molDrawingDetails.bondIds,
molDrawingDetails.atomMap.empty() ? nullptr
: &molDrawingDetails.atomMap,
molDrawingDetails.bondMap.empty() ? nullptr
: &molDrawingDetails.bondMap,
molDrawingDetails.radiiMap.empty() ? nullptr
: &molDrawingDetails.radiiMap,
-1, molDrawingDetails.kekulize, molDrawingDetails.addChiralHs,
molDrawingDetails.wedgeBonds, molDrawingDetails.forceCoords,
molDrawingDetails.wavyBonds);
} else {
MolDraw2DUtils::prepareMolForDrawing(
*drawnMol, molDrawingDetails.kekulize, molDrawingDetails.addChiralHs,
molDrawingDetails.wedgeBonds, molDrawingDetails.forceCoords,
molDrawingDetails.wavyBonds);
drawer().drawMoleculeWithHighlights(
*drawnMol, molDrawingDetails.legend, molDrawingDetails.atomMultiMap,
molDrawingDetails.bondMultiMap, molDrawingDetails.radiiMap,
molDrawingDetails.lineWidthMultiplierMap);
}
return finalizeDrawing();
}
std::string draw_rxn(const ChemicalReaction &rxn) {
Expand Down
14 changes: 14 additions & 0 deletions Code/MinimalLib/tests/tests.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3176,6 +3176,19 @@ function test_get_mol_copy() {
}
}

function test_multi_highlights() {
const mol = RDKitModule.get_mol('[H]c1cc2c(-c3ccnc(Nc4ccc(F)c(F)c4)n3)c(-c3cccc(C(F)(F)F)c3)nn2nc1C', JSON.stringify({removeHs: false}));
const details = '{"width":250,"height":200,"highlightAtomMultipleColors":{"15":[[0.941,0.894,0.259]],"17":[[0,0.62,0.451]],"21":[[0.902,0.624,0]],"22":[[0.902,0.624,0]],"23":[[0.902,0.624,0]],"24":[[0.902,0.624,0]],"25":[[0.902,0.624,0]],"26":[[0.902,0.624,0]],"27":[[0.902,0.624,0]],"28":[[0.902,0.624,0]],"29":[[0.902,0.624,0]],"30":[[0.902,0.624,0]],"35":[[0.337,0.706,0.914]]},"highlightBondMultipleColors":{"14":[[0.941,0.894,0.259]],"16":[[0,0.62,0.451]],"20":[[0.902,0.624,0]],"21":[[0.902,0.624,0]],"22":[[0.902,0.624,0]],"23":[[0.902,0.624,0]],"24":[[0.902,0.624,0]],"25":[[0.902,0.624,0]],"26":[[0.902,0.624,0]],"27":[[0.902,0.624,0]],"28":[[0.902,0.624,0]],"29":[[0.902,0.624,0]],"34":[[0.337,0.706,0.914]],"38":[[0.902,0.624,0]]},"highlightAtomRadii":{"15":0.4,"17":0.4,"21":0.4,"22":0.4,"23":0.4,"24":0.4,"25":0.4,"26":0.4,"27":0.4,"28":0.4,"29":0.4,"30":0.4,"35":0.4},"highlightLineWidthMultipliers":{"14":2,"16":2,"20":2,"21":2,"22":2,"23":2,"24":2,"25":2,"26":2,"27":2,"28":2,"29":2,"34":2,"38":2}}';
const svgWithDetails = mol.get_svg_with_highlights(details);
assert(svgWithDetails.includes('ellipse'));
const COLORS = ['#009E73', '#55B4E9', '#E69F00', '#EFE342'];
assert(COLORS.every((color) => svgWithDetails.includes(color)));
const svgWithOutDetails = mol.get_svg_with_highlights('');
assert(!svgWithOutDetails.includes('ellipse'));
assert(!COLORS.some((color) => svgWithOutDetails.includes(color)));
mol.delete();
}

initRDKitModule().then(function(instance) {
var done = {};
const waitAllTestsFinished = () => {
Expand Down Expand Up @@ -3257,6 +3270,7 @@ initRDKitModule().then(function(instance) {
test_assign_chiral_tags_from_mol_parity();
test_make_dummies_queries();
test_get_mol_copy();
test_multi_highlights();
waitAllTestsFinished().then(() =>
console.log("Tests finished successfully")
);
Expand Down

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