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Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier (#8857)

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* support direct property setting/getting in MolDraw2DOptions

* same thing for contourParams

* add getAtomPalette()
This commit is contained in:
Greg Landrum
2025-10-09 14:14:19 +02:00
committed by GitHub
parent 00583fc1ab
commit ad1fcb5b7b
2 changed files with 858 additions and 726 deletions
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87
Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
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@@ -519,6 +519,13 @@ void setAtomPalette(RDKit::MolDrawOptions &self, python::object cmap) {
self.atomColourPalette.clear();
updateAtomPalette(self, cmap);
}
python::dict getAtomPalette(const RDKit::MolDrawOptions &self) {
python::dict res;
for (const auto &pair : self.atomColourPalette) {
res[pair.first] = colourToPyTuple(pair.second);
}
return res;
}
void setMonochromeMode_helper1(RDKit::MolDrawOptions &options, python::tuple fg,
python::tuple bg) {
@@ -629,11 +636,22 @@ void setColoursHelper(RDKit::MolDraw2DUtils::ContourParams &params,
}
params.colourMap = cs;
}
python::tuple getColoursHelper(
const RDKit::MolDraw2DUtils::ContourParams &params) {
python::list res;
for (const auto &clr : params.colourMap) {
res.append(colourToPyTuple(clr));
}
return python::tuple(res);
}
void setContourColour(RDKit::MolDraw2DUtils::ContourParams &params,
python::tuple tpl) {
params.contourColour = pyTupleToDrawColour(tpl);
}
python::object getContourColour(
const RDKit::MolDraw2DUtils::ContourParams &params) {
return colourToPyTuple(params.contourColour);
}
void drawPolygonHelper(RDKit::MolDraw2D &self, python::object py_cds,
bool rawCoords) {
std::unique_ptr<std::vector<RDGeom::Point2D>> cds =
@@ -786,6 +804,38 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
&RDKit::MolDrawOptions::dummiesAreAttachments)
.def_readwrite("circleAtoms", &RDKit::MolDrawOptions::circleAtoms)
.def_readwrite("splitBonds", &RDKit::MolDrawOptions::splitBonds)
.add_property(
"backgroundColour", &RDKit::getBgColour, &RDKit::setBgColour,
"the background colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"queryColour", &RDKit::getQyColour, &RDKit::setQyColour,
"the query colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"highlightColour", &RDKit::getHighlightColour,
&RDKit::setHighlightColour,
"the highlight colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"symbolColour", &RDKit::getSymbolColour, &RDKit::setSymbolColour,
"the symbol colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"annotationColour", &RDKit::getAnnotationColour,
&RDKit::setAnnotationColour,
"the annotation colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"atomNoteColour", &RDKit::getAtomNoteColour,
&RDKit::setAtomNoteColour,
"the atom note colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"bondNoteColour", &RDKit::getBondNoteColour,
&RDKit::setBondNoteColour,
"the bond note colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"legendColour", &RDKit::getLegendColour, &RDKit::setLegendColour,
"the legend colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.add_property(
"variableAttachmentColour", &RDKit::getVariableAttachmentColour,
&RDKit::setVariableAttachmentColour,
"the variable attachment colour as an (R,G,B,A) tuple, values should be between 0 and 1")
.def("getBackgroundColour", &RDKit::getBgColour, python::args("self"),
"method returning the background colour")
.def("getQueryColour", &RDKit::getQyColour, python::args("self"),
@@ -843,6 +893,9 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
python::args("self", "cmap"),
"sets the palette for atoms and bonds from a dictionary mapping ints "
"to 3-tuples")
.def("getAtomPalette", &RDKit::getAtomPalette, python::args("self"),
"returns the current atom palette as a dictionary mapping ints "
"to 4-tuples")
.def_readwrite("atomLabels", &RDKit::MolDrawOptions::atomLabels,
"maps indices to atom labels")
.def_readwrite("atomLabelDeuteriumTritium",
@@ -1135,8 +1188,8 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
.def("FillPolys", &RDKit::MolDraw2D::fillPolys, python::args("self"),
"returns whether or not polygons are being filled")
.def("DrawLine",
(void (RDKit::MolDraw2D::*)(const Point2D &, const Point2D &,
bool))&RDKit::MolDraw2D::drawLine,
(void(RDKit::MolDraw2D::*)(const Point2D &, const Point2D &, bool)) &
RDKit::MolDraw2D::drawLine,
(python::arg("self"), python::arg("cds1"), python::arg("cds2"),
python::arg("rawCoords") = false),
"draws a line with the current drawing style. The coordinates "
@@ -1185,8 +1238,9 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
"are in the molecule frame unless rawCoords is true, "
"in which case the coordinates are in pixels.")
.def("DrawArc",
(void (RDKit::MolDraw2D::*)(const Point2D &, double, double, double,
bool))&RDKit::MolDraw2D::drawArc,
(void(RDKit::MolDraw2D::*)(const Point2D &, double, double, double,
bool)) &
RDKit::MolDraw2D::drawArc,
(python::arg("self"), python::arg("center"), python::arg("radius"),
python::arg("angle1"), python::arg("angle2"),
python::arg("rawCoords") = false),
@@ -1215,9 +1269,9 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
"are in the molecule frame unless rawCoords is true, "
"in which case the coordinates are in pixels.")
.def("DrawString",
(void (RDKit::MolDraw2D::*)(const std::string &,
const RDGeom::Point2D &,
bool))&RDKit::MolDraw2D::drawString,
(void(RDKit::MolDraw2D::*)(const std::string &,
const RDGeom::Point2D &, bool)) &
RDKit::MolDraw2D::drawString,
(python::arg("self"), python::arg("string"), python::arg("pos"),
python::arg("rawCoords") = false),
"add text to the canvas. The coordinates "
@@ -1232,14 +1286,14 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
"are in the molecule frame unless rawCoords is true, "
"in which case the coordinates are in pixels.")
.def("GetDrawCoords",
(RDGeom::Point2D (RDKit::MolDraw2D::*)(const RDGeom::Point2D &)
(RDGeom::Point2D(RDKit::MolDraw2D::*)(const RDGeom::Point2D &)
const) &
RDKit::MolDraw2D::getDrawCoords,
(python::arg("self"), python::arg("point")),
"get the coordinates in drawing space for a particular point in "
"molecule space")
.def("GetDrawCoords",
(RDGeom::Point2D (RDKit::MolDraw2D::*)(int) const) &
(RDGeom::Point2D(RDKit::MolDraw2D::*)(int) const) &
RDKit::MolDraw2D::getDrawCoords,
(python::arg("self"), python::arg("atomIndex")),
"get the coordinates in drawing space for a particular atom")
@@ -1269,7 +1323,7 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
python::args("self"),
"add the last bits of SVG to finish the drawing")
.def("AddMoleculeMetadata",
(void (RDKit::MolDraw2DSVG::*)(const RDKit::ROMol &, int) const) &
(void(RDKit::MolDraw2DSVG::*)(const RDKit::ROMol &, int) const) &
RDKit::MolDraw2DSVG::addMoleculeMetadata,
((python::arg("self"), python::arg("mol")),
python::arg("confId") = -1),
@@ -1381,6 +1435,12 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
"fillThresholdIsFraction",
&RDKit::MolDraw2DUtils::ContourParams::fillThresholdIsFraction,
"if true, fillThreshold is a fraction of the range of the data")
.add_property("colourMap", &RDKit::getColoursHelper,
&RDKit::setColoursHelper,
"the color map to use when filling the grid")
.add_property("contourColour", &RDKit::getContourColour,
&RDKit::setContourColour,
"the color to use for drawing the contours")
.def("setContourColour", &RDKit::setContourColour,
(python::arg("self"), python::arg("colour")))
.def("setColourMap", &RDKit::setColoursHelper,
@@ -1516,9 +1576,10 @@ https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_draw
(python::arg("mol"), python::arg("confId") = -1),
"Calculate the mean bond length for the molecule.");
python::def("SetDarkMode",
(void (*)(RDKit::MolDrawOptions &))&RDKit::setDarkMode,
(void (*)(RDKit::MolDrawOptions &)) & RDKit::setDarkMode,
python::args("d2d"), "set dark mode for a MolDrawOptions object");
python::def("SetDarkMode", (void (*)(RDKit::MolDraw2D &))&RDKit::setDarkMode,
python::def("SetDarkMode",
(void (*)(RDKit::MolDraw2D &)) & RDKit::setDarkMode,
python::args("d2d"), "set dark mode for a MolDraw2D object");
python::def("SetMonochromeMode", RDKit::setMonochromeMode_helper1,
(python::arg("options"), python::arg("fgColour"),

1497
Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py
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