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Expose highlighAtomColors, highlighBondColors and highlightAtomRadii to CFFI and JS (#5657)

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* expose highlighAtomColors, highlighBondColors and highlightAtomRadii to CFFI and JS

* removed comment

Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2022-10-18 05:00:35 +02:00
committed by GitHub
parent 7e90108081
commit 893affdff0
4 changed files with 213 additions and 63 deletions
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188
Code/MinimalLib/common.h
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@@ -256,40 +256,87 @@ ChemicalReaction *rxn_from_input(const std::string &input,
return rxn_from_input(input, json);
}
std::string process_details(const std::string &details, int &width, int &height,
int &offsetx, int &offsety, std::string &legend,
std::vector<int> &atomIds,
std::string parse_int_array(const rj::Document &doc, std::vector<int> &intVec,
const std::string &keyName,
const std::string &valueName) {
const auto it = doc.FindMember(keyName.c_str());
if (it != doc.MemberEnd()) {
if (!it->value.IsArray()) {
return "JSON contains '" + keyName + "' field, but it is not an array";
}
for (const auto &val : it->value.GetArray()) {
if (!val.IsInt()) {
return valueName + " should be integers";
}
intVec.push_back(val.GetInt());
}
}
return "";
}
std::string parse_rgba_array(const rj::Value &val, DrawColour &color,
const std::string &keyName) {
if (!val.IsArray() || val.Size() < 3 || val.Size() > 4) {
return "JSON contains '" + keyName +
"' field, but the "
"colors are not R,G,B[,A] arrays";
}
std::vector<double> rgba(4, 1.0);
unsigned int i = 0;
for (const auto &component : val.GetArray()) {
if (!component.IsNumber()) {
return "JSON contains '" + keyName +
"' field, but the "
"R,G,B[,A] arrays contain non-float values";
}
CHECK_INVARIANT(i < 4, "");
rgba[i++] = component.GetDouble();
}
color.r = rgba[0];
color.g = rgba[1];
color.b = rgba[2];
color.a = rgba[3];
return "";
}
std::string parse_highlight_colors(const rj::Document &doc,
std::map<int, DrawColour> &colorMap,
const std::string &keyName) {
const auto it = doc.FindMember(keyName.c_str());
if (it != doc.MemberEnd()) {
if (!it->value.IsObject()) {
return "JSON contains '" + keyName + "' field, but it is not an object";
}
for (const auto &entry : it->value.GetObject()) {
DrawColour color;
auto problems = parse_rgba_array(entry.value, color, keyName);
if (!problems.empty()) {
return problems;
}
int idx = std::atoi(entry.name.GetString());
colorMap[idx] = std::move(color);
}
}
return "";
}
std::string process_details(rj::Document &doc, const std::string &details,
int &width, int &height, int &offsetx, int &offsety,
std::string &legend, std::vector<int> &atomIds,
std::vector<int> &bondIds, bool &kekulize) {
rj::Document doc;
doc.Parse(details.c_str());
if (!doc.IsObject()) {
return "Invalid JSON";
}
const auto atomsIt = doc.FindMember("atoms");
if (atomsIt != doc.MemberEnd()) {
if (!atomsIt->value.IsArray()) {
return "JSON contains 'atoms' field, but it is not an array";
}
for (const auto &molval : atomsIt->value.GetArray()) {
if (!molval.IsInt()) {
return ("Atom IDs should be integers");
}
atomIds.push_back(molval.GetInt());
}
std::string problems;
problems = parse_int_array(doc, atomIds, "atoms", "Atom IDs");
if (!problems.empty()) {
return problems;
}
const auto bondsIt = doc.FindMember("bonds");
if (bondsIt != doc.MemberEnd()) {
if (!bondsIt->value.IsArray()) {
return "JSON contains 'bonds' field, but it is not an array";
}
for (const auto &molval : bondsIt->value.GetArray()) {
if (!molval.IsInt()) {
return ("Bond IDs should be integers");
}
bondIds.push_back(molval.GetInt());
}
problems = parse_int_array(doc, bondIds, "bonds", "Bond IDs");
if (!problems.empty()) {
return problems;
}
const auto widthIt = doc.FindMember("width");
@@ -345,21 +392,59 @@ std::string process_details(const std::string &details, int &width, int &height,
return "";
}
std::string process_mol_details(const std::string &details, int &width,
int &height, int &offsetx, int &offsety,
std::string &legend, std::vector<int> &atomIds,
std::vector<int> &bondIds,
std::map<int, DrawColour> &atomMap,
std::map<int, DrawColour> &bondMap,
std::map<int, double> &radiiMap,
bool &kekulize) {
rj::Document doc;
auto problems = process_details(doc, details, width, height, offsetx, offsety,
legend, atomIds, bondIds, kekulize);
if (!problems.empty()) {
return problems;
}
problems = parse_highlight_colors(doc, atomMap, "highlightAtomColors");
if (!problems.empty()) {
return problems;
}
problems = parse_highlight_colors(doc, bondMap, "highlightBondColors");
if (!problems.empty()) {
return problems;
}
const auto radiiMapit = doc.FindMember("highlightAtomRadii");
if (radiiMapit != doc.MemberEnd()) {
if (!radiiMapit->value.IsObject()) {
return "JSON contains 'highlightAtomRadii' field, but it is not an object";
}
for (const auto &entry : radiiMapit->value.GetObject()) {
if (!entry.value.IsNumber()) {
return "JSON contains 'highlightAtomRadii' field, but the radii"
"are not floats";
}
int idx = std::atoi(entry.name.GetString());
radiiMap[idx] = entry.value.GetDouble();
}
}
return "";
}
std::string process_rxn_details(
const std::string &details, int &width, int &height, int &offsetx,
int &offsety, std::string &legend, std::vector<int> &atomIds,
std::vector<int> &bondIds, bool &kekulize, bool &highlightByReactant,
std::vector<DrawColour> &highlightColorsReactants) {
auto problems = process_details(details, width, height, offsetx, offsety,
rj::Document doc;
auto problems = process_details(doc, details, width, height, offsetx, offsety,
legend, atomIds, bondIds, kekulize);
if (!problems.empty()) {
return problems;
}
rj::Document doc;
doc.Parse(details.c_str());
if (!doc.IsObject()) {
return "Invalid JSON";
}
auto highlightByReactantIt = doc.FindMember("highlightByReactant");
if (highlightByReactantIt != doc.MemberEnd()) {
if (!highlightByReactantIt->value.IsBool()) {
@@ -375,22 +460,13 @@ std::string process_rxn_details(
return "JSON contains 'highlightColorsReactants' field, but it is not an "
"array";
}
for (const auto &color : highlightColorsReactantsIt->value.GetArray()) {
if (!color.IsArray() || color.Size() < 3 || color.Size() > 4) {
return "JSON contains 'highlightColorsReactants' array, but the "
"elements are not R,G,B[,A] arrays";
for (const auto &rgbaArray : highlightColorsReactantsIt->value.GetArray()) {
DrawColour color;
problems = parse_rgba_array(rgbaArray, color, "highlightColorsReactants");
if (!problems.empty()) {
return problems;
}
std::vector<double> rgba(4, 1.0);
unsigned int i = 0;
for (const auto &component : color.GetArray()) {
if (!component.IsDouble()) {
return "JSON contains 'highlightColorsReactants' array, but the "
"R,G,B[,A] arrays contain non-float values";
}
CHECK_INVARIANT(i < 4, "");
rgba[i++] = component.GetDouble();
}
highlightColorsReactants.emplace_back(rgba[0], rgba[1], rgba[2], rgba[3]);
highlightColorsReactants.push_back(std::move(color));
}
}
return "";
@@ -426,18 +502,22 @@ std::string mol_to_svg(const ROMol &m, int w, int h,
const std::string &details = "") {
std::vector<int> atomIds;
std::vector<int> bondIds;
std::map<int, DrawColour> atomMap;
std::map<int, DrawColour> bondMap;
std::map<int, double> radiiMap;
std::string legend = "";
std::string problems;
int offsetx = 0;
int offsety = 0;
bool kekulize = true;
if (!details.empty()) {
auto problems = process_details(details, w, h, offsetx, offsety, legend,
atomIds, bondIds, kekulize);
problems =
process_mol_details(details, w, h, offsetx, offsety, legend, atomIds,
bondIds, atomMap, bondMap, radiiMap, kekulize);
if (!problems.empty()) {
return problems;
}
}
MolDraw2DSVG drawer(w, h);
if (!details.empty()) {
MolDraw2DUtils::updateDrawerParamsFromJSON(drawer, details);
@@ -445,8 +525,10 @@ std::string mol_to_svg(const ROMol &m, int w, int h,
drawer.setOffset(offsetx, offsety);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, m, legend, &atomIds, &bondIds,
nullptr, nullptr, nullptr, -1,
kekulize);
atomMap.empty() ? nullptr : &atomMap,
bondMap.empty() ? nullptr : &bondMap,
radiiMap.empty() ? nullptr : &radiiMap,
-1, kekulize);
drawer.finishDrawing();
return drawer.getDrawingText();