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epam · Nov 18, 2024 · 952f132 · 952f132
1 parent 4991bb0
commit 952f132
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Showing 14 changed files with 128 additions and 49 deletions.
diff --git a/api/c/indigo/src/indigo_reaction.cpp b/api/c/indigo/src/indigo_reaction.cpp
@@ -142,6 +142,7 @@ IndigoReaction::~IndigoReaction()
 void IndigoReaction::init(std::unique_ptr<BaseReaction>&& reaction)
 {
     rxn = reaction ? std::move(reaction) : std::make_unique<Reaction>();
+    _properties.copy(rxn->properties());
 }
 
 Reaction& IndigoReaction::getReaction()

diff --git a/core/indigo-core/layout/pathway_layout.h b/core/indigo-core/layout/pathway_layout.h
@@ -64,7 +64,7 @@ namespace indigo
             : _reaction(reaction), _depths(MAX_DEPTHS, 0), _maxDepth(0), _bond_length(options.DEFAULT_BOND_LENGTH),
               _default_arrow_size((float)options.DEFAULT_BOND_LENGTH * ARROW_LENGTH_FACTOR),
               _reaction_margin_size(options.reactionComponentMarginSize / options.ppi), _preserve_molecule_layout(true),
-              _text_height((float)options.DEFAULT_BOND_LENGTH * TEXT_LINE_HEIGHT)
+              _text_line_height((float)options.DEFAULT_BOND_LENGTH * TEXT_LINE_HEIGHT)
         {
         }
 
@@ -108,7 +108,7 @@ namespace indigo
                         mol.scale(center, bondLength / mean);
                     }
                     Rect2f boundingBox;
-                    mol.getBoundingBox(boundingBox);
+                    mol.getBoundingBox(boundingBox, Vec2f(bondLength, bondLength));
                     molecules.push_back(std::make_pair(reactantIdx, boundingBox));
                     width = boundingBox.width();
                     height = boundingBox.height();
@@ -263,7 +263,7 @@ namespace indigo
         std::vector<PathwayLayoutRootItem> _layoutRootItems;
 
         const float _bond_length;
-        const float _text_height;
+        const float _text_line_height;
         const float _default_arrow_size;
         const float _reaction_margin_size;
         bool _preserve_molecule_layout;

diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp
@@ -152,15 +152,18 @@ void PathwayLayout::buildLayoutTree()
 
             auto totalHeight = std::accumulate(currentLayoutItem.children.begin(), currentLayoutItem.children.end(), 0.0f,
                                                [](float summ, const PathwayLayoutItem* item) { return summ + item->height; });
+            auto totalSpacing = (currentLayoutItem.children.size() - 1) * VERTICAL_SPACING;
             totalHeight -= currentLayoutItem.children.front()->height / 2;
             totalHeight -= currentLayoutItem.children.back()->height / 2;
             totalHeight /= 2.0f;
-            float targetHeight = totalLines * _text_height + _reaction_margin_size;
+            float targetHeight = totalLines * _text_line_height + _reaction_margin_size;
             if (totalHeight < targetHeight)
             {
-                auto adjustHeight = (targetHeight - totalHeight) / (currentLayoutItem.children.size() - 1);
                 for (auto& child : currentLayoutItem.children)
-                    child->height += adjustHeight * TEXT_ADJUSTMENT; // should be 2.0f
+                {
+                    child->height *= (targetHeight - totalSpacing / 2);
+                    child->height /= totalHeight;
+                }
             }
         }
     }
@@ -197,7 +200,7 @@ void PathwayLayout::copyTextPropertiesToNode(const PathwayReaction::SimpleReacti
         }
     }
 
-    if (node.name_text.size())
+    if (node.name_text.size() && node.conditions_text.size())
         node.name_text.push().readString("", true);
 }
 
@@ -306,7 +309,7 @@ void PathwayLayout::applyLayout()
                 arrows.insert(arrows.end(), tails.begin(), tails.end());
 
                 // add spines
-                float text_height_limit = MIN_LINES_COUNT * _text_height;
+                float text_height_limit = MIN_LINES_COUNT * _text_line_height;
                 auto& node = _reaction.getReactionNode(layoutItem->reactionIndex);
                 Vec2f textPos_bl(0, head.y);
                 if (tails.size() > 1)
@@ -341,12 +344,12 @@ void PathwayLayout::generateTextBlocks(SimpleTextObjectBuilder& tob, const ObjAr
 {
     for (int i = 0; i < props.size(); ++i)
     {
-        if (height > _text_height)
+        if (std::ceil(height * 1000) >= std::ceil(_text_line_height * 1000))
         {
-            height -= _text_height;
+            height -= _text_line_height;
             SimpleTextLine textLine;
             textLine.text = props[i].ptr();
-            if (height < _text_height && props.size() - i > 1)
+            if (std::ceil(height * 1000) < std::ceil(_text_line_height * 1000) && props.size() - i > 1)
                 textLine.text += "...";
             auto& ts = textLine.text_styles.emplace_back();
             ts.offset = 0;
@@ -365,8 +368,9 @@ void PathwayLayout::addMetaText(PathwayReaction::ReactionNode& node, const Vec2f
     generateTextBlocks(tob, node.name_text, KFontBoldStr, height_limit);
     generateTextBlocks(tob, node.conditions_text, KFontItalicStr, height_limit);
     tob.finalize();
-    Vec3f text_pos_lr(text_pos_bl.x, text_pos_bl.y + _text_height / 2 + (text_height_limit - height_limit), 0.0f);
-    _reaction.meta().addMetaObject(new SimpleTextObject(text_pos_lr, tob.getJsonString()), true);
+    auto text_height = _text_line_height / 2 + (text_height_limit - height_limit);
+    Vec3f text_pos_tr(text_pos_bl.x, text_pos_bl.y + text_height, 0.0f);
+    _reaction.meta().addMetaObject(new SimpleTextObject(text_pos_tr, Vec2f(node.text_width, text_height), tob.getJsonString()), true);
 }
 
 std::vector<std::string> PathwayLayout::splitText(const std::string& text, float max_width, std::function<float(char ch)> symbol_width)

diff --git a/core/indigo-core/molecule/meta_commons.h b/core/indigo-core/molecule/meta_commons.h
@@ -159,16 +159,16 @@ namespace indigo
 
         static const std::uint32_t CID = "Simple text object"_hash;
 
-        SimpleTextObject(const Vec3f& pos, const std::string& content);
+        SimpleTextObject(const Vec3f& pos, const Vec2f& sz, const std::string& content);
 
         MetaObject* clone() const override
         {
-            return new SimpleTextObject(_pos, _content);
+            return new SimpleTextObject(_pos, _size, _content);
         }
 
         void getBoundingBox(Rect2f& bbox) const override
         {
-            bbox = Rect2f(Vec2f(_pos.x, _pos.y), Vec2f(_pos.x, _pos.y));
+            bbox = Rect2f(Vec2f(_pos.x, _pos.y), Vec2f(_pos.x + _size.x, _pos.y - _size.y));
         }
 
         void offset(const Vec2f& offset) override
@@ -185,6 +185,7 @@ namespace indigo
         std::string _content;
         std::list<SimpleTextLine> _block;
         Vec3f _pos;
+        Vec2f _size;
     };
 
     class SimpleTextObjectBuilder

diff --git a/core/indigo-core/molecule/molecule_cdxml_loader.h b/core/indigo-core/molecule/molecule_cdxml_loader.h
@@ -176,6 +176,16 @@ namespace indigo
         bool is_superatom;
     };
 
+    struct CdxmlText
+    {
+        CdxmlText(const Vec3f& pos, const Vec2f& size, const std::string& text) : pos(pos), size(size), text(text)
+        {
+        }
+        std::string text;
+        Vec3f pos;
+        Vec2f size;
+    };
+
     class BaseCDXProperty
     {
     public:
@@ -805,7 +815,7 @@ namespace indigo
         std::vector<CdxmlNode> nodes;
         std::vector<CdxmlBond> bonds;
         std::vector<CdxmlBracket> brackets;
-        std::vector<std::pair<Vec3f, std::string>> text_objects;
+        std::vector<CdxmlText> text_objects;
 
         static const int SCALE = 30;
 
@@ -820,7 +830,7 @@ namespace indigo
         void _parseBond(CdxmlBond& bond, BaseCDXProperty& prop);
 
         void _parseBracket(CdxmlBracket& bracket, BaseCDXProperty& prop);
-        void _parseText(BaseCDXElement& elem, std::vector<std::pair<Vec3f, std::string>>& text_parsed);
+        void _parseText(BaseCDXElement& elem, std::vector<CdxmlText>& text_parsed);
         void _parseLabel(BaseCDXElement& elem, std::string& label);
 
         void _parseGraphic(BaseCDXElement& elem);

diff --git a/core/indigo-core/molecule/molecule_json_saver.h b/core/indigo-core/molecule/molecule_json_saver.h
@@ -66,6 +66,8 @@ namespace indigo
         int getMonomerNumber(int mon_idx);
 
         void writeFloat(JsonWriter& writer, float f_value);
+        void writePos(JsonWriter& writer, const Vec3f& pos);
+
         void saveAtoms(BaseMolecule& mol, JsonWriter& writer);
         void saveBonds(BaseMolecule& mol, JsonWriter& writer);
         void saveRGroup(PtrPool<BaseMolecule>& fragments, int rgnum, JsonWriter& writer);

diff --git a/core/indigo-core/molecule/src/meta_commons.cpp b/core/indigo-core/molecule/src/meta_commons.cpp
@@ -162,10 +162,11 @@ namespace indigo
         return base64::encode(_image_data.c_str(), _image_data.size());
     }
 
-    SimpleTextObject::SimpleTextObject(const Vec3f& pos, const std::string& content) : MetaObject(CID)
+    SimpleTextObject::SimpleTextObject(const Vec3f& pos, const Vec2f& sz, const std::string& content) : MetaObject(CID)
     {
         using namespace rapidjson;
         _pos = pos;
+        _size = sz;
         _content = content;
         Document data;
         data.Parse(content.c_str());

diff --git a/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp b/core/indigo-core/molecule/src/molecule_cdxml_loader.cpp
@@ -509,7 +509,7 @@ void MoleculeCdxmlLoader::_parseCollections(BaseMolecule& mol)
         _addBracket(mol, brk);
 
     for (const auto& to : text_objects)
-        mol.meta().addMetaObject(new SimpleTextObject(to.first, to.second));
+        mol.meta().addMetaObject(new SimpleTextObject(to.pos, to.size, to.text));
 
     for (const auto& plus : _pluses)
         mol.meta().addMetaObject(new ReactionPlusObject(plus));
@@ -1683,7 +1683,7 @@ void MoleculeCdxmlLoader::_parseLabel(BaseCDXElement& elem, std::string& label)
     }
 }
 
-void MoleculeCdxmlLoader::_parseText(BaseCDXElement& elem, std::vector<std::pair<Vec3f, std::string>>& text_parsed)
+void MoleculeCdxmlLoader::_parseText(BaseCDXElement& elem, std::vector<CdxmlText>& text_parsed)
 {
     Vec3f text_pos;
     auto text_coordinates_lambda = [&text_pos, this](const std::string& data) { this->parsePos(data, text_pos); };
@@ -1816,8 +1816,7 @@ void MoleculeCdxmlLoader::_parseText(BaseCDXElement& elem, std::vector<std::pair
     std::string txt = s.GetString();
     if (!is_valid_utf8(txt))
         txt = latin1_to_utf8(txt);
-
-    text_parsed.emplace_back(tpos, txt.c_str());
+    text_parsed.emplace_back(tpos, Vec2f(text_bbox.width(), text_bbox.height()), txt.c_str());
 }
 
 void MoleculeCdxmlLoader::_parseBracket(CdxmlBracket& bracket, BaseCDXProperty& prop)

diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp
@@ -1867,7 +1867,19 @@ void MoleculeJsonLoader::loadMetaObjects(rapidjson::Value& meta_objects, MetaDat
                         text_origin.x = sobj["position"]["x"].GetFloat();
                         text_origin.y = sobj["position"]["y"].GetFloat();
                         text_origin.z = sobj["position"]["z"].GetFloat();
-                        meta_interface.addMetaObject(new SimpleTextObject(text_origin, content));
+                        Vec2f text_size;
+                        if (sobj.HasMember("pos"))
+                        {
+                            auto pos = sobj["pos"].GetArray();
+                            if (pos.Size())
+                            {
+                                Vec2f lt(pos[0]["x"].GetFloat(), pos[0]["y"].GetFloat());
+                                Vec2f rb(pos[2]["x"].GetFloat(), pos[2]["y"].GetFloat());
+                                text_size.x = rb.x - lt.x;
+                                text_size.y = lt.y - rb.y;
+                            }
+                        }
+                        meta_interface.addMetaObject(new SimpleTextObject(text_origin, text_size, content));
                     }
                 }
             }

diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -664,6 +664,18 @@ void MoleculeJsonSaver::writeFloat(JsonWriter& writer, float f_value)
         writer.Double(f_value);
 }
 
+void indigo::MoleculeJsonSaver::writePos(JsonWriter& writer, const Vec3f& pos)
+{
+    writer.StartObject();
+    writer.Key("x");
+    writeFloat(writer, pos.x);
+    writer.Key("y");
+    writeFloat(writer, pos.y);
+    writer.Key("z");
+    writeFloat(writer, pos.z);
+    writer.EndObject();
+}
+
 void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
 {
     QS_DEF(Array<char>, buf);
@@ -1609,8 +1621,8 @@ void MoleculeJsonSaver::saveMolecule(BaseMolecule& bmol, JsonWriter& writer)
                 }
                 // location
                 writer.Key("position");
-                writer.StartObject();
                 const auto& pos = mol->getAtomXyz(i);
+                writer.StartObject();
                 writer.Key("x");
                 writeFloat(writer, pos.x);
                 writer.Key("y");
@@ -1964,14 +1976,19 @@ void MoleculeJsonSaver::saveMetaData(JsonWriter& writer, MetaDataStorage& meta)
             writer.Key("content");
             writer.String(simple_obj->_content.c_str());
             writer.Key("position");
-            writer.StartObject();
-            writer.Key("x");
-            writeFloat(writer, simple_obj->_pos.x);
-            writer.Key("y");
-            writeFloat(writer, simple_obj->_pos.y);
-            writer.Key("z");
-            writeFloat(writer, simple_obj->_pos.z);
-            writer.EndObject(); // end position
+            writePos(writer, simple_obj->_pos);
+
+            writer.Key("pos");
+            writer.StartArray();
+            Vec2f pos_bbox(simple_obj->_pos.x, simple_obj->_pos.y);
+            writePos(writer, pos_bbox);
+            pos_bbox.y -= simple_obj->_size.y;
+            writePos(writer, pos_bbox);
+            pos_bbox.x += simple_obj->_size.x;
+            writePos(writer, pos_bbox);
+            pos_bbox.y += simple_obj->_size.y;
+            writePos(writer, pos_bbox);
+            writer.EndArray();
             writer.EndObject(); // end data
             writer.EndObject(); // end node
             break;

diff --git a/core/indigo-core/reaction/pathway_reaction.h b/core/indigo-core/reaction/pathway_reaction.h
@@ -106,6 +106,7 @@ namespace indigo
                 reaction->addProductCopy(*_molecules[pidx], 0, 0);
             for (auto ridx : sr.reactantIndexes)
                 reaction->addReactantCopy(*_molecules[ridx], 0, 0);
+            reaction->properties().copy(sr.properties);
             return reaction;
         }
 
@@ -131,7 +132,7 @@ namespace indigo
             return static_cast<int>(_molecules.size());
         }
 
-        const auto& getReaction(int reaction_idx)
+        auto& getReaction(int reaction_idx)
         {
             return _reactions[reaction_idx];
         }

diff --git a/core/indigo-core/reaction/reaction_multistep_detector.h b/core/indigo-core/reaction/reaction_multistep_detector.h
@@ -56,8 +56,8 @@ namespace indigo
 
         void constructPathwayReaction(PathwayReaction& rxn);
         void detectPathwayMetadata(PathwayReaction& rxn);
-        void collectMetadata(PathwayReaction& rxn, const Rect2f& bbox);
-        void collectProperties(PathwayReaction& rxn, const SimpleTextObject& text_obj);
+        void collectMetadata(int reaction_idx, PathwayReaction& rxn, const Rect2f& bbox);
+        void collectProperties(PathwayReaction::SimpleReaction& sr, const SimpleTextObject& text_obj);
 
         typedef std::pair<float, int> FLOAT_INT_PAIR;
         typedef std::vector<FLOAT_INT_PAIR> FLOAT_INT_PAIRS;