From 4991bb09033774b006801965563d9e0b557dc1d0 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Sun, 17 Nov 2024 13:45:29 +0100 Subject: [PATCH 01/24] ket rdf --- core/indigo-core/common/math/algebra.h | 5 ++ .../indigo-core/layout/src/pathway_layout.cpp | 2 +- core/indigo-core/molecule/meta_commons.h | 5 ++ core/indigo-core/molecule/metadata_storage.h | 9 ++-- .../molecule/src/metadata_storage.cpp | 24 ++++++---- .../reaction/reaction_multistep_detector.h | 3 ++ .../src/reaction_multistep_detector.cpp | 48 +++++++++++++++++++ utils/indigo-depict/main.c | 2 +- 8 files changed, 85 insertions(+), 13 deletions(-) diff --git a/core/indigo-core/common/math/algebra.h b/core/indigo-core/common/math/algebra.h index 5a9fa9be6c..9ec0be286b 100644 --- a/core/indigo-core/common/math/algebra.h +++ b/core/indigo-core/common/math/algebra.h @@ -379,6 +379,11 @@ namespace indigo return _leftBottom.x < pt.x && _leftBottom.y < pt.y && _rightTop.x > pt.x && _rightTop.y > pt.y; } + inline bool intersects(const Rect2f& other) const + { + return !(right() < other.left() || left() > other.right() || top() < other.bottom() || bottom() > other.top()); + } + inline bool rayIntersectsRect(const Vec2f& begin, const Vec2f& end) { auto lb = _leftBottom; diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index ceebacc02a..5a4efc4ec5 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -366,7 +366,7 @@ void PathwayLayout::addMetaText(PathwayReaction::ReactionNode& node, const Vec2f 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())); + _reaction.meta().addMetaObject(new SimpleTextObject(text_pos_lr, tob.getJsonString()), true); } std::vector PathwayLayout::splitText(const std::string& text, float max_width, std::function symbol_width) diff --git a/core/indigo-core/molecule/meta_commons.h b/core/indigo-core/molecule/meta_commons.h index 0e8fe94487..f1b6abf999 100644 --- a/core/indigo-core/molecule/meta_commons.h +++ b/core/indigo-core/molecule/meta_commons.h @@ -177,6 +177,11 @@ namespace indigo _pos.y += offset.y; } + const auto& getLines() const + { + return _block; + } + std::string _content; std::list _block; Vec3f _pos; diff --git a/core/indigo-core/molecule/metadata_storage.h b/core/indigo-core/molecule/metadata_storage.h index 0df2cee27a..0f3236d643 100644 --- a/core/indigo-core/molecule/metadata_storage.h +++ b/core/indigo-core/molecule/metadata_storage.h @@ -21,6 +21,7 @@ #include #include "base_cpp/ptr_array.h" +#include "base_cpp/ptr_pool.h" #include "common/math/algebra.h" namespace indigo @@ -49,7 +50,7 @@ namespace indigo { } - int addMetaObject(MetaObject* pobj); + int addMetaObject(MetaObject* pobj, bool explicit_reaction_object = false); void resetMetaData() { @@ -59,11 +60,12 @@ namespace indigo _simple_object_indexes.clear(); _text_object_indexes.clear(); _image_indexes.clear(); + _explicit_reaction_object_indexes.clear(); } void resetReactionData(); - const PtrArray& metaData() const + const PtrPool& metaData() const { return _meta_data; } @@ -75,13 +77,14 @@ namespace indigo int getMetaObjectIndex(uint32_t meta_type, int index) const; protected: - PtrArray _meta_data; // TODO: should be replaced with list of unique_ptr + PtrPool _meta_data; // TODO: should be replaced with list of unique_ptr Array _plus_indexes; Array _arrow_indexes; Array _multi_tail_indexes; Array _simple_object_indexes; Array _text_object_indexes; Array _image_indexes; + Array _explicit_reaction_object_indexes; }; } #endif \ No newline at end of file diff --git a/core/indigo-core/molecule/src/metadata_storage.cpp b/core/indigo-core/molecule/src/metadata_storage.cpp index 340440b63d..10564dde5e 100644 --- a/core/indigo-core/molecule/src/metadata_storage.cpp +++ b/core/indigo-core/molecule/src/metadata_storage.cpp @@ -6,11 +6,14 @@ using namespace indigo; IMPL_ERROR(MetaDataStorage, "metadata storage"); -int MetaDataStorage::addMetaObject(MetaObject* pobj) +bool isReactionObject(uint32_t class_id) { - int index = _meta_data.size(); - _meta_data.expand(index + 1); - _meta_data.set(index, pobj); + return class_id == ReactionArrowObject::CID || class_id == ReactionPlusObject::CID || class_id == ReactionMultitailArrowObject::CID; +} + +int MetaDataStorage::addMetaObject(MetaObject* pobj, bool explicit_reaction_object) +{ + int index = _meta_data.add(pobj); switch (pobj->_class_id) { @@ -35,6 +38,8 @@ int MetaDataStorage::addMetaObject(MetaObject* pobj) default: break; } + if (explicit_reaction_object && !isReactionObject(pobj->_class_id)) + _explicit_reaction_object_indexes.push(index); return index; } @@ -43,6 +48,7 @@ void MetaDataStorage::append(const MetaDataStorage& other) const auto& meta = other.metaData(); for (int i = 0; i < meta.size(); i++) addMetaObject(meta[i]->clone()); + _explicit_reaction_object_indexes.copy(other._explicit_reaction_object_indexes); } void MetaDataStorage::clone(const MetaDataStorage& other) @@ -122,9 +128,11 @@ void MetaDataStorage::resetReactionData() _arrow_indexes.clear(); _multi_tail_indexes.clear(); for (int i = _meta_data.size() - 1; i >= 0; i--) - { - if (_meta_data[i]->_class_id == ReactionArrowObject::CID || _meta_data[i]->_class_id == ReactionPlusObject::CID || - _meta_data[i]->_class_id == ReactionMultitailArrowObject::CID) + if (isReactionObject(_meta_data[i]->_class_id)) _meta_data.remove(i); - } + + for (auto i : _explicit_reaction_object_indexes) + _meta_data.remove(i); + + _explicit_reaction_object_indexes.clear(); } diff --git a/core/indigo-core/reaction/reaction_multistep_detector.h b/core/indigo-core/reaction/reaction_multistep_detector.h index 503d8e3745..d86afc29c1 100644 --- a/core/indigo-core/reaction/reaction_multistep_detector.h +++ b/core/indigo-core/reaction/reaction_multistep_detector.h @@ -55,6 +55,9 @@ namespace indigo void constructSimpleArrowReaction(BaseReaction& rxn); void constructPathwayReaction(PathwayReaction& rxn); + void detectPathwayMetadata(PathwayReaction& rxn); + void collectMetadata(PathwayReaction& rxn, const Rect2f& bbox); + void collectProperties(PathwayReaction& rxn, const SimpleTextObject& text_obj); typedef std::pair FLOAT_INT_PAIR; typedef std::vector FLOAT_INT_PAIRS; diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 0e085c0579..cdd1c3d17d 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -646,6 +646,54 @@ void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) } } } + detectPathwayMetadata(rxn); +} + +void ReactionMultistepDetector::detectPathwayMetadata(PathwayReaction& rxn) +{ + for (int i = 0; i < rxn.meta().getMetaCount(ReactionArrowObject::CID); ++i) + { + auto& arrow = static_cast(rxn.meta().getMetaObject(ReactionArrowObject::CID, i)); + Vec2f box_rt = arrow.getHead(); + box_rt.y += (arrow.getHead() - arrow.getTail()).length() / 2; + Rect2f lookup_box(arrow.getTail(), box_rt); + } + + for (int i = 0; i < rxn.meta().getMetaCount(ReactionMultitailArrowObject::CID); ++i) + { + auto& multi_arrow = static_cast(rxn.meta().getMetaObject(ReactionMultitailArrowObject::CID, i)); + Rect2f lookup_box(multi_arrow.getHead(), multi_arrow.getSpineBegin()); + } +} + +void ReactionMultistepDetector::collectMetadata(PathwayReaction& rxn, const Rect2f& bbox) +{ + for (int i = 0; i < rxn.meta().getMetaCount(SimpleTextObject::CID); ++i) + { + auto& text = static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, i)); + Rect2f text_bbox; + text.getBoundingBox(text_bbox); + if (bbox.intersects(text_bbox)) + collectProperties(rxn, text); + } +} + +void ReactionMultistepDetector::collectProperties(PathwayReaction& rxn, const SimpleTextObject& text_obj) +{ + for (const auto& line : text_obj.getLines()) + { + for (const auto& [key, value] : line.styles) + { + if (value.count(std::make_pair(SimpleTextObject::EBold, true))) + { + rxn.properties().insert(""); + } + + if (value.count(std::make_pair(SimpleTextObject::EItalic, true))) + { + } + } + } } void ReactionMultistepDetector::constructMultipleArrowReaction(BaseReaction& rxn) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index 74f0c58b84..d3586919bd 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -1058,7 +1058,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else if (p.out_ext == OEXT_RXN) From 952f1326e4b5fd5418929837e2277e47b4c96cea Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 10:04:56 +0100 Subject: [PATCH 02/24] ket rdf --- api/c/indigo/src/indigo_reaction.cpp | 1 + core/indigo-core/layout/pathway_layout.h | 6 +- .../indigo-core/layout/src/pathway_layout.cpp | 24 ++++---- core/indigo-core/molecule/meta_commons.h | 7 ++- .../molecule/molecule_cdxml_loader.h | 14 ++++- .../molecule/molecule_json_saver.h | 2 + .../indigo-core/molecule/src/meta_commons.cpp | 3 +- .../molecule/src/molecule_cdxml_loader.cpp | 7 +-- .../molecule/src/molecule_json_loader.cpp | 14 ++++- .../molecule/src/molecule_json_saver.cpp | 35 +++++++++--- core/indigo-core/reaction/pathway_reaction.h | 3 +- .../reaction/reaction_multistep_detector.h | 4 +- .../src/reaction_multistep_detector.cpp | 55 +++++++++++++++---- utils/indigo-depict/main.c | 2 +- 14 files changed, 128 insertions(+), 49 deletions(-) diff --git a/api/c/indigo/src/indigo_reaction.cpp b/api/c/indigo/src/indigo_reaction.cpp index d7707937fe..8c45094e58 100644 --- 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&& reaction) { rxn = reaction ? std::move(reaction) : std::make_unique(); + _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 index ab150c0d44..20f613fa9c 100644 --- 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 _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 index 5a4efc4ec5..734df6d1c4 100644 --- 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 PathwayLayout::splitText(const std::string& text, float max_width, std::function symbol_width) diff --git a/core/indigo-core/molecule/meta_commons.h b/core/indigo-core/molecule/meta_commons.h index f1b6abf999..79b1b20692 100644 --- 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 _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 index 6de550cae4..cf199214fa 100644 --- 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 nodes; std::vector bonds; std::vector brackets; - std::vector> text_objects; + std::vector 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>& text_parsed); + void _parseText(BaseCDXElement& elem, std::vector& 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 index 2d3d16431a..0dfd664d23 100644 --- 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& 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 index 0f1e270182..d09d41adc0 100644 --- 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 index d22d0b5f00..a6ad869d81 100644 --- 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>& text_parsed) +void MoleculeCdxmlLoader::_parseText(BaseCDXElement& elem, std::vector& 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, 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 index fc8685b929..58beb2b4c1 100644 --- 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(_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 index d86afc29c1..4a47c2e917 100644 --- 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_PAIR; typedef std::vector FLOAT_INT_PAIRS; diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index cdd1c3d17d..0b7e5e7257 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -17,6 +17,7 @@ ***************************************************************************/ #include +#include "layout/pathway_layout.h" #include "reaction/pathway_reaction.h" #include "reaction/reaction.h" #include "reaction/reaction_multistep_detector.h" @@ -651,48 +652,78 @@ void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) void ReactionMultistepDetector::detectPathwayMetadata(PathwayReaction& rxn) { + int ridx = 0; for (int i = 0; i < rxn.meta().getMetaCount(ReactionArrowObject::CID); ++i) { auto& arrow = static_cast(rxn.meta().getMetaObject(ReactionArrowObject::CID, i)); Vec2f box_rt = arrow.getHead(); box_rt.y += (arrow.getHead() - arrow.getTail()).length() / 2; Rect2f lookup_box(arrow.getTail(), box_rt); + auto& sr = rxn.getReaction(ridx); + collectMetadata(ridx, rxn, lookup_box); + ridx++; } for (int i = 0; i < rxn.meta().getMetaCount(ReactionMultitailArrowObject::CID); ++i) { auto& multi_arrow = static_cast(rxn.meta().getMetaObject(ReactionMultitailArrowObject::CID, i)); Rect2f lookup_box(multi_arrow.getHead(), multi_arrow.getSpineBegin()); + collectMetadata(ridx, rxn, lookup_box); + ridx++; } } -void ReactionMultistepDetector::collectMetadata(PathwayReaction& rxn, const Rect2f& bbox) +void ReactionMultistepDetector::collectMetadata(int reaction_idx, PathwayReaction& rxn, const Rect2f& bbox) { + auto& sr = rxn.getReaction(reaction_idx); + float min_dist; + int text_idx = -1; for (int i = 0; i < rxn.meta().getMetaCount(SimpleTextObject::CID); ++i) { auto& text = static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, i)); Rect2f text_bbox; text.getBoundingBox(text_bbox); if (bbox.intersects(text_bbox)) - collectProperties(rxn, text); + { + auto dist = Vec2f::dist(bbox.leftBottom(), text_bbox.leftBottom()); + if (text_idx < 0 || dist < min_dist) + { + text_idx = i; + min_dist = dist; + } + } } + if (text_idx >= 0) + collectProperties(sr, static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, text_idx))); } -void ReactionMultistepDetector::collectProperties(PathwayReaction& rxn, const SimpleTextObject& text_obj) +void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReaction& sr, const SimpleTextObject& text_obj) { + std::string name, condition; + bool is_condition = false; for (const auto& line : text_obj.getLines()) { - for (const auto& [key, value] : line.styles) + if (line.text.size()) { - if (value.count(std::make_pair(SimpleTextObject::EBold, true))) - { - rxn.properties().insert(""); - } - - if (value.count(std::make_pair(SimpleTextObject::EItalic, true))) - { - } + if (is_condition) + condition += line.text; + else + name += line.text; } + else + is_condition = true; + } + + if (name.size()) + { + int id = sr.properties.insert(PathwayLayout::REACTION_NAME); + sr.properties.value(id).readString(name.c_str(), true); + } + + if (condition.size()) + { + int id = sr.properties.insert(PathwayLayout::REACTION_CONDITIONS); + sr.properties.value(id).readString(condition.c_str(), true); } } diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index d3586919bd..970a0723cf 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -1058,7 +1058,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + // indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else if (p.out_ext == OEXT_RXN) From dc8220d4cd881e981eb07758574e1553eef4c7f1 Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 10:28:52 +0100 Subject: [PATCH 03/24] ket rdf --- .../integration/ref/formats/cdx_to_ket.py.out | 1032 ++++++++++++++++- .../ref/formats/cdxml_ket_superscript.py.out | 50 +- .../tests/formats/ref/961-text_size.ket | 24 +- .../integration/tests/formats/ref/agents.ket | 24 +- .../tests/formats/ref/pathway11.cdxml | 420 ++++--- .../tests/formats/ref/pathway11.ket | 2 +- .../tests/formats/ref/pathway12.cdxml | 319 +++-- .../tests/formats/ref/pathway12.ket | 2 +- 8 files changed, 1445 insertions(+), 428 deletions(-) diff --git a/api/tests/integration/ref/formats/cdx_to_ket.py.out b/api/tests/integration/ref/formats/cdx_to_ket.py.out index e5f5437986..fe2a8520be 100644 --- a/api/tests/integration/ref/formats/cdx_to_ket.py.out +++ b/api/tests/integration/ref/formats/cdx_to_ket.py.out @@ -15932,7 +15932,29 @@ invalid-ascii.cdx "x": 6.2833333015441898, "y": -0.1458333283662796, "z": 0.0 - } + }, + "pos": [ + { + "x": 6.2833333015441898, + "y": -0.1458333283662796, + "z": 0.0 + }, + { + "x": 6.2833333015441898, + "y": -0.30416667461395266, + "z": 0.0 + }, + { + "x": 6.416666507720947, + "y": -0.30416667461395266, + "z": 0.0 + }, + { + "x": 6.416666507720947, + "y": -0.1458333432674408, + "z": 0.0 + } + ] } }, { @@ -15943,7 +15965,29 @@ invalid-ascii.cdx "x": 6.25, "y": -2.8125, "z": 0.0 - } + }, + "pos": [ + { + "x": 6.25, + "y": -2.8125, + "z": 0.0 + }, + { + "x": 6.25, + "y": -2.9708333015441896, + "z": 0.0 + }, + { + "x": 6.449999809265137, + "y": -2.9708333015441896, + "z": 0.0 + }, + { + "x": 6.449999809265137, + "y": -2.8125, + "z": 0.0 + } + ] } } ] @@ -17765,7 +17809,29 @@ CDXML loader: Not a molecule. Found 1 arrows. "x": 9.713333129882813, "y": -1.4463328123092652, "z": 0.0 - } + }, + "pos": [ + { + "x": 9.713333129882813, + "y": -1.4463328123092652, + "z": 0.0 + }, + { + "x": 9.713333129882813, + "y": -1.4463328123092652, + "z": 0.0 + }, + { + "x": 9.713333129882813, + "y": -1.4463328123092652, + "z": 0.0 + }, + { + "x": 9.713333129882813, + "y": -1.4463328123092652, + "z": 0.0 + } + ] } }, { @@ -18346,7 +18412,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 18.868331909179689, "y": -2.632500171661377, "z": 0.0 - } + }, + "pos": [ + { + "x": 18.868331909179689, + "y": -2.632500171661377, + "z": 0.0 + }, + { + "x": 18.868331909179689, + "y": -3.024166822433472, + "z": 0.0 + }, + { + "x": 19.888330459594728, + "y": -3.024166822433472, + "z": 0.0 + }, + { + "x": 19.888330459594728, + "y": -2.632500171661377, + "z": 0.0 + } + ] } }, { @@ -18357,7 +18445,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 25.81833267211914, "y": -2.6658334732055666, "z": 0.0 - } + }, + "pos": [ + { + "x": 25.81833267211914, + "y": -2.6658334732055666, + "z": 0.0 + }, + { + "x": 25.81833267211914, + "y": -3.057500123977661, + "z": 0.0 + }, + { + "x": 26.838333129882817, + "y": -3.057500123977661, + "z": 0.0 + }, + { + "x": 26.838333129882817, + "y": -2.6658334732055666, + "z": 0.0 + } + ] } }, { @@ -18368,7 +18478,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 17.70600128173828, "y": -1.88266658782959, "z": 0.0 - } + }, + "pos": [ + { + "x": 17.70600128173828, + "y": -1.88266658782959, + "z": 0.0 + }, + { + "x": 17.70600128173828, + "y": -2.265999794006348, + "z": 0.0 + }, + { + "x": 18.24466896057129, + "y": -2.265999794006348, + "z": 0.0 + }, + { + "x": 18.24466896057129, + "y": -1.8826664686203004, + "z": 0.0 + } + ] } }, { @@ -18379,7 +18511,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 20.12933158874512, "y": -1.3268331289291382, "z": 0.0 - } + }, + "pos": [ + { + "x": 20.12933158874512, + "y": -1.3268331289291382, + "z": 0.0 + }, + { + "x": 20.12933158874512, + "y": -1.718499779701233, + "z": 0.0 + }, + { + "x": 20.314664840698247, + "y": -1.718499779701233, + "z": 0.0 + }, + { + "x": 20.314664840698247, + "y": -1.3268331289291382, + "z": 0.0 + } + ] } }, { @@ -18390,7 +18544,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 3.9159998893737795, "y": -4.514999866485596, "z": 0.0 - } + }, + "pos": [ + { + "x": 3.9159998893737795, + "y": -4.514999866485596, + "z": 0.0 + }, + { + "x": 3.9159998893737795, + "y": -4.986332416534424, + "z": 0.0 + }, + { + "x": 7.2126665115356449, + "y": -4.986332416534424, + "z": 0.0 + }, + { + "x": 7.2126665115356449, + "y": -4.514999866485596, + "z": 0.0 + } + ] } }, { @@ -18401,7 +18577,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 16.34583282470703, "y": -6.464666843414307, "z": 0.0 - } + }, + "pos": [ + { + "x": 16.34583282470703, + "y": -6.464666843414307, + "z": 0.0 + }, + { + "x": 16.34583282470703, + "y": -6.8480000495910648, + "z": 0.0 + }, + { + "x": 17.25550079345703, + "y": -6.8480000495910648, + "z": 0.0 + }, + { + "x": 17.25550079345703, + "y": -6.464666843414307, + "z": 0.0 + } + ] } }, { @@ -18412,7 +18610,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 26.246334075927736, "y": -7.201666355133057, "z": 0.0 - } + }, + "pos": [ + { + "x": 26.246334075927736, + "y": -7.201666355133057, + "z": 0.0 + }, + { + "x": 26.246334075927736, + "y": -7.5849995613098148, + "z": 0.0 + }, + { + "x": 27.155668258666993, + "y": -7.5849995613098148, + "z": 0.0 + }, + { + "x": 27.155668258666993, + "y": -7.201666355133057, + "z": 0.0 + } + ] } }, { @@ -18423,7 +18643,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 4.557000160217285, "y": -2.677499771118164, "z": 0.0 - } + }, + "pos": [ + { + "x": 4.557000160217285, + "y": -2.677499771118164, + "z": 0.0 + }, + { + "x": 4.557000160217285, + "y": -3.069166421890259, + "z": 0.0 + }, + { + "x": 5.577000141143799, + "y": -3.069166421890259, + "z": 0.0 + }, + { + "x": 5.577000141143799, + "y": -2.677499771118164, + "z": 0.0 + } + ] } }, { @@ -18434,7 +18676,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 1.664666771888733, "y": -3.627500057220459, "z": 0.0 - } + }, + "pos": [ + { + "x": 1.664666771888733, + "y": -3.627500057220459, + "z": 0.0 + }, + { + "x": 1.664666771888733, + "y": -4.019166946411133, + "z": 0.0 + }, + { + "x": 1.850000023841858, + "y": -4.019166946411133, + "z": 0.0 + }, + { + "x": 1.850000023841858, + "y": -3.62749981880188, + "z": 0.0 + } + ] } }, { @@ -18445,7 +18709,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 3.1116669178009039, "y": -1.892333507537842, "z": 0.0 - } + }, + "pos": [ + { + "x": 3.1116669178009039, + "y": -1.892333507537842, + "z": 0.0 + }, + { + "x": 3.1116669178009039, + "y": -2.2756667137146, + "z": 0.0 + }, + { + "x": 3.83566689491272, + "y": -2.2756667137146, + "z": 0.0 + }, + { + "x": 3.83566689491272, + "y": -1.8923333883285525, + "z": 0.0 + } + ] } }, { @@ -18456,7 +18742,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 4.813000202178955, "y": -3.5356669425964357, "z": 0.0 - } + }, + "pos": [ + { + "x": 4.813000202178955, + "y": -3.5356669425964357, + "z": 0.0 + }, + { + "x": 4.813000202178955, + "y": -3.919000148773194, + "z": 0.0 + }, + { + "x": 8.672333717346192, + "y": -3.919000148773194, + "z": 0.0 + }, + { + "x": 8.672333717346192, + "y": -3.5356669425964357, + "z": 0.0 + } + ] } }, { @@ -18467,7 +18775,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 5.392666816711426, "y": -1.279833436012268, "z": 0.0 - } + }, + "pos": [ + { + "x": 5.392666816711426, + "y": -1.279833436012268, + "z": 0.0 + }, + { + "x": 5.392666816711426, + "y": -1.6715000867843629, + "z": 0.0 + }, + { + "x": 5.578000068664551, + "y": -1.6715000867843629, + "z": 0.0 + }, + { + "x": 5.578000068664551, + "y": -1.279833436012268, + "z": 0.0 + } + ] } }, { @@ -18478,7 +18808,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 8.27400016784668, "y": -3.7074999809265138, "z": 0.0 - } + }, + "pos": [ + { + "x": 8.27400016784668, + "y": -3.7074999809265138, + "z": 0.0 + }, + { + "x": 8.27400016784668, + "y": -4.099166870117188, + "z": 0.0 + }, + { + "x": 8.459333419799805, + "y": -4.099166870117188, + "z": 0.0 + }, + { + "x": 8.459333419799805, + "y": -3.7075002193450929, + "z": 0.0 + } + ] } }, { @@ -18489,7 +18841,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 11.849666595458985, "y": -2.690833568572998, "z": 0.0 - } + }, + "pos": [ + { + "x": 11.849666595458985, + "y": -2.690833568572998, + "z": 0.0 + }, + { + "x": 11.849666595458985, + "y": -3.0825002193450929, + "z": 0.0 + }, + { + "x": 12.869667053222657, + "y": -3.0825002193450929, + "z": 0.0 + }, + { + "x": 12.869667053222657, + "y": -2.690833568572998, + "z": 0.0 + } + ] } }, { @@ -18500,7 +18874,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 10.71233367919922, "y": -1.4706664085388184, "z": 0.0 - } + }, + "pos": [ + { + "x": 10.71233367919922, + "y": -1.4706664085388184, + "z": 0.0 + }, + { + "x": 10.71233367919922, + "y": -1.8539997339248656, + "z": 0.0 + }, + { + "x": 11.39033317565918, + "y": -1.8539997339248656, + "z": 0.0 + }, + { + "x": 11.39033317565918, + "y": -1.4706664085388184, + "z": 0.0 + } + ] } }, { @@ -18511,7 +18907,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 27.751501083374025, "y": -3.7408337593078619, "z": 0.0 - } + }, + "pos": [ + { + "x": 27.751501083374025, + "y": -3.7408337593078619, + "z": 0.0 + }, + { + "x": 27.751501083374025, + "y": -4.132500648498535, + "z": 0.0 + }, + { + "x": 28.716501235961919, + "y": -4.132500648498535, + "z": 0.0 + }, + { + "x": 28.716501235961919, + "y": -3.740833997726441, + "z": 0.0 + } + ] } }, { @@ -18522,7 +18940,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 17.198833465576173, "y": -3.38266658782959, "z": 0.0 - } + }, + "pos": [ + { + "x": 17.198833465576173, + "y": -3.38266658782959, + "z": 0.0 + }, + { + "x": 17.198833465576173, + "y": -3.766000032424927, + "z": 0.0 + }, + { + "x": 17.923168182373048, + "y": -3.766000032424927, + "z": 0.0 + }, + { + "x": 17.923168182373048, + "y": -3.38266658782959, + "z": 0.0 + } + ] } }, { @@ -18533,7 +18973,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 0.3896666169166565, "y": -0.6631668210029602, "z": 0.0 - } + }, + "pos": [ + { + "x": 0.3896666169166565, + "y": -0.6631668210029602, + "z": 0.0 + }, + { + "x": 0.3896666169166565, + "y": -1.0548335313796998, + "z": 0.0 + }, + { + "x": 1.1689999103546145, + "y": -1.0548335313796998, + "z": 0.0 + }, + { + "x": 1.1689999103546145, + "y": -0.663166880607605, + "z": 0.0 + } + ] } }, { @@ -18544,7 +19006,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 1.4541666507720948, "y": -4.8663330078125, "z": 0.0 - } + }, + "pos": [ + { + "x": 1.4541666507720948, + "y": -4.8663330078125, + "z": 0.0 + }, + { + "x": 1.4541666507720948, + "y": -5.632999420166016, + "z": 0.0 + }, + { + "x": 2.660500049591065, + "y": -5.632999420166016, + "z": 0.0 + }, + { + "x": 2.660500049591065, + "y": -4.8663330078125, + "z": 0.0 + } + ] } }, { @@ -18555,7 +19039,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 7.121333122253418, "y": -4.8663330078125, "z": 0.0 - } + }, + "pos": [ + { + "x": 7.121333122253418, + "y": -4.8663330078125, + "z": 0.0 + }, + { + "x": 7.121333122253418, + "y": -5.249666213989258, + "z": 0.0 + }, + { + "x": 7.845333099365234, + "y": -5.249666213989258, + "z": 0.0 + }, + { + "x": 7.845333099365234, + "y": -4.8663330078125, + "z": 0.0 + } + ] } }, { @@ -18566,7 +19072,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 1.4541666507720948, "y": -5.966666698455811, "z": 0.0 - } + }, + "pos": [ + { + "x": 1.4541666507720948, + "y": -5.966666698455811, + "z": 0.0 + }, + { + "x": 1.4541666507720948, + "y": -6.733333110809326, + "z": 0.0 + }, + { + "x": 2.660500049591065, + "y": -6.733333110809326, + "z": 0.0 + }, + { + "x": 2.660500049591065, + "y": -5.966666698455811, + "z": 0.0 + } + ] } }, { @@ -18577,7 +19105,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 7.121333122253418, "y": -5.966666698455811, "z": 0.0 - } + }, + "pos": [ + { + "x": 7.121333122253418, + "y": -5.966666698455811, + "z": 0.0 + }, + { + "x": 7.121333122253418, + "y": -6.349999904632568, + "z": 0.0 + }, + { + "x": 7.845333099365234, + "y": -6.349999904632568, + "z": 0.0 + }, + { + "x": 7.845333099365234, + "y": -5.966666698455811, + "z": 0.0 + } + ] } }, { @@ -18588,7 +19138,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 13.628166198730469, "y": -4.860666751861572, "z": 0.0 - } + }, + "pos": [ + { + "x": 13.628166198730469, + "y": -4.860666751861572, + "z": 0.0 + }, + { + "x": 13.628166198730469, + "y": -5.24399995803833, + "z": 0.0 + }, + { + "x": 14.352498054504397, + "y": -5.24399995803833, + "z": 0.0 + }, + { + "x": 14.352498054504397, + "y": -4.860666751861572, + "z": 0.0 + } + ] } }, { @@ -18599,7 +19171,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 4.072500228881836, "y": -5.599833488464356, "z": 0.0 - } + }, + "pos": [ + { + "x": 4.072500228881836, + "y": -5.599833488464356, + "z": 0.0 + }, + { + "x": 4.072500228881836, + "y": -6.071500301361084, + "z": 0.0 + }, + { + "x": 7.682167053222656, + "y": -6.071500301361084, + "z": 0.0 + }, + { + "x": 7.682167053222656, + "y": -5.599833488464356, + "z": 0.0 + } + ] } }, { @@ -18610,7 +19204,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 13.628166198730469, "y": -5.941000461578369, "z": 0.0 - } + }, + "pos": [ + { + "x": 13.628166198730469, + "y": -5.941000461578369, + "z": 0.0 + }, + { + "x": 13.628166198730469, + "y": -6.324333667755127, + "z": 0.0 + }, + { + "x": 14.352498054504397, + "y": -6.324333667755127, + "z": 0.0 + }, + { + "x": 14.352498054504397, + "y": -5.941000461578369, + "z": 0.0 + } + ] } }, { @@ -18621,7 +19237,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 15.12166690826416, "y": -7.171666622161865, "z": 0.0 - } + }, + "pos": [ + { + "x": 15.12166690826416, + "y": -7.171666622161865, + "z": 0.0 + }, + { + "x": 15.12166690826416, + "y": -7.554999828338623, + "z": 0.0 + }, + { + "x": 16.04966735839844, + "y": -7.554999828338623, + "z": 0.0 + }, + { + "x": 16.04966735839844, + "y": -7.171666622161865, + "z": 0.0 + } + ] } }, { @@ -18632,7 +19270,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 20.52133560180664, "y": -6.979999542236328, "z": 0.0 - } + }, + "pos": [ + { + "x": 20.52133560180664, + "y": -6.979999542236328, + "z": 0.0 + }, + { + "x": 20.52133560180664, + "y": -7.363333225250244, + "z": 0.0 + }, + { + "x": 21.4306697845459, + "y": -7.363333225250244, + "z": 0.0 + }, + { + "x": 21.4306697845459, + "y": -6.979999542236328, + "z": 0.0 + } + ] } }, { @@ -18643,7 +19303,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 15.214333534240725, "y": -8.036666870117188, "z": 0.0 - } + }, + "pos": [ + { + "x": 15.214333534240725, + "y": -8.036666870117188, + "z": 0.0 + }, + { + "x": 15.214333534240725, + "y": -8.420000076293946, + "z": 0.0 + }, + { + "x": 16.327667236328126, + "y": -8.420000076293946, + "z": 0.0 + }, + { + "x": 16.327667236328126, + "y": -8.036666870117188, + "z": 0.0 + } + ] } }, { @@ -18654,7 +19336,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 20.52133560180664, "y": -7.836667060852051, "z": 0.0 - } + }, + "pos": [ + { + "x": 20.52133560180664, + "y": -7.836667060852051, + "z": 0.0 + }, + { + "x": 20.52133560180664, + "y": -8.220001220703125, + "z": 0.0 + }, + { + "x": 21.4306697845459, + "y": -8.220001220703125, + "z": 0.0 + }, + { + "x": 21.4306697845459, + "y": -7.836667537689209, + "z": 0.0 + } + ] } }, { @@ -18665,7 +19369,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 20.571334838867189, "y": -4.644000053405762, "z": 0.0 - } + }, + "pos": [ + { + "x": 20.571334838867189, + "y": -4.644000053405762, + "z": 0.0 + }, + { + "x": 20.571334838867189, + "y": -5.027333736419678, + "z": 0.0 + }, + { + "x": 21.48066902160645, + "y": -5.027333736419678, + "z": 0.0 + }, + { + "x": 21.48066902160645, + "y": -4.644000053405762, + "z": 0.0 + } + ] } }, { @@ -18676,7 +19402,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 28.60466766357422, "y": -7.7273335456848148, "z": 0.0 - } + }, + "pos": [ + { + "x": 28.60466766357422, + "y": -7.7273335456848148, + "z": 0.0 + }, + { + "x": 28.60466766357422, + "y": -8.110666275024414, + "z": 0.0 + }, + { + "x": 29.51400184631348, + "y": -8.110666275024414, + "z": 0.0 + }, + { + "x": 29.51400184631348, + "y": -7.727333068847656, + "z": 0.0 + } + ] } }, { @@ -18687,7 +19435,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 15.12166690826416, "y": -10.136667251586914, "z": 0.0 - } + }, + "pos": [ + { + "x": 15.12166690826416, + "y": -10.136667251586914, + "z": 0.0 + }, + { + "x": 15.12166690826416, + "y": -10.520000457763672, + "z": 0.0 + }, + { + "x": 16.04966735839844, + "y": -10.520000457763672, + "z": 0.0 + }, + { + "x": 16.04966735839844, + "y": -10.136667251586914, + "z": 0.0 + } + ] } }, { @@ -18698,7 +19468,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 16.75, "y": -9.50999927520752, "z": 0.0 - } + }, + "pos": [ + { + "x": 16.75, + "y": -9.50999927520752, + "z": 0.0 + }, + { + "x": 16.75, + "y": -9.893332481384278, + "z": 0.0 + }, + { + "x": 17.566665649414064, + "y": -9.893332481384278, + "z": 0.0 + }, + { + "x": 17.566665649414064, + "y": -9.50999927520752, + "z": 0.0 + } + ] } }, { @@ -18709,7 +19501,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 24.79716682434082, "y": -8.018333435058594, "z": 0.0 - } + }, + "pos": [ + { + "x": 24.79716682434082, + "y": -8.018333435058594, + "z": 0.0 + }, + { + "x": 24.79716682434082, + "y": -8.401666641235352, + "z": 0.0 + }, + { + "x": 25.72483253479004, + "y": -8.401666641235352, + "z": 0.0 + }, + { + "x": 25.72483253479004, + "y": -8.018333435058594, + "z": 0.0 + } + ] } }, { @@ -18720,7 +19534,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 20.77133560180664, "y": -9.994000434875489, "z": 0.0 - } + }, + "pos": [ + { + "x": 20.77133560180664, + "y": -9.994000434875489, + "z": 0.0 + }, + { + "x": 20.77133560180664, + "y": -10.377333641052246, + "z": 0.0 + }, + { + "x": 21.6806697845459, + "y": -10.377333641052246, + "z": 0.0 + }, + { + "x": 21.6806697845459, + "y": -9.994000434875489, + "z": 0.0 + } + ] } }, { @@ -18731,7 +19567,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 28.75466537475586, "y": -9.477333068847657, "z": 0.0 - } + }, + "pos": [ + { + "x": 28.75466537475586, + "y": -9.477333068847657, + "z": 0.0 + }, + { + "x": 28.75466537475586, + "y": -9.86066722869873, + "z": 0.0 + }, + { + "x": 29.66399955749512, + "y": -9.86066722869873, + "z": 0.0 + }, + { + "x": 29.66399955749512, + "y": -9.477333068847657, + "z": 0.0 + } + ] } }, { @@ -18742,7 +19600,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 25.946334838867189, "y": -9.4516658782959, "z": 0.0 - } + }, + "pos": [ + { + "x": 25.946334838867189, + "y": -9.4516658782959, + "z": 0.0 + }, + { + "x": 25.946334838867189, + "y": -9.834999084472657, + "z": 0.0 + }, + { + "x": 26.85566902160645, + "y": -9.834999084472657, + "z": 0.0 + }, + { + "x": 26.85566902160645, + "y": -9.4516658782959, + "z": 0.0 + } + ] } }, { @@ -18753,7 +19633,29 @@ CDXML loader: Not a molecule. Found 14 arrows. "x": 24.92216682434082, "y": -9.668333053588868, "z": 0.0 - } + }, + "pos": [ + { + "x": 24.92216682434082, + "y": -9.668333053588868, + "z": 0.0 + }, + { + "x": 24.92216682434082, + "y": -10.051666259765624, + "z": 0.0 + }, + { + "x": 25.84983253479004, + "y": -10.051666259765624, + "z": 0.0 + }, + { + "x": 25.84983253479004, + "y": -9.668333053588868, + "z": 0.0 + } + ] } }, { @@ -20345,7 +21247,29 @@ x_sup.cdx "x": 6.925000190734863, "y": -7.525000095367432, "z": 0.0 - } + }, + "pos": [ + { + "x": 6.925000190734863, + "y": -7.525000095367432, + "z": 0.0 + }, + { + "x": 6.925000190734863, + "y": -7.525000095367432, + "z": 0.0 + }, + { + "x": 6.925000190734863, + "y": -7.525000095367432, + "z": 0.0 + }, + { + "x": 6.925000190734863, + "y": -7.525000095367432, + "z": 0.0 + } + ] } } ] @@ -20363,7 +21287,29 @@ x_sup_sub_default_size.cdx "x": 8.300000190734864, "y": -10.050000190734864, "z": 0.0 - } + }, + "pos": [ + { + "x": 8.300000190734864, + "y": -10.050000190734864, + "z": 0.0 + }, + { + "x": 8.300000190734864, + "y": -10.050000190734864, + "z": 0.0 + }, + { + "x": 8.300000190734864, + "y": -10.050000190734864, + "z": 0.0 + }, + { + "x": 8.300000190734864, + "y": -10.050000190734864, + "z": 0.0 + } + ] } } ] diff --git a/api/tests/integration/ref/formats/cdxml_ket_superscript.py.out b/api/tests/integration/ref/formats/cdxml_ket_superscript.py.out index 8021b6b9dd..f5e2e575bc 100644 --- a/api/tests/integration/ref/formats/cdxml_ket_superscript.py.out +++ b/api/tests/integration/ref/formats/cdxml_ket_superscript.py.out @@ -10,7 +10,29 @@ "x": 4.449999809265137, "y": -7.900000095367432, "z": 0.0 - } + }, + "pos": [ + { + "x": 4.449999809265137, + "y": -7.900000095367432, + "z": 0.0 + }, + { + "x": 4.449999809265137, + "y": -7.900000095367432, + "z": 0.0 + }, + { + "x": 4.449999809265137, + "y": -7.900000095367432, + "z": 0.0 + }, + { + "x": 4.449999809265137, + "y": -7.900000095367432, + "z": 0.0 + } + ] } } ] @@ -27,7 +49,29 @@ "x": 8.399999618530274, "y": -9.475000381469727, "z": 0.0 - } + }, + "pos": [ + { + "x": 8.399999618530274, + "y": -9.475000381469727, + "z": 0.0 + }, + { + "x": 8.399999618530274, + "y": -9.475000381469727, + "z": 0.0 + }, + { + "x": 8.399999618530274, + "y": -9.475000381469727, + "z": 0.0 + }, + { + "x": 8.399999618530274, + "y": -9.475000381469727, + "z": 0.0 + } + ] } } ] @@ -141,4 +185,4 @@ } ] } -} \ No newline at end of file +} diff --git a/api/tests/integration/tests/formats/ref/961-text_size.ket b/api/tests/integration/tests/formats/ref/961-text_size.ket index d098373bf4..5ba6ba2fc8 100644 --- a/api/tests/integration/tests/formats/ref/961-text_size.ket +++ b/api/tests/integration/tests/formats/ref/961-text_size.ket @@ -33,7 +33,29 @@ "x": 7.425000190734863, "y": -4.5, "z": 0.0 - } + }, + "pos": [ + { + "x": 7.425000190734863, + "y": -4.5, + "z": 0.0 + }, + { + "x": 7.425000190734863, + "y": -4.5, + "z": 0.0 + }, + { + "x": 7.425000190734863, + "y": -4.5, + "z": 0.0 + }, + { + "x": 7.425000190734863, + "y": -4.5, + "z": 0.0 + } + ] } } ] diff --git a/api/tests/integration/tests/formats/ref/agents.ket b/api/tests/integration/tests/formats/ref/agents.ket index d401ef5687..25de6b4cef 100644 --- a/api/tests/integration/tests/formats/ref/agents.ket +++ b/api/tests/integration/tests/formats/ref/agents.ket @@ -36,7 +36,29 @@ "x": 10.149999618530274, "y": -5.574999809265137, "z": 0.0 - } + }, + "pos": [ + { + "x": 10.149999618530274, + "y": -5.574999809265137, + "z": 0.0 + }, + { + "x": 10.149999618530274, + "y": -5.574999809265137, + "z": 0.0 + }, + { + "x": 10.149999618530274, + "y": -5.574999809265137, + "z": 0.0 + }, + { + "x": 10.149999618530274, + "y": -5.574999809265137, + "z": 0.0 + } + ] } } ] diff --git a/api/tests/integration/tests/formats/ref/pathway11.cdxml b/api/tests/integration/tests/formats/ref/pathway11.cdxml index a1918d7349..285475818a 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway11.cdxml @@ -18,13 +18,13 @@ - - - - - - - + + + + + + + OH @@ -35,30 +35,30 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + OH - - + + @@ -72,35 +72,35 @@ - - - - - - - + + + + + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - + + @@ -119,14 +119,14 @@ - - + + Cl - - - + + + I @@ -134,37 +134,37 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + O - - - - + + + + O - - + + @@ -181,17 +181,17 @@ - - - - - + + + + + N - - - + + + S @@ -202,20 +202,20 @@ - - + + NH 2 - - - - - - - - + + + + + + + + OH @@ -229,28 +229,28 @@ - - - - - + + + + + NH - - - + + + N - - - - - - - - + + + + + + + + O @@ -270,43 +270,43 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + O - - - - + + + + OH - - - + + + Cl - - + + @@ -325,60 +325,60 @@ - - - - - + + + + + N - - - - + + + + OH - - - + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - - - - + + + + + N - - - - - - - - + + + + + + + + O @@ -414,46 +414,46 @@ - - - - - + + + + + NH - - - - + + + + OH - - - + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - + + @@ -474,83 +474,77 @@ - + Removal of benzoxazol-2-yl - + group from amines - - + + LAH.THF.reflux - + Alkylation of amines with - + alkyl halides - - + + KOH. toluene. PTC. catalyst - + or KI. base e.g. K2CO3 - + Published reaction - - + + Stage 1: 14 h, Copper(II) - + chloride, Dimethylformamide, - + Dichloromethane, CK2O3 - + Potassium carbonate | Stage 2 - + 5 h, 80 degree, acid, Dy(3+) - - salt C3Dy1F9O9S3, + + salt C3Dy1F9O9S3,... - - Dichloromethane, Acetonitrile - - + Addition of dihalomethane to - + aldehyde - - - SmI2.THF - - + + Ozonolysis - - + + O3.MeOH.CH2Cl2.PPh3 or Me2S - + low temperature - + Mitsunobu reaction - - + + DEAD.or.DCAD.or.DIAD.PPh3 - - + + diff --git a/api/tests/integration/tests/formats/ref/pathway11.ket b/api/tests/integration/tests/formats/ref/pathway11.ket index 6653e58057..b7d8b75e02 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.ket +++ b/api/tests/integration/tests/formats/ref/pathway11.ket @@ -1 +1 @@ -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"$ref":"mol3"},{"$ref":"mol4"},{"$ref":"mol5"},{"$ref":"mol6"},{"$ref":"mol7"},{"$ref":"mol8"},{"$ref":"mol9"},{"$ref":"mol10"},{"type":"text","data":{"content":"{\"blocks\":[{\"text\":\"Removal of benzoxazol-2-yl\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":26,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"group from amines\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":17,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"LAH.THF.reflux\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":14,\"style\":\"ITALIC\"}],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}","position":{"x":117.7531509399414,"y":-18.884170532226564,"z":0.0}}},{"type":"text","data":{"content":"{\"blocks\":[{\"text\":\"Alkylation of amines with\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":25,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"alkyl halides\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":13,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"KOH. toluene. 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\ No newline at end of file From c965efc312c2ac507b74dd46065aeebfd4cf002e Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 10:44:53 +0100 Subject: [PATCH 04/24] ket rdf --- core/indigo-core/molecule/meta_commons.h | 6 +++--- .../reaction/src/reaction_multistep_detector.cpp | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/core/indigo-core/molecule/meta_commons.h b/core/indigo-core/molecule/meta_commons.h index 79b1b20692..24788fd8f9 100644 --- a/core/indigo-core/molecule/meta_commons.h +++ b/core/indigo-core/molecule/meta_commons.h @@ -178,9 +178,9 @@ namespace indigo } const auto& getLines() const - { - return _block; - } + { + return _block; + } std::string _content; std::list _block; diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 0b7e5e7257..3454c45f31 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -694,7 +694,7 @@ void ReactionMultistepDetector::collectMetadata(int reaction_idx, PathwayReactio } } if (text_idx >= 0) - collectProperties(sr, static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, text_idx))); + collectProperties(sr, static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, text_idx))); } void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReaction& sr, const SimpleTextObject& text_obj) @@ -717,13 +717,13 @@ void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReactio if (name.size()) { int id = sr.properties.insert(PathwayLayout::REACTION_NAME); - sr.properties.value(id).readString(name.c_str(), true); + sr.properties.value(id).readString(name.c_str(), true); } if (condition.size()) { int id = sr.properties.insert(PathwayLayout::REACTION_CONDITIONS); - sr.properties.value(id).readString(condition.c_str(), true); + sr.properties.value(id).readString(condition.c_str(), true); } } From 045b57050204066e0e6b016d2a7a7c213be6d79c Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Nov 2024 11:19:58 +0100 Subject: [PATCH 05/24] node js fix --- api/wasm/indigo-ketcher/test/pathway_layout.ket | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/api/wasm/indigo-ketcher/test/pathway_layout.ket b/api/wasm/indigo-ketcher/test/pathway_layout.ket index d4668bf414..2ec7175258 100644 --- a/api/wasm/indigo-ketcher/test/pathway_layout.ket +++ b/api/wasm/indigo-ketcher/test/pathway_layout.ket @@ -1 +1 @@ -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"type":"multi-tailed-arrow","data":{"head":{"position":{"x":15.157186508178711,"y":-4.793466567993164,"z":0.0}},"spine":{"pos":[{"x":4.757185459136963,"y":-2.631371021270752,"z":0.0},{"x":4.757185459136963,"y":-6.955562114715576,"z":0.0}]},"tails":{"pos":[{"x":3.9571855068206789,"y":-2.631371021270752,"z":0.0},{"x":3.9571855068206789,"y":-6.955562114715576,"z":0.0}]},"zOrder":0}}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[17.646059036254884,-3.5623931884765627,0.0]},{"label":"C","location":[16.35163116455078,-4.502849578857422,0.0]},{"label":"C","location":[16.846059799194337,-6.024539947509766,0.0]},{"label":"C","location":[18.44605827331543,-6.024539947509766,0.0]},{"label":"C","location":[18.940486907958986,-4.502849578857422,0.0]}],"bonds":[{"type":1,"atoms":[0,4]},{"type":1,"atoms":[4,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,1]},{"type":1,"atoms":[1,0]}]},"mol1":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-1.5000001192092896,0.0]},{"label":"C","location":[0.49999964237213137,-2.631371021270752,0.0]},{"label":"C","location":[2.7627415657043459,-2.631371021270752,0.0]},{"label":"C","location":[1.6313706636428834,-3.762742042541504,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,0]}]},"mol2":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-6.262741565704346,0.0]},{"label":"C","location":[0.8313705921173096,-7.648382186889648,0.0]},{"label":"C","location":[2.431370496749878,-7.648382186889648,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":1,"atoms":[2,0]}]}} \ No newline at end of file +{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"type":"multi-tailed-arrow","data":{"head":{"position":{"x":15.157186508178711,"y":-4.8470563888549809,"z":0.0}},"spine":{"pos":[{"x":4.757185459136963,"y":-2.631371021270752,"z":0.0},{"x":4.757185459136963,"y":-7.062741756439209,"z":0.0}]},"tails":{"pos":[{"x":3.9571855068206789,"y":-2.631371021270752,"z":0.0},{"x":3.9571855068206789,"y":-7.062741756439209,"z":0.0}]},"zOrder":0}}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[17.646059036254884,-3.615983009338379,0.0]},{"label":"C","location":[16.35163116455078,-4.556439399719238,0.0]},{"label":"C","location":[16.846059799194337,-6.078129768371582,0.0]},{"label":"C","location":[18.44605827331543,-6.078129768371582,0.0]},{"label":"C","location":[18.940486907958986,-4.556439399719238,0.0]}],"bonds":[{"type":1,"atoms":[0,4]},{"type":1,"atoms":[4,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,1]},{"type":1,"atoms":[1,0]}]},"mol1":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-1.5000001192092896,0.0]},{"label":"C","location":[0.49999964237213137,-2.631371021270752,0.0]},{"label":"C","location":[2.7627415657043459,-2.631371021270752,0.0]},{"label":"C","location":[1.6313706636428834,-3.762742042541504,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,0]}]},"mol2":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-6.3699212074279789,0.0]},{"label":"C","location":[0.8313705921173096,-7.755561828613281,0.0]},{"label":"C","location":[2.431370496749878,-7.755561828613281,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":1,"atoms":[2,0]}]}} \ No newline at end of file From 6047e45652922e06db52eac3fb195a2c48ae48ea Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 11:34:27 +0100 Subject: [PATCH 06/24] ket rdf --- api/tests/integration/tests/formats/ref/issue_1777.b64cdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/api/tests/integration/tests/formats/ref/issue_1777.b64cdx b/api/tests/integration/tests/formats/ref/issue_1777.b64cdx index 338931573a..d1f2aacee6 100644 --- a/api/tests/integration/tests/formats/ref/issue_1777.b64cdx +++ b/api/tests/integration/tests/formats/ref/issue_1777.b64cdx @@ -1 +1 @@ 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\ No newline at end of file From d2ef1b2dfea0e47d157f8d61d2e457928c4849eb Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 20:36:14 +0100 Subject: [PATCH 07/24] ket rdf --- core/indigo-core/molecule/metadata_storage.h | 1 + core/indigo-core/molecule/src/metadata_storage.cpp | 5 +++++ .../indigo-core/reaction/src/reaction_multistep_detector.cpp | 4 ++++ utils/indigo-depict/main.c | 2 +- 4 files changed, 11 insertions(+), 1 deletion(-) diff --git a/core/indigo-core/molecule/metadata_storage.h b/core/indigo-core/molecule/metadata_storage.h index 0f3236d643..6b75f1cb1a 100644 --- a/core/indigo-core/molecule/metadata_storage.h +++ b/core/indigo-core/molecule/metadata_storage.h @@ -75,6 +75,7 @@ namespace indigo const MetaObject& getMetaObject(uint32_t meta_type, int index) const; int getMetaObjectIndex(uint32_t meta_type, int index) const; + void addExplicitReactionObjectIndex(int index); protected: PtrPool _meta_data; // TODO: should be replaced with list of unique_ptr diff --git a/core/indigo-core/molecule/src/metadata_storage.cpp b/core/indigo-core/molecule/src/metadata_storage.cpp index 10564dde5e..f2707c786f 100644 --- a/core/indigo-core/molecule/src/metadata_storage.cpp +++ b/core/indigo-core/molecule/src/metadata_storage.cpp @@ -84,6 +84,11 @@ int MetaDataStorage::getMetaObjectIndex(uint32_t meta_type, int index) const } } +void MetaDataStorage::addExplicitReactionObjectIndex(int index) +{ + _explicit_reaction_object_indexes.push(index); +} + const MetaObject& MetaDataStorage::getMetaObject(uint32_t meta_type, int index) const { return *_meta_data[getMetaObjectIndex(meta_type, index)]; diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 3454c45f31..e3712fceff 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -694,7 +694,11 @@ void ReactionMultistepDetector::collectMetadata(int reaction_idx, PathwayReactio } } if (text_idx >= 0) + { collectProperties(sr, static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, text_idx))); + int meta_id = rxn.meta().getMetaObjectIndex(SimpleTextObject::CID, text_idx); + rxn.meta().addExplicitReactionObjectIndex(reaction_idx); + } } void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReaction& sr, const SimpleTextObject& text_obj) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index 970a0723cf..74f0c58b84 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -1058,7 +1058,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - // indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else if (p.out_ext == OEXT_RXN) From 08c0afb658d964be4d76cc7b5385bba608524f3b Mon Sep 17 00:00:00 2001 From: even1024 Date: Tue, 19 Nov 2024 11:35:24 +0100 Subject: [PATCH 08/24] ket rdf --- core/indigo-core/layout/src/pathway_layout.cpp | 8 ++++++++ .../reaction/src/reaction_multistep_detector.cpp | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index 734df6d1c4..e061d792ca 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -171,6 +171,8 @@ void PathwayLayout::buildLayoutTree() void PathwayLayout::copyTextPropertiesToNode(const PathwayReaction::SimpleReaction& reaction, PathwayReaction::ReactionNode& node) { + node.name_text.clear(); + node.conditions_text.clear(); auto& props = reaction.properties; // split text labels and put them into the reaction node name_text and conditions_text auto text_max_width = _default_arrow_size - _reaction_margin_size * 2; @@ -386,6 +388,12 @@ std::vector PathwayLayout::splitText(const std::string& text, float while (current_pos < text.size() && width + symbol_width(text[current_pos]) <= max_width) { + if (text[current_pos] == '\n') + { + last_break_pos = current_pos; + ++current_pos; + break; + } width += symbol_width(text[current_pos]); if (std::isspace(text[current_pos]) || std::ispunct(text[current_pos])) { diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index e3712fceff..418f483532 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -710,9 +710,17 @@ void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReactio if (line.text.size()) { if (is_condition) + { + if (condition.size()) + condition += "\n"; condition += line.text; + } else + { + if (name.size()) + name += "\n"; name += line.text; + } } else is_condition = true; From 1ab554cf92a8532c15b20a2b15c886a42c5dcb36 Mon Sep 17 00:00:00 2001 From: even1024 Date: Tue, 19 Nov 2024 11:41:09 +0100 Subject: [PATCH 09/24] ket rdf --- core/indigo-core/reaction/src/reaction_multistep_detector.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 418f483532..a6883c2c5b 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -712,7 +712,7 @@ void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReactio if (is_condition) { if (condition.size()) - condition += "\n"; + condition += "\n"; condition += line.text; } else From b0c6564696ac8ac7976dc62cf95d9fa87c77a7df Mon Sep 17 00:00:00 2001 From: even1024 Date: Tue, 19 Nov 2024 13:02:24 +0100 Subject: [PATCH 10/24] ket rdf --- .../tests/formats/ref/pathway11.cdxml | 30 +++++++++++-------- .../tests/formats/ref/pathway11.ket | 2 +- .../tests/formats/ref/pathway12.cdxml | 26 +++++++++------- .../tests/formats/ref/pathway12.ket | 2 +- .../indigo-core/layout/src/pathway_layout.cpp | 4 +-- 5 files changed, 38 insertions(+), 26 deletions(-) diff --git a/api/tests/integration/tests/formats/ref/pathway11.cdxml b/api/tests/integration/tests/formats/ref/pathway11.cdxml index 285475818a..092e49b83a 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway11.cdxml @@ -497,35 +497,41 @@ or KI. base e.g. K2CO3 - + Published reaction - - + + Stage 1: 14 h, Copper(II) - + chloride, Dimethylformamide, - + Dichloromethane, CK2O3 - + Potassium carbonate | Stage 2 - + 5 h, 80 degree, acid, Dy(3+) - - salt C3Dy1F9O9S3,... + + salt C3Dy1F9O9S3, - + + Dichloromethane, Acetonitrile + + Addition of dihalomethane to - + aldehyde - + + + SmI2.THF + Ozonolysis diff --git a/api/tests/integration/tests/formats/ref/pathway11.ket b/api/tests/integration/tests/formats/ref/pathway11.ket index b7d8b75e02..d29b338bdc 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.ket +++ b/api/tests/integration/tests/formats/ref/pathway11.ket @@ -1 +1 @@ -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"$ref":"mol3"},{"$ref":"mol4"},{"$ref":"mol5"},{"$ref":"mol6"},{"$ref":"mol7"},{"$ref":"mol8"},{"$ref":"mol9"},{"$ref":"mol10"},{"type":"text","data":{"content":"{\"blocks\":[{\"text\":\"Removal of benzoxazol-2-yl\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":26,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"group from 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\ No newline at end of file diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index e061d792ca..3541ddb709 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -346,12 +346,12 @@ void PathwayLayout::generateTextBlocks(SimpleTextObjectBuilder& tob, const ObjAr { for (int i = 0; i < props.size(); ++i) { - if (std::ceil(height * 1000) >= std::ceil(_text_line_height * 1000)) + if (std::round(height * 1000) >= std::round(_text_line_height * 1000)) { height -= _text_line_height; SimpleTextLine textLine; textLine.text = props[i].ptr(); - if (std::ceil(height * 1000) < std::ceil(_text_line_height * 1000) && props.size() - i > 1) + if (std::round(height * 1000) < std::round(_text_line_height * 1000) && props.size() - i > 1) textLine.text += "..."; auto& ts = textLine.text_styles.emplace_back(); ts.offset = 0; From bfeedd37b3026a3e507d18568ea420b9bb402ee9 Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 01:10:30 +0100 Subject: [PATCH 11/24] ket rdf --- core/indigo-core/layout/src/pathway_layout.cpp | 10 +++++----- core/indigo-core/molecule/meta_commons.h | 2 ++ core/indigo-core/molecule/src/meta_commons.cpp | 8 +++++++- core/render2d/src/render_item_aux.cpp | 4 +++- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index 3541ddb709..488004f0ce 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -157,7 +157,7 @@ void PathwayLayout::buildLayoutTree() totalHeight -= currentLayoutItem.children.back()->height / 2; totalHeight /= 2.0f; float targetHeight = totalLines * _text_line_height + _reaction_margin_size; - if (totalHeight < targetHeight) + if (totalHeight + totalSpacing / 2 < targetHeight) { for (auto& child : currentLayoutItem.children) { @@ -329,7 +329,7 @@ void PathwayLayout::applyLayout() { insertSorted(metaObjects, std::make_pair(layoutItem->reactionIndex, std::make_unique(ReactionArrowObject::EFilledTriangle, tails.front(), head))); - textPos_bl.x = tails.front().x + (_default_arrow_size - node.text_width) / 2; + textPos_bl.x = tails.front().x + (_default_arrow_size - node.text_width - _reaction_margin_size * 2) / 2; } if (node.name_text.size() || node.conditions_text.size()) @@ -370,9 +370,9 @@ 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(); - 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); + auto text_height = _text_line_height * tob.getLineCounter(); + Vec3f text_pos_tl(text_pos_bl.x, text_pos_bl.y - _text_line_height / 2.0f + text_height + _reaction_margin_size, 0.0f); + _reaction.meta().addMetaObject(new SimpleTextObject(text_pos_tl, Vec2f(node.text_width, text_height), tob.getJsonString()), true); } std::vector PathwayLayout::splitText(const std::string& text, float max_width, std::function symbol_width) diff --git a/core/indigo-core/molecule/meta_commons.h b/core/indigo-core/molecule/meta_commons.h index 24788fd8f9..8e72c9eb5c 100644 --- a/core/indigo-core/molecule/meta_commons.h +++ b/core/indigo-core/molecule/meta_commons.h @@ -195,10 +195,12 @@ namespace indigo void addLine(const SimpleTextLine& line); void finalize(); std::string getJsonString() const; + int getLineCounter() const; private: rapidjson::Writer _writer; rapidjson::StringBuffer _buffer; + int _line_counter; }; class ReactionArrowObject : public MetaObject diff --git a/core/indigo-core/molecule/src/meta_commons.cpp b/core/indigo-core/molecule/src/meta_commons.cpp index d09d41adc0..ba4aa97501 100644 --- a/core/indigo-core/molecule/src/meta_commons.cpp +++ b/core/indigo-core/molecule/src/meta_commons.cpp @@ -230,12 +230,13 @@ namespace indigo } } - SimpleTextObjectBuilder::SimpleTextObjectBuilder() : _writer(_buffer) + SimpleTextObjectBuilder::SimpleTextObjectBuilder() : _writer(_buffer), _line_counter(0) { } void SimpleTextObjectBuilder::addLine(const SimpleTextLine& line) { + _line_counter++; if (_buffer.GetLength() == 0) { _writer.StartObject(); @@ -287,6 +288,11 @@ namespace indigo result = _buffer.GetString(); return result; } + + int SimpleTextObjectBuilder::getLineCounter() const + { + return _line_counter; + } } #ifdef _MSC_VER diff --git a/core/render2d/src/render_item_aux.cpp b/core/render2d/src/render_item_aux.cpp index eb6b7b7893..a0f4d37f3c 100644 --- a/core/render2d/src/render_item_aux.cpp +++ b/core/render2d/src/render_item_aux.cpp @@ -546,10 +546,12 @@ float RenderItemAuxiliary::_getMaxHeight(const SimpleTextObject::SimpleTextLine& int first_index = -1; int second_index = -1; FONT_STYLE_SET current_styles; - float sz = 0; TextItem ti; ti.size = KDefaultFontSize / KFontScaleFactor; // default size ti.ritype = RenderItem::RIT_TITLE; + ti.text.readString("!", true); + _rc.setTextItemSize(ti); + float sz = (float)ti.bbsz.y; for (auto& kvp : tl.styles) { if (first_index == -1) From 5c67311f474b689523fa1faf0d07adc72fba531e Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 01:50:24 +0100 Subject: [PATCH 12/24] ket rdf --- .../tests/formats/ref/pathway11.cdxml | 396 +++++++++--------- .../tests/formats/ref/pathway11.ket | 2 +- .../tests/formats/ref/pathway12.cdxml | 312 +++++++------- .../tests/formats/ref/pathway12.ket | 2 +- 4 files changed, 356 insertions(+), 356 deletions(-) diff --git a/api/tests/integration/tests/formats/ref/pathway11.cdxml b/api/tests/integration/tests/formats/ref/pathway11.cdxml index 092e49b83a..77febd5bc4 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway11.cdxml @@ -18,13 +18,13 @@ - - - - - - - + + + + + + + OH @@ -35,30 +35,30 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + OH - - + + @@ -72,35 +72,35 @@ - - - - - - - + + + + + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - + + @@ -119,14 +119,14 @@ - - + + Cl - - - + + + I @@ -134,37 +134,37 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + O - - - - + + + + O - - + + @@ -181,17 +181,17 @@ - - - - - + + + + + N - - - + + + S @@ -229,28 +229,28 @@ - - - - - + + + + + NH - - - + + + N - - - - - - - - + + + + + + + + O @@ -270,43 +270,43 @@ - - + + NH 2 - - - + + + O - - - - - - - + + + + + + + O - - - - + + + + OH - - - + + + Cl - - + + @@ -325,60 +325,60 @@ - - - - - + + + + + N - - - - + + + + OH - - - + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - - - - + + + + + N - - - - - - - - + + + + + + + + O @@ -414,46 +414,46 @@ - - - - - + + + + + NH - - - - + + + + OH - - - + + + O - - - - - - - - + + + + + + + + NH 2 - - + + O - - + + @@ -474,83 +474,83 @@ - + Removal of benzoxazol-2-yl - + group from amines - - + + LAH.THF.reflux - + Alkylation of amines with - + alkyl halides - - + + KOH. toluene. 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\ No newline at end of file From 3ec9b42fe7d93cf3eff789d60401041870dc19de Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 02:57:39 +0100 Subject: [PATCH 13/24] ket rdf --- core/render2d/src/render_item_aux.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/render2d/src/render_item_aux.cpp b/core/render2d/src/render_item_aux.cpp index a0f4d37f3c..d71ccd9ea9 100644 --- a/core/render2d/src/render_item_aux.cpp +++ b/core/render2d/src/render_item_aux.cpp @@ -549,7 +549,7 @@ float RenderItemAuxiliary::_getMaxHeight(const SimpleTextObject::SimpleTextLine& TextItem ti; ti.size = KDefaultFontSize / KFontScaleFactor; // default size ti.ritype = RenderItem::RIT_TITLE; - ti.text.readString("!", true); + // ti.text.readString("!", true); _rc.setTextItemSize(ti); float sz = (float)ti.bbsz.y; for (auto& kvp : tl.styles) From dee66d9051ce7b1bfef77d44fd31415102a3bd6f Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 03:09:59 +0100 Subject: [PATCH 14/24] ket rdf --- core/indigo-core/reaction/src/reaction_multistep_detector.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index a6883c2c5b..e268033c30 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -697,7 +697,7 @@ void ReactionMultistepDetector::collectMetadata(int reaction_idx, PathwayReactio { collectProperties(sr, static_cast(rxn.meta().getMetaObject(SimpleTextObject::CID, text_idx))); int meta_id = rxn.meta().getMetaObjectIndex(SimpleTextObject::CID, text_idx); - rxn.meta().addExplicitReactionObjectIndex(reaction_idx); + rxn.meta().addExplicitReactionObjectIndex(meta_id); } } From 6c8219720249a80781f208db253fe17efa89531e Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 10:08:25 +0100 Subject: [PATCH 15/24] ket rdf --- .../integration/ref/formats/ket_to_rdf.py.out | 1 + .../integration/tests/formats/ket_to_rdf.py | 1 + .../tests/formats/reactions/pathway11.ket | 1064 +---------------- .../tests/formats/reactions/pathway12.ket | 1 + .../tests/formats/ref/pathway11.rdf | 654 ++++++++-- .../tests/formats/ref/pathway3.rdf | 100 +- .../tests/formats/ref/pathway6.rdf | 68 +- .../tests/formats/ref/pathway8.rdf | 676 +++++------ .../tests/formats/ref/pathway9.rdf | 676 +++++------ .../src/reaction_multistep_detector.cpp | 4 +- 10 files changed, 1309 insertions(+), 1936 deletions(-) create mode 100644 api/tests/integration/tests/formats/reactions/pathway12.ket diff --git a/api/tests/integration/ref/formats/ket_to_rdf.py.out b/api/tests/integration/ref/formats/ket_to_rdf.py.out index a173cb969a..fbe2308b97 100644 --- a/api/tests/integration/ref/formats/ket_to_rdf.py.out +++ b/api/tests/integration/ref/formats/ket_to_rdf.py.out @@ -3,6 +3,7 @@ multi.rdf:SUCCEED pathway1.rdf:SUCCEED pathway10.rdf:SUCCEED pathway11.rdf:SUCCEED +pathway12.rdf:SUCCEED pathway2.rdf:SUCCEED pathway3.rdf:SUCCEED pathway4.rdf:SUCCEED diff --git a/api/tests/integration/tests/formats/ket_to_rdf.py b/api/tests/integration/tests/formats/ket_to_rdf.py index e490d71b37..463394b754 100644 --- a/api/tests/integration/tests/formats/ket_to_rdf.py +++ b/api/tests/integration/tests/formats/ket_to_rdf.py @@ -37,6 +37,7 @@ def find_diff(a, b): "pathway9", "pathway10", "pathway11", + "pathway12", ] files.sort() diff --git a/api/tests/integration/tests/formats/reactions/pathway11.ket b/api/tests/integration/tests/formats/reactions/pathway11.ket index b0fd857155..0406838e41 100644 --- a/api/tests/integration/tests/formats/reactions/pathway11.ket +++ b/api/tests/integration/tests/formats/reactions/pathway11.ket @@ -1,1063 +1 @@ -{ - "root": { - "nodes": [ - { - "$ref": "mol0" - }, - { - "$ref": "mol1" - }, - { - "$ref": "mol2" - }, - { - "$ref": "mol3" - }, - { - "$ref": "mol4" - }, - { - "$ref": "mol5" - }, - { - "$ref": 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115.2102 -19.0138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 114.4140 -17.6256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 112.8140 -17.6215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 112.0102 -19.0048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 110.4441 -19.3328 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 4 0 0 0 0 + 11 12 4 0 0 0 0 + 12 13 4 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 13 18 4 0 0 0 0 + 18 19 4 0 0 0 0 + 4 20 1 0 0 0 0 + 20 21 4 0 0 0 0 + 21 22 4 0 0 0 0 + 22 23 4 0 0 0 0 + 23 24 4 0 0 0 0 + 24 25 4 0 0 0 0 + 25 26 4 0 0 0 0 + 26 27 4 0 0 0 0 + 27 28 4 0 0 0 0 + 19 10 4 0 0 0 0 + 28 20 4 0 0 0 0 + 27 22 4 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 19 19 0 0 0 0 0 0 0 0999 V2000 + 128.7991 -19.2955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 130.1841 -20.0965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 130.1828 -21.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 131.5704 -19.2978 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 132.9555 -20.0988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 134.3418 -19.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 134.3430 -17.6999 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 135.7268 -20.1010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 137.1131 -19.3022 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 138.4981 -20.1032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 138.4969 -21.7033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 139.8819 -22.5043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 141.2682 -21.7056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 142.6532 -22.5066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 144.0396 -21.7078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 145.4246 -22.5088 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 144.0408 -20.1077 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 141.2695 -20.1055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 139.8845 -19.3045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 4 0 0 0 0 + 11 12 4 0 0 0 0 + 12 13 4 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 13 18 4 0 0 0 0 + 18 19 4 0 0 0 0 + 19 10 4 0 0 0 0 M END +$DTYPE Name +$DATUM Ozonolysis +$DTYPE Reaction Conditions +$DATUM O3.MeOH.CH2Cl2.PPh3 or Me2S +low temperature +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 $MOL -INDIGO-01000000002D - 5 5 0 0 0 0 0 0 0 0999 V2000 - 6.9277 -12.1136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.4281 -13.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.7373 -12.7074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.4273 -13.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.1180 -12.7074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 5 4 2 0 0 0 0 - 4 2 1 0 0 0 0 + 6 5 0 0 0 0 0 0 0 0999 V2000 + 7.4225 -30.4560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0375 -29.6550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0387 -28.0549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6512 -30.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2661 -29.6528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8799 -30.4518 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 0.5000 -36.1859 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8828 -35.3810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8770 -33.7810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2713 -36.1759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6540 -35.3711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0426 -36.1660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4253 -35.3609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4196 -33.7611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8023 -32.9560 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0310 -32.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6483 -33.7711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 2 3 2 0 0 0 0 - 3 1 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 8 10 4 0 0 0 0 + 10 11 4 0 0 0 0 + 11 5 4 0 0 0 0 M END $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 6.0616 -14.9114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0616 -15.9114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9277 -16.4114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.7937 -15.9114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.7937 -14.9114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9277 -14.4114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 23.7788 -32.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7774 -33.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3912 -34.7063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.1625 -34.7082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.5488 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9339 -34.7104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3199 -33.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7050 -34.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0913 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0928 -32.3139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4789 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4804 -29.9147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8665 -29.1159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0953 -29.1137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7076 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3211 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 + 2 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 4 0 0 0 0 + 9 10 4 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 10 15 4 0 0 0 0 + 15 16 4 0 0 0 0 + 16 7 4 0 0 0 0 M END +$DTYPE Name +$DATUM Removal of benzoxazol-2-yl +group from amines +$DTYPE Reaction Conditions +$DATUM LAH.THF.reflux +$RFMT +$RXN + + -INDIGO- 0100000000 + + 1 1 $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 10.1458 -12.4392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.8761 -12.4388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0126 -11.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.8761 -13.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.1458 -13.4442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0148 -13.9392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 23.7788 -32.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7774 -33.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3912 -34.7063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.1625 -34.7082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.5488 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9339 -34.7104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3199 -33.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7050 -34.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0913 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0928 -32.3139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4789 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4804 -29.9147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8665 -29.1159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0953 -29.1137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7076 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3211 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 2 3 1 0 0 0 0 + 2 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 4 0 0 0 0 + 9 10 4 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 10 15 4 0 0 0 0 + 15 16 4 0 0 0 0 + 16 7 4 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 14 14 0 0 0 0 0 0 0 0999 V2000 + 59.5443 -29.1160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1580 -29.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7730 -29.1138 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1567 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7705 -32.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7692 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3829 -34.7126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9979 -33.9116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6117 -34.7107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 51.2267 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 49.8404 -34.7085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 48.4554 -33.9072 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9992 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3855 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 8 13 4 0 0 0 0 + 13 14 4 0 0 0 0 + 14 5 4 0 0 0 0 M END +$DTYPE Name +$DATUM Mitsunobu reaction +$DTYPE Reaction Conditions +$DATUM DEAD.or.DCAD.or.DIAD.PPh3 $RFMT $RXN @@ -86,50 +307,178 @@ $MOL -INDIGO-01000000002D - 4 4 0 0 0 0 0 0 0 0999 V2000 - 9.0467 -21.2520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.0430 -20.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0348 -21.2391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0323 -20.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6 5 0 0 0 0 0 0 0 0999 V2000 + 56.7716 -6.6652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3854 -5.8661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3841 -4.2662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 54.0005 -6.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6143 -5.8684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 51.2281 -5.0693 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 2 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 1 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 2 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 8 8 0 0 0 0 0 0 0 0999 V2000 + 51.9204 -18.8226 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 53.3067 -18.0235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 54.6917 -18.8248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.0780 -18.0258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.0792 -16.4257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 54.6943 -15.6248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.3080 -16.4235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 51.9230 -15.6225 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 4 0 0 0 0 + 3 4 4 0 0 0 0 + 4 5 4 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 1 0 0 0 0 + 7 2 4 0 0 0 0 M END $MOL -INDIGO-01000000002D - 3 3 0 0 0 0 0 0 0 0999 V2000 - 11.4363 -21.2511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.4375 -21.2511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.9370 -20.3861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13 14 0 0 0 0 0 0 0 0999 V2000 + 73.3694 -10.5494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 74.9694 -10.5481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.7684 -9.1619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.7706 -11.9331 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 77.3709 -11.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.3098 -10.6364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 79.8320 -11.1299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.2169 -10.3289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.6032 -11.1276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.6044 -12.7276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.2195 -13.5285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 79.8333 -12.7298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.3117 -13.2258 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 4 0 0 0 0 + 9 10 4 0 0 0 0 + 10 11 4 0 0 0 0 + 11 12 4 0 0 0 0 + 12 13 4 0 0 0 0 + 13 5 4 0 0 0 0 + 12 7 4 0 0 0 0 M END +$DTYPE Name +$DATUM Addition of dihalomethane to +aldehyde +$DTYPE Reaction Conditions +$DATUM SmI2.THF +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 $MOL -INDIGO-01000000002D - 8 8 0 0 0 0 0 0 0 0999 V2000 - 16.6286 -21.7080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.6288 -20.7055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3340 -20.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3342 -22.4134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.3366 -22.4134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.0420 -21.7080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.0419 -20.7055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.3366 -20.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 1 4 1 0 0 0 0 + 3 2 0 0 0 0 0 0 0 0999 V2000 + 55.3854 -26.2144 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 54.0005 -25.4131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6143 -26.2122 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 14 14 0 0 0 0 0 0 0 0999 V2000 + 59.5443 -29.1160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1580 -29.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7730 -29.1138 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1567 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7705 -32.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7692 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3829 -34.7126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9979 -33.9116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6117 -34.7107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 51.2267 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 49.8404 -34.7085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 48.4554 -33.9072 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9992 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3855 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 6 7 1 0 0 0 0 - 7 8 1 0 0 0 0 - 8 3 1 0 0 0 0 - 3 2 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 8 13 4 0 0 0 0 + 13 14 4 0 0 0 0 + 14 5 4 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 73.1332 -23.6683 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 74.5194 -24.4670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9044 -23.6660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 74.5207 -26.0671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9067 -26.8661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9080 -28.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 77.2943 -29.2649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.6796 -28.4640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 80.0655 -29.2630 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 80.0668 -30.8631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.4531 -31.6618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.8381 -30.8608 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 81.4544 -33.2619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.8407 -34.0609 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 78.6783 -26.8639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 77.2920 -26.0652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 11 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 8 15 4 0 0 0 0 + 15 16 4 0 0 0 0 + 16 5 4 0 0 0 0 M END +$DTYPE Name +$DATUM Published reaction +$DTYPE Reaction Conditions +$DATUM Stage 1: 14 h, Copper(II) +chloride, Dimethylformamide, +Dichloromethane, CK2O3 +Potassium carbonate | Stage 2 +5 h, 80 degree, acid, Dy(3+) +salt C3Dy1F9O9S3, +Dichloromethane, Acetonitrile $RFMT $RXN @@ -140,57 +489,140 @@ $MOL -INDIGO-01000000002D - 5 5 0 0 0 0 0 0 0 0999 V2000 - 8.4733 -24.9313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2823 -25.5191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9733 -26.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.9733 -26.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.6643 -25.5191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 5 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 2 1 0 0 0 0 - 2 1 1 0 0 0 0 + 13 14 0 0 0 0 0 0 0 0999 V2000 + 73.3694 -10.5494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 74.9694 -10.5481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.7684 -9.1619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.7706 -11.9331 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 77.3709 -11.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.3098 -10.6364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 79.8320 -11.1299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.2169 -10.3289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.6032 -11.1276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.6044 -12.7276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.2195 -13.5285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 79.8333 -12.7298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.3117 -13.2258 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 4 0 0 0 0 + 9 10 4 0 0 0 0 + 10 11 4 0 0 0 0 + 11 12 4 0 0 0 0 + 12 13 4 0 0 0 0 + 13 5 4 0 0 0 0 + 12 7 4 0 0 0 0 M END $MOL -INDIGO-01000000002D - 7 7 0 0 0 0 0 0 0 0999 V2000 - 11.6427 -25.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.4266 -24.7908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.3996 -25.0133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.8337 -25.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6482 -26.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4003 -26.8162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.4266 -27.0387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 1 5 1 0 0 0 0 - 5 7 1 0 0 0 0 - 7 6 1 0 0 0 0 - 6 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 2 1 0 0 0 0 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 73.1332 -23.6683 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 74.5194 -24.4670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9044 -23.6660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 74.5207 -26.0671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9067 -26.8661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 75.9080 -28.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 77.2943 -29.2649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 78.6796 -28.4640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 80.0655 -29.2630 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 80.0668 -30.8631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 81.4531 -31.6618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.8381 -30.8608 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 81.4544 -33.2619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 82.8407 -34.0609 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 78.6783 -26.8639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 77.2920 -26.0652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 11 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 8 15 4 0 0 0 0 + 15 16 4 0 0 0 0 + 16 5 4 0 0 0 0 M END $MOL -INDIGO-01000000002D - 8 8 0 0 0 0 0 0 0 0999 V2000 - 17.0791 -26.3582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.0793 -25.3557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7845 -24.6505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7847 -27.0636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7871 -27.0636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4924 -26.3582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4923 -25.3557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7871 -24.6504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 1 4 1 0 0 0 0 + 28 30 0 0 0 0 0 0 0 0999 V2000 + 107.4924 -24.1159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 108.8802 -23.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 110.2636 -24.1236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 108.8847 -21.7197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 107.5013 -20.9159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 106.1135 -21.7120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 106.1090 -23.3121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 104.7301 -20.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 103.3419 -21.7044 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 101.9589 -20.9005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 101.9630 -19.3005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 100.5797 -18.4967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 99.1918 -19.2928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 97.8084 -18.4890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 97.8129 -16.8890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 96.4296 -16.0851 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 99.2008 -16.0928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 99.1877 -20.8928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 100.5707 -21.6967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 110.2729 -20.9236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 111.7324 -21.5789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 112.8063 -20.3927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 114.4060 -20.3968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.2102 -19.0138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 114.4140 -17.6256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 112.8140 -17.6215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 112.0102 -19.0048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 110.4441 -19.3328 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 - 7 8 1 0 0 0 0 - 8 3 1 0 0 0 0 - 3 2 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 4 0 0 0 0 + 11 12 4 0 0 0 0 + 12 13 4 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 13 18 4 0 0 0 0 + 18 19 4 0 0 0 0 + 4 20 1 0 0 0 0 + 20 21 4 0 0 0 0 + 21 22 4 0 0 0 0 + 22 23 4 0 0 0 0 + 23 24 4 0 0 0 0 + 24 25 4 0 0 0 0 + 25 26 4 0 0 0 0 + 26 27 4 0 0 0 0 + 27 28 4 0 0 0 0 + 19 10 4 0 0 0 0 + 28 20 4 0 0 0 0 + 27 22 4 0 0 0 0 M END +$DTYPE Name +$DATUM Alkylation of amines with +alkyl halides +$DTYPE Reaction Conditions +$DATUM KOH. toluene. PTC. catalyst +or KI. base e.g. K2CO3 diff --git a/api/tests/integration/tests/formats/ref/pathway3.rdf b/api/tests/integration/tests/formats/ref/pathway3.rdf index 069bf3bd7f..821bc32d99 100644 --- a/api/tests/integration/tests/formats/ref/pathway3.rdf +++ b/api/tests/integration/tests/formats/ref/pathway3.rdf @@ -3,6 +3,56 @@ $DATM 01/00/00 00:00 $RDFILE 1 $DATM 01/00/00 00:00 $RFMT +$RXN + + -INDIGO- 0100000000 + + 1 1 +$MOL + + -INDIGO-01000000002D + + 7 7 0 0 0 0 0 0 0 0999 V2000 + 5.2303 3.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2303 2.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0963 2.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9624 2.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9624 3.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0963 4.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8284 4.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6 1 1 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 9 9 0 0 0 0 0 0 0 0999 V2000 + 12.1944 3.9886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.9247 3.9891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.0612 4.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.9247 2.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.1944 2.9837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.0634 2.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.3284 2.4837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3563 1.7816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.6318 2.2811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 5 7 1 0 0 0 0 + 6 8 2 0 0 0 0 + 4 9 1 0 0 0 0 +M END +$RFMT $RXN -INDIGO- 0100000000 @@ -62,53 +112,3 @@ $MOL 5 6 1 0 0 0 0 5 7 1 0 0 0 0 M END -$RFMT -$RXN - - -INDIGO- 0100000000 - - 1 1 -$MOL - - -INDIGO-01000000002D - - 7 7 0 0 0 0 0 0 0 0999 V2000 - 5.2303 3.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.2303 2.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0963 2.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9624 2.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9624 3.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0963 4.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.8284 4.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 9 9 0 0 0 0 0 0 0 0999 V2000 - 12.1944 3.9886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.9247 3.9891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0612 4.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.9247 2.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.1944 2.9837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0634 2.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.3284 2.4837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.3563 1.7816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.6318 2.2811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 - 2 3 1 0 0 0 0 - 5 7 1 0 0 0 0 - 6 8 2 0 0 0 0 - 4 9 1 0 0 0 0 -M END diff --git a/api/tests/integration/tests/formats/ref/pathway6.rdf b/api/tests/integration/tests/formats/ref/pathway6.rdf index 7b7e755f8d..21c3292a7c 100644 --- a/api/tests/integration/tests/formats/ref/pathway6.rdf +++ b/api/tests/integration/tests/formats/ref/pathway6.rdf @@ -12,6 +12,40 @@ $MOL -INDIGO-01000000002D + 3 3 0 0 0 0 0 0 0 0999 V2000 + 0.7291 16.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 16.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2297 17.0581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 1 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 7.5782 17.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3872 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7692 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 5 4 1 0 0 0 0 + 4 3 1 0 0 0 0 + 3 2 1 0 0 0 0 + 2 1 1 0 0 0 0 +M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 1 1 +$MOL + + -INDIGO-01000000002D + 5 5 0 0 0 0 0 0 0 0999 V2000 7.5782 17.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3872 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -138,40 +172,6 @@ $MOL 12 3 1 0 0 0 0 M END $RFMT -$RXN - - -INDIGO- 0100000000 - - 1 1 -$MOL - - -INDIGO-01000000002D - - 3 3 0 0 0 0 0 0 0 0999 V2000 - 0.7291 16.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 16.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.2297 17.0581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 5 5 0 0 0 0 0 0 0 0999 V2000 - 7.5782 17.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3872 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.7692 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 5 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 2 1 0 0 0 0 - 2 1 1 0 0 0 0 -M END -$RFMT $RXN -INDIGO- 0100000000 diff --git a/api/tests/integration/tests/formats/ref/pathway8.rdf b/api/tests/integration/tests/formats/ref/pathway8.rdf index ba2e493c32..27f91ba084 100644 --- a/api/tests/integration/tests/formats/ref/pathway8.rdf +++ b/api/tests/integration/tests/formats/ref/pathway8.rdf @@ -12,6 +12,184 @@ $MOL -INDIGO-01000000002D + 5 5 0 0 0 0 0 0 0 0999 V2000 + 0.8097 4.8948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3101 3.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6194 4.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3094 3.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 4.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 5 4 2 0 0 0 0 + 4 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 1 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 59 73 0 0 0 0 0 0 0 0999 V2000 + 10.3580 1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.4308 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9467 0.7545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.3262 0.0421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.2534 1.5930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.7375 0.8386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.6725 0.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4721 1.8787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1279 1.0510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.3611 1.9943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.5614 0.4547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.9056 1.2823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0240 2.1739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4468 1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9149 2.2738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.0878 0.7308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6651 1.3525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1970 0.6309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9241 3.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1739 3.9860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8150 3.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6419 4.7076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3922 3.7863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7512 4.6077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9010 6.4198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6513 5.4985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.5421 5.5984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1194 6.2201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3690 7.1413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4782 7.0414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.0512 2.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.5013 3.0418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3025 3.4439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.4490 2.1469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.9990 2.0563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.1978 1.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.3504 4.3357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.9004 4.2450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.0991 3.8429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.9526 5.1399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.4027 5.2305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.2038 5.6327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.2517 6.5244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.8017 6.4338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.0005 6.0317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.8539 7.3287 0.0000 C 0 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0 0 0 0 0 0 0 0 0 0 0 + 17.9665 28.5705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.4166 28.6611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.2178 29.0632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3323 28.7234 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6909 29.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7947 29.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.1248 28.6907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7664 27.9390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6626 27.9227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.5934 28.9129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0176 27.5258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.3093 28.3735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1213 27.5414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.8591 28.3986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3 1 2 0 0 0 0 1 5 1 0 0 0 0 5 6 2 0 0 0 0 @@ -478,6 +628,20 @@ $MOL 52 59 1 0 0 0 0 57 47 1 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 4 4 0 0 0 0 0 0 0 0999 V2000 + 24.6782 24.8691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.6745 25.8642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.6663 24.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.6638 25.8642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 3 1 0 0 0 0 + 3 1 1 0 0 0 0 +M END $RFMT $RXN @@ -711,170 +875,6 @@ $MOL 57 47 1 0 0 0 0 M END $RFMT -$RXN - - -INDIGO- 0100000000 - - 1 1 -$MOL - - -INDIGO-01000000002D - - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0017 14.7456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 14.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8684 15.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 13.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0017 13.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8706 13.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 - 2 3 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 60 74 0 0 0 0 0 0 0 0999 V2000 - 10.6003 11.2320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.6656 9.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.2051 10.4719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.5214 9.7873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.4561 11.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.9167 10.5473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8066 10.0636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.6323 11.5370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.2941 10.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.4830 11.6377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.6573 10.1642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.9955 10.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.4171 11.8978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.7820 11.3157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.2676 12.0008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.4459 10.5278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0812 11.1099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5955 10.4248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3143 12.7482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.5007 13.6391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.1646 12.8512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9864 14.3242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.7999 13.4333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.1359 14.2212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.2195 15.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0329 15.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8834 15.1746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5186 15.7567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.7051 16.6476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.8547 16.5446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.1638 12.4943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.8192 13.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.6725 13.1960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4571 12.3450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.8018 11.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.9485 11.6433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.2532 14.6765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.5979 14.0494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7445 13.9748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.9599 14.8257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6152 15.4528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4686 15.5275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.0493 17.0079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.3940 16.3809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.5405 16.3062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.7560 17.1573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4113 17.7843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.2647 17.8590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5489 17.3760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.6862 18.3289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8425 18.1807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.2364 17.6723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.0990 16.7193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.9427 16.8674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.0529 18.7042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.3691 18.0194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.9086 18.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.9738 17.2594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.6576 17.9442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.1180 17.2218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 - 2 3 1 0 0 0 0 - 9 7 2 0 0 0 0 - 7 11 1 0 0 0 0 - 11 12 2 0 0 0 0 - 12 10 1 0 0 0 0 - 10 8 2 0 0 0 0 - 8 9 1 0 0 0 0 - 6 9 1 0 0 0 0 - 15 13 2 0 0 0 0 - 13 17 1 0 0 0 0 - 17 18 2 0 0 0 0 - 18 16 1 0 0 0 0 - 16 14 2 0 0 0 0 - 14 15 1 0 0 0 0 - 14 3 1 0 0 0 0 - 21 19 2 0 0 0 0 - 19 23 1 0 0 0 0 - 23 24 2 0 0 0 0 - 24 22 1 0 0 0 0 - 22 20 2 0 0 0 0 - 20 21 1 0 0 0 0 - 19 13 1 0 0 0 0 - 21 15 1 0 0 0 0 - 27 25 2 0 0 0 0 - 25 29 1 0 0 0 0 - 29 30 2 0 0 0 0 - 30 28 1 0 0 0 0 - 28 26 2 0 0 0 0 - 26 27 1 0 0 0 0 - 22 27 1 0 0 0 0 - 24 26 1 0 0 0 0 - 33 31 2 0 0 0 0 - 31 35 1 0 0 0 0 - 35 36 2 0 0 0 0 - 36 34 1 0 0 0 0 - 34 32 2 0 0 0 0 - 32 33 1 0 0 0 0 - 12 34 1 0 0 0 0 - 39 37 2 0 0 0 0 - 37 41 1 0 0 0 0 - 41 42 2 0 0 0 0 - 42 40 1 0 0 0 0 - 40 38 2 0 0 0 0 - 38 39 1 0 0 0 0 - 45 43 2 0 0 0 0 - 43 47 1 0 0 0 0 - 47 48 2 0 0 0 0 - 48 46 1 0 0 0 0 - 46 44 2 0 0 0 0 - 44 45 1 0 0 0 0 - 39 32 1 0 0 0 0 - 38 33 1 0 0 0 0 - 45 41 1 0 0 0 0 - 44 42 1 0 0 0 0 - 51 49 2 0 0 0 0 - 49 53 1 0 0 0 0 - 53 54 2 0 0 0 0 - 54 52 1 0 0 0 0 - 52 50 2 0 0 0 0 - 50 51 1 0 0 0 0 - 57 55 2 0 0 0 0 - 55 59 1 0 0 0 0 - 59 60 2 0 0 0 0 - 60 58 1 0 0 0 0 - 58 56 2 0 0 0 0 - 56 57 1 0 0 0 0 - 25 49 1 0 0 0 0 - 52 59 1 0 0 0 0 - 56 43 1 0 0 0 0 -M END -$RFMT $RXN -INDIGO- 0100000000 diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index e268033c30..6c0e977917 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -405,7 +405,7 @@ bool ReactionMultistepDetector::mapMultitailReactionComponents() else { auto& csb_min_prod = _component_summ_blocks[idx_cs_min_prod]; - csb_min_prod.reaction_idx = pathway_idx; + csb_min_prod.reaction_idx = pathway_idx + _bmol.meta().getMetaCount(ReactionArrowObject::CID); auto& rc_arrow = _reaction_components[_moleculeCount + _bmol.meta().getMetaCount(ReactionPlusObject::CID) + _bmol.meta().getMetaCount(ReactionArrowObject::CID) + pathway_idx]; rc_arrow.summ_block_idx = ReactionComponent::CONNECTED; // mark arrow as connected @@ -435,7 +435,7 @@ bool ReactionMultistepDetector::mapMultitailReactionComponents() csb_min_reac.arrows_to.push_back(idx_cs_min_prod); _component_summ_blocks[idx_cs_min_prod].arrows_from.push_back(reac.second); } - csb_min_reac.reaction_idx = pathway_idx; + csb_min_reac.reaction_idx = pathway_idx + _bmol.meta().getMetaCount(ReactionArrowObject::CID); } else bad_pathway = true; From 99977e564a93f2edc2d648325aadfa5585e1a54b Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 20:08:09 +0100 Subject: [PATCH 16/24] ket rdf --- .../tests/formats/ref/pathway10.rdf | 96 +++---- .../tests/formats/ref/pathway11.rdf | 268 +++++++++--------- .../tests/formats/ref/pathway12.cdxml | 4 +- .../tests/formats/ref/pathway12.ket | 2 +- .../tests/formats/ref/pathway6.rdf | 68 ++--- .../tests/formats/ref/pathway8.rdf | 60 ++-- .../tests/formats/ref/pathway9.rdf | 60 ++-- .../indigo-core/layout/src/pathway_layout.cpp | 19 +- core/indigo-core/molecule/metadata_storage.h | 3 +- .../molecule/src/metadata_storage.cpp | 14 +- .../src/reaction_multistep_detector.cpp | 41 +-- 11 files changed, 330 insertions(+), 305 deletions(-) diff --git a/api/tests/integration/tests/formats/ref/pathway10.rdf b/api/tests/integration/tests/formats/ref/pathway10.rdf index 024b45d7f9..2f76d9307d 100644 --- a/api/tests/integration/tests/formats/ref/pathway10.rdf +++ b/api/tests/integration/tests/formats/ref/pathway10.rdf @@ -12,54 +12,6 @@ $MOL -INDIGO-01000000002D - 4 4 0 0 0 0 0 0 0 0999 V2000 - 7.8497 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.8509 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3504 2.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.6092 3.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 - 3 4 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 6 6 0 0 0 0 0 0 0 0999 V2000 - 9.8367 11.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8367 10.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.7027 10.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.5687 10.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.5687 11.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.7027 12.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 5 5 0 0 0 0 0 0 0 0999 V2000 - 10.8653 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8616 2.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8534 1.7357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8509 2.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.5687 3.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 1 1 0 0 0 0 - 2 5 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - 5 5 0 0 0 0 0 0 0 0999 V2000 1.7303 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7266 0.9951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -120,6 +72,54 @@ $MOL 4 2 2 0 0 0 0 2 3 1 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 4 4 0 0 0 0 0 0 0 0999 V2000 + 7.8497 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8509 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3504 2.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.6092 3.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 1 1 0 0 0 0 + 3 4 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 9.8367 11.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8367 10.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7027 10.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5687 10.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5687 11.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7027 12.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6 1 1 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 10.8653 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.8616 2.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8534 1.7357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8509 2.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5687 3.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 3 1 0 0 0 0 + 3 1 1 0 0 0 0 + 2 5 1 0 0 0 0 +M END $MOL -INDIGO-01000000002D diff --git a/api/tests/integration/tests/formats/ref/pathway11.rdf b/api/tests/integration/tests/formats/ref/pathway11.rdf index 6226412390..a1c0e7dd05 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.rdf +++ b/api/tests/integration/tests/formats/ref/pathway11.rdf @@ -3,6 +3,89 @@ $DATM 01/00/00 00:00 $RDFILE 1 $DATM 01/00/00 00:00 $RFMT +$RXN + + -INDIGO- 0100000000 + + 1 1 +$MOL + + -INDIGO-01000000002D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 23.7788 -32.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7774 -33.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3912 -34.7063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.1625 -34.7082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.5488 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9339 -34.7104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3199 -33.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7050 -34.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0913 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0928 -32.3139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4789 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4804 -29.9147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8665 -29.1159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0953 -29.1137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7076 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3211 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 4 0 0 0 0 + 9 10 4 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 10 15 4 0 0 0 0 + 15 16 4 0 0 0 0 + 16 7 4 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 14 14 0 0 0 0 0 0 0 0999 V2000 + 59.5443 -29.1160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1580 -29.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7730 -29.1138 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 58.1567 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7705 -32.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 56.7692 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3829 -34.7126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9979 -33.9116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6117 -34.7107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 51.2267 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 49.8404 -34.7085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 48.4554 -33.9072 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9992 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 55.3855 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 4 0 0 0 0 + 6 7 4 0 0 0 0 + 7 8 4 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 8 13 4 0 0 0 0 + 13 14 4 0 0 0 0 + 14 5 4 0 0 0 0 +M END +$DTYPE Name +$DATUM Ozonolysis +$DTYPE Reaction Conditions +$DATUM O3.MeOH.CH2Cl2.PPh3 or Me2S +low temperature +$RFMT $RXN -INDIGO- 0100000000 @@ -117,10 +200,10 @@ $MOL 19 10 4 0 0 0 0 M END $DTYPE Name -$DATUM Ozonolysis +$DATUM Removal of benzoxazol-2-yl +group from amines $DTYPE Reaction Conditions -$DATUM O3.MeOH.CH2Cl2.PPh3 or Me2S -low temperature +$DATUM LAH.THF.reflux $RFMT $RXN @@ -211,53 +294,25 @@ $MOL 16 7 4 0 0 0 0 M END $DTYPE Name -$DATUM Removal of benzoxazol-2-yl -group from amines +$DATUM Mitsunobu reaction $DTYPE Reaction Conditions -$DATUM LAH.THF.reflux +$DATUM DEAD.or.DCAD.or.DIAD.PPh3 $RFMT $RXN -INDIGO- 0100000000 - 1 1 + 2 1 $MOL -INDIGO-01000000002D - 16 16 0 0 0 0 0 0 0 0999 V2000 - 23.7788 -32.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 23.7774 -33.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 22.3912 -34.7063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 25.1625 -34.7082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 26.5488 -33.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 27.9339 -34.7104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 29.3199 -33.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 30.7050 -34.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 32.0913 -33.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 32.0928 -32.3139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 33.4789 -31.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 33.4804 -29.9147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 34.8665 -29.1159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 32.0953 -29.1137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 30.7076 -31.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 29.3211 -32.3116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 2 0 0 0 0 0 0 0 0999 V2000 + 55.3854 -26.2144 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 54.0005 -25.4131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.6143 -26.2122 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 - 2 4 2 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 6 7 1 0 0 0 0 - 7 8 4 0 0 0 0 - 8 9 4 0 0 0 0 - 9 10 4 0 0 0 0 - 10 11 1 0 0 0 0 - 11 12 1 0 0 0 0 - 12 13 1 0 0 0 0 - 12 14 2 0 0 0 0 - 10 15 4 0 0 0 0 - 15 16 4 0 0 0 0 - 16 7 4 0 0 0 0 M END $MOL @@ -293,10 +348,49 @@ $MOL 13 14 4 0 0 0 0 14 5 4 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 73.1332 -23.6683 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 74.5194 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a/api/tests/integration/tests/formats/ref/pathway8.rdf b/api/tests/integration/tests/formats/ref/pathway8.rdf index 27f91ba084..9d392b6be9 100644 --- a/api/tests/integration/tests/formats/ref/pathway8.rdf +++ b/api/tests/integration/tests/formats/ref/pathway8.rdf @@ -172,24 +172,6 @@ $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0017 14.7456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 14.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8684 15.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 13.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0017 13.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8706 13.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 - 2 3 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - 60 74 0 0 0 0 0 0 0 0999 V2000 10.6003 11.2320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6656 9.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -326,6 +308,18 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 3 3 0 0 0 0 0 0 0 0999 V2000 + 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 1 1 0 0 0 0 +M END $RFMT $RXN @@ -336,6 +330,24 @@ $MOL -INDIGO-01000000002D + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0017 14.7456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7320 14.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8684 15.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7320 13.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0017 13.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8706 13.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + 60 74 0 0 0 0 0 0 0 0999 V2000 10.6003 11.2320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6656 9.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -472,18 +484,6 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END -$MOL - - -INDIGO-01000000002D - - 3 3 0 0 0 0 0 0 0 0999 V2000 - 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 -M END $RFMT $RXN diff --git a/api/tests/integration/tests/formats/ref/pathway9.rdf b/api/tests/integration/tests/formats/ref/pathway9.rdf index de3f055e85..84206b83f1 100644 --- a/api/tests/integration/tests/formats/ref/pathway9.rdf +++ b/api/tests/integration/tests/formats/ref/pathway9.rdf @@ -172,24 +172,6 @@ $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0017 14.7456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 14.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8684 15.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 13.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0017 13.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8706 13.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3 1 2 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 6 4 1 0 0 0 0 - 4 2 2 0 0 0 0 - 2 3 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - 60 74 0 0 0 0 0 0 0 0999 V2000 10.6003 11.2320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6656 9.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -326,6 +308,18 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 3 3 0 0 0 0 0 0 0 0999 V2000 + 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 1 1 0 0 0 0 +M END $RFMT $RXN @@ -336,6 +330,24 @@ $MOL -INDIGO-01000000002D + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0017 14.7456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7320 14.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8684 15.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7320 13.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0017 13.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8706 13.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + 60 74 0 0 0 0 0 0 0 0999 V2000 10.6003 11.2320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6656 9.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -472,18 +484,6 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END -$MOL - - -INDIGO-01000000002D - - 3 3 0 0 0 0 0 0 0 0999 V2000 - 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 -M END $RFMT $RXN diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index 488004f0ce..c0ab61af42 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -352,7 +352,13 @@ void PathwayLayout::generateTextBlocks(SimpleTextObjectBuilder& tob, const ObjAr SimpleTextLine textLine; textLine.text = props[i].ptr(); if (std::round(height * 1000) < std::round(_text_line_height * 1000) && props.size() - i > 1) - textLine.text += "..."; + { + const std::string ellipsis = "..."; + if (textLine.text.size() >= ellipsis.size()) + textLine.text.replace(textLine.text.size() - ellipsis.size(), ellipsis.size(), ellipsis); + else + textLine.text.append(ellipsis); + } auto& ts = textLine.text_styles.emplace_back(); ts.offset = 0; ts.size = textLine.text.size(); @@ -390,11 +396,11 @@ std::vector PathwayLayout::splitText(const std::string& text, float { if (text[current_pos] == '\n') { - last_break_pos = current_pos; - ++current_pos; break; } + width += symbol_width(text[current_pos]); + if (std::isspace(text[current_pos]) || std::ispunct(text[current_pos])) { last_break_pos = current_pos; @@ -402,6 +408,13 @@ std::vector PathwayLayout::splitText(const std::string& text, float ++current_pos; } + if (text[current_pos] == '\n') + { + result.push_back(text.substr(start, current_pos - start)); + start = current_pos + 1; + continue; + } + if (current_pos == text.size()) { result.push_back(text.substr(start)); diff --git a/core/indigo-core/molecule/metadata_storage.h b/core/indigo-core/molecule/metadata_storage.h index 6b75f1cb1a..09f372cbb0 100644 --- a/core/indigo-core/molecule/metadata_storage.h +++ b/core/indigo-core/molecule/metadata_storage.h @@ -22,6 +22,7 @@ #include "base_cpp/ptr_array.h" #include "base_cpp/ptr_pool.h" +#include "base_cpp/red_black.h" #include "common/math/algebra.h" namespace indigo @@ -85,7 +86,7 @@ namespace indigo Array _simple_object_indexes; Array _text_object_indexes; Array _image_indexes; - Array _explicit_reaction_object_indexes; + RedBlackSet _explicit_reaction_object_indexes; }; } #endif \ No newline at end of file diff --git a/core/indigo-core/molecule/src/metadata_storage.cpp b/core/indigo-core/molecule/src/metadata_storage.cpp index f2707c786f..ca89ee68ae 100644 --- a/core/indigo-core/molecule/src/metadata_storage.cpp +++ b/core/indigo-core/molecule/src/metadata_storage.cpp @@ -39,7 +39,7 @@ int MetaDataStorage::addMetaObject(MetaObject* pobj, bool explicit_reaction_obje break; } if (explicit_reaction_object && !isReactionObject(pobj->_class_id)) - _explicit_reaction_object_indexes.push(index); + _explicit_reaction_object_indexes.find_or_insert(index); return index; } @@ -48,7 +48,11 @@ void MetaDataStorage::append(const MetaDataStorage& other) const auto& meta = other.metaData(); for (int i = 0; i < meta.size(); i++) addMetaObject(meta[i]->clone()); - _explicit_reaction_object_indexes.copy(other._explicit_reaction_object_indexes); + for (auto it = other._explicit_reaction_object_indexes.begin(); it != other._explicit_reaction_object_indexes.end(); + it = other._explicit_reaction_object_indexes.next(it)) + { + _explicit_reaction_object_indexes.insert(other._explicit_reaction_object_indexes.key(it)); + } } void MetaDataStorage::clone(const MetaDataStorage& other) @@ -86,7 +90,7 @@ int MetaDataStorage::getMetaObjectIndex(uint32_t meta_type, int index) const void MetaDataStorage::addExplicitReactionObjectIndex(int index) { - _explicit_reaction_object_indexes.push(index); + _explicit_reaction_object_indexes.find_or_insert(index); } const MetaObject& MetaDataStorage::getMetaObject(uint32_t meta_type, int index) const @@ -136,8 +140,8 @@ void MetaDataStorage::resetReactionData() if (isReactionObject(_meta_data[i]->_class_id)) _meta_data.remove(i); - for (auto i : _explicit_reaction_object_indexes) - _meta_data.remove(i); + for (auto it = _explicit_reaction_object_indexes.begin(); it != _explicit_reaction_object_indexes.end(); it = _explicit_reaction_object_indexes.next(it) ) + _meta_data.remove(_explicit_reaction_object_indexes.key(it)); _explicit_reaction_object_indexes.clear(); } diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 6c0e977917..8b28bde896 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -435,7 +435,7 @@ bool ReactionMultistepDetector::mapMultitailReactionComponents() csb_min_reac.arrows_to.push_back(idx_cs_min_prod); _component_summ_blocks[idx_cs_min_prod].arrows_from.push_back(reac.second); } - csb_min_reac.reaction_idx = pathway_idx + _bmol.meta().getMetaCount(ReactionArrowObject::CID); + // csb_min_reac.reaction_idx = pathway_idx + _bmol.meta().getMetaCount(ReactionArrowObject::CID); } else bad_pathway = true; @@ -570,6 +570,7 @@ void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) csb_reactions.emplace_back().second.push_back(i); // add csb as product auto [sri, sr] = rxn.addReaction(); + sr.arrowMetaIndex = csb.reaction_idx; // add products for (auto rc_idx : csb.indexes) { @@ -652,24 +653,30 @@ void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) void ReactionMultistepDetector::detectPathwayMetadata(PathwayReaction& rxn) { - int ridx = 0; - for (int i = 0; i < rxn.meta().getMetaCount(ReactionArrowObject::CID); ++i) - { - auto& arrow = static_cast(rxn.meta().getMetaObject(ReactionArrowObject::CID, i)); - Vec2f box_rt = arrow.getHead(); - box_rt.y += (arrow.getHead() - arrow.getTail()).length() / 2; - Rect2f lookup_box(arrow.getTail(), box_rt); - auto& sr = rxn.getReaction(ridx); - collectMetadata(ridx, rxn, lookup_box); - ridx++; - } + auto arrow_count = rxn.meta().getMetaCount(ReactionArrowObject::CID); + auto multi_count = rxn.meta().getMetaCount(ReactionMultitailArrowObject::CID); - for (int i = 0; i < rxn.meta().getMetaCount(ReactionMultitailArrowObject::CID); ++i) + for (int i = 0; i < rxn.getReactionCount(); ++i) { - auto& multi_arrow = static_cast(rxn.meta().getMetaObject(ReactionMultitailArrowObject::CID, i)); - Rect2f lookup_box(multi_arrow.getHead(), multi_arrow.getSpineBegin()); - collectMetadata(ridx, rxn, lookup_box); - ridx++; + auto& sr = rxn.getReaction(i); + if (sr.arrowMetaIndex >= 0) + { + if (arrow_count && sr.arrowMetaIndex < arrow_count) + { + auto& arrow = static_cast(rxn.meta().getMetaObject(ReactionArrowObject::CID, sr.arrowMetaIndex)); + Vec2f box_rt = arrow.getHead(); + box_rt.y += (arrow.getHead() - arrow.getTail()).length() / 2; + Rect2f lookup_box(arrow.getTail(), box_rt); + collectMetadata(i, rxn, lookup_box); + } + else + { + auto& multi_arrow = static_cast( + rxn.meta().getMetaObject(ReactionMultitailArrowObject::CID, sr.arrowMetaIndex - arrow_count)); + Rect2f lookup_box(multi_arrow.getHead(), multi_arrow.getSpineBegin()); + collectMetadata(i, rxn, lookup_box); + } + } } } From d8ac22ff9abb305c4d348aa91c6236a5967d1e24 Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 20:39:02 +0100 Subject: [PATCH 17/24] ket rdf --- core/indigo-core/molecule/src/metadata_storage.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/indigo-core/molecule/src/metadata_storage.cpp b/core/indigo-core/molecule/src/metadata_storage.cpp index ca89ee68ae..e1d450b701 100644 --- a/core/indigo-core/molecule/src/metadata_storage.cpp +++ b/core/indigo-core/molecule/src/metadata_storage.cpp @@ -49,7 +49,7 @@ void MetaDataStorage::append(const MetaDataStorage& other) for (int i = 0; i < meta.size(); i++) addMetaObject(meta[i]->clone()); for (auto it = other._explicit_reaction_object_indexes.begin(); it != other._explicit_reaction_object_indexes.end(); - it = other._explicit_reaction_object_indexes.next(it)) + it = other._explicit_reaction_object_indexes.next(it)) { _explicit_reaction_object_indexes.insert(other._explicit_reaction_object_indexes.key(it)); } @@ -140,7 +140,7 @@ void MetaDataStorage::resetReactionData() if (isReactionObject(_meta_data[i]->_class_id)) _meta_data.remove(i); - for (auto it = _explicit_reaction_object_indexes.begin(); it != _explicit_reaction_object_indexes.end(); it = _explicit_reaction_object_indexes.next(it) ) + for (auto it = _explicit_reaction_object_indexes.begin(); it != _explicit_reaction_object_indexes.end(); it = _explicit_reaction_object_indexes.next(it)) _meta_data.remove(_explicit_reaction_object_indexes.key(it)); _explicit_reaction_object_indexes.clear(); From ec6039137c8731edabfc4052e85958c0f48080b7 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 20 Nov 2024 20:45:43 +0100 Subject: [PATCH 18/24] node js fix --- api/wasm/indigo-ketcher/test/pathway_layout.ket | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/api/wasm/indigo-ketcher/test/pathway_layout.ket b/api/wasm/indigo-ketcher/test/pathway_layout.ket index 18a3c2b6f8..8348afcc55 100644 --- a/api/wasm/indigo-ketcher/test/pathway_layout.ket +++ b/api/wasm/indigo-ketcher/test/pathway_layout.ket @@ -1,5 +1 @@ -<<<<<<< HEAD -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"type":"multi-tailed-arrow","data":{"head":{"position":{"x":15.157186508178711,"y":-4.8470563888549809,"z":0.0}},"spine":{"pos":[{"x":4.757185459136963,"y":-2.631371021270752,"z":0.0},{"x":4.757185459136963,"y":-7.062741756439209,"z":0.0}]},"tails":{"pos":[{"x":3.9571855068206789,"y":-2.631371021270752,"z":0.0},{"x":3.9571855068206789,"y":-7.062741756439209,"z":0.0}]},"zOrder":0}}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[17.646059036254884,-3.615983009338379,0.0]},{"label":"C","location":[16.35163116455078,-4.556439399719238,0.0]},{"label":"C","location":[16.846059799194337,-6.078129768371582,0.0]},{"label":"C","location":[18.44605827331543,-6.078129768371582,0.0]},{"label":"C","location":[18.940486907958986,-4.556439399719238,0.0]}],"bonds":[{"type":1,"atoms":[0,4]},{"type":1,"atoms":[4,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,1]},{"type":1,"atoms":[1,0]}]},"mol1":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-1.5000001192092896,0.0]},{"label":"C","location":[0.49999964237213137,-2.631371021270752,0.0]},{"label":"C","location":[2.7627415657043459,-2.631371021270752,0.0]},{"label":"C","location":[1.6313706636428834,-3.762742042541504,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,0]}]},"mol2":{"type":"molecule","atoms":[{"label":"C","location":[1.6313705444335938,-6.3699212074279789,0.0]},{"label":"C","location":[0.8313705921173096,-7.755561828613281,0.0]},{"label":"C","location":[2.431370496749878,-7.755561828613281,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":1,"atoms":[2,0]}]}} -======= -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"type":"multi-tailed-arrow","data":{"head":{"position":{"x":10.108657836914063,"y":-4.027166366577148,"z":0.0}},"spine":{"pos":[{"x":3.6086575984954836,"y":-2.207106590270996,"z":0.0},{"x":3.6086575984954836,"y":-5.847226142883301,"z":0.0}]},"tails":{"pos":[{"x":3.1086575984954836,"y":-2.207106590270996,"z":0.0},{"x":3.1086575984954836,"y":-5.847226142883301,"z":0.0}]},"zOrder":0}}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[12.112119674682618,-3.2577455043792726,0.0]},{"label":"C","location":[11.303102493286133,-3.8455305099487306,0.0]},{"label":"C","location":[11.612119674682618,-4.796586990356445,0.0]},{"label":"C","location":[12.612119674682618,-4.796586990356445,0.0]},{"label":"C","location":[12.921136856079102,-3.8455307483673097,0.0]}],"bonds":[{"type":1,"atoms":[0,4]},{"type":1,"atoms":[4,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,1]},{"type":1,"atoms":[1,0]}]},"mol1":{"type":"molecule","atoms":[{"label":"C","location":[1.207106590270996,-1.499999761581421,0.0]},{"label":"C","location":[0.4999998211860657,-2.207106590270996,0.0]},{"label":"C","location":[1.9142134189605713,-2.207106590270996,0.0]},{"label":"C","location":[1.2071067094802857,-2.914213180541992,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,3]},{"type":1,"atoms":[3,2]},{"type":1,"atoms":[2,0]}]},"mol2":{"type":"molecule","atoms":[{"label":"C","location":[1.207106590270996,-5.414213180541992,0.0]},{"label":"C","location":[0.7071065902709961,-6.280238628387451,0.0]},{"label":"C","location":[1.707106590270996,-6.280238628387451,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":1,"atoms":[2,0]}]}} ->>>>>>> 532604726e4fc935a931308d71717316082843b9 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\ No newline at end of file From bd1332bb67d8cbe1602d7cd00ba52ef5d62b2a00 Mon Sep 17 00:00:00 2001 From: even1024 Date: Wed, 20 Nov 2024 21:19:04 +0100 Subject: [PATCH 19/24] ket rdf --- .../tests/formats/ref/pathway12.rdf | 462 ++++++++++++++++++ 1 file changed, 462 insertions(+) create mode 100644 api/tests/integration/tests/formats/ref/pathway12.rdf diff --git a/api/tests/integration/tests/formats/ref/pathway12.rdf b/api/tests/integration/tests/formats/ref/pathway12.rdf new file mode 100644 index 0000000000..d375b8b979 --- /dev/null +++ b/api/tests/integration/tests/formats/ref/pathway12.rdf @@ -0,0 +1,462 @@ +$RDFILE 1 +$DATM 01/00/00 00:00 +$RDFILE 1 +$DATM 01/00/00 00:00 +$RFMT +$RXN + + -INDIGO- 0100000000 + + 1 1 +$MOL + + -INDIGO-01000000002D + + 2 1 0 0 0 0 0 0 0 0999 V2000 + 0.6072 -23.2264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9928 -22.4264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 17.0745 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From bb2a8e70926ed022ae891f521839181184628d3a Mon Sep 17 00:00:00 2001 From: even1024 Date: Fri, 22 Nov 2024 04:53:23 +0100 Subject: [PATCH 20/24] ket rdf --- .../integration/ref/formats/ket_to_rdf.py.out | 1 + .../integration/tests/formats/ket_to_rdf.py | 1 + .../reactions/2404-metadata_detect.ket | 2791 +++++++++++++++++ .../formats/ref/2404-metadata_detect.ket | 2791 +++++++++++++++++ .../tests/formats/ref/2558-missed.cdxml | 270 +- ...e_arrow_retro_arrow_sum_of_products.b64cdx | 2 +- ...le_arrow_retro_arrow_sum_of_products.cdxml | 66 +- ...mple_arrow_retro_arrow_sum_of_products.cml | 26 +- ...e_arrow_retro_arrow_sum_of_products.smarts | 2 +- ...mple_arrow_retro_arrow_sum_of_products.smi | 2 +- ...arrow_retro_arrow_sum_of_products_2000.rxn | 26 +- ...arrow_retro_arrow_sum_of_products_3000.rxn | 28 +- .../formats/ref/ket_two_retro_arrows.b64cdx | 2 +- .../formats/ref/ket_two_retro_arrows.cdxml | 54 +- .../tests/formats/ref/multi_overlap.cdxml | 74 +- .../tests/formats/ref/pathway12.cdxml | 4 +- .../tests/formats/ref/pathway12.ket | 2 +- .../tests/formats/ref/pathway12.rdf | 8 + .../formats/ref/retro_arrow_diagonal.cdxml | 38 +- core/indigo-core/layout/pathway_layout.h | 1 + .../indigo-core/layout/src/pathway_layout.cpp | 10 +- .../reaction/pathway_reaction_builder.h | 1 - .../reaction/reaction_multistep_detector.h | 1 - .../reaction/src/pathway_reaction_builder.cpp | 7 +- .../src/reaction_multistep_detector.cpp | 20 +- 25 files changed, 5906 insertions(+), 322 deletions(-) create mode 100644 api/tests/integration/tests/formats/reactions/2404-metadata_detect.ket create mode 100644 api/tests/integration/tests/formats/ref/2404-metadata_detect.ket diff --git a/api/tests/integration/ref/formats/ket_to_rdf.py.out b/api/tests/integration/ref/formats/ket_to_rdf.py.out index fbe2308b97..9ad5628411 100644 --- a/api/tests/integration/ref/formats/ket_to_rdf.py.out +++ b/api/tests/integration/ref/formats/ket_to_rdf.py.out @@ -1,4 +1,5 @@ *** KET to RDF *** +2404-metadata_detect.rdf:SUCCEED multi.rdf:SUCCEED pathway1.rdf:SUCCEED pathway10.rdf:SUCCEED diff --git a/api/tests/integration/tests/formats/ket_to_rdf.py b/api/tests/integration/tests/formats/ket_to_rdf.py index 463394b754..7c3f8aec7b 100644 --- a/api/tests/integration/tests/formats/ket_to_rdf.py +++ b/api/tests/integration/tests/formats/ket_to_rdf.py @@ -26,6 +26,7 @@ def find_diff(a, b): files = [ "multi", + "2404-metadata_detect", "pathway1", "pathway2", "pathway3", diff --git a/api/tests/integration/tests/formats/reactions/2404-metadata_detect.ket b/api/tests/integration/tests/formats/reactions/2404-metadata_detect.ket new file mode 100644 index 0000000000..32d5e24a8d --- /dev/null +++ b/api/tests/integration/tests/formats/reactions/2404-metadata_detect.ket @@ -0,0 +1,2791 @@ +{ + "root": { + "nodes": [ + { + "$ref": "mol0" + }, + { + "$ref": "mol1" + }, + { + "$ref": "mol2" + }, + { + "$ref": "mol3" + }, + { + "$ref": "mol4" + }, + { + "$ref": "mol5" + }, + { + "$ref": "mol6" + }, + { + "$ref": "mol7" + }, + { + "$ref": "mol8" + }, + { + "$ref": "mol9" + }, + { + "$ref": "mol10" + }, + { + "$ref": "mol11" + }, + { + "$ref": "mol12" + }, + { + "$ref": "mol13" + }, + { + "$ref": "mol14" + }, + { + "type": "arrow", + "data": { + "mode": "filled-triangle", + "pos": [ + { + "x": 13.365317797904297, + "y": -16.91036502334189, + "z": 0 + }, + { + "x": 20.36532142107432, + "y": -16.91036502334189, + "z": 0 + } + ] + } + }, + { + "type": "arrow", + "data": { + "mode": "filled-triangle", + "pos": [ + { + "x": 26.937129102591086, + "y": -16.91036502334189, + "z": 0 + }, + { + "x": 33.93713272576112, + "y": -16.91036502334189, + "z": 0 + } + ] + } + }, + { + "type": "text", + "data": { + "content": "{\"blocks\":[{\"text\":\"C-H functionalization of\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":24,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"heteroarenes by\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":15,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"alkanesulfinate salts\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":21,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"TBHP.90C\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":8,\"style\":\"ITALIC\"}],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}", + "position": { + "x": 46.338289815195054, + "y": -16.206120287027993, + "z": 0 + }, + "pos": [ + { + "x": 46.338289815195054, + "y": -16.206120287027993, + "z": 0 + }, + { + "x": 46.338289815195054, + "y": -17.94259241684977, + "z": 0 + }, + { + "x": 49.99138887525365, + "y": -17.94259241684977, + "z": 0 + }, + { + "x": 49.99138887525365, + "y": -16.206120287027993, + "z": 0 + } + ] + } + }, + { + "type": "text", + "data": { + "content": "{\"blocks\":[{\"text\":\"Synthesis of sulfinyl acids\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":27,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"from alkyl or aryl halides\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":26,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"1. 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\ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cdxml b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cdxml index a795d4ecc4..a72a9a8af9 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cdxml +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cdxml @@ -18,42 +18,42 @@ - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + NH 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + @@ -75,8 +75,8 @@ - - + + diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cml b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cml index a72e11c694..e3758cd197 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cml +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.cml @@ -2,19 +2,6 @@ - - - - - - - - - - - - - @@ -51,6 +38,19 @@ + + + + + + + + + + + + + diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smarts b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smarts index ef43a39c45..3168821c16 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smarts +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smarts @@ -1 +1 @@ -[#6]-[#6](-[#7])-[#6].[#6]1-[#6]-[#6]-[#6]-[#6]-1.[#6]1-[#6]=[#6]-[#6]=[#6]-1>>[#8]-[#6]-[#8] \ No newline at end of file +[#6]1-[#6]-[#6]-[#6]-[#6]-1.[#6]1-[#6]=[#6]-[#6]=[#6]-1.[#6]-[#6](-[#7])-[#6]>>[#8]-[#6]-[#8] \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smi b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smi index 1ad2aa86f0..aab9da2128 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smi +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.smi @@ -1 +1 @@ -CC(N)C.C1CCCC1.C1C=CC=C1>>OCO \ No newline at end of file +C1CCCC1.C1C=CC=C1.CC(N)C>>OCO \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_2000.rxn b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_2000.rxn index 564592aaf7..2a4d964e8a 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_2000.rxn +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_2000.rxn @@ -7,19 +7,6 @@ $MOL -INDIGO-01000000002D - 4 3 0 0 0 0 0 0 0 0999 V2000 - 10.1817 -8.8140 0.0000 C 0 0 0 0 0 0 0 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b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_3000.rxn index 2514843869..c8eae2944a 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_3000.rxn +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products_3000.rxn @@ -5,20 +5,6 @@ $RXN V3000 M V30 COUNTS 3 1 M V30 BEGIN REACTANT M V30 BEGIN CTAB -M V30 COUNTS 4 3 0 0 0 -M V30 BEGIN ATOM -M V30 1 C 10.1817 -8.81398 0.0 0 -M V30 2 C 10.1817 -7.81398 0.0 0 -M V30 3 C 9.3157 -7.31398 0.0 0 -M V30 4 N 11.0478 -7.31398 0.0 0 -M V30 END ATOM -M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 1 2 3 -M V30 3 1 2 4 -M V30 END BOND -M V30 END CTAB -M V30 BEGIN CTAB M V30 COUNTS 5 5 0 0 0 M V30 BEGIN ATOM M V30 1 C 22.8103 -7.14454 0.0 0 @@ -52,6 +38,20 @@ M V30 4 2 2 3 M V30 5 1 3 1 M V30 END BOND M V30 END CTAB +M V30 BEGIN CTAB +M V30 COUNTS 4 3 0 0 0 +M V30 BEGIN ATOM +M V30 1 C 10.1817 -8.81398 0.0 0 +M V30 2 C 10.1817 -7.81398 0.0 0 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\ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/pathway12.rdf b/api/tests/integration/tests/formats/ref/pathway12.rdf index d375b8b979..c4d1a2765e 100644 --- a/api/tests/integration/tests/formats/ref/pathway12.rdf +++ b/api/tests/integration/tests/formats/ref/pathway12.rdf @@ -97,6 +97,8 @@ $DATUM 123456789012345678901234567890 123456789012345678901234567890 123456789012345678901234567890 123456789012345678901234567890... +$DTYPE Reaction Conditions +$DATUM Not available $RFMT $RXN @@ -150,6 +152,8 @@ ABCDEFGHIJKLMNOPQRSTUVWXYZABCD ABCDEFGHIJKLMNOPQRSTUVWXYZABCD ABCDEFGHIJKLMNOPQRSTUVWXYZABCD ABCDEFGHIJKLMNOPQRSTUVWXYZABCD +$DTYPE Reaction Conditions +$DATUM Not available $RFMT $RXN @@ -336,6 +340,8 @@ M END $DTYPE Name $DATUM 123456789012345678901234567890 12 +$DTYPE Reaction Conditions +$DATUM Not available $RFMT $RXN @@ -460,3 +466,5 @@ $DATUM 123456789012345678901234567890 123456789012345678901234567890 123456789012345678901234567890 123456789012345678901234567890... +$DTYPE Reaction Conditions +$DATUM Not available diff --git a/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml b/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml index bd95a29bc2..d6e4d872a0 100644 --- a/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml +++ b/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml @@ -18,24 +18,24 @@ - - - - - - - - - - + + + + + + - - - - - - - + + + + + + + + + + + @@ -58,8 +58,8 @@ - - + + diff --git a/core/indigo-core/layout/pathway_layout.h b/core/indigo-core/layout/pathway_layout.h index 20f613fa9c..9eb993ae82 100644 --- a/core/indigo-core/layout/pathway_layout.h +++ b/core/indigo-core/layout/pathway_layout.h @@ -59,6 +59,7 @@ namespace indigo static constexpr int MIN_LINES_COUNT = 9; static constexpr auto REACTION_CONDITIONS = "Reaction Conditions"; static constexpr auto REACTION_NAME = "Name"; + static constexpr auto REACTION_PROPERTY_NA = "Not available"; PathwayLayout(PathwayReaction& reaction, const LayoutOptions& options) : _reaction(reaction), _depths(MAX_DEPTHS, 0), _maxDepth(0), _bond_length(options.DEFAULT_BOND_LENGTH), diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index c0ab61af42..ac3d88c40e 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -180,9 +180,13 @@ void PathwayLayout::copyTextPropertiesToNode(const PathwayReaction::SimpleReacti auto italicWidthLambda = [text_max_width](char ch) { return text_max_width / MAX_SYMBOLS; }; // TODO: implement italic font width for (auto prop_idx = props.begin(); prop_idx != props.end(); prop_idx = props.next(prop_idx)) { + std::string prop_val = props.value(prop_idx).ptr(); + if (prop_val == REACTION_PROPERTY_NA) + continue; + if (props.key(prop_idx) == std::string(REACTION_NAME)) { - auto splitted_name = splitText(props.value(prop_idx).ptr(), text_max_width, boldWidthLambda); + auto splitted_name = splitText(prop_val, text_max_width, boldWidthLambda); for (auto& line : splitted_name) { node.name_text.push().readString(line.c_str(), true); @@ -192,7 +196,7 @@ void PathwayLayout::copyTextPropertiesToNode(const PathwayReaction::SimpleReacti } else if (props.key(prop_idx) == std::string(REACTION_CONDITIONS)) { - auto splitted_conditions = splitText(props.value(prop_idx).ptr(), text_max_width, italicWidthLambda); + auto splitted_conditions = splitText(prop_val, text_max_width, italicWidthLambda); for (auto& line : splitted_conditions) { node.conditions_text.push().readString(line.c_str(), true); @@ -202,7 +206,7 @@ void PathwayLayout::copyTextPropertiesToNode(const PathwayReaction::SimpleReacti } } - if (node.name_text.size() && node.conditions_text.size()) + if (node.conditions_text.size()) node.name_text.push().readString("", true); } diff --git a/core/indigo-core/reaction/pathway_reaction_builder.h b/core/indigo-core/reaction/pathway_reaction_builder.h index 87bdecf693..0bafa9a894 100644 --- a/core/indigo-core/reaction/pathway_reaction_builder.h +++ b/core/indigo-core/reaction/pathway_reaction_builder.h @@ -71,7 +71,6 @@ namespace indigo std::unordered_map> _reactantToReactions; std::unique_ptr _pathwayReaction; std::unordered_map, int, pair_hash> _moleculeMapping; - static constexpr auto kPropNA = "Not available"; }; } // namespace indigo diff --git a/core/indigo-core/reaction/reaction_multistep_detector.h b/core/indigo-core/reaction/reaction_multistep_detector.h index 4a47c2e917..b93ccc1f5c 100644 --- a/core/indigo-core/reaction/reaction_multistep_detector.h +++ b/core/indigo-core/reaction/reaction_multistep_detector.h @@ -53,7 +53,6 @@ namespace indigo ReactionType detectReaction(); void constructMultipleArrowReaction(BaseReaction& rxn); void constructSimpleArrowReaction(BaseReaction& rxn); - void constructPathwayReaction(PathwayReaction& rxn); void detectPathwayMetadata(PathwayReaction& rxn); void collectMetadata(int reaction_idx, PathwayReaction& rxn, const Rect2f& bbox); diff --git a/core/indigo-core/reaction/src/pathway_reaction_builder.cpp b/core/indigo-core/reaction/src/pathway_reaction_builder.cpp index 7bbc634931..97b96fa3f9 100644 --- a/core/indigo-core/reaction/src/pathway_reaction_builder.cpp +++ b/core/indigo-core/reaction/src/pathway_reaction_builder.cpp @@ -107,11 +107,8 @@ void PathwayReactionBuilder::buildReactions() for (auto& prop : rid.properties) { - if (prop.second.size() && prop.second != kPropNA) - { - auto prop_idx = sr.properties.insert(prop.first.c_str()); - sr.properties.value(prop_idx).readString(prop.second.c_str(), true); - } + auto prop_idx = sr.properties.insert(prop.first.c_str()); + sr.properties.value(prop_idx).readString(prop.second.c_str(), true); } } } diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index 8b28bde896..d38e45ad80 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -340,7 +340,7 @@ bool ReactionMultistepDetector::mapReactionComponents() // idx_cs_min_reac <-> idx_cs_min_prod csb_min_reac.arrows_to.push_back(idx_cs_min_prod); csb_min_prod.arrows_from.push_back(idx_cs_min_reac); - csb_min_reac.reaction_idx = reaction_index; + // csb_min_reac.reaction_idx = reaction_index; csb_min_prod.reaction_idx = reaction_index; } } @@ -733,17 +733,11 @@ void ReactionMultistepDetector::collectProperties(PathwayReaction::SimpleReactio is_condition = true; } - if (name.size()) - { - int id = sr.properties.insert(PathwayLayout::REACTION_NAME); - sr.properties.value(id).readString(name.c_str(), true); - } + int id = sr.properties.insert(PathwayLayout::REACTION_NAME); + sr.properties.value(id).readString(name.empty() ? PathwayLayout::REACTION_PROPERTY_NA : name.c_str(), true); - if (condition.size()) - { - int id = sr.properties.insert(PathwayLayout::REACTION_CONDITIONS); - sr.properties.value(id).readString(condition.c_str(), true); - } + id = sr.properties.insert(PathwayLayout::REACTION_CONDITIONS); + sr.properties.value(id).readString(condition.empty() ? PathwayLayout::REACTION_PROPERTY_NA : condition.c_str(), true); } void ReactionMultistepDetector::constructMultipleArrowReaction(BaseReaction& rxn) @@ -804,7 +798,7 @@ void ReactionMultistepDetector::constructMultipleArrowReaction(BaseReaction& rxn } } -void indigo::ReactionMultistepDetector::constructSimpleArrowReaction(BaseReaction& rxn) +void ReactionMultistepDetector::constructSimpleArrowReaction(BaseReaction& rxn) { for (auto& csb : _component_summ_blocks) { @@ -846,4 +840,4 @@ void indigo::ReactionMultistepDetector::constructSimpleArrowReaction(BaseReactio break; } } -} +} \ No newline at end of file From 8923db4a9a6babf0165a6de4e34b6afafd1ad5d3 Mon Sep 17 00:00:00 2001 From: even1024 Date: Fri, 22 Nov 2024 05:50:12 +0100 Subject: [PATCH 21/24] ket rdf --- .../formats/ref/2404-metadata_detect.ket | 2791 ----------------- .../formats/ref/2404-metadata_detect.rdf | 639 ++++ .../indigo-core/layout/src/pathway_layout.cpp | 2 +- 3 files changed, 640 insertions(+), 2792 deletions(-) delete mode 100644 api/tests/integration/tests/formats/ref/2404-metadata_detect.ket create mode 100644 api/tests/integration/tests/formats/ref/2404-metadata_detect.rdf diff --git a/api/tests/integration/tests/formats/ref/2404-metadata_detect.ket b/api/tests/integration/tests/formats/ref/2404-metadata_detect.ket deleted file mode 100644 index 32d5e24a8d..0000000000 --- a/api/tests/integration/tests/formats/ref/2404-metadata_detect.ket +++ /dev/null @@ -1,2791 +0,0 @@ -{ - "root": { - "nodes": [ - { - "$ref": "mol0" - }, - { - "$ref": "mol1" - }, - { - "$ref": "mol2" - }, - { - "$ref": "mol3" - }, - { - "$ref": "mol4" - }, - { - "$ref": "mol5" - }, - { - "$ref": "mol6" - }, - { - "$ref": "mol7" - }, - { - "$ref": "mol8" - }, - { - "$ref": "mol9" - }, - { - "$ref": "mol10" - }, - { - "$ref": "mol11" - }, - { - "$ref": "mol12" - }, - { - "$ref": "mol13" - }, - { - "$ref": "mol14" - }, - { - "type": "arrow", - "data": { - "mode": "filled-triangle", - "pos": [ - { - "x": 13.365317797904297, - "y": -16.91036502334189, - "z": 0 - }, - { - "x": 20.36532142107432, - "y": -16.91036502334189, - "z": 0 - } - ] - } - }, - { - "type": "arrow", - "data": { - "mode": "filled-triangle", - "pos": [ - { - "x": 26.937129102591086, - "y": -16.91036502334189, - "z": 0 - }, - { - "x": 33.93713272576112, - "y": -16.91036502334189, - "z": 0 - } - ] - } - }, - { - "type": "text", - "data": { - "content": "{\"blocks\":[{\"text\":\"C-H functionalization of\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":24,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"heteroarenes by\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":15,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"alkanesulfinate salts\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":21,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"TBHP.90C\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":8,\"style\":\"ITALIC\"}],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}", - "position": { - "x": 46.338289815195054, - "y": -16.206120287027993, - "z": 0 - }, - "pos": [ - { - "x": 46.338289815195054, - "y": -16.206120287027993, - "z": 0 - }, - { - "x": 46.338289815195054, - "y": -17.94259241684977, - "z": 0 - }, - { - "x": 49.99138887525365, - "y": -17.94259241684977, - "z": 0 - }, - { - "x": 49.99138887525365, - "y": -16.206120287027993, - "z": 0 - } - ] - } - }, - { - "type": "text", - "data": { - "content": "{\"blocks\":[{\"text\":\"Synthesis of sulfinyl acids\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":27,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"from alkyl or aryl halides\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":26,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"1. 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0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 23 25 0 0 1 0 0 0 0 0999 V2000 + 38.9539 -27.9570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5024 -28.8500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.9615 -29.7389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 38.2572 -30.4486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.4182 -31.4360 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 39.3533 -31.7899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.1276 -31.1568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.5143 -32.7773 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 38.8103 -33.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.2691 -34.3759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.2546 -34.2152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.4074 -33.2266 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 41.2958 -32.7693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 42.1369 -33.3102 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 41.3438 -31.7703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3641 -29.9993 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 37.5172 -29.0107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8055 -28.3062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.8412 -28.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1316 -27.8656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.3848 -26.8979 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3495 -26.6357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0607 -27.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 6 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 4 16 1 0 0 0 0 + 16 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 2 0 0 0 0 + 19 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 21 22 1 0 0 0 0 + 22 23 2 0 0 0 0 + 17 2 2 0 0 0 0 + 23 18 1 0 0 0 0 + 12 8 1 0 0 0 0 +M END +$DTYPE Name +$DATUM Synthesis of ureas +$DTYPE Reaction Conditions +$DATUM S8.CO (1 atm).DMF then O2 (1 +atm) +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$MOL + + -INDIGO-01000000002D + + 10 9 0 0 0 0 0 0 0 0999 V2000 + 39.1326 -18.0947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6341 -17.2277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.1325 -18.0927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7691 -16.7261 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7713 -15.7260 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 36.9021 -17.2243 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.5014 -16.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0029 -15.8624 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 40.0030 -15.8644 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 40.3664 -17.2311 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 4 6 1 0 0 0 0 + 2 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 10 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 23 25 0 0 1 0 0 0 0 0999 V2000 + 38.9539 -27.9570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5024 -28.8500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.9615 -29.7389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 38.2572 -30.4486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.4182 -31.4360 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 39.3533 -31.7899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.1276 -31.1568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.5143 -32.7773 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 38.8103 -33.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.2691 -34.3759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.2546 -34.2152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.4074 -33.2266 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 41.2958 -32.7693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 42.1369 -33.3102 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 41.3438 -31.7703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3641 -29.9993 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 37.5172 -29.0107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8055 -28.3062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.8412 -28.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1316 -27.8656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.3848 -26.8979 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3495 -26.6357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0607 -27.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 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+ 57.8943 -27.2909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 58.7354 -27.8320 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 57.9423 -26.2919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9629 -24.5210 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 54.1157 -23.5324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.4041 -22.8279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.4398 -23.0921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 51.7304 -22.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 51.9834 -21.4194 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 52.9483 -21.1574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.2031 -20.1896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 54.1701 -20.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 53.9071 -19.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 52.4928 -19.4857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 51.7888 -20.1962 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 51.5258 -19.2313 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 52.7473 -18.5187 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + 53.6593 -21.8609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 6 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 4 16 1 0 0 0 0 + 16 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 2 0 0 0 0 + 19 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 21 22 1 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 23 25 1 0 0 0 0 + 23 26 1 0 0 0 0 + 26 27 1 0 0 0 0 + 26 28 1 0 0 0 0 + 26 29 1 0 0 0 0 + 22 30 2 0 0 0 0 + 17 2 2 0 0 0 0 + 30 18 1 0 0 0 0 + 12 8 1 0 0 0 0 +M END +$DTYPE Name +$DATUM C-H functionalization of +heteroarenes by +alkanesulfinate salts +$DTYPE Reaction Conditions +$DATUM TBHP.90C diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index ac3d88c40e..1a89d12f59 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -396,7 +396,7 @@ std::vector PathwayLayout::splitText(const std::string& text, float size_t last_break_pos = start; size_t current_pos = start; - while (current_pos < text.size() && width + symbol_width(text[current_pos]) <= max_width) + while (current_pos < text.size() && width + symbol_width(text[current_pos]) < max_width) { if (text[current_pos] == '\n') { From c41c29d94df701aa6c92a9a6ec2c4faa3dddfd5a Mon Sep 17 00:00:00 2001 From: even1024 Date: Fri, 22 Nov 2024 07:13:04 +0100 Subject: [PATCH 22/24] ket rdf --- core/indigo-core/layout/src/pathway_layout.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index 1a89d12f59..e052c826c0 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -412,7 +412,7 @@ std::vector PathwayLayout::splitText(const std::string& text, float ++current_pos; } - if (text[current_pos] == '\n') + if (text[current_pos] == '\n' || text[current_pos] == ' ') { result.push_back(text.substr(start, current_pos - start)); start = current_pos + 1; From bbd67f22a8922f6a1272f2c9b2507721613ef3ef Mon Sep 17 00:00:00 2001 From: even1024 Date: Fri, 22 Nov 2024 07:27:08 +0100 Subject: [PATCH 23/24] ket rdf --- api/tests/integration/tests/formats/ref/pathway11.cdxml | 6 +++--- api/tests/integration/tests/formats/ref/pathway11.ket | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/api/tests/integration/tests/formats/ref/pathway11.cdxml b/api/tests/integration/tests/formats/ref/pathway11.cdxml index 6c731df050..44d70b2402 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway11.cdxml @@ -492,10 +492,10 @@ - KOH. toluene. PTC. catalyst + KOH. toluene. PTC. catalyst or - or KI. base e.g. K2CO3 + KI. base e.g. K2CO3 Published reaction @@ -511,7 +511,7 @@ Dichloromethane, CK2O3 - Potassium carbonate | Stage 2 + Potassium carbonate | Stage 2: 5 h, 80 degree, acid, Dy(3+) diff --git a/api/tests/integration/tests/formats/ref/pathway11.ket b/api/tests/integration/tests/formats/ref/pathway11.ket index 82a420e46a..4a53e8d08f 100644 --- a/api/tests/integration/tests/formats/ref/pathway11.ket +++ b/api/tests/integration/tests/formats/ref/pathway11.ket @@ -1 +1 @@ -{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"$ref":"mol3"},{"$ref":"mol4"},{"$ref":"mol5"},{"$ref":"mol6"},{"$ref":"mol7"},{"$ref":"mol8"},{"$ref":"mol9"},{"$ref":"mol10"},{"type":"text","data":{"content":"{\"blocks\":[{\"text\":\"Removal of benzoxazol-2-yl\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":26,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"group from amines\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":17,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"LAH.THF.reflux\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":14,\"style\":\"ITALIC\"}],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}","position":{"x":77.3457260131836,"y":-11.969417572021485,"z":0.0},"pos":[{"x":77.3457260131836,"y":-11.969417572021485,"z":0.0},{"x":77.3457260131836,"y":-13.409418106079102,"z":0.0},{"x":82.20868682861328,"y":-13.409418106079102,"z":0.0},{"x":82.20868682861328,"y":-11.969417572021485,"z":0.0}]}},{"type":"text","data":{"content":"{\"blocks\":[{\"text\":\"Alkylation of amines with\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":25,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"alkyl halides\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":13,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"\",\"inlineStyleRanges\":[{\"offset\":0,\"length\":0,\"style\":\"BOLD\"}],\"entityRanges\":[],\"data\":{}},{\"text\":\"KOH. toluene. 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0; i < props.size(); ++i) { - if (std::round(height * 1000) >= std::round(_text_line_height * 1000)) + if (std::round(height * ROUNDING_FACTOR) >= std::round(_text_line_height * ROUNDING_FACTOR)) { height -= _text_line_height; SimpleTextLine textLine; textLine.text = props[i].ptr(); - if (std::round(height * 1000) < std::round(_text_line_height * 1000) && props.size() - i > 1) + if (std::round(height * ROUNDING_FACTOR) < std::round(_text_line_height * ROUNDING_FACTOR) && props.size() - i > 1) { const std::string ellipsis = "..."; - if (textLine.text.size() >= ellipsis.size()) + if (textLine.text.size() >= ellipsis.size() && (textLine.text.size() + ellipsis.size()) > MAX_SYMBOLS) textLine.text.replace(textLine.text.size() - ellipsis.size(), ellipsis.size(), ellipsis); else textLine.text.append(ellipsis); @@ -399,24 +399,14 @@ std::vector PathwayLayout::splitText(const std::string& text, float while (current_pos < text.size() && width + symbol_width(text[current_pos]) < max_width) { if (text[current_pos] == '\n') - { break; - } width += symbol_width(text[current_pos]); if (std::isspace(text[current_pos]) || std::ispunct(text[current_pos])) - { last_break_pos = current_pos; - } - ++current_pos; - } - if (text[current_pos] == '\n' || text[current_pos] == ' ') - { - result.push_back(text.substr(start, current_pos - start)); - start = current_pos + 1; - continue; + ++current_pos; } if (current_pos == text.size()) @@ -425,20 +415,32 @@ std::vector PathwayLayout::splitText(const std::string& text, float break; } - if (last_break_pos > start) + if (text[current_pos] == '\n' || text[current_pos] == ' ') { - result.push_back(text.substr(start, last_break_pos - start)); - start = last_break_pos + 1; - while (start < text.size() && std::isspace(text[start])) - { - ++start; - } + // if the line ends with a space or a new line + result.push_back(text.substr(start, current_pos - start)); + start = current_pos + 1; } - else + else if (std::ispunct(text[current_pos]) || last_break_pos == start) { + // if the line ends with a punctuation result.push_back(text.substr(start, current_pos - start)); start = current_pos; } + else if (last_break_pos > start) + { + // last break position is found + if (std::isspace(text[last_break_pos])) + result.push_back(text.substr(start, last_break_pos - start)); + else + result.push_back(text.substr(start, last_break_pos - start + 1)); + + start = last_break_pos + 1; + } + + // skip spaces after break to avoid next line starting with space + while (start < text.size() && std::isspace(text[start])) + ++start; } return result;