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even1024Mikalai Sukhikh
even1024
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Mikalai Sukhikh
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Backmerge: Bugfix/950 cdx aromatized structures (#954)
* rgroups (#946) Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com> * CDX import: Reaction arrows disappear when opening a file #943 (#948) * marvin cdx fix * clang fix Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com> * CDX import: Aromatized structures are not recognized when Pasting from Clipboard #950 (#953) * bond order fix * clang fix * test fix Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com> Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com>
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‎api/tests/integration/ref/formats/cdx_to_ket.py.out‎

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*** CDXML to mol ***
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arom64.cdx
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{"root":{"nodes":[{"$ref":"mol0"}]},"mol0":{"type":"molecule","atoms":[{"label":"Br","location":[0.27766722440719607,-3.042332887649536,0.0]},{"label":"C","location":[0.6933329105377197,-2.8023335933685304,0.0]},{"label":"C","location":[0.6933329105377197,-2.322333812713623,0.0]},{"label":"C","location":[1.1090006828308106,-2.0823333263397219,0.0]},{"label":"C","location":[1.5246663093566895,-2.322333812713623,0.0]},{"label":"C","location":[1.9403340816497803,-2.0823333263397219,0.0]},{"label":"O","location":[2.355999708175659,-2.322333812713623,0.0]},{"label":"C","location":[2.77166748046875,-2.0823333263397219,0.0]},{"label":"C","location":[3.187666893005371,-2.322333812713623,0.0]},{"label":"N","location":[3.603334665298462,-2.0823333263397219,0.0]},{"label":"C","location":[3.653334617614746,-1.6049997806549073,0.0]},{"label":"C","location":[4.123000144958496,-1.5049997568130494,0.0]},{"label":"N","location":[4.363000392913818,-1.9206664562225342,0.0]},{"label":"C","location":[4.041666507720947,-2.2776663303375246,0.0]},{"label":"C","location":[2.77166748046875,-1.6023335456848145,0.0]},{"label":"C","location":[3.187666893005371,-1.3623331785202027,0.0]},{"label":"C","location":[3.187666893005371,-0.8823333978652954,0.0]},{"label":"C","location":[2.77166748046875,-0.6423329710960388,0.0]},{"label":"Cl","location":[2.77166748046875,-0.1623331755399704,0.0]},{"label":"C","location":[2.355999708175659,-0.8823333978652954,0.0]},{"label":"C","location":[2.355999708175659,-1.3623331785202027,0.0]},{"label":"Cl","location":[1.9403340816497803,-1.6023335456848145,0.0]},{"label":"C","location":[1.5246663093566895,-2.8023335933685304,0.0]},{"label":"Cl","location":[1.9403340816497803,-3.042332887649536,0.0]},{"label":"C","location":[1.1090006828308106,-3.042332887649536,0.0]}],"bonds":[{"type":1,"atoms":[0,1]},{"type":4,"atoms":[1,2]},{"type":4,"atoms":[2,3]},{"type":4,"atoms":[3,4]},{"type":1,"atoms":[4,5]},{"type":1,"atoms":[5,6]},{"type":1,"atoms":[6,7]},{"type":1,"atoms":[7,8]},{"type":1,"atoms":[8,9]},{"type":4,"atoms":[9,10]},{"type":4,"atoms":[10,11]},{"type":4,"atoms":[11,12]},{"type":4,"atoms":[12,13]},{"type":4,"atoms":[9,13]},{"type":1,"atoms":[7,14]},{"type":4,"atoms":[14,15]},{"type":4,"atoms":[15,16]},{"type":4,"atoms":[16,17]},{"type":1,"atoms":[17,18]},{"type":4,"atoms":[17,19]},{"type":4,"atoms":[19,20]},{"type":4,"atoms":[14,20]},{"type":1,"atoms":[20,21]},{"type":4,"atoms":[4,22]},{"type":1,"atoms":[22,23]},{"type":4,"atoms":[22,24]},{"type":4,"atoms":[1,24]}]}}
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marvin.cdx
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CDXML loader: Not a molecule. Found 1 arrows.
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*** Try as Reaction ***

‎api/tests/integration/tests/formats/molecules/cdx/arom64.cdx‎

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‎core/indigo-core/molecule/CDXCommons.h‎

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CDXFontStyle
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};
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const std::unordered_map<int, std::string> kBondOrderIntToStr = {{kCDXBondOrder_Single, "1"},
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{kCDXBondOrder_Double, "2"},
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{kCDXBondOrder_Triple, "3"},
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{kCDXBondOrder_Quadruple, "4"},
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{kCDXBondOrder_Quintuple, "5"},
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{kCDXBondOrder_Sextuple, "6"},
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{kCDXBondOrder_Half, "0.5"},
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{kCDXBondOrder_OneHalf, "1.5"},
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{kCDXBondOrder_TwoHalf, "2.5"},
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{kCDXBondOrder_ThreeHalf, "3.5"},
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{kCDXBondOrder_FourHalf, "4.5"},
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{kCDXBondOrder_FiveHalf, "5.5"},
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{kCDXBondOrder_Dative, "dative"},
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{kCDXBondOrder_Ionic, "ionic"},
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{kCDXBondOrder_Hydrogen, "hydrogen"},
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{kCDXBondOrder_ThreeCenter, "threecenter"},
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{kCDXBondOrder_SingleOrDouble, "singleordouble"},
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{kCDXBondOrder_SingleOrAromatic, "singleoraromatic"},
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{kCDXBondOrder_DoubleOrAromatic, "doubleoraromatic"}};
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const std::unordered_map<std::string, CDXBondOrder> kBondOrderStrToId = {{"1", kCDXBondOrder_Single},
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{"2", kCDXBondOrder_Double},
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{"3", kCDXBondOrder_Triple},
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{"4", kCDXBondOrder_Quadruple},
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{"5", kCDXBondOrder_Quintuple},
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{"6", kCDXBondOrder_Sextuple},
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{"0.5", kCDXBondOrder_Half},
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{"1.5", kCDXBondOrder_OneHalf},
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{"2.5", kCDXBondOrder_TwoHalf},
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{"3.5", kCDXBondOrder_ThreeHalf},
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{"4.5", kCDXBondOrder_FourHalf},
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{"5.5", kCDXBondOrder_FiveHalf},
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{"dative", kCDXBondOrder_Dative},
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{"ionic", kCDXBondOrder_Ionic},
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{"hydrogen", kCDXBondOrder_Hydrogen},
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{"threecenter", kCDXBondOrder_ThreeCenter},
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{"singleordouble", kCDXBondOrder_SingleOrDouble},
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{"singleoraromatic", kCDXBondOrder_SingleOrAromatic},
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{"doubleoraromatic", kCDXBondOrder_DoubleOrAromatic}};
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const std::unordered_map<std::string, CDXArrowType> kCDXProp_Arrow_TypeStrToID = {{"NoHead", kCDXArrowType_NoHead},
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{"HalfHead", kCDXArrowType_HalfHead},
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{"FullHead", kCDXArrowType_FullHead},

‎core/indigo-core/molecule/molecule_cdxml_loader.h‎

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{
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switch (tag)
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{
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case kCDXProp_Bond_Order: {
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return kBondOrderIntToStr.at(val);
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}
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case kCDXProp_Node_Type: {
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return KNodeTypeIntToName.at(val);
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}

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