From dc8220d4cd881e981eb07758574e1553eef4c7f1 Mon Sep 17 00:00:00 2001 From: even1024 Date: Mon, 18 Nov 2024 10:28:52 +0100 Subject: [PATCH] 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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