diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml index 7aca4c692e..e17a2b321d 100644 --- a/.github/workflows/indigo-ci.yaml +++ b/.github/workflows/indigo-ci.yaml @@ -1406,4 +1406,4 @@ jobs: export clean_tag=${tag/refs\/tags\/indigo-/} docker tag epmlsop/indigo-service:enhanced-latest epmlsop/indigo-service:enhanced-${clean_tag} docker push epmlsop/indigo-service:enhanced-${clean_tag} - docker push epmlsop/indigo-service:enhanced-latest + docker push epmlsop/indigo-service:enhanced-latest \ No newline at end of file diff --git a/api/tests/integration/ref/formats/ket_cdxml.py.out b/api/tests/integration/ref/formats/ket_cdxml.py.out index d233b3c449..4275afbbaf 100644 --- a/api/tests/integration/ref/formats/ket_cdxml.py.out +++ b/api/tests/integration/ref/formats/ket_cdxml.py.out @@ -1,4 +1,6 @@ *** KET to CDXML to KET *** +2558-missed.cdxml:SUCCEED +2558-missed.ket:SUCCEED 961-text_size.cdxml:SUCCEED 961-text_size.ket:SUCCEED agents.cdxml:SUCCEED 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 8442abe18b..a173cb969a 100644 --- a/api/tests/integration/ref/formats/ket_to_rdf.py.out +++ b/api/tests/integration/ref/formats/ket_to_rdf.py.out @@ -2,6 +2,7 @@ multi.rdf:SUCCEED pathway1.rdf:SUCCEED pathway10.rdf:SUCCEED +pathway11.rdf:SUCCEED pathway2.rdf:SUCCEED pathway3.rdf:SUCCEED pathway4.rdf:SUCCEED diff --git a/api/tests/integration/ref/formats/rdf_to_cdxml.py.out b/api/tests/integration/ref/formats/rdf_to_cdxml.py.out index 730aa7c8b8..549a3331a0 100644 --- a/api/tests/integration/ref/formats/rdf_to_cdxml.py.out +++ b/api/tests/integration/ref/formats/rdf_to_cdxml.py.out @@ -1,6 +1,7 @@ *** RDF to CDXML *** pathway1.cdxml:SUCCEED pathway10.cdxml:SUCCEED +pathway11.cdxml:SUCCEED pathway2.cdxml:SUCCEED pathway3.cdxml:SUCCEED pathway4.cdxml:SUCCEED diff --git a/api/tests/integration/ref/formats/rxn_to_ket.py.out b/api/tests/integration/ref/formats/rxn_to_ket.py.out new file mode 100644 index 0000000000..8d892eab3d --- /dev/null +++ b/api/tests/integration/ref/formats/rxn_to_ket.py.out @@ -0,0 +1,3 @@ +*** RXN to KET *** +2485-bad-layout.ket:SUCCEED +2531-bad-layout.ket:SUCCEED diff --git a/api/tests/integration/ref/reaction/pathway.py.out b/api/tests/integration/ref/reaction/pathway.py.out index c4790116ae..adadd52e90 100644 --- a/api/tests/integration/ref/reaction/pathway.py.out +++ b/api/tests/integration/ref/reaction/pathway.py.out @@ -8,3 +8,4 @@ pathway7.rdf:SUCCEED pathway8.rdf:SUCCEED pathway9.rdf:SUCCEED pathway10.rdf:SUCCEED +pathway11.rdf:SUCCEED diff --git a/api/tests/integration/tests/formats/ket_cdxml.py b/api/tests/integration/tests/formats/ket_cdxml.py index ab0437fb38..25eca0c543 100644 --- a/api/tests/integration/tests/formats/ket_cdxml.py +++ b/api/tests/integration/tests/formats/ket_cdxml.py @@ -28,6 +28,7 @@ def find_diff(a, b): "multi_overlap", "961-text_size", "generic", + "2558-missed", ] files.sort() diff --git a/api/tests/integration/tests/formats/ket_to_rdf.py b/api/tests/integration/tests/formats/ket_to_rdf.py index 6179ae694b..e490d71b37 100644 --- a/api/tests/integration/tests/formats/ket_to_rdf.py +++ b/api/tests/integration/tests/formats/ket_to_rdf.py @@ -36,6 +36,7 @@ def find_diff(a, b): "pathway8", "pathway9", "pathway10", + "pathway11", ] files.sort() diff --git a/api/tests/integration/tests/formats/rdf_to_cdxml.py b/api/tests/integration/tests/formats/rdf_to_cdxml.py index da54f91e7f..f80e971e4f 100644 --- a/api/tests/integration/tests/formats/rdf_to_cdxml.py +++ b/api/tests/integration/tests/formats/rdf_to_cdxml.py @@ -33,6 +33,7 @@ def find_diff(a, b): "pathway8", "pathway9", "pathway10", + "pathway11", ] files.sort() diff --git a/api/tests/integration/tests/formats/reactions/2485-bad-layout.rxn b/api/tests/integration/tests/formats/reactions/2485-bad-layout.rxn new file mode 100644 index 0000000000..0ad4b98394 --- /dev/null +++ b/api/tests/integration/tests/formats/reactions/2485-bad-layout.rxn @@ -0,0 +1,65 @@ +$RXN V3000 + + -INDIGO- 1021241118 + +M V30 COUNTS 2 1 +M V30 BEGIN REACTANT +M V30 BEGIN CTAB +M V30 COUNTS 5 5 0 0 0 +M V30 BEGIN ATOM +M V30 1 C -29.801 19.8069 0.0 0 +M V30 2 C -29.3006 18.2668 0.0 0 +M V30 3 C -28.9913 19.213 0.0 0 +M V30 4 C -30.3014 18.2668 0.0 0 +M V30 5 C -30.6107 19.213 0.0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 1 1 5 +M V30 2 2 5 4 +M V30 3 1 4 2 +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 6 6 0 0 0 +M V30 BEGIN ATOM +M V30 1 C -29.6854 16.8444 0.0 0 +M V30 2 C -27.9551 16.8449 0.0 0 +M V30 3 C -28.8186 17.3445 0.0 0 +M V30 4 C -27.9551 15.844 0.0 0 +M V30 5 C -29.6854 15.8395 0.0 0 +M V30 6 C -28.8164 15.3445 0.0 0 +M V30 END ATOM +M V30 BEGIN BOND +M V30 1 2 3 1 +M V30 2 1 1 5 +M V30 3 2 5 6 +M V30 4 1 6 4 +M V30 5 2 4 2 +M V30 6 1 2 3 +M V30 END BOND +M V30 END CTAB +M V30 END REACTANT +M V30 BEGIN PRODUCT +M V30 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\ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/ket_retro_arrow_and_simple_arrow.cdxml b/api/tests/integration/tests/formats/ref/ket_retro_arrow_and_simple_arrow.cdxml index 32fa979257..5b4c946057 100644 --- a/api/tests/integration/tests/formats/ref/ket_retro_arrow_and_simple_arrow.cdxml +++ b/api/tests/integration/tests/formats/ref/ket_retro_arrow_and_simple_arrow.cdxml @@ -18,33 +18,33 @@ - - - - - - NH - 2 - - - - - - - - + OH - - + + OH + + + + + + + + + + NH + 2 + + + - + @@ -62,8 +62,8 @@ - - + + diff --git a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.b64cdx b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.b64cdx index 93638d480d..6f97122a37 100644 --- a/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.b64cdx +++ b/api/tests/integration/tests/formats/ref/ket_simple_arrow_retro_arrow_sum_of_products.b64cdx @@ -1 +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 a72a9a8af9..a795d4ecc4 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 e3758cd197..a72e11c694 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 @@ -2,6 +2,19 @@ + + + + + + + + + + + + + @@ -38,19 +51,6 @@ - - - - - - - - - - - - - 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 3168821c16..ef43a39c45 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]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 +[#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 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 aab9da2128..1ad2aa86f0 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 @@ -C1CCCC1.C1C=CC=C1.CC(N)C>>OCO \ No newline at end of file +CC(N)C.C1CCCC1.C1C=CC=C1>>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 2a4d964e8a..564592aaf7 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 @@ -7,6 +7,19 @@ $MOL -INDIGO-01000000002D + 4 3 0 0 0 0 0 0 0 0999 V2000 + 10.1817 -8.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1817 -7.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3157 -7.3140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0478 -7.3140 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + 5 5 0 0 0 0 0 0 0 0999 V2000 22.8103 -7.1445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 23.6193 -7.7323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -39,19 +52,6 @@ $MOL -INDIGO-01000000002D - 4 3 0 0 0 0 0 0 0 0999 V2000 - 10.1817 -8.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.1817 -7.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.3157 -7.3140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0478 -7.3140 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 2 4 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - 3 2 0 0 0 0 0 0 0 0999 V2000 14.9228 -7.8140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 15.7888 -8.3140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 diff --git 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 index c8eae2944a..2514843869 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 @@ -5,6 +5,20 @@ $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 @@ -38,20 +52,6 @@ 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 -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 END REACTANT M V30 BEGIN PRODUCT M V30 BEGIN CTAB diff --git a/api/tests/integration/tests/formats/ref/multi_overlap.cdxml b/api/tests/integration/tests/formats/ref/multi_overlap.cdxml index b8b04bc8d1..ee59976467 100644 --- a/api/tests/integration/tests/formats/ref/multi_overlap.cdxml +++ b/api/tests/integration/tests/formats/ref/multi_overlap.cdxml @@ -18,88 +18,88 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - O - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + NH 2 - - - - - - - + + + + + + + - - + + ClH + + + + + + + + + + O + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + diff --git a/api/tests/integration/tests/formats/ref/pathway1.cdxml b/api/tests/integration/tests/formats/ref/pathway1.cdxml index 1e95025aa6..62e8365daa 100644 --- a/api/tests/integration/tests/formats/ref/pathway1.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway1.cdxml @@ -18,12 +18,12 @@ - - - - - - + + + + + + @@ -32,11 +32,11 @@ - - - - - + + + + + @@ -44,13 +44,13 @@ - - - - - - - + + + + + + + @@ -60,13 +60,13 @@ - - - - - - - + + + + + + + @@ -76,14 +76,14 @@ - - - - - - - - + + + + + + + + @@ -94,15 +94,15 @@ - - - - - - - - - + + + + + + + + + diff --git a/api/tests/integration/tests/formats/ref/pathway1.rdf b/api/tests/integration/tests/formats/ref/pathway1.rdf index d3cff0b676..2a300e5499 100644 --- a/api/tests/integration/tests/formats/ref/pathway1.rdf +++ b/api/tests/integration/tests/formats/ref/pathway1.rdf @@ -3,66 +3,6 @@ $DATM 01/00/00 00:00 $RDFILE 1 $DATM 01/00/00 00:00 $RFMT -$RXN - - -INDIGO- 0100000000 - - 2 1 -$MOL - - -INDIGO-01000000002D - - 5 5 0 0 0 0 0 0 0 0999 V2000 - 0.9206 13.6931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4210 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.4203 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1109 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 5 4 2 0 0 0 0 - 4 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 1 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0000 9.1529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 9.1534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8668 9.6530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 8.1524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 8.1479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8690 7.6529 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 -$MOL - - -INDIGO-01000000002D - - 7 7 0 0 0 0 0 0 0 0999 V2000 - 5.7891 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.7891 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.6551 9.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.5212 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.5212 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.6551 11.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3872 11.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 1 0 0 0 0 -M END -$RFMT $RXN -INDIGO- 0100000000 @@ -154,3 +94,63 @@ $MOL 6 8 2 0 0 0 0 4 9 1 0 0 0 0 M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 0.9206 13.6931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4210 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4203 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1109 13.0993 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 +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0000 9.1529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 9.1534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8668 9.6530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 8.1524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 8.1479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8690 7.6529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 7 7 0 0 0 0 0 0 0 0999 V2000 + 5.7891 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7891 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 9.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 11.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3872 11.7880 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 diff --git a/api/tests/integration/tests/formats/ref/pathway10.cdxml b/api/tests/integration/tests/formats/ref/pathway10.cdxml index 211ea1d8d8..e89971e211 100644 --- a/api/tests/integration/tests/formats/ref/pathway10.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway10.cdxml @@ -18,12 +18,12 @@ - - - - - - + + + + + + F @@ -34,11 +34,11 @@ - - - - - + + + + + Cl @@ -48,11 +48,11 @@ - - - - - + + + + + @@ -60,12 +60,12 @@ - - - - - - + + + + + + @@ -74,11 +74,11 @@ - - - - - + + + + + OH @@ -88,12 +88,12 @@ - - - - - - + + + + + + @@ -102,12 +102,12 @@ - - - - - - + + + + + + NH 2 @@ -119,13 +119,13 @@ - - - - - - - + + + + + + + SH @@ -137,12 +137,12 @@ - - - - - - + + + + + + PH 2 @@ -154,42 +154,42 @@ - - + + OH - - + + OH - - + + OH - - + + OH - - + + O - - + + OH - - - - - - + + + + + + @@ -202,8 +202,8 @@ - - + + Chiral diff --git a/api/tests/integration/tests/formats/ref/pathway10.rdf b/api/tests/integration/tests/formats/ref/pathway10.rdf index 136f00f28c..024b45d7f9 100644 --- a/api/tests/integration/tests/formats/ref/pathway10.rdf +++ b/api/tests/integration/tests/formats/ref/pathway10.rdf @@ -12,6 +12,54 @@ $MOL -INDIGO-01000000002D + 4 4 0 0 0 0 0 0 0 0999 V2000 + 7.8497 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8509 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3504 2.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.6092 3.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 1 1 0 0 0 0 + 3 4 1 0 0 0 0 +M END +$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 @@ -76,49 +124,31 @@ $MOL -INDIGO-01000000002D - 4 4 0 0 0 0 0 0 0 0999 V2000 - 7.8497 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.8509 1.7228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3504 2.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.6092 3.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 - 3 4 1 0 0 0 0 -M END -$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 + 12 12 0 0 1 0 0 0 0 0999 V2000 + 19.5055 8.6403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 19.5055 6.7652 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 17.6861 5.8247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.8666 6.7651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 17.6805 8.6403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0687 8.0460 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 18.5957 8.1812 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 18.5957 7.2298 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 17.6805 6.7651 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 16.7709 7.2296 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 16.7709 8.1811 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 15.8666 8.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6 12 1 0 0 0 0 + 11 5 1 0 0 0 0 + 5 7 1 0 0 0 0 + 7 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 1 0 0 0 + 7 1 1 6 0 0 0 + 8 2 1 6 0 0 0 + 9 3 1 6 0 0 0 + 10 4 1 6 0 0 0 M END $MOL @@ -154,33 +184,3 @@ $MOL 3 1 1 0 0 0 0 2 5 1 0 0 0 0 M END -$MOL - - -INDIGO-01000000002D - - 12 12 0 0 1 0 0 0 0 0999 V2000 - 19.5055 8.6403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 19.5055 6.7652 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.6861 5.8247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8666 6.7651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.6805 8.6403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 15.0687 8.0460 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 18.5957 8.1812 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 - 18.5957 7.2298 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 - 17.6805 6.7651 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 - 16.7709 7.2296 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 - 16.7709 8.1811 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 - 15.8666 8.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 12 1 0 0 0 0 - 11 5 1 0 0 0 0 - 5 7 1 0 0 0 0 - 7 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 1 0 0 0 - 7 1 1 6 0 0 0 - 8 2 1 6 0 0 0 - 9 3 1 6 0 0 0 - 10 4 1 6 0 0 0 -M END diff --git a/api/tests/integration/tests/formats/ref/pathway11.cdxml b/api/tests/integration/tests/formats/ref/pathway11.cdxml new file mode 100644 index 0000000000..563cfafb00 --- /dev/null +++ b/api/tests/integration/tests/formats/ref/pathway11.cdxml @@ -0,0 +1,484 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + OH + + + + + + + + + + + + NH + 2 + + + + + + O + + + + + + + + + + OH + + + + + + + + + + + + + + + + + + + + + + + + + O + + + + + + + + + + + NH + 2 + + + + + O + + + + + + + + + + + + + + + + + + + + + + + + + Cl + + + + + + I + + + + + + + + + NH + 2 + + + + + + O + + + + + + + + + + O + + + + + + + O + + + + + + + + + + + + + + + + + + + + + + + + + + N + + + + + + S + + + + + + + + + + + + NH + 2 + + + + + + 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-INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 6.8165 -9.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.6255 -10.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3165 -11.3753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3165 -11.3753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0076 -10.4242 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 +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 6.9277 -12.1136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4281 -13.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7373 -12.7074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4273 -13.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1180 -12.7074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 5 4 2 0 0 0 0 + 4 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 1 1 0 0 0 0 +M END +$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 + 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 +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 10.1458 -12.4392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.8761 -12.4388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0126 -11.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.8761 -13.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1458 -13.4442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0148 -13.9392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$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 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+ + @@ -44,13 +44,13 @@ - - - - - - - + + + + + + + @@ -60,13 +60,13 @@ - - - - - - - + + + + + + + @@ -76,15 +76,15 @@ - - - - - - - - - + + + + + + + + + diff --git a/api/tests/integration/tests/formats/ref/pathway2.rdf b/api/tests/integration/tests/formats/ref/pathway2.rdf index 8e25eb284e..e3139b414b 100644 --- a/api/tests/integration/tests/formats/ref/pathway2.rdf +++ b/api/tests/integration/tests/formats/ref/pathway2.rdf @@ -12,66 +12,6 @@ $MOL -INDIGO-01000000002D - 5 5 0 0 0 0 0 0 0 0999 V2000 - 0.9206 8.9452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4210 7.4051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 8.3514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.4203 7.4051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1109 8.3514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 5 4 2 0 0 0 0 - 4 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 1 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0000 4.4050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 4.4055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8668 4.9051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 3.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 3.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8690 2.9050 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 -$MOL - - -INDIGO-01000000002D - - 7 7 0 0 0 0 0 0 0 0999 V2000 - 5.2303 6.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.2303 5.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0963 5.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9624 5.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.9624 6.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0963 7.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.8284 7.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 1 0 0 0 0 -M END -$RFMT -$RXN - - -INDIGO- 0100000000 - - 2 1 -$MOL - - -INDIGO-01000000002D - 7 7 0 0 0 0 0 0 0 0999 V2000 5.2303 6.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2303 5.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -132,3 +72,63 @@ $MOL 6 8 2 0 0 0 0 4 9 1 0 0 0 0 M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 0.9206 8.9452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4210 7.4051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 8.3514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4203 7.4051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1109 8.3514 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 +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0000 4.4050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 4.4055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8668 4.9051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 3.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 3.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8690 2.9050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 7 7 0 0 0 0 0 0 0 0999 V2000 + 5.2303 6.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2303 5.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0963 5.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9624 5.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9624 6.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0963 7.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8284 7.0401 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 diff --git a/api/tests/integration/tests/formats/ref/pathway3.cdxml b/api/tests/integration/tests/formats/ref/pathway3.cdxml index 07a0db1abf..b49f31a2a5 100644 --- a/api/tests/integration/tests/formats/ref/pathway3.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway3.cdxml @@ -18,12 +18,12 @@ - - - - - - + + + + + + @@ -32,11 +32,11 @@ - - - - - + + + + + @@ -44,13 +44,13 @@ - - - - - - - + + + + + + + @@ -60,15 +60,15 @@ - - - - - - - - - + + + + + + + + + @@ -79,9 +79,9 @@ - + - + diff --git a/api/tests/integration/tests/formats/ref/pathway4.cdxml b/api/tests/integration/tests/formats/ref/pathway4.cdxml index 693041a2dd..1ed864bed8 100644 --- a/api/tests/integration/tests/formats/ref/pathway4.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway4.cdxml @@ -18,11 +18,11 @@ - - - - - + + + + + @@ -30,13 +30,13 @@ - - - - - - - + + + + + + + @@ -46,15 +46,15 @@ - - - - - - - - - + + + + + + + + + @@ -65,8 +65,8 @@ - - + + diff --git a/api/tests/integration/tests/formats/ref/pathway5.cdxml b/api/tests/integration/tests/formats/ref/pathway5.cdxml index 543aabc4ab..3987968848 100644 --- a/api/tests/integration/tests/formats/ref/pathway5.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway5.cdxml @@ -18,13 +18,13 @@ - - - - - - - + + + + + + + @@ -34,15 +34,15 @@ - - - - - - - - - + + + + + + + + + @@ -53,7 +53,7 @@ - + diff --git a/api/tests/integration/tests/formats/ref/pathway6.cdxml b/api/tests/integration/tests/formats/ref/pathway6.cdxml index 49426978b3..677e4eb1e9 100644 --- a/api/tests/integration/tests/formats/ref/pathway6.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway6.cdxml @@ -18,12 +18,12 @@ - - - - - - + + + + + + @@ -32,11 +32,11 @@ - - - - - + + + + + @@ -44,13 +44,13 @@ - - - - - - - + + + + + + + @@ -60,13 +60,13 @@ - - - - - - - + + + + + + + @@ -76,14 +76,14 @@ - - - - - - - - + + + + + + + + @@ -94,19 +94,19 @@ - - - + + + - - - - - + + + + + @@ -114,15 +114,15 @@ - - - - - - - - - + + + + + + + + + @@ -134,14 +134,14 @@ - - - - - - - - + + + + + + + + @@ -152,22 +152,22 @@ - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -186,11 +186,11 @@ - - + + - + diff --git a/api/tests/integration/tests/formats/ref/pathway6.rdf b/api/tests/integration/tests/formats/ref/pathway6.rdf index df5f611c61..7b7e755f8d 100644 --- a/api/tests/integration/tests/formats/ref/pathway6.rdf +++ b/api/tests/integration/tests/formats/ref/pathway6.rdf @@ -7,60 +7,135 @@ $RXN -INDIGO- 0100000000 - 2 1 + 1 1 $MOL -INDIGO-01000000002D 5 5 0 0 0 0 0 0 0 0999 V2000 - 0.9206 13.6931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4210 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.4203 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1109 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 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 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 + 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 $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0000 9.1529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 9.1534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8668 9.6530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7303 8.1524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 8.1479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8690 7.6529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 12.7773 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7775 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4826 17.8321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4828 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4852 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.1906 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.1905 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4852 17.8322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 1 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 3 1 0 0 0 0 + 3 2 1 0 0 0 0 +M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$MOL + + -INDIGO-01000000002D + + 8 8 0 0 0 0 0 0 0 0999 V2000 + 12.7773 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7775 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4826 17.8321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4828 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4852 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.1906 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.1905 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4852 17.8322 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 + 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 +M END +$MOL + + -INDIGO-01000000002D + + 9 9 0 0 0 0 0 0 0 0999 V2000 + 12.7532 6.8825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4835 6.8830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6200 7.3826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.4835 5.8821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7532 5.8776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6222 5.3826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.8872 5.3776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.9151 4.6755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.1906 5.1750 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 $MOL -INDIGO-01000000002D - 7 7 0 0 0 0 0 0 0 0999 V2000 - 5.7891 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.7891 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.6551 9.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.5212 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.5212 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.6551 11.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3872 11.7880 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 + 16 17 0 0 0 0 0 0 0 0999 V2000 + 18.6906 9.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.6908 10.2244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3960 10.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3962 8.5165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3986 8.5165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1040 9.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1039 10.2244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3986 10.9297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.7740 12.4302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.7742 13.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.4793 14.1380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.4795 11.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4819 11.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1873 12.4302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1872 13.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4819 14.1381 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 4 5 1 0 0 0 0 5 6 1 0 0 0 0 - 5 7 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 + 10 9 1 0 0 0 0 + 9 12 1 0 0 0 0 + 12 13 1 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 + 16 11 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 3 1 0 0 0 0 M END $RFMT $RXN @@ -193,133 +268,58 @@ $RXN -INDIGO- 0100000000 - 1 1 + 2 1 $MOL -INDIGO-01000000002D 5 5 0 0 0 0 0 0 0 0999 V2000 - 7.5782 17.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3872 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.0782 15.8561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.7692 16.8072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9206 13.6931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4210 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4203 12.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1109 13.0993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 - 5 4 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 2 1 0 0 0 0 - 2 1 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 8 8 0 0 0 0 0 0 0 0999 V2000 - 12.7773 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.7775 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4826 17.8321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4828 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.4852 15.4189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.1906 16.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.1905 17.1269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.4852 17.8322 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 - 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 -M END -$RFMT -$RXN - - 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0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 21.1039 10.2244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.3986 10.9297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7740 12.4302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7742 13.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4793 14.1380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4795 11.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.4819 11.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 21.1873 12.4302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 21.1872 13.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.4819 14.1381 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 + 7 7 0 0 0 0 0 0 0 0999 V2000 + 5.7891 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7891 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 9.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 10.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 11.2880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 11.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3872 11.7880 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 - 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 - 10 9 1 0 0 0 0 - 9 12 1 0 0 0 0 - 12 13 1 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 - 16 11 1 0 0 0 0 - 11 10 1 0 0 0 0 - 12 3 1 0 0 0 0 + 5 7 1 0 0 0 0 M END diff --git a/api/tests/integration/tests/formats/ref/pathway7.cdxml b/api/tests/integration/tests/formats/ref/pathway7.cdxml index 4886913be3..df7e1c3743 100644 --- a/api/tests/integration/tests/formats/ref/pathway7.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway7.cdxml @@ -18,11 +18,11 @@ - - - - - + + + + + @@ -30,12 +30,12 @@ - - - - - - + + + + + + @@ -44,13 +44,13 @@ - - - - - - - + + + + + + + @@ -60,66 +60,66 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -196,73 +196,73 @@ - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -338,14 +338,14 @@ - - - - - - - - + + + + + + + + @@ -355,9 +355,9 @@ - + - + diff --git a/api/tests/integration/tests/formats/ref/pathway7.rdf b/api/tests/integration/tests/formats/ref/pathway7.rdf index 1d23e6b07a..76e1934e49 100644 --- a/api/tests/integration/tests/formats/ref/pathway7.rdf +++ b/api/tests/integration/tests/formats/ref/pathway7.rdf @@ -165,60 +165,18 @@ $RXN -INDIGO- 0100000000 - 3 1 -$MOL - - -INDIGO-01000000002D - - 7 7 0 0 0 0 0 0 0 0999 V2000 - 13.5150 8.9987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.5113 9.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.5023 9.0116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.4998 9.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.9648 10.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.0916 10.6227 0.0000 C 0 0 0 0 0 0 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32.6062 18.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.1584 17.2274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0541 17.2274 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 + 2 3 1 0 0 0 0 3 1 1 0 0 0 0 - 5 4 1 0 0 0 0 M END $MOL @@ -358,23 +316,87 @@ $MOL 52 59 1 0 0 0 0 57 47 1 0 0 0 0 M END +$MOL + + -INDIGO-01000000002D + + 8 8 0 0 0 0 0 0 0 0999 V2000 + 37.7244 12.5030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5519 12.1602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.8947 11.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8969 12.1602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5541 11.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8969 10.5052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7244 10.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5519 10.5052 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 + 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 +M END $RFMT $RXN -INDIGO- 0100000000 - 2 1 + 3 1 $MOL -INDIGO-01000000002D - 3 3 0 0 0 0 0 0 0 0999 V2000 - 32.6062 18.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 32.1584 17.2274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 33.0541 17.2274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7 7 0 0 0 0 0 0 0 0999 V2000 + 13.5150 8.9987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.5113 9.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.5023 9.0116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.4998 9.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9648 10.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0916 10.6227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.6338 8.0370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 4 3 1 0 0 0 0 + 3 1 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 2 1 0 0 0 0 + 7 1 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 13.7708 4.0406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.7671 5.0365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7580 4.0535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7555 5.0365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.2206 5.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.6338 5.5370 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 + 5 4 1 0 0 0 0 + 2 6 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 14.6338 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.6301 0.9959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6210 0.0130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6185 0.9959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.6249 1.5406 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 + 5 4 1 0 0 0 0 M END $MOL @@ -514,25 +536,3 @@ $MOL 52 59 1 0 0 0 0 57 47 1 0 0 0 0 M END -$MOL - - -INDIGO-01000000002D - - 8 8 0 0 0 0 0 0 0 0999 V2000 - 37.7244 12.5030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 38.5519 12.1602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 38.8947 11.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 36.8969 12.1602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 36.5541 11.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 36.8969 10.5052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 37.7244 10.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 38.5519 10.5052 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 - 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 -M END diff --git a/api/tests/integration/tests/formats/ref/pathway8.cdxml b/api/tests/integration/tests/formats/ref/pathway8.cdxml index 97709c65b6..a81eefbfd2 100644 --- a/api/tests/integration/tests/formats/ref/pathway8.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway8.cdxml @@ -18,11 +18,11 @@ - - - - - + + + + + @@ -30,12 +30,12 @@ - - - - - - + + + + + + @@ -44,66 +44,66 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -180,12 +180,12 @@ - - - - - - + + + + + + @@ -194,65 +194,65 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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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 @@ -166,46 +148,24 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END -$RFMT -$RXN - - -INDIGO- 0100000000 - - 2 1 $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0000 27.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 26.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8660 26.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 26.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 27.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8660 28.4989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 + 3 3 0 0 0 0 0 0 0 0999 V2000 + 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 + 3 1 1 0 0 0 0 M END -$MOL +$RFMT +$RXN - -INDIGO-01000000002D + -INDIGO- 0100000000 - 5 5 0 0 0 0 0 0 0 0999 V2000 - 0.9282 23.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4250 22.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 23.4092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.4315 22.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1243 23.4092 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 + 1 1 $MOL -INDIGO-01000000002D @@ -344,6 +304,20 @@ $MOL 52 59 1 0 0 0 0 57 47 1 0 0 0 0 M END +$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 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b/api/tests/integration/tests/formats/ref/pathway9.cdxml index 965e3765bb..2ddecd89a7 100644 --- a/api/tests/integration/tests/formats/ref/pathway9.cdxml +++ b/api/tests/integration/tests/formats/ref/pathway9.cdxml @@ -18,11 +18,11 @@ - - - - - + + + + + @@ -30,12 +30,12 @@ - - - - - - + + + + + + @@ -44,66 +44,66 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -180,12 +180,12 @@ - - - - - - + + + + + + @@ -194,65 +194,65 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -328,11 +328,11 @@ - - - - - + + + + + @@ -340,30 +340,30 @@ - - - + + + - - - - + + + + - - - - - - + + + + + + @@ -372,11 +372,11 @@ 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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 @@ -166,46 +148,24 @@ $MOL 52 59 1 0 0 0 0 56 43 1 0 0 0 0 M END -$RFMT -$RXN - - -INDIGO- 0100000000 - - 2 1 $MOL -INDIGO-01000000002D - 6 6 0 0 0 0 0 0 0 0999 V2000 - 0.0000 27.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 26.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8660 26.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 26.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.7320 27.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8660 28.4989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6 1 1 0 0 0 0 + 3 3 0 0 0 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0100000000 - - 2 1 -$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 -$MOL - - -INDIGO-01000000002D - - 3 3 0 0 0 0 0 0 0 0999 V2000 - 23.6769 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.6782 13.8132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.1776 14.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 1 1 0 0 0 0 -M END -$MOL - - -INDIGO-01000000002D - - 8 8 0 0 0 0 0 0 0 0999 V2000 - 28.1782 19.3050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 28.1784 20.3074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 28.8836 21.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 28.8838 18.5995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 29.8862 18.5995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 30.5916 19.3050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 30.5915 20.3074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 29.8862 21.0127 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 - 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 + 56 43 1 0 0 0 0 M END $RFMT $RXN @@ -1026,3 +966,63 @@ $MOL 6 8 2 0 0 0 0 4 9 1 0 0 0 0 M END +$RFMT +$RXN + + -INDIGO- 0100000000 + + 2 1 +$MOL + + -INDIGO-01000000002D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 0.9206 44.6845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4210 43.1444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 44.0907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4203 43.1444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1109 44.0907 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 +$MOL + + -INDIGO-01000000002D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0000 40.1443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 40.1448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8668 40.6444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7303 39.1438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 39.1393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8690 38.6443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 2 0 0 0 0 + 1 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 4 1 0 0 0 0 + 4 2 2 0 0 0 0 + 2 3 1 0 0 0 0 +M END +$MOL + + -INDIGO-01000000002D + + 7 7 0 0 0 0 0 0 0 0999 V2000 + 5.7891 42.2794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7891 41.2794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 40.7794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 41.2794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5212 42.2794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6551 42.7794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3872 42.7794 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 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 22f7f1117e..bd95a29bc2 100644 --- a/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml +++ b/api/tests/integration/tests/formats/ref/retro_arrow_diagonal.cdxml @@ -18,39 +18,39 @@ - - - - - - + + + + + + + + + + - - - - - - - - - + + + + + + + - - - - + + + + + + + + + - - - - - - - - - - - + + + + @@ -58,9 +58,9 @@ - - - + + + diff --git a/api/tests/integration/tests/formats/rxn_to_ket.py b/api/tests/integration/tests/formats/rxn_to_ket.py new file mode 100644 index 0000000000..f99fb1f83b --- /dev/null +++ b/api/tests/integration/tests/formats/rxn_to_ket.py @@ -0,0 +1,45 @@ +import difflib +import os +import sys + + +def find_diff(a, b): + return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines())) + + +sys.path.append( + os.path.normpath( + os.path.join(os.path.abspath(__file__), "..", "..", "..", "common") + ) +) +from env_indigo import * # noqa + +indigo = Indigo() +indigo.setOption("json-saving-pretty", True) +indigo.setOption("ignore-stereochemistry-errors", True) + +print("*** RXN to KET ***") + +root = joinPathPy("reactions/", __file__) +ref_path = joinPathPy("ref/", __file__) + +files = [ + "2531-bad-layout", + "2485-bad-layout", +] + +files.sort() +for filename in files: + mol = indigo.loadReactionFromFile(os.path.join(root, filename + ".rxn")) + + # with open(os.path.join(ref_path, filename) + ".ket", "w") as file: + # file.write(mol.json()) + with open(os.path.join(ref_path, filename) + ".ket", "r") as file: + ket_ref = file.read() + ket = mol.json() + diff = find_diff(ket_ref, ket) + if not diff: + print(filename + ".ket:SUCCEED") + else: + print(filename + ".ket:FAILED") + print(diff) diff --git a/api/tests/integration/tests/reaction/pathway.py b/api/tests/integration/tests/reaction/pathway.py index e2bd05f00f..b3771c01e7 100644 --- a/api/tests/integration/tests/reaction/pathway.py +++ b/api/tests/integration/tests/reaction/pathway.py @@ -29,6 +29,7 @@ def find_diff(a, b): "pathway8", "pathway9", "pathway10", + "pathway11", ] for filename in files: diff --git a/api/tests/integration/tests/reaction/reactions/pathway11.rdf b/api/tests/integration/tests/reaction/reactions/pathway11.rdf new file mode 100644 index 0000000000..e32da0593a --- /dev/null +++ b/api/tests/integration/tests/reaction/reactions/pathway11.rdf @@ -0,0 +1,671 @@ +$RDFILE 1 +$DATM 2/8/2024, 10:14:53 AM +$RFMT +$RXN + + RDKit + + 2 1 +$MOL + + RDKit 2D + + 6 5 0 0 0 0 0 0 0 0999 V2000 + -0.2893 -0.4179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1549 0.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1541 1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0213 -0.4165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8869 0.0841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7533 -0.4153 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 2 0 + 4 5 1 0 + 5 6 1 0 +M END +$MOL + + RDKit 2D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + -3.6362 -0.9186 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7720 -0.4156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7756 0.5844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9042 -0.9124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0400 -0.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1722 -0.9062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6920 -0.4030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6884 0.5968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5526 1.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1794 1.0938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0436 0.5906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 2 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 1 0 + 8 10 4 0 + 10 11 4 0 + 11 5 4 0 +M END +$MOL + + RDKit 2D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + -4.1340 0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1348 -0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0012 -1.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2692 -1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4028 -0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5372 -1.2805 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6710 -0.7813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1948 -1.2819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0612 -0.7827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0620 0.2173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9284 0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9292 1.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7956 2.2159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0636 2.2173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1964 0.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6702 0.2187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 2 0 + 4 5 1 0 + 5 6 1 0 + 6 7 1 0 + 7 8 4 0 + 8 9 4 0 + 9 10 4 0 + 10 11 1 0 + 11 12 1 0 + 12 13 1 0 + 12 14 2 0 + 10 15 4 0 + 15 16 4 0 + 16 7 4 0 +M END + +$DTYPE Name +$DATUM Mitsunobu reaction +$DTYPE Reference +$DATUM [10.1021/jo0345751]: https://doi.org/10.1021/jo0345751 [10.1021/ol0618757]: https://doi.org/10.1021/ol0618757 +$DTYPE Reaction Conditions +$DATUM DEAD.or.DCAD.or.DIAD.PPh3 +$DTYPE SMILES +$DATUM CC(C)=CCO.NC(=O)Cc1ccc(O)cc1>>CC(C)=CCOc1ccc(CC(N)=O)cc1 +$DTYPE Protections +$DATUM Not available +$DTYPE Inventory +$DATUM Not available +$RFMT +$RXN + + RDKit + + 1 1 +$MOL + + RDKit 2D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + -7.6865 0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6874 -0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -8.5537 -1.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.8217 -1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.9553 -0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0897 -1.2805 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2235 -0.7813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3578 -1.2819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4914 -0.7827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4905 0.2173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6242 0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6233 1.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7570 2.2159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4889 2.2173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3562 0.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2227 0.2187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 2 0 + 4 5 1 0 + 5 6 1 0 + 6 7 1 0 + 7 8 4 0 + 8 9 4 0 + 9 10 4 0 + 10 11 1 0 + 11 12 1 0 + 12 13 1 0 + 12 14 2 0 + 10 15 4 0 + 15 16 4 0 + 16 7 4 0 +M END +$MOL + + RDKit 2D + + 14 14 0 0 0 0 0 0 0 0999 V2000 + 0.2544 2.1405 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6120 1.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4776 2.1419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6128 0.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4792 0.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4800 -0.8581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3464 -1.3573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2120 -0.8567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0784 -1.3561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.9440 -0.8553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8104 -1.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6760 -0.8539 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2112 0.1433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3448 0.6425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 2 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 2 0 + 8 13 4 0 + 13 14 4 0 + 14 5 4 0 +M END + +$DTYPE Name +$DATUM Ozonolysis +$DTYPE Reference +$DATUM [10.1016/j.tet.2017.03.039]: https://doi.org/10.1016/j.tet.2017.03.039 +$DTYPE Reaction Conditions +$DATUM O3.MeOH.CH2Cl2.PPh3 or Me2S.low temperature +$DTYPE SMILES +$DATUM CC(C)=CCOc1ccc(CC(N)=O)cc1>>NC(=O)Cc1ccc(OCC=O)cc1 +$DTYPE Protections +$DATUM Not available +$DTYPE Inventory +$DATUM Not available +$RFMT +$RXN + + RDKit + + 2 1 +$MOL + + RDKit 2D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + -0.0003 -0.1674 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8659 0.3334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7323 -0.1660 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 +M END +$MOL + + RDKit 2D + + 14 14 0 0 0 0 0 0 0 0999 V2000 + 1.0110 2.1405 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1446 1.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7210 2.1419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1438 0.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7226 0.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7234 -0.8581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5898 -1.3573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4554 -0.8567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3218 -1.3561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1874 -0.8553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0538 -1.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.9194 -0.8539 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4546 0.1433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5882 0.6425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 2 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 2 0 + 8 13 4 0 + 13 14 4 0 + 14 5 4 0 +M END +$MOL + + RDKit 2D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + -3.2719 2.9350 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4055 2.4358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5399 2.9364 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4047 1.4358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5385 0.9364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5377 -0.0636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6713 -0.5628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1945 -0.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0607 -0.5616 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0615 -1.5616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9279 -2.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7935 -1.5602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9287 -3.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7951 -3.5602 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1937 0.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6727 1.4370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 2 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 1 0 + 11 13 1 0 + 13 14 1 0 + 8 15 4 0 + 15 16 4 0 + 16 5 4 0 +M END + +$DTYPE Name +$DATUM Addition of dihalomethane to aldehyde +$DTYPE Reference +$DATUM [10.1016/j.tetlet.2005.02.093]: https://doi.org/10.1016/j.tetlet.2005.02.093 [10.1021/jo970318i]: https://doi.org/10.1021/jo970318i [10.1016/j.tet.2012.02.033]: https://doi.org/10.1016/j.tet.2012.02.033 +$DTYPE Reaction Conditions +$DATUM SmI2.THF +$DTYPE SMILES +$DATUM ClCI.NC(=O)Cc1ccc(OCC=O)cc1>>NC(=O)Cc1ccc(OCC(O)CCl)cc1 +$DTYPE Protections +$DATUM Not available +$DTYPE Inventory +$DATUM Not available +$RFMT +$RXN + + RDKit + + 2 1 +$MOL + + RDKit 2D + + 6 5 0 0 0 0 0 0 0 0999 V2000 + -0.2885 -0.5821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1549 -0.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1557 0.9173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0205 -0.5835 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8869 -0.0841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7533 0.4153 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 1 0 + 4 5 2 0 + 5 6 2 0 +M END +$MOL + + RDKit 2D + + 8 8 0 0 0 0 0 0 0 0999 V2000 + -0.8881 -0.9990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0217 -0.4996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8439 -1.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7103 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7111 0.4990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8455 0.9996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0209 0.5004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8865 1.0010 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 4 0 + 3 4 4 0 + 4 5 4 0 + 5 6 4 0 + 6 7 4 0 + 7 8 1 0 + 7 2 4 0 +M END +$MOL + + RDKit 2D + + 13 14 0 0 0 0 0 0 0 0999 V2000 + -2.7676 0.5970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7676 0.5978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2682 1.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2668 -0.2678 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2666 -0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3202 0.5426 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2716 0.2342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1372 0.7348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0036 0.2356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0044 -0.7644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1388 -1.2650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2724 -0.7658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3214 -1.0758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 4 0 + 9 10 4 0 + 10 11 4 0 + 11 12 4 0 + 12 13 4 0 + 13 5 4 0 + 12 7 4 0 +M END + +$DTYPE Name +$DATUM Published reaction +$DTYPE Reference +$DATUM [10.1002/ANIE.201201451]: https://doi.org/10.1002/ANIE.201201451 +$DTYPE Reaction Conditions +$DATUM Stage 1: 14 h, Copper(II) chloride, Dimethylformamide, Dichloromethane, CK2O3 Potassium carbonate | Stage 2: 5 h, 80 degree, acid, Dy(3+)-salt C3Dy1F9O9S3, Dichloromethane, Acetonitrile +$DTYPE SMILES +$DATUM CC(C)N=C=S.Nc1ccccc1O>>CC(C)Nc1nc2ccccc2o1 +$DTYPE Protections +$DATUM Not available +$DTYPE Inventory +$DATUM Not available +$RFMT +$RXN + + RDKit + + 2 1 +$MOL + + RDKit 2D + + 13 14 0 0 0 0 0 0 0 0999 V2000 + -6.4787 0.5970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.4787 0.5978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.9793 1.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.9779 -0.2678 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9777 -0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3909 0.5426 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4395 0.2342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5739 0.7348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7075 0.2356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7067 -0.7644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5723 -1.2650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4387 -0.7658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3897 -1.0758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 1 0 + 4 5 1 0 + 5 6 4 0 + 6 7 4 0 + 7 8 4 0 + 8 9 4 0 + 9 10 4 0 + 10 11 4 0 + 11 12 4 0 + 12 13 4 0 + 13 5 4 0 + 12 7 4 0 +M END +$MOL + + RDKit 2D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + -4.9897 2.9350 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1233 2.4358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2577 2.9364 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1225 1.4358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2563 0.9364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2555 -0.0636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3891 -0.5628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5233 -0.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6571 -0.5616 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6563 -1.5616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2101 -2.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0757 -1.5602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2109 -3.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0773 -3.5602 0.0000 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0 + 22 23 4 0 + 23 24 4 0 + 24 25 4 0 + 25 26 4 0 + 26 27 4 0 + 27 28 4 0 + 19 10 4 0 + 28 20 4 0 + 27 22 4 0 +M END + +$DTYPE Name +$DATUM Alkylation of amines with alkyl halides +$DTYPE Reference +$DATUM [10.1016/s0040-4039(00)74286-9]: https://doi.org/10.1016/s0040-4039(00)74286-9 [10.1021/acs.oprd.8b00074]: https://doi.org/10.1021/acs.oprd.8b00074 [10.1016/S0040-4020(01)00989-9]: https://doi.org/10.1016/S0040-4020(01)00989-9 [10.1080/00397911.2013.828077]: https://doi.org/10.1080/00397911.2013.828077 [10.1016/j.bmcl.2012.08.032]: https://doi.org/10.1016/j.bmcl.2012.08.032 +$DTYPE Reaction Conditions +$DATUM KOH. toluene. 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-1.3714 0.2349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2370 0.7355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 1 0 + 4 5 1 0 + 5 6 1 0 + 6 7 1 0 + 6 8 1 0 + 8 9 1 0 + 9 10 1 0 + 10 11 4 0 + 11 12 4 0 + 12 13 4 0 + 13 14 1 0 + 14 15 1 0 + 15 16 1 0 + 15 17 2 0 + 13 18 4 0 + 18 19 4 0 + 19 10 4 0 +M END + +$DTYPE Name +$DATUM Removal of benzoxazol-2-yl group from amines +$DTYPE Reference +$DATUM [10.1021/ol501935d]: https://doi.org/10.1021/ol501935d +$DTYPE Reaction Conditions +$DATUM LAH.THF.reflux +$DTYPE SMILES +$DATUM CC(C)N(CC(O)COc1ccc(CC(N)=O)cc1)c1nc2ccccc2o1>>CC(C)NCC(O)COc1ccc(CC(N)=O)cc1 +$DTYPE Protections +$DATUM Not available +$DTYPE Inventory +$DATUM Not available + +END diff --git a/api/tests/integration/tests/reaction/ref/arom/pathway1.ket b/api/tests/integration/tests/reaction/ref/arom/pathway1.ket index 9af7ed7592..6a6e4618c4 100644 --- a/api/tests/integration/tests/reaction/ref/arom/pathway1.ket +++ b/api/tests/integration/tests/reaction/ref/arom/pathway1.ket @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/core/indigo-core/layout/pathway_layout.h b/core/indigo-core/layout/pathway_layout.h index 0073ad65a5..bb9a69092c 100644 --- a/core/indigo-core/layout/pathway_layout.h +++ b/core/indigo-core/layout/pathway_layout.h @@ -48,7 +48,7 @@ namespace indigo static constexpr float ARROW_TAIL_LENGTH = 0.5f; static constexpr float VERTICAL_SPACING = 2.5f; static constexpr float MULTIPATHWAY_VERTICAL_SPACING = 1.5f; - static constexpr float ARROW_LENGTH_FACTOR = 6.5f; + static constexpr float ARROW_LENGTH_FACTOR = 7.0f; static constexpr float MIN_BOND_MEAN = 0.01f; static constexpr int MAX_DEPTHS = 10; @@ -79,7 +79,7 @@ namespace indigo parent(nullptr), nextSibling(nullptr), prevSibling(nullptr), reaction(pwr), boundingBox() { auto& reactionNode = reaction.getReactionNode(nodeIdx); - auto& simpleReaction = reaction.getReaction(reactionNode.reactionIdx); + reactionIndex = reactionNode.reactionIdx; // create as a final reactant child if (reactantIdx != -1) { @@ -105,6 +105,7 @@ namespace indigo } else { + auto& simpleReaction = reaction.getReaction(reactionIndex); for (auto pidx : simpleReaction.productIndexes) { auto& mol = reaction.getMolecule(pidx); @@ -128,25 +129,6 @@ namespace indigo width += boundingBox.width(); // add some spacing for plus height = std::max(boundingBox.height(), height); } - - // add precursors free reactants as children - for (int i = 0; i < simpleReaction.reactantIndexes.size(); ++i) - { - // check if it is a final reactant - if (!reactionNode.connectedReactants.find(i)) - { - auto ridx = simpleReaction.reactantIndexes[i]; - reactantsNoPrecursors.emplace_back(reaction, pwl, nodeIdx, bondLength, ridx); - PathwayLayoutItem* item = &reactantsNoPrecursors.back(); - children.push_back(item); - item->parent = this; - if (children.size() > 1) - { - children[children.size() - 2]->nextSibling = item; - item->prevSibling = children[children.size() - 2]; - } - } - } } width += COMPONENTS_MARGIN * molecules.size(); } @@ -214,6 +196,7 @@ namespace indigo std::vector> molecules; PathwayReaction& reaction; Rect2f boundingBox; + int reactionIndex; }; struct PathwayLayoutRootItem @@ -243,9 +226,9 @@ namespace indigo PathwayLayoutItem* apportion(PathwayLayoutItem* currentNode, PathwayLayoutItem* ancestorNode); - PathwayLayoutItem* nextTop(PathwayLayoutItem* node); + PathwayLayoutItem* nextUpper(PathwayLayoutItem* node); - PathwayLayoutItem* nextBottom(PathwayLayoutItem* node); + PathwayLayoutItem* nextLower(PathwayLayoutItem* node); void moveSubtree(PathwayLayoutItem* parent, PathwayLayoutItem* wp, float shift); diff --git a/core/indigo-core/layout/reaction_layout.h b/core/indigo-core/layout/reaction_layout.h index 858471e2b0..5df591c04b 100644 --- a/core/indigo-core/layout/reaction_layout.h +++ b/core/indigo-core/layout/reaction_layout.h @@ -46,6 +46,9 @@ namespace indigo void makePathwayFromSimple(); // layout if reaction components are not in the places + static bool hasAnyIntersect(const std::vector& bblist); + static bool validVerticalRange(const std::vector& bblist); + void fixLayout(); void processSideBoxes(std::vector& pluses, Rect2f& type_box, int side); @@ -65,6 +68,20 @@ namespace indigo }; private: + struct SweepEvent + { + float x; + bool is_start; + float y_start, y_end; + + bool operator<(const SweepEvent& other) const + { + if (x != other.x) + return x < other.x; + return is_start > other.is_start; + } + }; + void _makePathway(); void _updateMetadata(); void _pushMol(Metalayout::LayoutLine& line, int id, bool is_agent = false); diff --git a/core/indigo-core/layout/src/pathway_layout.cpp b/core/indigo-core/layout/src/pathway_layout.cpp index be26ce8d2e..ac739683f6 100644 --- a/core/indigo-core/layout/src/pathway_layout.cpp +++ b/core/indigo-core/layout/src/pathway_layout.cpp @@ -38,7 +38,7 @@ void PathwayLayout::make() PathwayLayoutItem* root = &_layoutItems[rootIndexes]; std::vector>> depths; - traverse(root, [&rootItem, &depths](PathwayLayoutItem* item, int level) { + traverse(root, [&rootItem, &depths, this](PathwayLayoutItem* item, int level) { int item_index = (int)rootItem.layoutItems.size(); if ((int)depths.size() > level) { @@ -78,12 +78,12 @@ void PathwayLayout::make() } rootItem.boundingBox = pathwayBoundingBox; + yShift += pathwayBoundingBox.height() + MULTIPATHWAY_VERTICAL_SPACING; for (size_t i = 0; i < layoutItems.size(); ++i) { auto& layoutItem = *layoutItems[i]; - layoutItem.boundingBox.offset(Vec2f(-pathwayBoundingBox.left(), -pathwayBoundingBox.bottom() + yShift)); + layoutItem.boundingBox.offset(Vec2f(-pathwayBoundingBox.left(), -pathwayBoundingBox.bottom() - yShift)); } - yShift += pathwayBoundingBox.height() + MULTIPATHWAY_VERTICAL_SPACING; } applyLayout(); } @@ -100,19 +100,47 @@ void PathwayLayout::buildLayoutTree() for (int i = 0; i < _reaction.getReactionNodeCount(); ++i) { auto& reactionNode = _reaction.getReactionNode(i); + auto& simpleReaction = _reaction.getReaction(i); + auto& currentLayoutItem = _layoutItems[i]; // add successor reactants to layout items - for (int j : reactionNode.precursorReactionIndexes) + + std::unordered_set already_added; + for (int j = 0; j < simpleReaction.reactantIndexes.size(); ++j) { - auto& precursorLayoutItem = _layoutItems[j]; - auto lastChild = currentLayoutItem.getLastChild(); - if (lastChild != nullptr) + // check if it is a final reactant + auto pcr = reactionNode.connectedReactants.at2(j); + if (pcr) { - lastChild->nextSibling = &precursorLayoutItem; - precursorLayoutItem.prevSibling = lastChild; + if (!already_added.count(*pcr)) + { + // add connected child + already_added.insert(*pcr); + auto& precursorLayoutItem = _layoutItems[*pcr]; + auto lastChild = currentLayoutItem.getLastChild(); + if (lastChild != nullptr) + { + lastChild->nextSibling = &precursorLayoutItem; + precursorLayoutItem.prevSibling = lastChild; + } + currentLayoutItem.children.push_back(&precursorLayoutItem); + precursorLayoutItem.parent = ¤tLayoutItem; + } + } + else + { + // add free reactant without precursors + auto ridx = simpleReaction.reactantIndexes[j]; + currentLayoutItem.reactantsNoPrecursors.emplace_back(_reaction, *this, i, _bond_length, ridx); + PathwayLayoutItem* item = ¤tLayoutItem.reactantsNoPrecursors.back(); + currentLayoutItem.children.push_back(item); + item->parent = ¤tLayoutItem; + if (currentLayoutItem.children.size() > 1) + { + currentLayoutItem.children[currentLayoutItem.children.size() - 2]->nextSibling = item; + item->prevSibling = currentLayoutItem.children[currentLayoutItem.children.size() - 2]; + } } - currentLayoutItem.children.push_back(&precursorLayoutItem); - precursorLayoutItem.parent = ¤tLayoutItem; } } } @@ -141,13 +169,14 @@ void PathwayLayout::firstWalk(PathwayLayoutItem* node, int level, int depth) if (node->children.empty()) { PathwayLayoutItem* layoutItem = node->prevSibling; - node->prelim = (layoutItem == nullptr) ? 0 : (layoutItem->prelim + spacing(layoutItem, node, true)); + node->prelim = layoutItem ? layoutItem->prelim + spacing(layoutItem, node, true) : 0; } else { PathwayLayoutItem* topMost = node->getFirstChild(); PathwayLayoutItem* bottomMost = node->getLastChild(); PathwayLayoutItem* defaultAncestor = topMost; + for (auto child : node->children) { firstWalk(child, level++, depth + 1); @@ -178,10 +207,21 @@ void PathwayLayout::secondWalk(PathwayLayoutItem* node, PathwayLayoutItem* paren node->clear(); } +void insertSorted(std::vector>>& objs, std::pair> newPair) +{ + auto it = std::lower_bound(objs.begin(), objs.end(), newPair, + [](const std::pair>& element, const std::pair>& value) { + return element.first < value.first; + }); + + objs.emplace(it, std::move(newPair)); +} + void PathwayLayout::applyLayout() { // upload coordinates back to the reaction _reaction.meta().resetReactionData(); + std::vector>> metaArrows; for (auto& rootItem : _layoutRootItems) { auto& layoutItems = rootItem.layoutItems; @@ -212,38 +252,43 @@ void PathwayLayout::applyLayout() // add spines if (tails.size() > 1) { - Vec2f spineTop(tails.front().x + ARROW_TAIL_LENGTH, tails.front().y); - Vec2f spineBottom(tails.back().x + ARROW_TAIL_LENGTH, tails.back().y); + Vec2f spineTop(tails.front().x + ARROW_TAIL_LENGTH * _bond_length, tails.front().y); + Vec2f spineBottom(tails.back().x + ARROW_TAIL_LENGTH * _bond_length, tails.back().y); arrows.push_back(spineBottom); arrows.push_back(spineTop); - _reaction.meta().addMetaObject(new KETReactionMultitailArrow(arrows.begin(), arrows.end())); + insertSorted(metaArrows, + std::make_pair(layoutItem->reactionIndex, std::make_unique(arrows.begin(), arrows.end()))); } else if (tails.size()) { - _reaction.meta().addMetaObject(new KETReactionArrow(KETReactionArrow::EFilledTriangle, tails.front(), head)); + insertSorted(metaArrows, std::make_pair(layoutItem->reactionIndex, + std::make_unique(KETReactionArrow::EFilledTriangle, tails.front(), head))); } } } } + + for (auto& arrow : metaArrows) + _reaction.meta().addMetaObject(arrow.second.release()); } PathwayLayout::PathwayLayoutItem* PathwayLayout::apportion(PathwayLayoutItem* currentNode, PathwayLayoutItem* ancestorNode) { PathwayLayoutItem* previousSibling = currentNode->prevSibling; - if (previousSibling != nullptr) + if (previousSibling) { PathwayLayoutItem *innerNode = currentNode, *siblingInner = previousSibling, *outerNode = currentNode, *siblingOuter = currentNode->parent->getFirstChild(); float modInner = innerNode->mod, modSiblingInner = siblingInner->mod, modOuter = outerNode->mod, modSiblingOuter = siblingOuter->mod; - PathwayLayoutItem* nextLower = nextBottom(siblingInner); - PathwayLayoutItem* nextUpper = nextTop(innerNode); + PathwayLayoutItem* next_lower = nextLower(siblingInner); + PathwayLayoutItem* next_upper = nextUpper(innerNode); - while (nextLower != nullptr && nextUpper != nullptr) + while (next_lower && next_upper) { - siblingInner = nextLower; - innerNode = nextUpper; - siblingOuter = nextTop(siblingOuter); - outerNode = nextBottom(outerNode); + siblingInner = next_lower; + innerNode = next_upper; + siblingOuter = nextUpper(siblingOuter); + outerNode = nextLower(outerNode); outerNode->ancestor = currentNode; float shift = (siblingInner->prelim + modSiblingInner) - (innerNode->prelim + modInner) + spacing(siblingInner, innerNode, false); if (shift > 0) @@ -257,17 +302,17 @@ PathwayLayout::PathwayLayoutItem* PathwayLayout::apportion(PathwayLayoutItem* cu modSiblingOuter += siblingOuter->mod; modOuter += outerNode->mod; - nextLower = nextBottom(siblingInner); - nextUpper = nextTop(innerNode); + next_lower = nextLower(siblingInner); + next_upper = nextUpper(innerNode); } - if (nextLower != nullptr && nextBottom(outerNode) == nullptr) + if (next_lower != nullptr && nextLower(outerNode) == nullptr) { - outerNode->thread = nextLower; + outerNode->thread = next_lower; outerNode->mod += modSiblingInner - modOuter; } - if (nextUpper != nullptr && nextTop(siblingOuter) == nullptr) + if (next_upper != nullptr && nextUpper(siblingOuter) == nullptr) { - siblingOuter->thread = nextUpper; + siblingOuter->thread = next_upper; siblingOuter->mod += modInner - modSiblingOuter; ancestorNode = currentNode; } @@ -297,13 +342,13 @@ void PathwayLayout::executeShifts(PathwayLayoutItem* node) } } -PathwayLayout::PathwayLayoutItem* PathwayLayout::nextTop(PathwayLayoutItem* node) +PathwayLayout::PathwayLayoutItem* PathwayLayout::nextUpper(PathwayLayoutItem* node) { PathwayLayoutItem* child = node->getFirstChild(); return (child != nullptr) ? child : node->thread; } -PathwayLayout::PathwayLayoutItem* PathwayLayout::nextBottom(PathwayLayoutItem* node) +PathwayLayout::PathwayLayoutItem* PathwayLayout::nextLower(PathwayLayoutItem* node) { PathwayLayoutItem* child = node->getLastChild(); return (child != nullptr) ? child : node->thread; @@ -332,8 +377,6 @@ void PathwayLayout::traverse(PathwayLayoutItem* root, std::functionchildren) - { queue.push({child, level + 1}); - } } } diff --git a/core/indigo-core/layout/src/reaction_layout.cpp b/core/indigo-core/layout/src/reaction_layout.cpp index 229526bf88..eafb1b3f37 100644 --- a/core/indigo-core/layout/src/reaction_layout.cpp +++ b/core/indigo-core/layout/src/reaction_layout.cpp @@ -53,6 +53,50 @@ ReactionLayout::ReactionLayout(BaseReaction& r, bool smart_layout, const LayoutO { } +bool ReactionLayout::hasAnyIntersect(const std::vector& bblist) +{ + std::vector events; + events.reserve(bblist.size() * 2); + for (const auto& rect : bblist) + { + events.emplace_back(SweepEvent{rect.left(), true, rect.bottom(), rect.top()}); + events.emplace_back(SweepEvent{rect.left() + rect.width(), false, rect.bottom(), rect.top()}); + } + std::sort(events.begin(), events.end()); + std::set> active; + for (const auto& event : events) + { + if (event.is_start) + { + auto it = active.lower_bound({event.y_start, event.y_end}); + if (it != active.begin()) + { + auto prev = std::prev(it); + if (prev->second > event.y_start) + return true; + } + if (it != active.end() && it->first < event.y_end) + return true; + active.emplace(event.y_start, event.y_end); + } + else + { + active.erase({event.y_start, event.y_end}); + } + } + return false; +} + +bool ReactionLayout::validVerticalRange(const std::vector& bblist) +{ + if (bblist.empty()) + return true; + + float max_start = std::max_element(bblist.begin(), bblist.end(), [](const Rect2f& a, const Rect2f& b) { return a.bottom() < b.bottom(); })->bottom(); + float min_end = std::min_element(bblist.begin(), bblist.end(), [](const Rect2f& a, const Rect2f& b) { return a.top() < b.top(); })->top(); + return max_start <= min_end; +} + void ReactionLayout::fixLayout() { int arrows_count = _r.meta().getMetaCount(KETReactionArrow::CID); @@ -62,6 +106,7 @@ void ReactionLayout::fixLayout() return; Rect2f bb; + std::vector bboxes; // Calculate rightTop of reactant bounding box bool invalid_layout = false; float cur_left = 0, cur_right = 0; @@ -69,6 +114,7 @@ void ReactionLayout::fixLayout() i = _r.isRetrosyntetic() ? _r.productNext(i) : _r.reactantNext(i)) { _r.getBaseMolecule(i).getBoundingBox(bb); + bboxes.push_back(bb); if (i == 0 || (bb.left() > cur_left && bb.right() > cur_right)) { cur_left = bb.left(); @@ -78,20 +124,37 @@ void ReactionLayout::fixLayout() invalid_layout = true; } + bool first_after_arrow = true; // Calculate leftBottom of product bounding box for (int i = _r.isRetrosyntetic() ? _r.reactantBegin() : _r.productBegin(); i != (_r.isRetrosyntetic() ? _r.reactantEnd() : _r.productEnd()); i = _r.isRetrosyntetic() ? _r.reactantNext(i) : _r.productNext(i)) { _r.getBaseMolecule(i).getBoundingBox(bb); + bboxes.push_back(bb); if (bb.left() > cur_left && bb.right() > cur_right) { + if (first_after_arrow) + { + first_after_arrow = false; + if (bb.left() - cur_left < default_arrow_size) + { + invalid_layout = true; + break; + } + } cur_left = bb.left(); cur_right = bb.right(); } else + { invalid_layout = true; + break; + } } + if (!invalid_layout) + invalid_layout = hasAnyIntersect(bboxes) || !validVerticalRange(bboxes); + // if left side of product bb at left of right side of reactant bb - fix layout if (invalid_layout) { diff --git a/core/indigo-core/molecule/ket_commons.h b/core/indigo-core/molecule/ket_commons.h index 6feed635ac..2b355a2af2 100644 --- a/core/indigo-core/molecule/ket_commons.h +++ b/core/indigo-core/molecule/ket_commons.h @@ -483,12 +483,13 @@ namespace indigo struct MolSumm { - MolSumm() : bbox(Vec2f(0, 0), Vec2f(0, 0)), role(BaseReaction::UNDEFINED){}; - MolSumm(const Rect2f& box) : bbox(box), role(BaseReaction::UNDEFINED){}; + MolSumm() : bbox(Vec2f(0, 0), Vec2f(0, 0)), role(BaseReaction::UNDEFINED), reaction_idx(-1){}; + MolSumm(const Rect2f& box) : bbox(box), role(BaseReaction::UNDEFINED), reaction_idx(-1){}; Rect2f bbox; std::vector indexes; int role; + int reaction_idx; std::vector arrows_to; std::vector arrows_from; }; @@ -577,5 +578,6 @@ namespace indigo } }; + std::string getDebugSmiles(BaseMolecule& mol); } #endif diff --git a/core/indigo-core/molecule/src/ket_commons.cpp b/core/indigo-core/molecule/src/ket_commons.cpp index 5ac804a31c..9ab2dc1a28 100644 --- a/core/indigo-core/molecule/src/ket_commons.cpp +++ b/core/indigo-core/molecule/src/ket_commons.cpp @@ -21,8 +21,10 @@ #endif #include "molecule/ket_commons.h" +#include "base_cpp/output.h" #include "base_cpp/scanner.h" #include "molecule/monomer_commons.h" +#include "molecule/smiles_saver.h" #include namespace indigo @@ -133,6 +135,16 @@ namespace indigo return res; } + std::string getDebugSmiles(BaseMolecule& mol) + { + Array out_buffer; + ArrayOutput output(out_buffer); + SmilesSaver saver(output); + saver.saveMolecule(mol.asMolecule()); + out_buffer.push('\0'); + return out_buffer.ptr(); + } + KETImage::KETImage(const Rect2f& bbox, KETImage::ImageFormat format, const std::string& data, bool is_base64) : MetaObject(CID), _bbox(bbox), _image_format(format) { diff --git a/core/indigo-core/reaction/pathway_reaction.h b/core/indigo-core/reaction/pathway_reaction.h index 48e881ac08..3c997b924a 100644 --- a/core/indigo-core/reaction/pathway_reaction.h +++ b/core/indigo-core/reaction/pathway_reaction.h @@ -77,7 +77,7 @@ namespace indigo // vector of precursor reactions indexes Array precursorReactionIndexes; // utility information - RedBlackSet connectedReactants; // where the precursors' products are connected to + RedBlackMap connectedReactants; // where the precursors' products are connected to int multiTailMetaIndex; }; diff --git a/core/indigo-core/reaction/reaction_multistep_detector.h b/core/indigo-core/reaction/reaction_multistep_detector.h index de0716a28d..db58436ddd 100644 --- a/core/indigo-core/reaction/reaction_multistep_detector.h +++ b/core/indigo-core/reaction/reaction_multistep_detector.h @@ -65,8 +65,10 @@ namespace indigo private: void createSummBlocks(); - bool detectArrows(); - bool detectMultitailArrows(); + void sortSummblocks(); + + bool mapReactionComponents(); + bool mapMultitailReactionComponents(); bool findPlusNeighbours(const Vec2f& plus_pos, const FLOAT_INT_PAIRS& mol_tops, const FLOAT_INT_PAIRS& mol_bottoms, const FLOAT_INT_PAIRS& mol_lefts, const FLOAT_INT_PAIRS& mol_rights, std::pair& connection); diff --git a/core/indigo-core/reaction/src/pathway_reaction_builder.cpp b/core/indigo-core/reaction/src/pathway_reaction_builder.cpp index 4b7df442bb..20d48302ca 100644 --- a/core/indigo-core/reaction/src/pathway_reaction_builder.cpp +++ b/core/indigo-core/reaction/src/pathway_reaction_builder.cpp @@ -166,8 +166,6 @@ void PathwayReactionBuilder::buildNodes(std::deque& reactions) { auto j = m_it->first; auto& val = m_it->second; - Array val_arr; - val_arr.copy(val); if (rn.successorReactionIndexes.size() == 0) { auto& rnj = _pathwayReaction->getReactionNode(j); @@ -185,7 +183,7 @@ void PathwayReactionBuilder::buildNodes(std::deque& reactions) rn.successorReactionIndexes.push(j); rnj.precursorReactionIndexes.push(i); for (auto ridx : val) - rnj.connectedReactants.insert(ridx); + rnj.connectedReactants.insert(ridx, i); } else { @@ -218,7 +216,7 @@ void PathwayReactionBuilder::buildRootReaction(PathwayReaction& reaction) const auto& root_reactions = reaction.getRootReactions(); if (root_reactions.size()) { - auto& first_root = reaction.getReaction(root_reactions.back()); + auto& first_root = reaction.getReaction(root_reactions.front()); for (auto& idx : first_root.reactantIndexes) { auto& mol = reaction.getMolecule(idx); diff --git a/core/indigo-core/reaction/src/reaction_cdxml_saver.cpp b/core/indigo-core/reaction/src/reaction_cdxml_saver.cpp index 90b7900682..91f1612981 100644 --- a/core/indigo-core/reaction/src/reaction_cdxml_saver.cpp +++ b/core/indigo-core/reaction/src/reaction_cdxml_saver.cpp @@ -363,7 +363,7 @@ void ReactionCdxmlSaver::_addStep(BaseReaction& rxn, MoleculeCdxmlSaver& molsave } else { - if (rxn.reactionBlocksCount()) + if (rxn.reactionBlocksCount() && arrow_id.second < rxn.reactionBlocksCount()) { auto& rb = rxn.reactionBlock(arrow_id.second); auto& reactants = rxn.isRetrosyntetic() ? rb.products : rb.reactants; @@ -390,7 +390,7 @@ void ReactionCdxmlSaver::_addStep(BaseReaction& rxn, MoleculeCdxmlSaver& molsave } else { - if (rxn.reactionBlocksCount()) + if (rxn.reactionBlocksCount() && arrow_id.second < rxn.reactionBlocksCount()) { auto& rb = rxn.reactionBlock(arrow_id.second); auto& products = rxn.isRetrosyntetic() ? rb.reactants : rb.products; diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp index a02ca5d415..d11d5655bc 100644 --- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp +++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp @@ -19,6 +19,7 @@ #include "reaction/reaction_multistep_detector.h" #include "reaction/pathway_reaction.h" #include "reaction/reaction.h" +#include using namespace indigo; @@ -236,22 +237,58 @@ void ReactionMultistepDetector::createSummBlocks() } } +void ReactionMultistepDetector::sortSummblocks() +{ + // Create a list of original indices + std::vector indices(_component_summ_blocks.size()); + std::iota(indices.begin(), indices.end(), 0); + + // Sort the indices based on reaction_idx + std::sort(indices.begin(), indices.end(), + [&](int a, int b) -> bool { return _component_summ_blocks[a].reaction_idx < _component_summ_blocks[b].reaction_idx; }); + + // Create a mapping from old index to new index + std::vector old_to_new(_component_summ_blocks.size()); + for (int new_idx = 0; new_idx < static_cast(indices.size()); ++new_idx) + old_to_new[indices[new_idx]] = new_idx; + + // Sort the blocks based on the sorted indices + std::vector sorted_blocks; + sorted_blocks.reserve(_component_summ_blocks.size()); + for (auto idx : indices) + sorted_blocks.emplace_back(std::move(_component_summ_blocks[idx])); + _component_summ_blocks = std::move(sorted_blocks); + + // Update arrows_to and arrows_from with new indices + for (auto& block : _component_summ_blocks) + { + auto update_arrow = [&](int& arrow) { + if (arrow >= 0 && arrow < static_cast(old_to_new.size())) + arrow = old_to_new[arrow]; + }; + + std::for_each(block.arrows_to.begin(), block.arrows_to.end(), update_arrow); + std::for_each(block.arrows_from.begin(), block.arrows_from.end(), update_arrow); + } +} + ReactionMultistepDetector::ReactionType ReactionMultistepDetector::detectReaction() { createSummBlocks(); - bool has_multistep = detectArrows(); - bool has_multitail = detectMultitailArrows(); + bool has_multistep = mapReactionComponents(); + bool has_multitail = mapMultitailReactionComponents(); + sortSummblocks(); return has_multitail ? ReactionType::EPathwayReaction : (has_multistep ? ReactionType ::EMutistepReaction : ReactionType::ESimpleReaction); } -bool ReactionMultistepDetector::detectArrows() +bool ReactionMultistepDetector::mapReactionComponents() { int arrow_count = _bmol.meta().getMetaCount(KETReactionArrow::CID); if (arrow_count == 0) return false; - for (int i = 0; i < arrow_count; ++i) + for (int reaction_index = 0; reaction_index < arrow_count; ++reaction_index) { - auto& arrow = (const KETReactionArrow&)_bmol.meta().getMetaObject(KETReactionArrow::CID, i); + auto& arrow = (const KETReactionArrow&)_bmol.meta().getMetaObject(KETReactionArrow::CID, reaction_index); int arrow_type = arrow.getArrowType(); bool reverseReactionOrder = arrow_type == KETReactionArrow::ERetrosynthetic; const Vec2f& arr_begin = !reverseReactionOrder ? arrow.getTail() : arrow.getHead(); @@ -285,7 +322,7 @@ bool ReactionMultistepDetector::detectArrows() // TODO: add upper limit if (min_dist_prod > 0 && min_dist_reac > 0) // if both ends present { - auto& rc_arrow = _reaction_components[_moleculeCount + _bmol.meta().getMetaCount(KETReactionPlus::CID) + i]; + auto& rc_arrow = _reaction_components[_moleculeCount + _bmol.meta().getMetaCount(KETReactionPlus::CID) + reaction_index]; rc_arrow.summ_block_idx = ReactionComponent::CONNECTED; // mark arrow as connected auto& csb_min_prod = _component_summ_blocks[idx_cs_min_prod]; if (csb_min_prod.role == BaseReaction::UNDEFINED) @@ -302,12 +339,14 @@ bool ReactionMultistepDetector::detectArrows() // 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_prod.reaction_idx = reaction_index; } } return arrow_count > 1; } -bool ReactionMultistepDetector::detectMultitailArrows() +bool ReactionMultistepDetector::mapMultitailReactionComponents() { int pathway_count = _bmol.meta().getMetaCount(KETReactionMultitailArrow::CID); @@ -316,9 +355,9 @@ bool ReactionMultistepDetector::detectMultitailArrows() bool bad_pathway = false; - for (int i = 0; i < pathway_count; ++i) + for (int pathway_idx = 0; pathway_idx < pathway_count; ++pathway_idx) { - auto& multi = (const KETReactionMultitailArrow&)_bmol.meta().getMetaObject(KETReactionMultitailArrow::CID, i); + auto& multi = (const KETReactionMultitailArrow&)_bmol.meta().getMetaObject(KETReactionMultitailArrow::CID, pathway_idx); float min_dist_prod = -1; int idx_cs_min_prod = -1; auto arr_begin = multi.getHead(); @@ -359,20 +398,15 @@ bool ReactionMultistepDetector::detectMultitailArrows() } } - for (auto& [min_dist, idx_cs_min_rc] : min_dist_reactants) - { - if (min_dist < 0) - bad_pathway = true; - } - // TODO: add upper limit if (idx_cs_min_prod < 0) bad_pathway = true; else { auto& csb_min_prod = _component_summ_blocks[idx_cs_min_prod]; - auto& rc_arrow = - _reaction_components[_moleculeCount + _bmol.meta().getMetaCount(KETReactionPlus::CID) + _bmol.meta().getMetaCount(KETReactionArrow::CID) + i]; + csb_min_prod.reaction_idx = pathway_idx; + auto& rc_arrow = _reaction_components[_moleculeCount + _bmol.meta().getMetaCount(KETReactionPlus::CID) + + _bmol.meta().getMetaCount(KETReactionArrow::CID) + pathway_idx]; rc_arrow.summ_block_idx = ReactionComponent::CONNECTED; // mark arrow as connected if (csb_min_prod.role == BaseReaction::UNDEFINED) csb_min_prod.role = BaseReaction::PRODUCT; @@ -400,7 +434,10 @@ bool ReactionMultistepDetector::detectMultitailArrows() 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; } + else + bad_pathway = true; } } for (auto& csb : _component_summ_blocks) @@ -499,7 +536,7 @@ bool ReactionMultistepDetector::findPlusNeighbours(const Vec2f& plus_pos, const if (tops_col_it != tops_col.end() && bottoms_col_it != bottoms_col.end()) { - min_distance_v = std::min(tops_col_it->first - plus_pos_y.first, bottoms_col_it->first - plus_pos_y.first); + min_distance_v = std::min(std::fabs(tops_col_it->first - plus_pos_y.first), std::fabs(bottoms_col_it->first - plus_pos_y.first)); if (!result || min_distance_v < min_distance_h) { connection.first = tops_col_it->second; @@ -514,21 +551,21 @@ bool ReactionMultistepDetector::findPlusNeighbours(const Vec2f& plus_pos, const void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) { std::unordered_map rc_to_molecule; - std::vector> csb_to_reaction; std::vector, std::vector>> csb_reactions; + + std::vector csb_product_to_reaction; std::vector> csb_to_reactant_indexes; for (int i = 0; i < (int)_component_summ_blocks.size(); ++i) { - csb_to_reaction.emplace_back(); + csb_product_to_reaction.push_back(-1); auto& csb = _component_summ_blocks[i]; if (csb.role == BaseReaction::PRODUCT || csb.role == BaseReaction::INTERMEDIATE) { // one product = one reaction, one reaction node // map reactionNode <> csb_reaction auto& rcidx_to_reactant = csb_to_reactant_indexes.emplace_back(); - rxn.addReactionNode(); - csb_to_reaction.back().emplace((int)csb_reactions.size()); + csb_product_to_reaction.back() = (int)csb_reactions.size(); csb_reactions.emplace_back().second.push_back(i); // add csb as product auto [sri, sr] = rxn.addReaction(); @@ -572,41 +609,39 @@ void ReactionMultistepDetector::constructPathwayReaction(PathwayReaction& rxn) } } + // fill reaction nodes for (int i = 0; i < (int)csb_reactions.size(); ++i) { auto& csb_reaction = csb_reactions[i]; - auto& rn = rxn.getReactionNode(i); + auto& rn = rxn.addReactionNode(); // normally we have only one summblock here for (auto csb_product_idx : csb_reaction.second) { auto& csb_product = _component_summ_blocks[csb_product_idx]; for (auto reactant_csb_idx : csb_product.arrows_to) { - // look up for reactions where the reactant_csb_idx summ block presents - auto successors = csb_to_reaction[reactant_csb_idx]; - // remove the current reaction - successors.erase(i); // remove the current reaction - // add successor reactions - for (auto reac_idx : successors) + // look up for reactions where the product plays a role of reactant + auto reac_idx = csb_product_to_reaction[reactant_csb_idx]; + if (reac_idx >= 0 && reac_idx != i) rn.successorReactionIndexes.push(reac_idx); } } + // iterate reactant summ blocks for (auto csb_reactant_idx : csb_reaction.first) { auto& csb_reactant = _component_summ_blocks[csb_reactant_idx]; - auto precursors = csb_to_reaction[csb_reactant_idx]; - for (auto reac_idx : precursors) - rn.precursorReactionIndexes.push(reac_idx); - - if (csb_reactant.arrows_from.size()) + // find reactions where the reactant plays a role of product + auto reac_idx = csb_product_to_reaction[csb_reactant_idx]; + if (reac_idx >= 0 && reac_idx != i) { + rn.precursorReactionIndexes.push(reac_idx); auto& rcidx_to_reactant = csb_to_reactant_indexes[i]; for (auto ridx : csb_reactant.indexes) { auto rcidx_it = rcidx_to_reactant.find(ridx); if (rcidx_it != rcidx_to_reactant.end()) - rn.connectedReactants.insert(rcidx_it->second); + rn.connectedReactants.insert(rcidx_it->second, reac_idx); } } }