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Feature/861 cdxml enhanced stereochemistry #882

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Oct 28, 2022
Merged

Feature/861 cdxml enhanced stereochemistry #882

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22d19ca
enhanced stereochemistry support
even1024 Oct 25, 2022
01263b7
tests updated
even1024 Oct 25, 2022
b17e701
1 changed to the true
even1024 Oct 26, 2022
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156 changes: 139 additions & 17 deletions api/tests/integration/ref/formats/cdxml_to_mol.py.out
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Original file line number Diff line number Diff line change
@@ -1,4 +1,126 @@
*** CDXML to mol ***
enhanced_stereo1.cdxml

-INDIGO-01000000002D

13 13 0 0 1 0 0 0 0 0999 V2000
0.3703 -0.1623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7860 -0.4023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7860 -0.8823 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
1.2017 -1.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2017 -1.6023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6173 -1.8423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6173 -2.3223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2017 -2.5623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7860 -2.3223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7860 -1.8423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3703 -1.1223 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3703 -1.6023 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
1.2017 -0.1623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 13 2 0 0 0 0
3 4 1 0 0 0 0
3 11 1 1 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
11 12 1 0 0 0 0
M END

enhanced_stereo2.cdxml

-INDIGO-01000000002D

0 0 0 0 0 0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 13 13 0 0 0
M V30 BEGIN ATOM
M V30 1 O 0.370333 -0.162333 0.0 0
M V30 2 C 0.786 -0.402334 0.0 0
M V30 3 C 0.786 -0.882333 0.0 0 CFG=1
M V30 4 C 1.20167 -1.12233 0.0 0
M V30 5 C 1.20167 -1.60233 0.0 0
M V30 6 C 1.61733 -1.84233 0.0 0
M V30 7 C 1.61733 -2.32233 0.0 0
M V30 8 C 1.20167 -2.56233 0.0 0
M V30 9 C 0.786 -2.32233 0.0 0
M V30 10 C 0.786 -1.84233 0.0 0
M V30 11 N 0.370333 -1.12233 0.0 0
M V30 12 I 0.370333 -1.60233 0.0 0
M V30 13 O 1.20167 -0.162333 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 2 2 13
M V30 4 1 3 4
M V30 5 1 3 11 CFG=1
M V30 6 1 4 5
M V30 7 2 5 6
M V30 8 1 5 10
M V30 9 1 6 7
M V30 10 2 7 8
M V30 11 1 8 9
M V30 12 2 9 10
M V30 13 1 11 12
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEREL1 ATOMS=(1 3)
M V30 END COLLECTION
M V30 END CTAB
M END

enhanced_stereo3.cdxml

-INDIGO-01000000002D

0 0 0 0 0 0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 14 0 0 0
M V30 BEGIN ATOM
M V30 1 O 0.370334 -0.162333 0.0 0
M V30 2 C 0.786 -0.402334 0.0 0
M V30 3 C 0.786 -0.882333 0.0 0 CFG=1
M V30 4 C 1.20167 -1.12233 0.0 0 CFG=2
M V30 5 C 1.20167 -1.60233 0.0 0
M V30 6 C 1.61733 -1.84233 0.0 0
M V30 7 C 1.61733 -2.32233 0.0 0
M V30 8 C 1.20167 -2.56233 0.0 0
M V30 9 C 0.786 -2.32233 0.0 0
M V30 10 C 0.786 -1.84233 0.0 0
M V30 11 N 0.370334 -1.12233 0.0 0
M V30 12 I 0.370334 -1.60233 0.0 0
M V30 13 O 1.20167 -0.162333 0.0 0
M V30 14 C 1.61733 -0.882333 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 2 2 13
M V30 4 1 3 4
M V30 5 1 3 11 CFG=1
M V30 6 1 4 5
M V30 7 2 5 6
M V30 8 1 5 10
M V30 9 1 6 7
M V30 10 2 7 8
M V30 11 1 8 9
M V30 12 2 9 10
M V30 13 1 11 12
M V30 14 1 4 14 CFG=1
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEREL1 ATOMS=(1 3)
M V30 MDLV30/STERAC1 ATOMS=(1 4)
M V30 END COLLECTION
M V30 END CTAB
M END

sgroups.cdxml

-INDIGO-01000000002D
Expand Down Expand Up @@ -102,14 +224,14 @@ test-multi.cdxml

-INDIGO-01000000002D

196212 0 0 0 0 0 0 0 0999 V2000
196212 0 0 1 0 0 0 0 0999 V2000
7.6673 -2.0793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8013 -2.5793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9353 -2.0793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6673 -1.0793 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0693 -2.5793 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.0973 -8.1650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0947 -7.1650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0947 -7.1650 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.9593 -6.6627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2273 -6.6677 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.9567 -5.6627 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -123,7 +245,7 @@ test-multi.cdxml
8.4860 -11.3550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7947 -10.4100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9573 -8.1650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9547 -7.1650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9547 -7.1650 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
9.8193 -6.6627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0873 -6.6677 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.8167 -5.6627 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -138,8 +260,8 @@ test-multi.cdxml
8.6547 -10.4100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1253 -5.5903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1933 -3.8593 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.6590 -4.7443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6583 -4.7837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6590 -4.7443 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.6583 -4.7837 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
7.1240 -5.6687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1920 -3.9380 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.1263 -5.5510 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -157,7 +279,7 @@ test-multi.cdxml
1.2263 -17.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9583 -16.2313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3603 -17.7313 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.8243 -17.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8243 -17.2313 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
5.6903 -17.7313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9583 -17.7313 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.6903 -18.7313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -171,7 +293,7 @@ test-multi.cdxml
6.5967 -16.1333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6897 -15.7310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8240 -16.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.5563 -17.7313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.5563 -17.7313 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
8.4223 -17.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6903 -17.2313 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.4223 -16.2313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -187,8 +309,8 @@ test-multi.cdxml
7.5560 -18.7313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8867 -17.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0207 -18.7313 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.0207 -17.7313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1547 -17.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0207 -17.7313 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
10.1547 -17.2313 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
10.1547 -16.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2887 -17.7313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.8867 -16.2313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -206,7 +328,7 @@ test-multi.cdxml
6.4203 -36.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6883 -37.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.5543 -35.9810 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -39.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -39.4810 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.2863 -38.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5543 -38.9810 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.1523 -39.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -220,7 +342,7 @@ test-multi.cdxml
5.4497 -41.9757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5543 -40.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -40.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1523 -37.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1523 -37.4810 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
8.1523 -36.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2863 -37.9810 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.0183 -35.9810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -236,8 +358,8 @@ test-multi.cdxml
9.0183 -37.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5543 -34.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -33.4810 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -34.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2863 -34.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4203 -34.4810 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
7.2863 -34.9810 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
8.1523 -34.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2863 -35.9810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.6883 -34.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
Expand All @@ -251,16 +373,16 @@ test-multi.cdxml
2.0900 -32.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9563 -33.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.9960 -16.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.0177 -15.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3487 -16.5603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.0177 -15.8170 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
27.3487 -16.5603 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
26.3703 -16.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.7013 -17.0957 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
26.0613 -15.4013 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
25.0833 -15.1933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.0833 -15.1933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
24.7743 -14.2423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.7960 -14.0343 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
25.4433 -13.4993 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
25.1343 -12.5480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.1343 -12.5480 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
25.8033 -11.8050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.4943 -10.8540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
26.7817 -12.0130 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
Expand Down
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