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bandaid to prevent exception from bubbling up during structure parsing
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adding some data files for unit tests, omitted earlier.
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@ChemMitch
ChemMitch committed Sep 3, 2024
1 parent f879b8c commit 02a5c9d
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Showing 4 changed files with 158 additions and 1 deletion.
2 changes: 1 addition & 1 deletion src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
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Expand Up @@ -256,7 +256,7 @@ public static void setMaxUndefinedStereoCenters(int maxUndefinedStereoCenters) {
} else {
Logger.getLogger(this.getClass().getName()).fine("This molecule is considered NOT complex");
try {
//The call to label generates an Exception down in the bowels of CDK.
//The call to label generates an Exception down in the bowels of CDK for *some* structures.
// trapping it in a try/catch allows the process to continue
CIPToolMod.label(cimp.getContainer());
} catch (NoSuchAtomException ex) {
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53 changes: 53 additions & 0 deletions src/test/resources/mols/calcium benzoate monohydrate confusing.mol
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Calcium benzoate monohydrate


22 18 0 0 0 0 0 0 0 0999 V2000
7.5718 -14.9911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.6141 -14.9905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.5949 -14.4008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.6141 -16.1720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.5718 -16.1773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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10.6373 -13.2183 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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10.8128 -16.5197 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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20 21 1 0 0 0 0
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M CHG 4 8 -1 10 2 12 -1 21 -1
M STY 1 1 MUL
M SLB 1 1 1
M SAL 1 15 1 2 3 4 5 6 7 8 9 14 15 16 17 18 19
M SAL 1 2 20 21
M SPA 1 9 1 2 3 4 5 6 7 8 9
M SDI 1 4 6.8840 -17.4493 6.8840 -12.4871
M SDI 1 4 12.3692 -12.4871 12.3692 -17.4493
M SMT 1 2
M END
53 changes: 53 additions & 0 deletions src/test/resources/mols/calcium benzoate monohydrate-18.mol
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ACCLDraw05242413082D

20 18 0 0 0 0 0 0 0 0999 V2000
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9.1350 -16.1719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0927 -16.1772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1184 -16.7615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1582 -14.3997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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M CHG 3 8 -1 10 2 19 -1
M ISO 1 11 18
M STY 1 1 MUL
M SLB 1 1 1
M SAL 1 15 1 2 3 4 5 6 7 8 9 12 13 14 15 16 17
M SAL 1 3 18 19 20
M SPA 1 9 1 2 3 4 5 6 7 8 9
M SDI 1 4 6.4049 -17.4493 6.4049 -12.4871
M SDI 1 4 11.8902 -12.4871 11.8902 -17.4493
M SMT 1 2
M END
51 changes: 51 additions & 0 deletions src/test/resources/mols/calcium benzoate.mol
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ACCLDraw05242410442D

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M CHG 3 8 -1 10 2 18 -1
M STY 1 1 MUL
M SLB 1 1 1
M SAL 1 15 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16
M SAL 1 3 17 18 19
M SPA 1 9 1 2 3 4 5 6 7 8 9
M SDI 1 4 4.6337 -10.7109 4.6337 -5.7487
M SDI 1 4 10.1190 -5.7487 10.1190 -10.7109
M SMT 1 2
M END

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