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ideaconsult / cdk

The Chemistry Development Kit
https://cdk.github.io/
GNU Lesser General Public License v2.1
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Changes rinchitoreaction #7

Closed uli-f closed 1 year ago

uli-f commented 1 year ago

This PR consists of two commits.

The first commit contains all the changes other than fixing the indentation.

The second commit only contains the changes to the indentation.

ntk73 commented 1 year ago

Merged only commit 080dfa5f7d650a0cb528def53268dc4481c8899f, modified to resolve conflicts and to fix 11 j-unit test failings. Merged as 3aa56b020be86e10591fb9067414c1289e7e003f. Formatting commit 7365d2dca2fb7f4a67b381d35e417afc50dc37fc is not applied. Formatting will be done after fixing java code and javadoc analogously to the PR #4. For some reason RInChI must work with empty structures as well, therefore line

     if (atomContainer.isEmpty())  {

was replaced with original check for null pointer:

    if (atomContainer != null) {

Btw, first I noticed that this line had a bug and the correct one should have been with logical negation: 

    if (!atomContainer.isEmpty())  {

But, even with this change, 11 tests failed. If needed, we can investigate and improve this matter further after handling the other PRs

uli-f commented 1 year ago

For some reason RInChI must work with empty structures as well, [...]

I think I understand why that is the case.

Thank you so much for fixing this 🐛