AlkylStructureFragmenter Implementation

Mila1004 commented 1 year ago

First steps for a complete alkyl structure fragmentation. Currently only contains fragmentation logic for cyclic structures and non-cyclic side-chains.

JonasSchaub commented 1 year ago

One general thing: Do i see it correctly that right now, there are settings offered in the GUI for the fragmenter that are actually without function, just mocks? Please, comment them out remove them. It cannot go to the master branch in this state.

JonasSchaub commented 11 months ago

@Mila1004 what does the new setting do? Does it turn the fragmentation of alkyl chains on/off?

Mila1004 commented 11 months ago

@Mila1004 what does the new setting do? Does it turn the fragmentation of alkyl chains on/off?

Short answer: yes. Long answer: It defines whether the given maximum chain length shall be used as restrictions for side chain fragmentation. If put on false, no restrictions are applied and the chains returned as they are. If a value >=1 is set, a switch decides the fragmentation steps. If 0 is given and the setting on false, a warning is given in the log.

JonasSchaub commented 11 months ago

@Mila1004 what does the new setting do? Does it turn the fragmentation of alkyl chains on/off?

Short answer: yes. Long answer: It defines whether the given maximum chain length shall be used as restrictions for side chain fragmentation. If put on false, no restrictions are applied and the chains returned as they are. If a value >=1 is set, a switch decides the fragmentation steps. If 0 is given and the setting on false, a warning is given in the log.

Ok, I don't get it 100 %, you will have to explain that to me on Friday. Preferably with examples.

JonasSchaub commented 11 months ago

@Mila1004 remember to run spotless check/apply before committing.

sonarcloud[bot] commented 9 months ago

Quality Gate failed

Failed conditions

8.1% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

FelixBaensch commented 6 months ago

Note: this PR points to main branch

JonasSchaub commented 6 months ago

@Mila1004 we will look at the merge conflicts together.

JonasSchaub commented 6 months ago

I guess the instance variables in your test class are creating problems. You can try fixing that by adding a static initializer setting the default locale to English to your test class:

static {
        Locale.setDefault(Locale.of("en", "GB"));
    }

If I do that, I am "only" getting file not found exceptions because the test resources are not imported correctly.

sonarcloud[bot] commented 6 months ago

Quality Gate failed

Failed conditions
7.6% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

sonarcloud[bot] commented 1 month ago

Quality Gate failed

Failed conditions
5.7% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

JonasSchaub commented 1 month ago

@Mila1004, when you have time, please merge the current production branch into your branch and adjust your code to the changes made there in the meantime.

JonasSchaub commented 1 month ago

@Mila1004 where did you get the example molecules in the MOL and SD files from? There should be a source/reference given somewhere.

sonarcloud[bot] commented 2 weeks ago

Quality Gate failed

Failed conditions
5.7% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

FelixBaensch / MORTAR