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Commits : Listings

Analyzed about 15 hours ago. based on code collected about 18 hours ago.
Nov 11, 2024 — Nov 11, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
improve and document agent handling in MDLRXNV2000Reader (#1138)
Uli
More... 11 months ago
adjust comments in RInChIGeneratorTest;
Felix Bänsch
More... 11 months ago
Adjust 'invalid symbol' tests and remove the bullet point from RInChIGenerator javdoc;
Felix Bänsch
More... 11 months ago
fixed merge errors introduced in previous commit
Uli
More... 11 months ago
Merge branch 'main' into rinchi-logic
Uli
More... 11 months ago
Updated dependencies (#1136)
Egon Willighagen
More... 11 months ago
remove deprecated calls from InChIGeneratorTest (#1134)
Uli
More... 11 months ago
This fixes a problem with the ordering of &. (#1131)
stefhk3
More... 11 months ago
work in progress: fixing for end atoms not in container
ToLeWeiss
More... 11 months ago
add test for IReaction getAgentCount
Uli
More... 11 months ago
add getAgentCount method to IReaction interface; replace StringBuilder with String concatenation as recommended for fixed number of string concatenations
Uli
More... 11 months ago
remove unused RdfileReader import; rename test01 to dielsAlderReaction_test; add comments regarding non-specification-compliant RDfiles; update text of select Disabled test annotations
Uli
More... 11 months ago
work in progress: figuring out why the end atoms are in a different container
ToLeWeiss
More... 11 months ago
Add limitations to RInChIGenerator javadoc; fix typo in RInChIGeneratorTest.test01();
Felix Bänsch
More... 11 months ago
Merge pull request #1129 from uli-f/smiles-generation-empty-reaction
John Mayfield
More... 11 months ago
remove RInChIGeneratorFactory; refactor RInChIGenerator and RInChIToReaction to work without the factory; add package-info.java; add to javaodcs
Uli
More... 11 months ago
add handling for empty atom containers in InChINumbersTools; remove unnecessary isEmpty checks in SmilesGenerator; fix typo in InChINumbersTools javadoc
Uli
More... 11 months ago
make RInChIDecomposition class usable without RInChIGeneratorFactory; add @cdk.module annotations to unit tests; change exception type from CDKException to RInChIException; add detailed documentation to RInChIDecomposition methods; disable specific RInChIGeneratorTest tests for undefined stereocenters in RAuxInfo; improve documentation in other classes related to RInChI processing
Uli
More... 11 months ago
disable failing test in InChIGeneratorTest; add reaction files for malate and oxaloacetate equilibrium reaction
Uli
More... 11 months ago
fix SmilesGenerator to handle empty reaction components in case of smiles flavor (Canonical | Stereo) and add corresponding tests in EmptyReactionSmilesGenerationTest; add assertj-core to pom.xml of inchi module; replaced calls to deprecated methods with non-deprecated ones in ReactionManipulatorTest and SmilesGeneratorTest; remove unnecessary throws statement from methods in ReactionManipulatorTest
Uli
More... 11 months ago
add license header and class-level javadoc
Uli
More... 11 months ago
add RInChIException class for package specific exceptions; update RInChIDecomposition methods to use RInChIException; modify test cases to expect RInChIException; update RInChIToReaction to accept a IChemObjectBuilder argument in constructor; add cdk-smiles dependency in pom.xml of rinchi package for testing scope; add RInChIToReactionTest; adjust RInChIGeneratorFactory functions to include IChemObjectBuilder parameter
Uli
More... 11 months ago
update test method, resource file names and resource files from r28_forceEquilibrium to r29_forceEquilibrium
Uli
More... 11 months ago
replace RInChIOption enum with RInChIOptions class that provides a timeout; add test for force equilibrium option; add tests in InChIGeneratorTest that demonstrate differences in InChI layers /t, /m, /s and AuxInfo layer /rA
Uli
More... 11 months ago
make all test classes extend CDKTestCase; ensure components list is final in RInChIDecomposition; add TODO for timeout option in RInChIGenerator; InChIGeneratorTest: fix auxiliary spelling mistake, refactor andEnantiomer_test to use try-with-resources and add AuxInfo assert
Uli
More... 11 months ago
implement business logic RInChIDecomposition and add an initial batch of unit tests
Uli
More... 12 months ago
work in progress: fix size limitation of the subset generation
ToLeWeiss
More... 12 months ago
work in progress: switch to primitive int matrices for subset generation and added more comprehensive comments for subset generation
ToLeWeiss
More... 12 months ago
work in progress: fixed indexing and fix of check for size constraint
ToLeWeiss
More... 12 months ago
switching to primitive integers because java Lists are indexed by these and therefore cant have more elements than 2^31 - 1
ToLeWeiss
More... 12 months ago