Activity for The Chemistry Development Kit
-
Egon Willighagen committed [01d7ab] on Code
Additional code smells - unused functions.
-
Code Smell: Variable renaming.
-
Clean up how option overiding works, when we add a single setting we should check if it already exists. This allows the base V2000/3000 writers to not emit SD tags by default, but when they are used in the SDWriter then they can emit the tags
-
Options to write out the SD tags from the V2000/V3000 writer.
-
Move the writing of non-structural data to the V2000 writer.
-
Cleaner Iterating SDF loop
-
Null check needed for reaction (RXN) readers - should probably also read the properties there as well.
-
Missed changes for test files.
-
Now the V2000/V3000 read the SD properties we can simplify the IteratingSdfReader.
-
Read in SDfile properties from single V3000 files to be consistent with V2000.
-
GitHub committed [99548a] on Code
List the latest release
-
GitHub committed [904c8f] on Code
Merge pull request #1060 from JonasSchaub/ElectronDonation-small-doc-fix
-
GitHub committed [6f66c3] on Code
small doc fix for cdkAllowingExocyclic()
-
Fix a corner case when depicting cc(C)c
-
GitHub committed [16f6bc] on Code
Merge pull request #1055 from cdk/update/CITATION.cff
-
GitHub committed [bb49c4] on Code
Merge branch 'main' into update/CITATION.cff
-
GitHub committed [9ccb3b] on Code
Merge pull request #1054 from egonw/update/jna-inchi
-
Updated JNA-InChI (updating the JNA dependency)
-
GitHub committed [c5572e] on Code
Applied suggested changes
-
GitHub committed [2ca780] on Code
Create CITATION.cff
-
Add missing import
-
Added the catching and exception of the Intractable exception
-
added test case for initial cycles oom
-
The number of essential/relevant cycles can be exponential for some molecules - e.g. cyclo-phanes.
-
SonarCloud complains if the capturing groups are removed (Group parts of the regex together).
-
Fix test value
-
Address some SonarCloud issues
-
Tests are all now enabled.
-
Reinstate test which is fine but not perfect.
-
Fix an error mesg in the AtomContainer implementation
-
Make sure we fail currently on bond order unknown.
-
Add in the option to recompute hydrogens.
-
Add the option to remove unmapped parts of a transformed molecule.
-
Make sure the bonds are ordered correctly when setting DB stereo.
-
Preliminary work on some SMIRKS options and mimicking other implementations.
-
Allow reactions to be run backwards.
-
Valence check only when pedantic.
-
Cleaner if condition for PEDANTIC erorr checking
-
Add in SMIRKS options, currently just a PEDANTIC mode which does additional checks. The valence checking is a WIP but the basics are there.
-
Make sure bond position arrays grow correctly. Use ORDER=1 for UP/DOWN stereobonds, this makes it possible for SMIRKS to avoid the warning. Some tweaks are needed to SMARTS writing.
-
If we can't work out the bond order, make a guess (if possible). In strict/pedantic mode this will warn/fail.
-
Track atom/bond indexes from input SMARTS allowing better warning/error messages.
-
Additional unit tests
-
Distinction between total vs implicit hydrogen count, fix default valences for new atoms.
-
Some extra test coverage.
-
Make the Unique/All application of transforms lazy with an iterator.
-
Only call resyncStereo() once (after all ops have been applied) and make sure reactive centre gets marked correctly. These two tests are nice tests which should keep stereo but currently don't.
-
SonarCloud - damn'd if you do damn'd if you don't
-
Cleanup recommended by SonarCloud.
-
New op: PromoteH to handle the case where we need to possible move and create an explicit H in the product.
-
Another iffy aromatic pattern.
-
When we optimize our op-codes (replace-atom) we need to remap the atom numbers in other op-codes.
-
AromaticBond implies aromatic atoms, aliphatic bond does not imply aliphatic atoms.
-
Another test case.
-
Fix an ordering issue in the op codes, we need a better comparator so this is a band aid for now.
-
Improved assertion error to show what the generated output was.
-
Make sure AromaticBond gets printed.
-
Better aromaticity semantics and warn on dubious patterns with an aromatic bond between aliphatic atoms. Some tests need to be adjusted since the patterns were not quite correct.
-
Improved some corner cases w.r.t atom maps and warnings.
-
Make the results list unmodifiable, in future we will return an iterator.
-
added more test cases
-
Ensure a deep copy of the molecule occurs for iterative mapping modes.
-
Remove unused field (aromaticity)
-
added convenient method to SmirksTest to assert different Transform.Mode modes; added more test cases
-
added more test cases
-
added two test cases; reverted system.err to logger output; commented out some other system.err; removed unused local variables
-
Removed unused field, we deletage to the SmartsPattern.
-
Fix an issue with beg/end ordering when pairing up bonds.
-
Remove stray print, allready got a debug here
-
Correct bond index
-
SonarCloud suggestions.
-
Add transform/SMIRKS support to CDK.
-
Actually deprecate.
-
Deprecate the method that took in the GraphUtil/EdgeMap cache
-
Some unit tests for the marking of ring/atoms bonds.
-
More efficient determination of ring flags/count.
-
New tests for flags
-
Move the CDKConstants flags to IChemObject.
-
Move the more useful flags to IChemObject we will deprecate and move the others.
-
Better error message for the most common reason this happens.
-
Improved the ChemObject flags API. We can now directly clear/set a flag without having a branch (if/else). Likewise due to padding a 16-bit integer does not take less space than 32-bit in this case and the 32-bit int is cleaner to work with.
-
Fix issues with reference/identity checking.
-
Fix regressions due to bonds being added before atoms
-
Renaming
-
Some left overs in the removal of using the implementation class
-
Fix all unused imports
-
New convenience methods on the Atom API.
-
Missed unused import
-
Use the DefaultChemObject builder to initialise the AtomContainer (default).
-
Fix a wrong test value - this molecule should not have any wavy bonds.
-
Fix a missed corner case with passing null atoms into indexOf(IAtom).
-
GitHub committed [3ca2b8] on Code
Merge pull request #1043 from Mailaender/osgi-imports
-
Matthias Mailänder committed [373d2b] on Code
Refine OSGi import rules.
-
Enforce that the AtomContainer (silent) is created through the builder.
-
New author
-
Added more documentation and unit tests;
-
Added isMetalloid utility method to Elements class
-
GitHub committed [737abd] on Code
Merge pull request #1042 from egonw/missing/ElementsTest
-
Removed copy/paste artifact
-
Added a test for a method that wasn't tested at all