cdk/cdk: CDK 2.8

$ git shortlog -s -n $v1..$v2
 278 John Mayfield
  13 Egon Willighagen
  11 Uli Fechner
   5 Mark Williamson
   3 Valentyn Kolesnikov
   2 MehmetAzizYirik
   2 Marco Foscato
   1 dependabot[bot]
   1 Tim Dudgeon
   1 Otto Brinkhaus
   1 Christoph Steinbeck
   1 Alex

• Dev version 2.8-SNAPSHOT ready for changes. John Mayfield on 2022-01-11
• Update InChINumbersTools to use the new JNA InChI options - note the auxInfo method is package private (phew). John Mayfield on 2022-01-11
• SDF change for MAYGEN. Valentyn Kolesnikov on 2022-01-12
• Added new contributor Egon Willighagen on 2022-01-13
• Bumped the copyright year Egon Willighagen on 2022-01-13
• Update xerces and make sure we use a specific version of xml-apis. John Mayfield on 2022-01-30
• Fixup John Mayfield on 2022-01-30
• We don't need or want xml-apis since this was rolled in to main JDK a long time ago. John Mayfield on 2022-01-30
• Attempt 2 - we need 1.4.01 because xerces is using funny APIs John Mayfield on 2022-01-30
• Bump xercesImpl from 2.12.1 to 2.12.2 dependabot[bot] on 2022-01-30
• Add sonar cloud John Mayfield on 2022-01-30
• Fix YAML indent John Mayfield on 2022-01-30
• Add in POM props for SonarCloud John Mayfield on 2022-01-30
• Fixup - correct property syntax John Mayfield on 2022-01-30
• Prevent parsing of external resources by the XMLFactory John Mayfield on 2022-01-30
• Use try-with-resources to ensure the IO is closed in the case of an exception John Mayfield on 2022-01-30
• Another try-with-resources John Mayfield on 2022-01-30
• Fix - questionable null-primitive assetions John Mayfield on 2022-01-30
• Fix - Correct way to test for an expected exception John Mayfield on 2022-01-30
• Possible fix - indicate the seed is set later John Mayfield on 2022-01-30
• Fix - Correct test for exception John Mayfield on 2022-01-30
• Resources is now local to class John Mayfield on 2022-01-30
• Resolves #734 John Mayfield on 2022-01-30
• Overflow logic was not quite correct. Restrict based on number of digits, in base 10, 7 digits is enough for 9.9 million atoms which is more than enough for any molecule. John Mayfield on 2022-02-01
• Update test case, expected value is not needed John Mayfield on 2022-02-01
• Better state management for stereochemistry. When an stereo element is added to a molecule it's atom/bond components are remapped to the internal AtomRef/BondRef of the molecule in question. This ensure any future actions such as swapping and atom for another work correctly. This is now more robust and we get an error if we try to add stereochemistry that includes atom/bonds not in this molecule - this makes sense. John Mayfield on 2022-02-03
• An unexpected consequence is some miss-use of the partition molecules function in the structure diagram generator. This is a bit of a missue but reasonable - we now need check if the stereochemistry has not be split between two molecules. We should also do the same of Sgroups (issue openned). John Mayfield on 2022-02-03
• CXSMILES optimisation - don't create and swap a new Pseudo atom if the atom to set the label on is already a pseudo atom. John Mayfield on 2022-02-03
• Integrating MAYGEN project to structgen package MehmetAzizYirik on 2022-02-06
• Added the JavaDoc to the source and test classes. MehmetAzizYirik on 2022-02-06
• Added dependencies, formatted sources. Valentyn Kolesnikov on 2022-02-06
• Fix up some dependencies lost in the rebase. We should not be calling new Atom() directly. John Mayfield on 2022-02-06
• Split out the command line parsing from the main entry point. For now we can put this in the test/ root John Mayfield on 2022-02-06
• Pass in the IChemObjectBuilder John Mayfield on 2022-02-06
• Fix copyright header John Mayfield on 2022-02-06
• Remove commons-lang3, a specicalled MF range parse would be better but for now we only need this function. John Mayfield on 2022-02-06
• Avoid reflective calls. John Mayfield on 2022-02-06
• removeHydrogens creates a copy of the molecule, use suppressHydrogens instead John Mayfield on 2022-02-06
• Replace seperate output modes with a single "emit" which will consumer our IAtomContainer's. John Mayfield on 2022-02-06
• Remove redundant ForkJoinPool, submitting and then waiting is just running on a background thread. John Mayfield on 2022-02-06
• May SonarCloud happier by not using a for-loop here? John Mayfield on 2022-02-06
• Parameterized tests John Mayfield on 2022-02-06
• Split out IO concerns from the generator, using a consumer. John Mayfield on 2022-02-06
• Forgot to remove the SmilesGenerator from here. John Mayfield on 2022-02-06
• Test IO generation, this is a little tricky since for example the coordinates may change causing a failing test. John Mayfield on 2022-02-06
• Add back in the brittle ForkJoin hack. John Mayfield on 2022-02-06
• SonarCloud: Use the logger for verbose output. If needed the format could be configured by the command line. John Mayfield on 2022-02-06
• Relicense header as LGPL to be inline with rest of CDK John Mayfield on 2022-02-06
• Document usage of the class. John Mayfield on 2022-02-06
• SonarCloud suggestion, move these tests into the Parameterized ones. John Mayfield on 2022-02-06
• Additional SonarCloud suggestions. John Mayfield on 2022-02-06
• Added support for the smiles and sdf generator. Valentyn Kolesnikov on 2022-02-06
• Less code smell. John Mayfield on 2022-02-06
• More efficient component splitting, if a single component is found return a singleton with the input molecule rather than a copy. John Mayfield on 2022-02-06
• Split out single test into three and tidy up. John Mayfield on 2022-02-06
• Add some additional test cases to weighted path descriptor. John Mayfield on 2022-02-06
• Simplify weight calculation removing the temporary double[] array. John Mayfield on 2022-02-06
• Compute the paths once and reuse - it is a little odd the later values are not unique. John Mayfield on 2022-02-06
• A faster way to collect all the paths, insteed of doing the N^2 tests we can just flood fill from every atom. John Mayfield on 2022-02-06
• Rather than computing all the paths and then suming the values we can just sum them as we go along. John Mayfield on 2022-02-06
• We can precompute the bond weights, reducing the number of SQRTs. John Mayfield on 2022-02-06
• Calculate the weight as we go traverse the path. John Mayfield on 2022-02-06
• Resolve SonarCloud issues, since degree is typically going to be small i.e. 1-5 the result will always fit in an integer. John Mayfield on 2022-02-06
• DictionaryDatabase complaining as it is missing a file, relocate from cdk-extra to cdk-dict John Mayfield on 2022-02-06
• Add a comment explaining this descriptor only applies to certain protons. John Mayfield on 2022-02-06
• Fix bug - annotations were not added for single bonds. Add a test to check it doesn't break again. John Mayfield on 2022-02-06
• Utility functions for determining the smallest ring size of an atom/bond. John Mayfield on 2022-02-07
• Cleaner logic for checking which component each Sgroup is in. For some reason we used to copy the Sgroup but I don't think this is need since the new logic is either the entire Sgroup is included or ignored. John Mayfield on 2022-02-07
• When an atom is removed from a molecule remove any Sgroups it is involved in. John Mayfield on 2022-02-07
• Consider Sgroups when where an atom is removed is is setAtom(i, atoms); this is useful for a "swap" like operation where we replace one atom with another. We can preserve the Sgroup here but need to update it's storage. John Mayfield on 2022-02-07
• Additional consistency check when setAtoms() or setBonds() as called. This can cause stereo and sgroups to become invalid. John Mayfield on 2022-02-07
• Minor code issues - SonarCloud John Mayfield on 2022-02-07
• Basic logical fix for the construction of the BurdenMatrix. We should only set matrix[i][j] once we have checked all bonds. John Mayfield on 2022-02-07
• More efficient matrix construction, do a single linear loop rather than a tripply nested for-loop. John Mayfield on 2022-02-07
• Rename and make options consistent between V2000/V3000 reader. We also add a new option allow us to turn on/off 0d stereo perception. John Mayfield on 2022-02-07
• Sort out coordinate reading, we now set only Point3d or Point2d not both. After the molecule is parsed we determine how many dimensions we have based on the header and avaliable data. John Mayfield on 2022-02-07
• Add ForceAs3D test case John Mayfield on 2022-02-07
• Add isotope support from V3000 and the option to default read D/T as 2H and 3H. John Mayfield on 2022-02-07
• Only set stereochemistry if specificed. John Mayfield on 2022-02-07
• Move logic around such that the final steps all get done in finalizeMol(). John Mayfield on 2022-02-07
• Reading of 0D stereochemistry from the CFG=1 and CFG=2 values in MDLV3000 to be more consistent with V2000. This is a corner case and I may change to off by default. John Mayfield on 2022-02-07
• Logging and additional checks where perceiving 2D stereochemistry from wedges. John Mayfield on 2022-02-08
• Additional strict mode check for stereochemistry, checking the wedge/hatch idioms. We could be even stricter ala-InChI but basic determinant calculations sort most of the obvious cases out. John Mayfield on 2022-02-08
• The intention of setupCustomizers is to load the default customerizers - this had the wrong logic on the if statement. John Mayfield on 2022-02-08
• Interface constants are public static final by default. It is much more convient if these are ints rather than bytes. John Mayfield on 2022-02-08
• First batch of converting symbol equality to int comparissions John Mayfield on 2022-02-08
• Negation of {string}.equals({var}.getSymbol()). John Mayfield on 2022-02-08
• {string}.equals({var}.getSymbol()) John Mayfield on 2022-02-08
• Some missing imports John Mayfield on 2022-02-08
• Mocked object needs updating John Mayfield on 2022-02-08
• Also now if atomic num is null John Mayfield on 2022-02-08
• Replace with switch John Mayfield on 2022-02-08
• Additional null check John Mayfield on 2022-02-08
• A few equalsIgnoreCases John Mayfield on 2022-02-08
• Replace comparisson between atom ref with Integer rather than String John Mayfield on 2022-02-08
• Replace String comparission on chained symbol access. John Mayfield on 2022-02-08
• Bug detected by SonarCloud - the if condition does nothing. Reading the original paper we see this is meant to be the SQRT(RADII) where this is different for each atom type. John Mayfield on 2022-02-08
• Less code smell John Mayfield on 2022-02-08
• Swap ordering of test assertions John Mayfield on 2022-02-08
• Cleanup the loading of customerizers. John Mayfield on 2022-02-09
• First a bug in the PiContactDescriptor - wrong atom was cloned. John Mayfield on 2022-02-09
• Add Kazuya's test case (slightly modified to match the expected behaviour) and add document that pi-systems with a single double bond are not considered conjugated. John Mayfield on 2022-02-09
• Use SMARTS in XLogP instead of the UniversalIsomorphismTester. This is now clearer what each pattern is and should run slightly faster since UIT is an MCS finding alogrithm instead of a simple substructure match. John Mayfield on 2022-02-09
• We no longer need the adjacency cache - AtomContainer2 takes care of this. John Mayfield on 2022-02-09
• Remove main() from FingerprinterTest John Mayfield on 2022-02-09
• Cuts in half the number of paths we need to encode, only do the more expensive canonical store when the start and end of the path are ordered lexicographically. John Mayfield on 2022-02-09
• Move some methods arround to make it easier to add either hashed features or strings. John Mayfield on 2022-02-09
• Add the option to create Raw and Count fingerprints for the path based fingerprints. A nice property of some of these is the hash is based of the feature string and see if needed we can refold loss-lessly back to the binary fingerprint. John Mayfield on 2022-02-09
• Issues found by SonarCloud John Mayfield on 2022-02-09
• Use the diamond operator. John Mayfield on 2022-02-10
• Collapse identical catch blocks John Mayfield on 2022-02-10
• for-each instead of for-i John Mayfield on 2022-02-10
• Replace String.indexOf with String.contains John Mayfield on 2022-02-10
• Replace StringBuffer with StringBuilder John Mayfield on 2022-02-10
• Removed unneeded boxing John Mayfield on 2022-02-10
• Use Java style array. John Mayfield on 2022-02-10
• Use List.sort(); John Mayfield on 2022-02-10
• Use a method-reference John Mayfield on 2022-02-10
• Remove unboxing John Mayfield on 2022-02-10
• Left over John Mayfield on 2022-02-10
• Remove redundant casts John Mayfield on 2022-02-10
• Remove redundant types John Mayfield on 2022-02-10
• Strings are immutable - we don't need a new one. John Mayfield on 2022-02-10
• Fields may be final John Mayfield on 2022-02-10
• while(iterator) loop can now use for-each John Mayfield on 2022-02-10
• Remove duplicate throws - majority in tests where throwing java.lang.Exception is OK. John Mayfield on 2022-02-10
• Final method not needed John Mayfield on 2022-02-10
• Interface members are public by default John Mayfield on 2022-02-10
• Redundant semi-colon John Mayfield on 2022-02-10
• Don't need to call toString() John Mayfield on 2022-02-10
• More toString() not needed John Mayfield on 2022-02-10
• Qualifier on enum not needed John Mayfield on 2022-02-10
• List replace indexOf with contains John Mayfield on 2022-02-10
• Unusued imports John Mayfield on 2022-02-10
• Remove redundant initalizers - unlike C in Java int defaults to 0, bool to false, etc. Object is not defaulted null but if this is later assigned then you don't need to set it to null in the first place. John Mayfield on 2022-02-10
• More final declarations John Mayfield on 2022-02-10
• Use RoundingMode enum John Mayfield on 2022-02-10
• Use Interger.parseInt when we need an int and not an Integer John Mayfield on 2022-02-10
• "Reinflate" convex rings in macrocycles. The macrocycle layout can end up with the ugly looking rings - we now detect if we get a convex ring and reinflate. Fixes #591. John Mayfield on 2022-02-10
• Removed unused varaible. John Mayfield on 2022-02-10
• Disable external entities. John Mayfield on 2022-02-10
• Try-with-resources around byte channl John Mayfield on 2022-02-10
• Avoid divide by 0 in random access SDF - it's not completely clear what this code was meant to be doing. John Mayfield on 2022-02-10
• Fix divide by 0 in geometry functions, most of the time we default ot 0 for central points, but we use 1 for an scaling factor and 0 for RMSD's again. John Mayfield on 2022-02-10
• Division by zero in taniomoto calcs - what the tanimoto (0.0 or 1.0) of two empty fingerprints is perhaps up for debate. John Mayfield on 2022-02-10
• Check for division by zero in some descriptors. John Mayfield on 2022-02-10
• MMFF - we can't share the charge if there were no terminal atoms. John Mayfield on 2022-02-10
• Okay so we can't use the non-deprecated SAXParserFactory - odd. John Mayfield on 2022-02-10
• Minor code smells John Mayfield on 2022-02-10
• Correct fix for disabling external entities and avoid using the deprecated XMLReaderFactory. John Mayfield on 2022-02-10
• Fix possesive Regex's and add a deprecation note pointing to the better implementation John Mayfield on 2022-02-10
• Unused imports John Mayfield on 2022-02-10
• Replace all cases of printStackTrace() - we log this as either a warning or error. Since this was ignore anyways these errors were effectively ignored and this gives more control via logging. John Mayfield on 2022-02-10
• Additional stereo wedge checks and corner cases. We need to check the angle of stereo with only 3 explict neighbours to know what a valid wedge pattern is. Also check for the 180 cases. John Mayfield on 2022-02-12
• Fix a corner case in repeat crossing bonds when we have variable attachments. John Mayfield on 2022-02-12
• Additional null check needed John Mayfield on 2022-02-12
• Fix copyright John Mayfield on 2022-02-12
• Compute correct HuLuIndex values and add a test case for a closed bug that still existed. John Mayfield on 2022-02-14
• Suggestions from SonarCloud John Mayfield on 2022-02-14
• Fix copyright John Mayfield on 2022-02-14
• "EXIT" extension command was duplicated - these are skipped anyways. https://www.noah-itn.eu/wp-content/uploads/2019/03/shelx-manual.pdf John Mayfield on 2022-02-15
• These methods should either all be synchronised or none at all. John Mayfield on 2022-02-15
• Remove dodgy comparator it's not clear what this was doing but possibly some hack to allow the enum comparator to be overridden - bonkers. John Mayfield on 2022-02-15
• Make equals work properly - the exception is converted to a runtime exception, maybe return false is better. John Mayfield on 2022-02-15
• Un-useful if conditions John Mayfield on 2022-02-15
• Fix reference comparissions - objects are compared with equals John Mayfield on 2022-02-15
• You really probably don't need BigDecimal for Tanimoto's John Mayfield on 2022-02-15
• Additional synchronisation. John Mayfield on 2022-02-19
• String's are immutable, trim() and subtring() return the new value. John Mayfield on 2022-02-19
• Copy-paste errors, SMSD 2 just has the single check. The ChemicalFilters check was checking the same atom pair twice. John Mayfield on 2022-02-19
• Some always-false conditions, some minor bugs found. John Mayfield on 2022-02-19
• As far as I can tell - this is could be SonarCloud misreporting. Use local loop variables to make things clearer. John Mayfield on 2022-02-19
• Remove non-loops. RandomAccessSDFReader had a comment that MDLV2000Reader(IAtomContainer) didn't read properties which is why it used a IChemModel - this is no longer the case. The reset were cases where we want to select the first match. John Mayfield on 2022-02-19
• Minor code-smells, unused imports and isEmpty(). John Mayfield on 2022-02-19
• First batch of NPE checks John Mayfield on 2022-02-19
• Cleanup John Mayfield on 2022-02-19
• RgroupList parsing - did not loop. We really just need if/else John Mayfield on 2022-02-20
• Rewrite this logic to make it clearer. John Mayfield on 2022-02-20
• SMSD NPR checks John Mayfield on 2022-02-20
• Various NPE checks and guards John Mayfield on 2022-02-20
• Correct logic of if John Mayfield on 2022-02-20
• try-with-resources much better here. John Mayfield on 2022-02-20
• Unused import John Mayfield on 2022-02-20
• Remaining NPE exceptions. John Mayfield on 2022-02-21
• Better handling of blank readLine() - SonarCloud will still complain but we should assert we have a blank line and not reached the end of input. John Mayfield on 2022-02-21
• Fix issues - RXN reader depends on brittle null handling to read a list of reactions. A push-back line reader would work better. John Mayfield on 2022-02-21
• Unused import John Mayfield on 2022-02-21
• atom1/2 are never null but suppress the warning John Mayfield on 2022-02-21
• Can be suppress the warning by loading it into a variable. John Mayfield on 2022-02-21
• Use a temporary variable for our blank lines. In the RXN reader we actually expected $MOL/$MDL. John Mayfield on 2022-02-21
• Ignore this test that does sometimes fail - as noted the XorShift PRNG is good enough for our purposes but it is not perfect. John Mayfield on 2022-02-21
• Comment out duplicate keys with a comment. Also add a DOI, we could add cdk.cite but this is in cdk-extra so less used than a descriptor. John Mayfield on 2022-02-21
• Ensure correct math operands, when storing a result in a double we probably don't want an double = int int. [John Mayfield* on 2022-02-21](https://github.com/cdk/cdk/commit/5b5fcd3d5d)
• Fix test case John Mayfield on 2022-02-21
• QueryChemObject is not Serializable so the subclass should not be. John Mayfield on 2022-02-21
• Don't need Math.abs() here. Actually cap the max number of rotations. John Mayfield on 2022-02-21
• Need float here. John Mayfield on 2022-02-21
• Avoid double brace initialisation. John Mayfield on 2022-02-21
• Check the type of the object. John Mayfield on 2022-02-21
• Add hashCode since there is an equals method. John Mayfield on 2022-02-21
• Boxing not needed John Mayfield on 2022-02-21
• Don't ignore important return values - the iterators were actually ok due to shared state but it is clearer to act on the return value. John Mayfield on 2022-02-21
• Use a temporary variable for ignored lines. John Mayfield on 2022-02-22
• Avoid NPE if firstAtom/secondAtom is null. John Mayfield on 2022-02-22
• We only need volatile if something is likely and inefficient to be accessed from multiple threads at once. In places like RingSearch this is very unlikely since you could just have a different RingSearch per thread/molecule. John Mayfield on 2022-02-22
• Avoid volatile in ChemObjectBuilders. The most robust way of implementing Singletons is with an Enum. John Mayfield on 2022-02-22
• Add NoSuchElement exceptions to cdk-default iterators. John Mayfield on 2022-02-22
• Add NoSuchElementException to cdk-standard iterators. John Mayfield on 2022-02-22
• Add NoSuchElement to iterators in cdk-silent. John Mayfield on 2022-02-22
• Misc NoSuchElementException needed on these iterators. John Mayfield on 2022-02-22
• Fix JavaDoc errors due to copy-paste John Mayfield on 2022-02-22
• Update README.md John Mayfield on 2022-02-22
• Enable Jacoco for SonarCloud John Mayfield on 2022-02-22
• restore space as delimiter for string-based definition of InChI options Marco Foscato on 2022-03-06
• allows both space and comma as separator for InChI options Marco Foscato on 2022-03-07
• javadoc improvements for SmallRingDescriptor Tim Dudgeon on 2022-03-19
• Two new contributors Egon Willighagen on 2022-03-19
• Another release of log4j Egon Willighagen on 2022-03-24
• Update FiguerasSSSRFinder.java Christoph Steinbeck on 2022-04-06
• Update FreeHepWrapper.java Otto Brinkhaus on 2022-04-06
• Fix a stuble corner case. When we split a molecule we now update the Sgroups accordingly. If an sgroups spans multiple components (e.g. a mixture bracket) we now delete it since it is redundant or inconsistent (the other option would be to add it to all parts it occurs in). To make things work nicely we should leave the original Sgroups intact. John Mayfield on 2022-04-07
• These methods are not implemented/supported and should therefore throw an exception. John Mayfield on 2022-04-20
• Update mockito-core to 4.5.1 Mark Williamson on 2022-04-22
• Update actions/cache to 3 Mark Williamson on 2022-04-22
• Update to actions/setup-java@v3 Mark Williamson on 2022-04-22
• Make use of setup-java's maven caching Mark Williamson on 2022-04-22
• Update actions checkout to v3 Mark Williamson on 2022-04-22
• Fix a v. subtle issue in up/down bond handling in SMILES. It's quite a corner case but it turns out some toolkits do write records like this (found one in ChEMBL). Only happens if the bond is written on the ring open (unusual but ok) and then multiple directional bonds are written. BEAM does more in recent releases to check/ignore innconsitent behaviour allready but we can add the correct check in the BEAM2CDK conversion. John Mayfield on 2022-06-03
• Updated to Apache Jena 4.2 Egon Willighagen on 2022-06-04
• Fixed the error message: correct writer description Egon Willighagen on 2022-06-04
• Reupdated, resolving merge conflict Egon Willighagen on 2022-06-04
• Move to Jena 4.4.0 and only include cdk-iordf if you are using Java 11 John Mayfield on 2022-06-04
• Remove stack trace dumping John Mayfield on 2022-06-04
• Update to latest dependency versions. John Mayfield on 2022-06-04
• Test for the proper output of the alpha value Egon Willighagen on 2022-06-06
• Use the US locale which uses a period for floats Egon Willighagen on 2022-06-06
• ROOT instead of US Egon Willighagen on 2022-06-07
• Update the documentation and make a comment on making sure the leading slash is not included. John Mayfield on 2022-06-30
• Check string bounds on PDB COMPND line. Fixes #870 John Mayfield on 2022-07-13
• Log4j 2.18.0 Egon Willighagen on 2022-08-21
• JNA-InChI 1.1 Egon Willighagen on 2022-08-21
• CMLXOM 4.3 Egon Willighagen on 2022-08-22
• Catching the more specific SecurityException instead of the general Exception to avoid just swallowing all exceptions that might occur Uli Fechner on 2022-08-22
• Breaking Change! Renaming LoggingTool to Log4jLoggingTool and make it package private so users don't create it in their own code (it should be via the factory). We also remove the compile time dependency on log4j-core, a use should include this them selves and may wish to use something like log4j-to-slf4j. John Mayfield on 2022-08-23
• Deprecate SystemOut logging tool and just put a StdErr tool in the same module so we can initialize it directly and don't need to use reflection. John Mayfield on 2022-08-23
• Removing log4j-core removes the ability to set the level and configure explictly. We can switch on a system property in the XML now which I've done. John Mayfield on 2022-08-23
• The only plase setLevel is called is from MayGen, this will now possibly throw an exception and is better controlled with Log Config John Mayfield on 2022-08-23
• • fixed and amended some javadocs in ReactionManipulator Uli Fechner on 2022-08-25
• Test this condition after checking -Dcdk.logging.level. Otherwise it defaults to warn John Mayfield on 2022-08-25
• • added methods to perceive and unset the atom type configurations in ReactionManipulator - fixed a javadoc errors wrt content in AtomContainerManipulator#percieveAtomTypesAndConfigureUnsetProperties Uli Fechner on 2022-08-26
• • added simple tests for newly added methods in ReactionManipulator - added null pointer checks for perceiveAtomTypesAndConfigureAtoms, perceiveAtomTypesAndConfigureUnsetProperties, and clearAtomConfigurations Uli Fechner on 2022-08-26
• Update maven.yml Alex on 2022-08-29
• Add MAVE_OPTS that shuould improve the timeout. John Mayfield on 2022-08-30
• Improved CML XSD loading using an entity resolver. Also use try-with-resources to ensure all streams are closed correctly. John Mayfield on 2022-08-31
• Fix test on windows we just use \n instead of \r\n. OK in this case. John Mayfield on 2022-08-31
• • fixed test in XMLIsotopeFactoryTest following John's work in AtomTypeFactoryTest - AtomTypeFactoryTest: removal of unused code, small beautifications Uli Fechner on 2022-08-31
• added dedicated method newReaction() for instantiation of Reaction objects to IChemObjectBuilder and implementations thereof Uli Fechner on 2022-09-05
• Utilities for selecting a substructure of a molecule. John Mayfield on 2022-09-10
• Correct the "resync" operation. John Mayfield on 2022-09-10
• More efficient single electron/lone pair handling based on how these are implemented we want to do a single pass over them. John Mayfield on 2022-09-10
• • improved javadocs for new copy method in AtomContainerManipulator - added a first very simply test for the copy method in AtomContainerManipulatorTest Uli Fechner on 2022-09-10
• • re-wrote extractSubstructure(IAtomContainer,int[]) to use extractSubstructure(IAtomContainer,Collection) instead - put an ignore on the method to test extractSubstructure(IAtomContainer,int[]) in AtomContainerManipulatorTest Uli Fechner on 2022-09-10
• Use mol.indexOf() instead of atom.getIndex(), also make sure the bond remapping is indexed correctly. John Mayfield on 2022-09-10
• un-ignore tests, fix sonar cloud smells. John Mayfield on 2022-09-10
• Missed removal of throws John Mayfield on 2022-09-10
• Remove @throws John Mayfield on 2022-09-10
• • fixed a bug in AtomContainerManipulator.copy(IAtomContainer,IAtomContainer,Predicate,Predicate) - added more tests for the copy method to AtomContainerManipulatorTest Uli Fechner on 2022-09-10
• re-wrote tests for methods copy and extractSubstructure based on Hamcrest's assertThat Uli Fechner on 2022-09-10
• Add slf4j logging redirect. John Mayfield on 2022-09-10
• Optimise unique (atom) match filtering, add a new filter for providing exclusive matches. John Mayfield on 2022-09-10
• Remove use of ThreadLocal in favour of an encapsulate SmartsResults. The getLastErrorMesg() is no longer thread safe but can be used in simple usages, the SmartsResult should be used in threaded environments. John Mayfield on 2022-09-10
• Set a flag on "complex" atom expressions, in some case down stream tools may wish to treat "simple" expressions (i.e. not in square brackets) differently. John Mayfield on 2022-09-10
• Minor fix to the message John Mayfield on 2022-09-10
• Make these check vs update package-private, this allows us to check a filter before we apply it. John Mayfield on 2022-09-10
• Add a deprecation comment to remind me where to look. John Mayfield on 2022-09-10
• Extra documentation on the exclusive atom mapping filter. John Mayfield on 2022-09-10
• Fix test by introducting a new Mappings filter, there is a subtle different between unique atoms (more efficient) and unique atom sets and both can be useful. Consider matching OSO against OS()(O)O, there are 2 unique matches over the atoms but 3 over the set of atoms (i.e. we see a new combinatation). [John Mayfield* on 2022-09-10](https://github.com/cdk/cdk/commit/a4ca3cb5d2)
• Mocktio v4.8.0 John Mayfield on 2022-09-10
• Rollback the UniqueAtomFilter changes - it makes sense to keep behaviour aligned with convention of other toolkits. Added a test to avoid making the change in future. John Mayfield on 2022-09-10
• Additional test John Mayfield on 2022-09-10
• As far as I can tell these specific exclusions are no longer needed. John Mayfield on 2022-09-11
• Move to Junit5 engine John Mayfield on 2022-09-11
• First pass with automated regactorings (IntelliJ) and manually putting in the assertThrows and assertTimeout. John Mayfield on 2022-09-11
• IntelliJ "replace Junit4 assertion with Junit5 assertion" John Mayfield on 2022-09-11
• Removed unused imports John Mayfield on 2022-09-11
• Rebase on master John Mayfield on 2022-09-11
• Final uses of Junit4 Assert. John Mayfield on 2022-09-11
• Junit5 parameterized tests - all uses of org.junit.Test updated. John Mayfield on 2022-09-11
• Increase timeout John Mayfield on 2022-09-11
• Replace SlowTest category annotation with JUnit5 tag John Mayfield on 2022-09-11
• Remove the vintage engine dependency. All tests fully ported to JUnit5 John Mayfield on 2022-09-11
• SonarCloud "bugs" John Mayfield on 2022-09-11
• Make all the timeouts longer here John Mayfield on 2022-09-11
• Fix missing test annotation John Mayfield on 2022-09-11
• These methods don't need to be public, as noted by SonarCloud John Mayfield on 2022-09-11
• Some missing test annotations John Mayfield on 2022-09-11
• Final removal of Junit4, these "Suites" are no longer needed and actually led to classes being run twice. John Mayfield on 2022-09-11
• re-introduced CloneNotSupportedException to retain compatability for any downstream code that calls AtomContainerManipulator::extractSubstructure(IAtomContainer,int[]) - removed unnecessary final modifier from private static method Uli Fechner on 2022-09-12
• A subtle bug introduced by a SonarCloud suggestion in ModelBuilder. 1/180 is a const expression and int div was probably not intended. Updating to 1.0/180π was not correct. The intended expression should have been 1/(180π) but a better idiom is Math.toRadians(). John Mayfield on 2022-09-12
• freehep (graphics) and cmlxom include Junit4 as a compile time dependency. John Mayfield on 2022-09-12
• Need to update the main branch in workflows. John Mayfield on 2022-09-12
• Identical but simpler logic, use JDK sort and compartor, avoid redundant loop variable. John Mayfield on 2022-09-12
• More tidying up - the sort in these two places does nothing since it only compares the "stringScore" John Mayfield on 2022-09-12
• Compare the parent node then the current sphere - fixes #588. Comparator chaining here is a little harder to read so we do it the old-fassioned way. Another test need updating but we can see the expected output is clear wrong. For example "C-3;CCC(CC,C,CC,O/..." is wrong since we have three nodes in the first sphere C,C,C then 4 in the second CC,C,CC,O. This is now correctly encoded as CC,CO,CC. [John Mayfield* on 2022-09-12](https://github.com/cdk/cdk/commit/756a0b1edf)
• Tests fixed - but we probably need to deprecate and remove this descriptor unless we can regenerate the DBs. John Mayfield on 2022-09-12
• SonarCloud bug complaint. John Mayfield on 2022-09-12
• Less varriable masking. John Mayfield on 2022-09-12
• Simplify sorting logic - we don't need the stringscore, these looks to be a hack to try and fix the nesting issue and can't work since the parents may be idential. Now we have a proper comparator we can sory in the correct places. John Mayfield on 2022-09-12
• Junit5 John Mayfield on 2022-09-12
• Add a flag to switch between LEGACY and DEFAULT (correct) mode. John Mayfield on 2022-09-12
• Move all existing usages of HOSE codes to LEGACY_MODE. John Mayfield on 2022-09-12
• More tweaks needed to be fully match the old legacy behaviour. John Mayfield on 2022-09-12
• Revert "Tests fixed - but we probably need to deprecate and remove this descriptor unless we can regenerate the DBs." John Mayfield on 2022-09-12
• Bug highlighted by SonarCloud John Mayfield on 2022-09-12
• Cleanup code smells. John Mayfield on 2022-09-12
• CDK v2.8 Release John Mayfield on 2022-09-13
• Move cdk-test main/ classes to test/ and make the test-jar the dependency. John Mayfield on 2022-09-14
• Update stylesheet for Java 17 John Mayfield on 2022-09-14
• Update the cdk-build-util dependency. John Mayfield on 2022-09-14