* first steps towards flexible colour palettes
* add B&W palette and a test for it
* add python support;
this is, once again, not the best API due to the inability to auto-translate boost::tuples at this point
* more palette control from python
* rename some of the swig-wrapped types to make them more consistent
* handle palettes that do not have a default value
* a bit of cleanup and modernization
* switch to -j3
* back to -j2
* disable static libs
* allow dynamic linking of swig wrappers
* turn off the py27 builds while we are testing
* Install java and SWIG
* re-enable python2.7
* Wrap Chem.FindPotentialStereoBonds into Python.
* findPotentialStereoBonds now sets the Bond.GetStereo property of the double bond to Bond::STEREOANY.
Some of the doc strings indicated this as the desired behavior, but
some others also indicated otherwise. So I've cleaned up and
refactored those doc strings as well to be consistent. Pulled all the
doc string comments from the .cpp file up to the .h file and merged
all the necessary prose, including adding some about the fact rings
are ignored.
Previously, users would have to test the size of the GetStereoAtoms
vector to determine whether this function found potential double bond
stereo. Testing for Bond::STEREOANY instead is way more straight
forward.
* Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper
* Added missing argument
Added missing argument to call to getAlignmentTransform causing build failure
* Added test case for getAlignmentTransform
* Update AlignTests.java
* Update AlignTests.java
* Update AlignTests.java
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
* Fixes csharp build for 64 bit systems
* Need to support make and make install stages
* switch to an alternate strategy and get it working for the java wrappers too
this now builds for me on 64bit win10 with MSVC14
* add missing files from that last commit
* Hopefully fixes unix and osx builds while maintaining msvc builds
* Fixes mono builds, removes python check
* update .gitignore
* foundation for 3D descriptors
move PBF into core
* cleanup work
* a bit more cleanup
* move the principal moments calc to MolTransforms
* cleanup
* cleanups
* add caching of the principal moments and values
* do not include the 3D descriptors in MolDescriptors.h
* the properties are computed
* add PMI descriptors and tests
* add tests for NPR descriptors
* return 0 when the largest PMI is zero
* PMI edge case tests
* NPR edge case tests
* PBF edge case tests
* PBF edge case tests
* more edge cases
* add a few more 3d descriptors
* add defns to docs
* tests for the new descriptors
* add versions to new descriptors
* add 3d descriptors to python wrapper
* add eigen support to the travis build
* try to get non-windows builds working
* remove computeCovarianceMatrix() from java wrapper
* make pmi property names "private"
* Adds replaceCore function that takes a matchVect
* Fixes error reporting, adds tests
* Switches PRECONDITION to ValueError exceptions
* Fixes MatchVectType annoyance in swig. Don't know why this is necessary.
* Silences warnings
* Adds working doctests and better explanations.
There seems to be a problem in some travis builds where some java wrapper files aren't finished writing before the next step of the build happens. This is an attempt to resolve that.
* Adds RDAny (smaller generic holder) Updates all used dictionaries
This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.
* Removes code duplication
* Converts CHECK_INVARIANT to TEST_ASSERT
* Fixes DoubleTag issue
* Adds Bool to DoubleMagic implementation
* Removes reference to property pickler
* download junit.jar automatically when it is needed
* do not need to download junit anymore
* doc update
* try a different maven url to see if that solves the MD5 problems
