* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
* 3D Descriptors Dragons
* stripped down, not yet working
* get this building on a non C++-11 compiler
* move the python test to the python directory
* move the python test to the python directory
* add the python test
* now at least those tests runn
* warning comment
* some basic refactoring and cleanup
* get python wrapper "working" (completely untested)
* fix Name
* fixing AutoCorr & RDF
* AutoCorr test added
* RDF reviewed based on AutoCorr comments
* fix Morse code
* Morse reviewed
* Correct Morse & start Getaway
* correct MORSE test
* start Getaway clean up
* simplification of Whim
* better
* fix Getaway
* fix RCON
* merge repaired
* adding Dragon 2D autocorrelations descriptors
* fix the 3D autocorrelation descriptors based on the modification in
Dragon.
* Adding the 2D autocorrelation descriptors (no need of Eigen
dependency for this one)
* Adding 2D test case
* IState … no idea for the moment
* there is an error in 2D computation (memory error ???)
* fix the IState for molecules with Hs
* need to use getTotalNumHs(true) not getTotalNumHs()
* also need to remove Hs in both dv and d!
* fixing Rcov values
I fix the Rcov values
* fix Getaway
* remove push_back
* remove call to sum
* improve tests
* fix getaway
* adding precision parameter to GETAWAY
* adding rouding (1e-3)
* fix WHIM
* use void in declarations of function
* update MolDescriptors link
* remove print option in WHIM
* fix python wrapper to 3D descriptors.
- all modifications reduce computation time by a factor of 3!
* final fix for Getaway
* all output are fixed except the 2 first values due to clustering
approach.
* cluster cannot be fixed du tu float precision issue between Java &
c++
* best fix of ITH and ISH
* use the same algorithm as in Dragon 6 but there is still a deviation
* remove std::move
* std:move only works on c++ 11
* fixing issue based on Greg Comments
* auto2D still not working on my env
* update 3d test.py
* auto 2D not working after the first loop test
* tighten up the tests
* change name
* update, but still does not pass
* make this run (though it does not work)
* re-enable test3D
* some cleanup
* add GETAWAY test data. Note that the tests fail
* fix the ATS and ATSC autocorrelation 2D
Broto Moreau and Geary autocorrelation are not correct again a specificity of Dragon to compute them. The result are not consistant with Padel because we use the relative weigth not in Padel.
* one minor change to get things to compile
* fix the M & G matrix computation
fix inversion in the computation of the equations for both M & G matrixes
* update autocorr2d tests
* 192 examples
* fix issue in cluster 0.01 0.009 case
this is not correct all the cases
* update GETAWAY expected values to reflect the fact that we cannot reproduce the literature values exactly
fix a leak in GETAWAY
* fix the negative values in gamma
this is strickly the implementation that we find in the book molecular descriptors for chemoinformatics (except the case where an atom is already in the axis in this case it should be added in the symetric list which is not the case in this implementation)
* Update WHIM.cpp
adding the axis atoms to the symetrical list
* update WHIM tests
* add AUTOCORR2D to MolDescriptors and the python wrappers
* start adding tests
* test the python versions of the new descriptors
* update list of descriptors
* Support more formats and add new method returning deleted fragments
* Reduce number of changes and make more visible what has really changed
* Add 'UnitTestSaltRemover' and perform changes suggested by review
* Add support for 'smi' file
* Improve doctest regarding new functionality
* Following suggestions made by collaborator
* Be consistent with 'ValueError' and add an example without tuple destructuring
* 3D Descriptors Dragons
* stripped down, not yet working
* get this building on a non C++-11 compiler
* move the python test to the python directory
* move the python test to the python directory
* add the python test
* now at least those tests runn
* warning comment
* some basic refactoring and cleanup
* get python wrapper "working" (completely untested)
* fix Name
* fixing AutoCorr & RDF
* AutoCorr test added
* RDF reviewed based on AutoCorr comments
* fix Morse code
* Morse reviewed
* Correct Morse & start Getaway
* correct MORSE test
* start Getaway clean up
* simplification of Whim
* better
* fix Getaway
* fix RCON
* merge repaired
* adding Dragon 2D autocorrelations descriptors
* fix the 3D autocorrelation descriptors based on the modification in
Dragon.
* Adding the 2D autocorrelation descriptors (no need of Eigen
dependency for this one)
* Adding 2D test case
* IState … no idea for the moment
* there is an error in 2D computation (memory error ???)
* fix the IState for molecules with Hs
* need to use getTotalNumHs(true) not getTotalNumHs()
* also need to remove Hs in both dv and d!
* fixing Rcov values
I fix the Rcov values
* fix Getaway
* remove push_back
* remove call to sum
* improve tests
* fix getaway
* adding precision parameter to GETAWAY
* adding rouding (1e-3)
* fix WHIM
* use void in declarations of function
* update MolDescriptors link
* remove print option in WHIM
* fix python wrapper to 3D descriptors.
- all modifications reduce computation time by a factor of 3!
* final fix for Getaway
* all output are fixed except the 2 first values due to clustering
approach.
* cluster cannot be fixed du tu float precision issue between Java &
c++
* best fix of ITH and ISH
* use the same algorithm as in Dragon 6 but there is still a deviation
* remove std::move
* std:move only works on c++ 11
* fixing issue based on Greg Comments
* auto2D still not working on my env
* update 3d test.py
* auto 2D not working after the first loop test
* tighten up the tests
* change name
* update, but still does not pass
* make this run (though it does not work)
* re-enable test3D
* some cleanup
* add GETAWAY test data. Note that the tests fail
* fix the ATS and ATSC autocorrelation 2D
Broto Moreau and Geary autocorrelation are not correct again a specificity of Dragon to compute them. The result are not consistant with Padel because we use the relative weigth not in Padel.
* one minor change to get things to compile
* fix the M & G matrix computation
fix inversion in the computation of the equations for both M & G matrixes
* update autocorr2d tests
* 192 examples
* fix issue in cluster 0.01 0.009 case
this is not correct all the cases
* update GETAWAY expected values to reflect the fact that we cannot reproduce the literature values exactly
fix a leak in GETAWAY
* fix the negative values in gamma
this is strickly the implementation that we find in the book molecular descriptors for chemoinformatics (except the case where an atom is already in the axis in this case it should be added in the symetric list which is not the case in this implementation)
* Update WHIM.cpp
adding the axis atoms to the symetrical list
* update WHIM tests
* add AUTOCORR2D to MolDescriptors and the python wrappers
* start adding tests
* test the python versions of the new descriptors
* update list of descriptors
* Support more formats and add new method returning deleted fragments
* Reduce number of changes and make more visible what has really changed
* Add 'UnitTestSaltRemover' and perform changes suggested by review
* Add support for 'smi' file
* Improve doctest regarding new functionality
* Following suggestions made by collaborator
* Be consistent with 'ValueError' and add an example without tuple destructuring
* 1194: Review assignments of range in Python code
Task-Url: https://github.com/rdkit/rdkit/issues/1194
Either wrapped the range expression into a list or made sure that the
code is working with a range object.
* Removed use of deprecated string module functions
* 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"
