* Fixes#2057
docs still need to be updated
* docs update
* Update getting started doc.
This still needs to have the doctests run and should probably be
proofread and tweaked
* some doc updates
* change in response to review
* add basic fingerprint bit rendering code
This was inspired by/adapted from the CheTo code from Nadine
* add some tests
* add documentation
add option to control which example of the bit is used
* first pass at something that kind of works
* no need to document sping
* add some imported modules
* forgot to add this before
* switch to using a file per module
* disable the old api copy
* update the way links are handled
* stop auto-running doctests (sigh)
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
* 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
* Start of GettingStartedInC++ documentation.
* Changed GettingStartedInC++ from rst to markdown format. Added some more text.
* Added Working with Molecules to GettingStartedInC++
* Expanded on behaviour of Kekulize wrt clearing aromatic flags on atoms and bonds.
* Added section Modifying Molecules.
* More plodding progress.
* A load more documentation.
* Undid change to global CMakeLists.txt
* Minor editing of docs.
* Changed examples so they use RDBASE to find test data rather than relative
path.
* Fixed use of -std=c++ in CMakeLists.txt. Extra waffling about memory.
* Modifications to examples and documentation as requested.
* Couple of minor changes.
* Change to example11.cpp and associated text in docs.
* Fix a bug in the python DistGeom tests.
* test new features
* add simple parameter objects for ETDG, ETKDG, and KDG
* Update conformation generation documentation to use the new parameter objects.
constructor (which is overkill, if the molecule had already been
sanitized) with a call to MolOps::Kekulize(). Thus it is not
necessary to call Kekulize() either from Python or from C++,
and no changes are required to the scripts/source codes
previously used for UFF
- removed the code which throws an exception asking to reload the
molecule with sanitize=false since it is not necessary:
only one test in the MMFF validation suite fails if the
molecule is aromatized and then re-kekulized (CIKSEU10), and
it represents a case where the position of double bonds in
a conjugated, non-aromatic system makes a difference for atom
type assignments, which in general is a nonsense. This is not
due to a bug in the code, but rather depends on MMFF atom
typing rules. Hence, I kept the sanitize=false and the call to
sanitizeMMFFMol() in testMMFFForceField.cpp, but I would not
generalize this requirement to "normal" molecules, because it
is really not necessary, since you do not have a reference
kekulization to refer to in the real world.
- updated Docs/Book/GettingStartedInPython.rst accordingly
- updated tests accordingly
