* add function to convert embedParams to json
* add catch test
* add function to python wrapper
* test python function
* update copyright
* undo formatting and cleanup
* more cleanup
* remove the map flag and added round trip
* add bounds mat output
* run clang-format
* expose symmetrizeTerminalAtoms() to the public API
* support symmetrizing terminal groups in RMS pruning in confgen
* add that to the python wrapper
* add backwards compatibility note
* allow JSON config of the new option
* change a define to a "using"
* basic atropiosomer support for confgen
currently only supports bonds with two exo substituents on each end
* support systems with two exo bonds
* cleanup
* add test for #7109Fixes#7109
* clean the tests up a bit
* first pass at allowing setting the coordmap from Python
* plug the memory leak
* implemented tidier coordMap memory management
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fix macrocycle bounds calculation, and make it accessible from Python
* Previously, C=C([#1])-C([#1])=C groups in a macrocycle were always
cis. Although the bounds within the group allowed cis or trans, the
1-4 bounds of the H atoms were always set to trans, which forces the
carbons into the cis position. This change fixes this behavior to
allow cis or trans conformations
* Previously, the useMacrocycle14config flag could only be used from
Python by creating an ETKDGv3 object, and defaulted to False
otherwise. This change adds the flag to EmbedMolecule,
EmbedMultipleConfs, and the EmbedParameters Python interface.
* The new default for useMacrocycle14config is True to be consistent
with the default for useMacrocycleTorsions. Since the old default was
False, this could change the output of existing scripts.
* Add test case for updated macrocycle distance bounds
* Remove 2 unused variables
* Fix a python test that set .seed instead of .randomSeed on an ETKDGv3
---------
Co-authored-by: Franz Waibl <waiblfranz@gmail.com>
* fix a float comparison in a test
* make ETKDGv3 (i.e. v2 of the torsion parameters) the default.
This should have been done a long time ago.
* change default for onlyHeavyAtomsForRMS too
* release notes update
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* a bit of minor refactoring
* create API function to get experimental torsion bonds
* put the torsion index in the dictionary
in this case it's silly to return tuples to python
* allow passing an EmbedParameters object from python
* capture the torsion index too
* add an atomIndices component
we should typedef the torsionBonds type
* test torsion index
* changers in response to review
* changes in response to review
* fix merge mistake
* support tracking where the conformer generation code fails
* less verbose output
* tests now pass
* fix a stupid typo
* fix SWIG wrappers
* changes in response to review
* add custom parameter to tune the relative weights of distance bounds to all the other force terms during ETKDG conformer generation
* fixes as per reviewer comments
* backup
* bug fix: ensure getTotalNumHs() alwasy considers neighbors
* make trans amides the default
ensure it works
cleanup expected tests
* note results-changing fix
* fix docs and run some clang-format
* cleanup in response to review
* improvements for smal anr large ring conformer generation
* add documentation and reorder parameters in EmbedParam
* resolve merge conflict due to coordMap null pointer
* minor changes to address merge comments
* reorder variables in EmbedParameters
* add regression test for small ring and macrocycle torsion preferences
* not apply small ring torsions to bridged ring systems
* fix and test for bridged small rings torsion pattern exclusion
* add ETKDGv3 and srETKDGv3 option to keep compatiblity for original ETKDG
* EKTDG version 3 related minor fix
* add reference to doc string
* Java wrapper for ETKDGv3
* fix doc
* change CPCI to shared_ptr, but it seems to be much slower
* minor modifications to small bridged ring systems, and share_ptr from previous commit is fine
* rollback from shared_ptr(map) to just map
* run clang-format
Co-authored-by: Shuzhe Wang <shuwang@eu-login-10.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-14.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-17.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-45.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-05.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-15.euler.ethz.ch>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* Support providing a distance matrix for molecule embedding
* a bit of parameter checking
* allow fragmentation before embedding to be disabled
* fix a build problem on windows
change in response to review
* 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
* Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0.
Fixing two distinct bugs:
- A randomSeed of 0 didn't use '0' as the seed even though the
documentation said that it should.
- Very large seeds could overflow the 'int' representation during
calculation of a new internal seed. This would make
EmbedMultipleConfs non-deterministic even though the user provided a
valid seed.
* Adding a C++ test for case pull request #1635.
* version 2 of ETKDG
* setting default and changing to unsigned int
* ETversion 2 only via EmbedParams available
* Some refactoring so that the DG functions that take the parameter object are the primaries.
This should allow new parameters to be added without having to modify the API
* test and wrapper changes to go along with that
* update cookbook to use etkdg
* 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.
* 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
