Paolo Tosco 97bb4a7f37 Improvements to 2D depiction and alignment/RMSD calculation (#5598) ...

* update AvalonTools to version 2.0.1

* Improvements to 2D depiction and alignment/RMSD calculation
- Refactored the straightenDepiction code which is now much simpler and more readable and supports a minimizeRotation parameter
- added C++, Python and JS tests for the new minimizeRotation parameter
- refactored tests to use CalcRMS rather than an internal implementation to compute RMS deviations
- Removed duplicated code in CalcRMS() and getBestRMS() and made their APIs consistent with respect to supported parameters
  IMPORTANT NOTE: for backwards compatibility I set the CalcRMS() default for the  new symmetrizeConjugatedTerminalGroups
  to false as this parameter was not originally supported. @greg: I would be very much in favor of setting this to true instead
  if you agree, even though it might change results for existing scripts, as I think it is a much more sensible default.
- Improved documentation to clarify the difference between CalcRMS() and getBestRMS()
- Added unit tests for CalcRMS() as there was none previously
- Added tests for the additional CalcRMS() and getBestRMS() parameters
- Added a new getBestAlignmentTransform() function
- The CFFI function set_2d_coords_aligned() now returns the matching atoms similarly to the C++, Python and JS counterparts
  IMPORTANT NOTE: this required an API change for the additional char ** parameter used to return the match.
  Existing code using set_2d_coords_aligned() will fail to compile and will require a last NULL parameter to be added to compile again
- Removed duplicated code between CFFI set_2d_coords_aligned() and JS generate_aligned_coords()
- Added has_2d_coords() to the CFFI library
- generate_aligned_coords() now supports JSON parameters and the previous versions are deprecated
- set_2d_coords_aligned() and generate_aligned_coords() both support an alignOnly parameter (which defaults to false).
  If set to true, rather than re-generating a fresh 2D layout around templateMol, the existing coordinates (if any) are simply aligned
  to the provided templateMol. If the molecule has no coordinates, a set of 2D coordinates is generated independently of templateMol
  and then aligned to the provided templateMol
- avoid that when acceptFailure is false set_2d_coords_aligned() and generate_aligned_coords() overwrite existing coordinates

* - explicitly link testDepictor to MolAlign library

* - add MolAlign dependency to testDepictor (rather than to the catch test as in the previous commit)
- add a couple of tweaks

* suppress compiler warnings (1st pass)

* warnings: 2nd pass

* warnings: 3rd pass

* - alignOnly mode should also support allowRGroups

* - fixed C++ build
- added tests for allowRGroups+alignOnly combination

* changes in response to review

* added an entry to backward incompatible changes regarding set_2d_coords_aligned()

Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>

2022-10-02 06:24:01 +02:00

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