* make sure 13 bounds constraints are added to angles that are part of an impropper torsion
* make sure angles are constrained with higher force constant to prevent rings from folding
* adapt tests to new behavior
* move comment to correct place
* add min bounds test
* make sure we are not terribly outside of the bounds matrix
* add angles and distances
* add Inversions
* add torsiona angle contribs
* use new contribs in test
* use new inversion and torsion contribs in dg
* use new distance contribs in dg
* use new angle constraints in dg
* use new constraints in FF tests
* update docstrings
* remove unused import
* include new contribs
* cleanup includes
* make changes requested by @greglandrum
* use std::move instead of release
* refactor skeleton
* fix contribs
* adapt documentation
* clarify function names
* make variable names more readable and update documentation
* switch boost dynamic bitset with std::vector<bool>
* clearer const name
* fix typo and go back to dynamic bitset
* go back to old function signature
* add inline overload with fewer arguments
* remove unecessary doc lines and add tol to distance directly in function call
* use constexpr for known distance force constant
* update documentation
* enhance documentation
* english
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* make changes requested by @greglandrum
* make all constexprs
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* First try at using DistViolationContribs
only the most basic of testing has been done
also add ForceField::distance2 to allow some optimizations
* allow testing using old approach
* optimization
At this point testUFFForceFieldHelpers fails since the check for std::max_element
in the e_contribs vector at Embedder.cpp:513 is now doing something totally different
(instead of a bunch of small distance violation contribs, we have one big one).
We'll need to come up with something for this.
With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules
using 10 threads - this runs in almost 10% less time than master.
* backup;
builds, tests do not pass
* all tests pass except the old failure
* more constification
* backup/debugging
* add fourthdim contribs the same way
* tests now pass
* deprecations
* remove unused vars and code
* changes in response to review
* first try
* do over with @greglandrum: fix atomPairs, lower SP angle force constant.
* change test file for 'update parameters from JSON':'ETKDGv2'
* adapt length to fix
* remove overwritten random seed
* adapt test files to changes
* adapt amide test, check with Greg
* fix python tests and remove unused imports
* proposal for new test molecule
* remove double comparison, increase threshold. Check with greg
* remove TODO comments
* remove debugging statements
* same code for both since they are doing the same
* format docstring to make more readable
* remove todo comments
* add indentation to angle param
* adapt doctest to newly generated conformers
* fix test to pass with fewer failures and move mol to mol file for less cluttered test.
* a bit of modernization
* remove cerrs and format correcly
* reverted test to old behavior
* use insert and make force field contribs exception safe
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Fixes#7181
adds a new constrainedAtoms member to the etkdgdetails structure which is used to propagate info about the coordMap into the ETK minimizations
* Update Code/DistGeom/DistGeomUtils.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/DistGeom/DistGeomUtils.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* 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
* 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
* move _embedPoints over to use EmbedArgs structure
* move _embedWithExpTorsions over
* a few pointer cleanups
* step by step
* more
* wrap the ETKDG paramaters into a struct
* fix a typo
* additional cleanup
* more
* simplify the embedargs struct
* pass embedParams instead of having them in embedargs
* a bit more cleanup
* response to code review
* enforce planarity
* increase the force constant for the impropers
* force constant adapted
* reduced tolerance for planarity and force constants changed for some torsions
* tolerance for planarity increased a bit again
* cerr outputs removed
* planarity tolerance increased
* boost log added in planarity check
GraphMol/DistGeomHelpers/:
Support generating random initial coordinates of atoms as an alternative to embedding. This has so far only been tested on windows (all tests pass) and it needs to be optimized (particularly force field parameters).
Other changes here are primarily cosmetic code cleanups.
