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* Add library path with os.add_dll_directory()

* Update path for Visual Studio

* Improved handling of CRYST1 records #3446

* Apply suggestions from code review
Co-authored-by: Jason Swails <jason@entos.ai>
Co-authored-by: Jason Swails <jason@entos.ai>

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

Without this restriction, the compilation fails if the project folder has parent folders called "tests", "internal" or other words in these generic patterns.

* Support prmtop files created by chamber

* Support CHARMM CMAP flags

* Changed handling of SCEE and SCNB scale factors

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests

* Atom types in CHARMM FF are non-case-sensitive

* Atom type name in CHARMM RTF

* Make atom section in CHARMM PSF file to be uppercase

* Improved handling of atoms with alternate locations

* Fixed a test failure caused by an invalid PDB file

* Added option for CheckpointReporter to save States

* Try to fix test failure on Windows

* Allow querying current step count

* Fixed error building Python wrapper

* Check for keyword args to createSystem() that are never used

* Fixed incorrect arguments in test cases

* Created OBC2 that works with current force fields

* Created HCT, OBC1, GBn, and GBn2 that works with current force fields

* Added documentation for GB models

* Updates to documentation and tests based on comments

* Added formula for screening parameter

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies

* Remove tri-sulfite bond formation.

Pdbfixer attempts to add di-sulfide bonds to any pair of CYS "S" atoms that are less than 3 A. This procedure fails when multiple such bonds are assigned to a given atom. 

Here we rectify this issue by a greedy algorithm: Atom I is chosen to be bonded to `argmin(distance([:I-1, I])` over all candidate di-sulfide bonds. This procedure will not generally result in a set of minimal distance di-sulfide bonds, but will fix the "tri-sulfide bond" problem. Fixing the more general case would require a solution to global constraint satisfaction problem.

**Legal**
This patch is provided under the CC0 license (https://creativecommons.org/share-your-work/public-domain/cc0/).
This is not an officially-supported Google product. It is provided ‘as-is’ without any warranty of any kind, whether expressed or implied.

* Update topology.py

Remove a redundant comment.

* Support of Amber FF19SB CMAP

* Update: Support of Amber FF19SB CMAP
Co-authored-by: Kye Won Wang <kyw220@sol.cc.lehigh.edu>