PR into main for 2024.2.0 release #207
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…tomMapping objects to mutate or merge molecules.
…ed at both end states. This means we now have the full information in this object to be able to properly construct merged and mutated molecules. Added a unit test to verify this works for mapping an alanine to a lysine within a protein (mapping works on subsets of molecules, meaning we can do a region of interest mapping and merge just be passing in the residues that we want to map - see test_match.py) Also, removed the C++ code for mutate as I realised that mutation is a merge followed by extracting the perturbed state. This is still a WIP - have got matching working, and have added the necessary info to AtomMapping. The next step is to fill in the C++ code for merge based on the information in AtomMapping.
…ntial energy of internal terms via the Cursor
Gone a little down the rabbit hole in the merge code by adding in support for alternate names for atoms and residues. This will enable the names of the perturbed end state to be saved, so that we can get something sensible out when we extract the end states. Will not compile
…ernate atom and residue names. Needs testing, plus then integrating with the merge code
Added in code for fix_170
…t hole and ready to go back to the merge code ;-)
…to store the mappings - and then this could be passed to the properties so that they can update themselves internally
Working on the code to move the merge into the properties themselves (where they know what they are doing)
…ters. Also beginning to fill in the various merge functions
…e, so that we can emit debug, log, warning and error messages from C++ that correctly get printed up in the Python layer (and can be properly customised and controlled in the Python layer). This is the first step to consolidating all of the messaging into a single Python logging-compatible framework (i.e. also removing some of the rich.console layer)
…Properties, plus have generated the new wrappers. Mostly compiling now - just need to fill in missing atomidxmapping.h includes in the wrappers.
…ses, and have now added all of the python wrappers. This all compiles, links and passes unit tests. Next step is to actually write the underlying merge code...
Next onto internal merging
…merge the connectivities together, as well as create a single merged connectivity.
…ity object. Testing it...
…ok like they are merging properly :-)
…st only in the perturbed state are copied into the reference state
…re now merging angles, dihedrals and impropers. But this all needs testing. Will do that after I have added in the code to merge the CLJNBPairs
…bonds/angles/dihedrals for atoms unmapped in the perturbed state copied from the match in the reference state
Changed `fix_ghost_sigmas` into `fix_perturbable_zero_sigmas` and moved the test into PerturbableOpenMMMolecule. Added ability to pass `map` to this constructor so that the option can be passed through to the right place. Most of the diff is because I had to regeneate the wrappers, and so the MM wrappers all got the new copy<T>() functions for their copy and deepcopy functions.
…eys is not iterable, so should be a list. Not triggering CI as this is a minor fix. Adding it here as it isn't big enough to warrant a new branch and PR [ci skip]
Add map option to prevent peturbation of the LJ sigma value for ghost atoms
…re_exclude_opposite_ghosts
… on Windows find MSVC
…ported at the moment)
…re_exclude_opposite_ghosts
…re_exclude_opposite_ghosts
Fix issue #200
…re_exclude_opposite_ghosts
…hangelog and defined QT_NO_SIGNALS_SLOTS_KEYWORDS at the gccxml level when generating headers. [ci skip]
Feature exclude opposite ghosts
…AtomIdx order. This works really well, except that it fails when merging submolecules, because the CGAtomIdx order changes on commit. I need to fix this. I suspect it will be by converting merged proteins into a single cutgroup?
…m is correct for its position in the molecule (i.e. is one higher than the AtomIdx of the last atom in the residue)
…plus legacy.System.System). Also added "origin" and "zero" as recognised options for constructing vectors, e.g. ``` c = mols.cursor() c.make_whole(center="origin") ``` will work.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
2024.2.0 prep