Feature merge #175
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Feature merge #175
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…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
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CI errors look like a crash on Linux in mol/test_mapping.py, and on Windows pulling in kartograf doesn't work as it can't find a matching ambertools... A good example of the benefit of a WIP PR... |
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I've found and fixed the source of the crash locally, and have removed kartograf from Windows. Hopefully this will work... |
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This PR brings in a draft version of the new merge and mutate code. I'm submitting it to check that everything builds ok, and also to give a heads up to check things work with BioSimSpace. The only changes now are debugging and adding in more documentation and examples. There should be no major changes now before the end of month release.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@lohedges
Any additional context of information?
I don't plan to merge this - this is just to test things via GH Actions, plus to give you something stable against which to test BSS (i.e. this has changed the properties, and added lots of underlying code changes). I'll continue working in
feature_merge2adding in more tests, tutorials, optimisations etc. The real PR will befeature_merge2, which will hopefully be less work because you've already seenfeature_merge.