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Feature merge#175

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chryswoods wants to merge 53 commits intodevelOpenBioSim/sire:develfrom feature_mergeOpenBioSim/sire:feature_mergeCopy head branch name to clipboard

+10,633-594

Commits

Commits on Feb 18, 2024

• WIP - adding in mutate and merge functions to make it easier to use AtomMapping

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  chryswoods

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  f5a307b

Commits on Feb 19, 2024

• Added the ability in AtomMapping to store the atoms that weren't mapped at both end states.

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  chryswoods

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  5a8d34e

Commits on Feb 20, 2024

• Added quick functions to get and set the expression used for the potential energy

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  chryswoods

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  326032a

• Merge branch 'fix_164' of https://github.com/openbiosim/sire into feature_merge

  chryswoods

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  605e820

Commits on Feb 21, 2024

• Merge branch 'fix_164' of https://github.com/openbiosim/sire into feature_merge

  chryswoods

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  807270b

• Merge branch 'fix_164' of https://github.com/openbiosim/sire into feature_merge

  chryswoods

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  f31f5c8

Commits on Feb 22, 2024

• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_merge

  chryswoods

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  7c31ecb

• WIP - VERY WIP

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  chryswoods

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  e3668f8

• WIP - filling in missing functions and fixing wrappers

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  469e284

• All functions implemented - can now compile and run code that has alternate atom

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  chryswoods

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  85b2419

Commits on Feb 23, 2024

• Added functions to switch to or remove the alternate names.

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  chryswoods

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  1d87e8f

• Merge branch 'fix_170' of https://github.com/openbiosim/sire into feature_merge

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  8b2cdca

• Fixed new code - all compiles, links and tests pass. Out of the rabbit hole and ready

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  dc43473

• Making good progress - realised that can use properties of the atoms to store

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Commits on Feb 25, 2024

• WIP (not compiling yet)

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  chryswoods

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  8d33ce3

• WIP (still) - added ability to control the value of ghost atom parameters.

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  chryswoods

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  2338e91

Commits on Feb 26, 2024

• Merge branch 'fix_170' of https://github.com/openbiosim/sire into feature_merge

  chryswoods

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  52156d1

• Added a SireBase::Console that connects through the sire.utils.Console, so that

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  chryswoods

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  4588f20

• Added a warning that these higher-level properties aren't being merged yet.

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Commits on Feb 27, 2024

• WIP - I've been filling in the merge function for most of the MolViewProperties, plus have generated

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  chryswoods

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  60abd65

Commits on Feb 28, 2024

• Finished filling in null merge functions for the MolViewProperty classes, and have

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  chryswoods

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  e6a3223

• AtomProperty merging is working quite well :-)

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  chryswoods

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  04f103e

• WIP - working out how to merge bonds...

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  44a4eaa

Commits on Mar 1, 2024

• Making progress - am merging the bonds. To test this, I need to next merge the connectivities

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  chryswoods

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  6bdf012

Commits on Mar 2, 2024

• Added code to merge the connectivities, plus build a shared connectivity object. Testing it...

  chryswoods

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  ce46594

• Connectivity, atomtype, charge, LJ, mass, name and bond properties look like they are merging properly :-)

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Commits on Mar 3, 2024

• Some optimisation, plus made sure that bonds involving atoms that exist only in the

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  chryswoods

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  9b1005c

• Added the same code to ThreeAtomFunctions and FourAtomFunctions and are now merging

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  e0f3674

• Make sure to add connections from ghosts to reference atoms in the reference state

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• Fixed a bug in AtomIdxMapping, and remembered to add the connections/bonds/angles/dihedrals for

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  42ff6bd

Commits on Mar 4, 2024

• Merge branch 'fix_constraints' of https://github.com/openbiosim/sire into feature_merge

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  e5ae14e

• Added the code to merge the CLJNBPairs.

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  1dab9f3

• Added a "to_xml" function so that it is easier to convert sire OpenMM objects to XML

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  f53bae3

• Added an AtomNumMatcher as this perfectly re-matches the separated existing

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  5348fcd

Commits on Mar 5, 2024

• I've added alignment and also got the mutation working. A quick look in Jupyter shows

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  0a6c0ae

• Working on adding in the checks for ring size breaking and changing, ported from Python to C++

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  51a68eb

Commits on Mar 6, 2024

• Added in the ring growing and breaking checks, ported from Python to C++

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  e344caa

• Added function-level documentation, plus also the sr.morph.decouple function to

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  ec46c5c

Commits on Mar 7, 2024

• Fixes to make the merge, mutate and decouple work for the demo

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Commits on Mar 8, 2024

• Added kartograf support to the match function. Can now pass in a KartografAtomMapper as

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  chryswoods

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  5cf821c

Commits on Mar 9, 2024

• Optimised the code that edits proteins, so that the merge is not O(N2) but is instead closer

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Commits on Mar 10, 2024

• Optimised the CLJNBPairs makeCompatible function, so that it works and is not O(n2)

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• Merge branch 'devel' of https://github.com/openbiosim/sire into feature_merge

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• Bringing in the fix for Mol2 atom types

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• Copying ghost NBSCL parameters from the alternate end state.

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• Added more to the merge test

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  ae47981

• Optimised the perturbation object, fixed a small bug in the merge code, added

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  f724cf8

• Remerged does give the same energy as original merge

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  c639827

• Added in lambda=0.5 check - it is different - worth checking why

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Commits on Mar 17, 2024

• Fixed the crash (I think) caused by not removing atoms from the connectivity

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• Updated requirements to not pull in kartograf on Windows

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• Added decorators to skip tests for functionality not supported on windows

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Commits on Mar 18, 2024

• Merge branch 'devel' into feature_merge

  chryswoods

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