Code

Feature restraint#105

Code

Merged

chryswoods merged 65 commits intodevelOpenBioSim/sire:develfrom feature_restraintOpenBioSim/sire:feature_restraintCopy head branch name to clipboardSep 18, 2023

+15,846-2,705

Commits

Commits on Aug 7, 2023

• Working on bringing perturbation into the dynamics interface. This will let you

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

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• Updating the dynamics object so that it can save energies during the trajectory. This

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• Letting the user set temperature, pressure and device from the function arguments.

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• Added a new EnergyTrajectory class that keeps track of the energies during a dynamics simulation.

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Commits on Aug 8, 2023

• Moved the underlying code in Properties to use shared pointers for all metadata, plus to have

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• Added the concept of linked properties. These let you add symbolic links to properties

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• Forgot that I need to update the global version number of a molecule when

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• Added lots of API documentation for the minimisation and dynamics functions.

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• Working on how I will update the constraints for different lambdas. In reality, I won't,

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• Working more on the constraints. Making sure that we use the largest mass of the

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Commits on Aug 9, 2023

• Added functions to System to make it easier to get and set energy trajectories. An empty one is

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• Fixed a bug in the openmm code which failed to correctly align perturbed internals. The code

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• Only default to PME for periodic spaces

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• I've separated out the non-bonded interactions that involve perturbations to or

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• Was a bug - I had been re-adding the 1-4 terms to cljff via the LambdaLever ;-)

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Commits on Aug 10, 2023

• Now calculating all exceptions in sire, not using the function from CLJFF. This is

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• I've now added in the ghost-14 CustomBondForce to calculate 1-4 terms involving

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Commits on Aug 11, 2023

• Only using the custom exceptions code for perturbable molecules. This speeds

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Commits on Aug 14, 2023

• Updated the dynamics runner so that it uses the perturbable property maps when

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• I've added in a Perturbation object that will make it easier to view

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Commits on Aug 15, 2023

• Moved functions and classes relating to perturbations to a new sire.morph module.

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• Some simple code cleaning

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• Added in a soft coulomb potential :-)

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Commits on Aug 16, 2023

• I've switched the code over to use alpha to control softening. Now have full LJ and coulomb

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• Adding in documentation for the new perturbation code. Added some convenience

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

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• Updated the changelog for the PR

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• Fix for link error on Windows

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• WIP - starting to sketch out what the restraint code could look like

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Commits on Aug 17, 2023

• I've now got working positional restraints :-)

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• Quick fix caused by me breaking dynamics when auto-converting openmm units...

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Commits on Aug 18, 2023

• WIP - refactor of the restraints code and cleaning up of the sire to openmm converter.

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• Finished refactoring the code. The sire_to_openmm_system is now in its own file

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Commits on Aug 21, 2023

• I've fixed the positional restraint to be a proper flat-bottom well potential.

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Commits on Aug 22, 2023

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

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• Added the ability to fix atoms. You can do this by passing in the search

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Commits on Aug 23, 2023

• Added most of the boilerplate code for Boresch restraints. Need to now fill in the actual

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Commits on Aug 24, 2023

• I've added the code to create and calculate the energies for the Boresch restraints.

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Commits on Sep 3, 2023

• Fixed loss of exception in minimisation, plus added in some docs and functions suggested by GitHub copilot

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Commits on Sep 4, 2023

• Energy trajectory pandas tables use floats for the column names (if they are numbers).

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• Reverted the change - gone back to using strings for the column names in pandas

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• Moved record of walltime to the dynamics block, because calculated dynamics speed

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• Call takeProperty on the trajectory, then save frame, then setProperty,

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Commits on Sep 5, 2023

• I've fixed a performance regression when creating OpenMM contexts. I was appending

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• Moved the restraints functions into a dedicated sr.restraints module. Added unit tests for

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• Added support for abs(unit) to GeneralUnit. Fixed logic that detects an exploded simulation

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Commits on Sep 6, 2023

• Working on the documentation...

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Commits on Sep 7, 2023

• More work on the documentation. Changed default shift_delta to 2. Allowed

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Commits on Sep 8, 2023

• Finished the basic restraint tutorials. Cleaned up the API a little by making

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• Adding in the alchemical restraints chapter

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Commits on Sep 10, 2023

• Continuing work on the tutorial

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Commits on Sep 11, 2023

• Finished the feature_restraints tutorial and cleaned up bits of the API.

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

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• Added last tests for the restraints code and fixed the bugs that these found

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• Added the changes to the changelog

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Commits on Sep 12, 2023

• Added a new sire.morph.replica_exchange function to perform replica exchange moves

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• Added functions to change the ensemble of a dynamics object. This will let

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Commits on Sep 15, 2023

• Fix small bug when the System space does not match the molecule space when shared

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• Added back the constraint flag for minimisation

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Commits on Sep 17, 2023

• Added in support for Rich Taylor's LJ softening function as this seems to give a better-shaped

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• Thanks to Julien I now know that shift_delta is a length ;-)

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Commits on Sep 18, 2023

• Fixed incorrect parsing of default shift delta

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• Fixed circular import of sire.cas. Fixed missing function in the mixed api.

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• Better handling of exceptions/exclusions for positional restraints.

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