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Atomtype parameterization methods for parameterizing a topology in GMSO. #644

Merged
merged 46 commits into from
Jun 15, 2022
Merged

Atomtype parameterization methods for parameterizing a topology in GMSO. #644

merged 46 commits into from
Jun 15, 2022

Commits on Apr 14, 2022

  1. Atomtype parameterization methods for parameterizing a topology in GMSO. 

    This PR will add the atomtyping module to GMSO for passing a GMSO.Forcefield
and a GMSO.Topology and match atomtype using foyer as the backend. Then,
the corresponding connection types will be found in the Forcefield and
applied to the connections in the topology.

* Create parameterize.py, which has the apply function which can take a
topology, and a gmso forcefield to apply to it. This can use subgraph
isomorphism to identify molecular structures in the topology through
the bondgraph and bin those into unique molecules that match a specified
forcefield. This apply function can also do the standard atomtyping of
the entire topology in one step.
* Create isomorph.py which uses networkx graphs to identify disconnected
components and isomorphism to identify repeated structures.
    @CalCraven
    CalCraven committed Apr 14, 2022
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  2. Move module imports for apply into atomtyping to prevent circular imp… 

    …orts
    @CalCraven
    CalCraven committed Apr 14, 2022
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Commits on Apr 25, 2022

  1. Add a quick fix which will do atomtyping if no residue flag is passed

    @CalCraven
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on Apr 26, 2022

  1. Merge branch 'master' of https://github.com/mosdef-hub/gmso into deve… 

    …lop-gmsoff-parameterize
    @daico007
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  2. correctly update sites when adding subtop

    @daico007
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Commits on Apr 28, 2022

  1. Merge branch 'develop' into develop-gmsoff-parameterize

    @daico007
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  2. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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Commits on Apr 29, 2022

  1. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  2. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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Commits on May 2, 2022

  1. Changes to doc strings for clarity. Add a subtop_label variable to ge… 

    …neralize where the molecule definition is pulled from
    @CalCraven
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on May 6, 2022

  1. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  2. More modular architecture

    @umesh-timalsina
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  3. WIP- Add testing, minor refactoring of the APIs.

    @umesh-timalsina
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Commits on May 9, 2022

  1. WIP- Better error handling

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Commits on May 25, 2022

  1. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
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Commits on May 31, 2022

  1. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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Commits on Jun 1, 2022

  1. Misc Changes 

    1. Update Topology after parametrization
2. Add dependency for forcefield_utilities in env files
3. Add tests for trappe forcefield
4. Patch parmed (should be moved to a cal's PR mosdef-hub#658
    @umesh-timalsina
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  2. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  3. WIP- Skip opls for now, full TrappE tests

    @umesh-timalsina
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Commits on Jun 3, 2022

  1. Avoid accidental overwriting of typemap when using isomorphism

    @umesh-timalsina
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  2. WIP- Remove unused import

    @umesh-timalsina
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  3. Use enumerate for atom index while converting to TopologyGraph

    @umesh-timalsina
    umesh-timalsina committed Jun 3, 2022
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  4. Fix argument order

    @umesh-timalsina
    umesh-timalsina committed Jun 3, 2022
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  5. WIP- Add test for subtopology parameterization

    @umesh-timalsina
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Commits on Jun 6, 2022

  1. Make opls/trappe global fixtures, Add tests for isomorphism

    @umesh-timalsina
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  2. Further testing isomorphism

    @umesh-timalsina
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Commits on Jun 7, 2022

  1. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  2. REVERT - skip OPLS tests

    @umesh-timalsina
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  3. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  4. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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  5. Copy scaling factors and combining rules after parametrization

    @umesh-timalsina
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  6. Proper OPLS tests

    @umesh-timalsina
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  7. WIP- Refactor the test module

    @umesh-timalsina
    umesh-timalsina committed Jun 7, 2022
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  8. WIP- Remove unused import

    @umesh-timalsina
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Commits on Jun 9, 2022

  1. WIP- Add test for parameterization with impropers

    @umesh-timalsina
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  2. Merge remote-tracking branch 'upstream/develop' into develop-gmsoff-p… 

    …arameterize
    @umesh-timalsina
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Commits on Jun 15, 2022

  1. WIP- Additional impropers test; Separate module for testing impropers

    @umesh-timalsina
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  2. Minor refacotors; additional edge cases coverage/tests

    @umesh-timalsina
    umesh-timalsina committed Jun 15, 2022
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  3. Docstring minor fix

    @umesh-timalsina
    umesh-timalsina committed Jun 15, 2022
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  4. Remove rel_to_module as is obsolete in forcefield_utilities

    @umesh-timalsina
    umesh-timalsina committed Jun 15, 2022
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  5. Change trappe_ua to trappe-ua for correct loading

    @umesh-timalsina
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  6. fix typo, add note about specific use case

    @daico007
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  7. Merge branch 'develop-gmsoff-parameterize' of https://github.com/CalC… 

    …raven/gmso into develop-gmsoff-parameterize
    @daico007
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  8. pip install forcefield-utilites until new release

    @daico007
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