fix: Implement EnhancedSampling class and fix import error #9

devin-ai-integration · 2024-11-13T17:31:27Z

This PR fixes the EnhancedSampling implementation and CI workflow issues:

Fixed EnhancedSampling class implementation in simulation.py
Updated CI workflow to fix package installation order
Added proper test data files
Resolved import issues in dynamics module
All tests passing locally

Link to Devin run: https://preview.devin.ai/devin/c0ba3e0f83574b5fbb3d16c0d3de8aa7

Testing:

Ran all tests locally with pytest
Verified EnhancedSampling functionality
Checked CI workflow execution

- Added EnhancedSampling class extending MolecularDynamics - Implemented replica exchange molecular dynamics functionality - Fixed import in __init__.py - Added proper error handling and logging

coderabbitai · 2024-11-13T17:31:36Z

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…lica exchange

- Add flexibility analysis modules - Add optimization utilities - Add pipeline implementations - Add prediction interfaces - Add comprehensive documentation - Add integration and unit tests

- Add flexibility analysis modules (backbone, sidechain, domain) - Add optimization utilities (GPU, data, progress, checkpointing) - Add pipeline implementations (flexibility, analysis) - Add prediction interfaces (AlphaFold, structure conversion) - Add comprehensive documentation and benchmarks Part of #8

…THONPATH

… CI workflow

…pdate method signature

…replica states

… EnhancedSampling

…st data

…thod

…ementation

…ator

…ation

fix: Implement EnhancedSampling class and fix import error

73d965b

- Added EnhancedSampling class extending MolecularDynamics - Implemented replica exchange molecular dynamics functionality - Fixed import in __init__.py - Added proper error handling and logging

devin-ai-integration bot added 28 commits November 13, 2024 17:38

fix: Add models/__init__.py to ensure proper package imports

4e4e83c

test: Add TestEnhancedSampling class with comprehensive tests for rep…

383a879

…lica exchange

feat: Add complete protein flexibility analysis implementation

cf086be

- Add flexibility analysis modules - Add optimization utilities - Add pipeline implementations - Add prediction interfaces - Add comprehensive documentation - Add integration and unit tests

fix: Install package in development mode before running tests

2113cc4

fix: Update test paths and add test data

83bc464

fix: Add valid alanine-dipeptide.pdb test data

8aeaed6

fix: Update test PDB generation with proper terminal residues

e056daf

feat: Add EnhancedSampling class and update imports

3a93425

fix: Resolve merge conflicts and update EnhancedSampling implementation

431138b

fix: Update CI workflow to run tests from project root with proper PY…

746d313

…THONPATH

fix: Update mdtraj installation in CI workflow to avoid GIL issues

25d2981

fix: Update package installation order and add explicit PYTHONPATH in…

7ef3c54

… CI workflow

fix: Rename setup_replica_simulations to setup_replica_exchange and u…

4b24c69

…pdate method signature

fix: Update run_replica_exchange to handle dynamics_steps and return …

aef36ca

…replica states

fix: Handle OpenMM units properly in EnhancedSampling class

7f0cb52

chore: Add test protein PDB file

d148d8f

chore: Update test data files with correct content

c45c58a

chore: Add test protein PDB file with proper structure

cc2ed27

fix: Update temperature ladder generation in EnhancedSampling

c748aa4

fix: Restore MolecularDynamics class and update temperature ladder in…

5e76bd7

… EnhancedSampling

fix: Update simulation.py with proper imports and add test data

558787e

fix: Update simulation.py with complete implementation and restore te…

3e3fcfb

…st data

fix: Update simulation.py with complete implementation and restore te…

08c5dae

…st data

fix: Update simulation.py with CutoffNonPeriodic and fix duplicate me…

179a671

…thod

fix: Update tests for non-periodic boundaries and fix simulation impl…

fc8e012

…ementation

fix: Remove duplicate _create_integrator and fix atom count calculation

c2cef0a

fix: Handle OpenMM units properly and remove duplicate _create_integr…

9ac450a

…ator

devin-ai-integration bot added 3 commits November 13, 2024 19:35

fix: Update simulation.py with proper unit handling and OpenMM integr…

c79c62d

…ation

fix: Update OpenMM version to 8.2.0 in requirements.txt

4591f82

fix: Update CI workflow to fix package installation order

a8437da

kasinadhsarma closed this Nov 14, 2024

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fix: Implement EnhancedSampling class and fix import error #9

fix: Implement EnhancedSampling class and fix import error #9

devin-ai-integration bot commented Nov 13, 2024 •

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fix: Implement EnhancedSampling class and fix import error #9

fix: Implement EnhancedSampling class and fix import error #9

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devin-ai-integration bot commented Nov 13, 2024 •

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