{"action":"created","comment":{"url":"https://api.github.com/repos/choderalab/perses/pulls/comments/229902063","pull_request_review_id":170513108,"id":229902063,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIyOTkwMjA2Mw==","diff_hunk":"@@ -0,0 +1,172 @@\n+import numpy as np\n+from perses.rjmc import geometry\n+from openmmtools import states, mcmc\n+from simtk import openmm, unit\n+from simtk.openmm import app\n+from openmmtools import cache\n+from perses.storage import NetCDFStorageView, NetCDFStorage\n+from typing import List, Dict\n+\n+cache.global_context_cache.platform = openmm.Platform.getPlatformByName(\"CUDA\")\n+cache.global_context_cache.capacity = 30\n+\n+\n+class HydrationPersesRun(object):\n+    \"\"\"\n+    This class encapsulates the necessary objects to run RJ calculations for relative hydration free energies","path":"examples/freesolv/freesolv_testsystem.py","position":17,"original_position":16,"commit_id":"03438d4db5dd1a89e736b4cf39b97fce03572af2","original_commit_id":"5f1719add85115221e86eb3291ef313d7ef9027c","user":{"login":"pgrinaway","id":4674712,"node_id":"MDQ6VXNlcjQ2NzQ3MTI=","avatar_url":"https://avatars2.githubusercontent.com/u/4674712?v=4","gravatar_id":"","url":"https://api.github.com/users/pgrinaway","html_url":"https://github.com/pgrinaway","followers_url":"https://api.github.com/users/pgrinaway/followers","following_url":"https://api.github.com/users/pgrinaway/following{/other_user}","gists_url":"https://api.github.com/users/pgrinaway/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrinaway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrinaway/subscriptions","organizations_url":"https://api.github.com/users/pgrinaway/orgs","repos_url":"https://api.github.com/users/pgrinaway/repos","events_url":"https://api.github.com/users/pgrinaway/events{/privacy}","received_events_url":"https://api.github.com/users/pgrinaway/received_events","type":"User","site_admin":false},"body":"Sure, it's to focus on the most favorable hydration free energies. I'll add that to the `README.md`","created_at":"2018-10-31T23:36:54Z","updated_at":"2018-10-31T23:36:55Z","html_url":"https://github.com/choderalab/perses/pull/490#discussion_r229902063","pull_request_url":"https://api.github.com/repos/choderalab/perses/pulls/490","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/choderalab/perses/pulls/comments/229902063"},"html":{"href":"https://github.com/choderalab/perses/pull/490#discussion_r229902063"},"pull_request":{"href":"https://api.github.com/repos/choderalab/perses/pulls/490"}},"in_reply_to_id":229899422},"pull_request":{"url":"https://api.github.com/repos/choderalab/perses/pulls/490","id":227420860,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI3NDIwODYw","html_url":"https://github.com/choderalab/perses/pull/490","diff_url":"https://github.com/choderalab/perses/pull/490.diff","patch_url":"https://github.com/choderalab/perses/pull/490.patch","issue_url":"https://api.github.com/repos/choderalab/perses/issues/490","number":490,"state":"open","locked":false,"title":"Add 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adds:\r\n\r\n- [x] A hydration free energy example based on FreeSolv\r\n\r\n- [x] Fixes to feptasks to allow the use of `DummyContextCache`\r\n\r\n- [x] Corrects the number of integrator steps\r\n\r\n- [x] Includes storage of `GeometryEngine` quantities.\r\n\r\n- [x] Ensures hydrogens are excluded from small molecule atom maps\r\n\r\n- [x] Correctly handles writing of NCMC trajectories\r\n\r\n- [x] Correctly resets integrator\r\n\r\n- [x] Finish 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