rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
https://rinikerlab.github.io/reeds/
MIT License
30 stars 8 forks source link

WIP: Energy offset rebalancing #51

Closed RiesBen closed 3 years ago

RiesBen commented 3 years ago

Description

This branch is work in progress. It contains the shall contains:

Todos

Notable points that this PR has either accomplished or will accomplish.

Status

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts when merging 2450fe671be72ef11df3cb8eec5e4a3248398ab8 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 2 alerts and fixes 12 when merging 280df2f941fa975536cc208ecb4184c49aa14cdb into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 2 alerts and fixes 12 when merging 8fdf06a6c98beac7f0b48afda63ebc0e2ad55c2e into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 3 alerts and fixes 17 when merging 130c99c90cbcf9f633fa610d2594025a5ce9e24a into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 3 alerts and fixes 17 when merging d7b9fe2a61c6b26922a1243982984ef72df461cd into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 3 alerts and fixes 17 when merging a96ea925f1ad317ce92ac279f5c5720912f6e5de into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 5 alerts and fixes 19 when merging 3e120dc5b02239210c3784a33864f67b87fdbea6 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 5 alerts and fixes 19 when merging 570c929b403dca2b352c8a98785f6abcebc77684 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 5 alerts and fixes 19 when merging 08be74209714dcb0b1ac87fff41f8a403ba9a5f9 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 6 alerts and fixes 19 when merging 5f3764613b0e96fa024e43852ed1fcbef2cfa4dc into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 6 alerts and fixes 19 when merging 881a24e5b5f8113b859b08012738c7d49b7946f6 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts and fixes 19 when merging 15b8133a4e084100d52e107c5ece2a80f70dedf0 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts and fixes 19 when merging dae78fb8e66a774449a490e9f4ee61b6b001e815 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts and fixes 19 when merging dc08b6afe6e1386683c5ce84addef714c0b0aee4 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts and fixes 19 when merging 694a6c0a3aee174c641b4433b16b4ac9fcdc8b63 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 9 alerts and fixes 19 when merging 357cd52a26f7c205a6eb7e11b88910a1853a5550 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 12 alerts and fixes 19 when merging f78fb4e8d68c480c438ab1c8be5b6f71b895bba3 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

RiesBen commented 3 years ago

Update I remove the double sided functionality, as we are ditching the idea. I corrected the pseudocount-form.

lgtm-com[bot] commented 3 years ago

This pull request introduces 5 alerts and fixes 20 when merging 1a5162f2465f5d8382d98d349251b10d59b03426 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 5 alerts and fixes 20 when merging 2b823d6f636b2654a19f21d296acb5bda5b701f0 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 22 when merging 230e475779ab35e619ef288ffa2f6dca42a71136 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 22 when merging 730b43ff425fe0991c310552f8c61fd389699f62 into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

SalomeRonja commented 3 years ago

I tested both the sopt and the eoff rebalancing modules, and didn't find any problems. nice work!

I would suggest we merge #54 to this branch, and then we can merge this branch to the main one.

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 22 when merging dd356491868a00142261783d8d5a4d9621f56cdf into 54579e52be26605612d6afcab89c5d3c34139fe5 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 2226b62fbbc022d9250ce852686e4e4a84fdcccb into 6964bfa7521dd02bd46c995ca1ae5ef535ffcbe9 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 861ea4484c327adf9eb1dd8e91a1eac0fc95e868 into 6964bfa7521dd02bd46c995ca1ae5ef535ffcbe9 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 0b89e5bc04c446191a34646bb5da80ffc8f12166 into 6964bfa7521dd02bd46c995ca1ae5ef535ffcbe9 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 6d963b3cd89758dfb607509e9dec55c3eed16243 into 6964bfa7521dd02bd46c995ca1ae5ef535ffcbe9 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging f616a164701e49482d92ba32b67d915344f63794 into 6964bfa7521dd02bd46c995ca1ae5ef535ffcbe9 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging d1c7f6bb4be7dfd2710853713b4f915528da28c2 into 8ab00bdf1e63014faa56e5fac304485d7b9e0a62 - view on LGTM.com

new alerts:

fixed alerts:

SalomeRonja commented 3 years ago

Hey @SchroederB , I changed the default analysis dict for preparing the next input folder in the eoff estimation module from write_eoff to write_eoffRB and write_eoffEstm, as I got an error message with the old setting. Hope that change is ok :)

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 20aefa50a81ac524e54eec502c3dbbc175087175 into 8ab00bdf1e63014faa56e5fac304485d7b9e0a62 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 5a445925151beacd554bf1a637909e28ba2f6d5c into 8ab00bdf1e63014faa56e5fac304485d7b9e0a62 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 3 years ago

This pull request introduces 4 alerts and fixes 24 when merging 34da54d3e13ca9c08115cc21217a62e4e4f830ee into 8ab00bdf1e63014faa56e5fac304485d7b9e0a62 - view on LGTM.com

new alerts:

fixed alerts:

SalomeRonja commented 3 years ago

Thanks again for the great work @SchroederB !!