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Notebook cleanup #44

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Notebook cleanup #44

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f72fd4b
begin moving code to helper module
EzryStIago Apr 14, 2024
9e352fb
remove outputs
EzryStIago Apr 14, 2024
177cfcc
add plotting functions
EzryStIago Apr 15, 2024
28db5ea
replace plotting scripts with functions
EzryStIago Apr 15, 2024
40aa303
add required arguments to convergence plot
EzryStIago Apr 15, 2024
ab7a15b
update argument names. PEP8
EzryStIago Apr 15, 2024
42e136a
remove interruption
EzryStIago Apr 15, 2024
1910649
consolidate cells and make bulk a fepdata object
EzryStIago Apr 15, 2024
886a602
rewrote classes into dGData which is a parent for TIData and FEPData.
EzryStIago Apr 15, 2024
13637e5
offload TI and misc values to the helpers module
EzryStIago Apr 15, 2024
af40080
fix references to dG_DBC which should have been DBC.dG with the new c…
EzryStIago Apr 15, 2024
2e02515
add documentation
EzryStIago Apr 15, 2024
5dd4d61
documentation
EzryStIago Apr 15, 2024
87749b1
blackify
EzryStIago Apr 15, 2024
2fe10ed
adding VMD and NAMD tutorial links
EzryStIago Apr 15, 2024
d50638d
Fix parameter order
jhenin Apr 15, 2024
05f5e60
remove unused imports
EzryStIago Apr 26, 2024
3b87593
replace kwargs with positional arguments to preserve backward/forward…
EzryStIago Apr 26, 2024
4ca486b
linting
EzryStIago Apr 26, 2024
a318892
update to agree with notebook_helpers
EzryStIago Apr 26, 2024
896e5b7
rename
EzryStIago Apr 26, 2024
f1c7d33
PEP8 compliance and rename file
EzryStIago Apr 26, 2024
3844873
Merge branch 'notebook_cleanup' of https://github.com/jhenin/SAFEP_tu…
EzryStIago Apr 26, 2024
16b2326
use field(default_factory=...) instead of mutable default objects
EzryStIago May 6, 2024
87c4e13
replace numpy ndarray default_factory with None
EzryStIago May 6, 2024
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -2,6 +2,9 @@
This repository contains all the files needed to calculate the binding free energy of phenol to lysozyme following the SAFEP Tutorial.
Available here: https://www.biorxiv.org/content/10.1101/2022.12.09.519809v1

If you are not yet familiar with VMD, see this tutorial: https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/
If you are not familiar with NAMD, see this tutorial: https://www.ks.uiuc.edu/Training/Tutorials/namd-index.html

Related tools can be found in the SAFEP repository: https://github.com/BranniganLab/safep

Structure of supplementary files:
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