All the changes from Shahlo's copy of FAST and some of mine too#8

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Pandapip1 wants to merge 27 commits intobowman-lab:masterfrom

Pandapip1:upstream-changes

Commits on Jul 31, 2025

added specific contacts analysis wrapper

Artur Meller
authored and
Pandapip1
committed
new analysis methods and no pocket edge case

Artur Meller
authored and
Pandapip1
committed
added new analysis methods and sasa clustering

Artur Meller
authored and
Pandapip1
committed
added analysis script for calculating axial angle defined by reference crystal structures

Artur Meller
authored and
Pandapip1
committed
fixed minor bug in top pockets which double summed pocket volumes

Artur Meller
authored and
Pandapip1
committed
added case for pbc cluster in gromacs processing

Ayan Bhattacharjee
authored and
Pandapip1
committed

Commits on Aug 19, 2025

A few bug fixes

Ayan Bhattacharjee
authored and
Pandapip1
committed
support for singularity run in gromacs submission and processing

Ayan Bhattacharjee
authored and
Pandapip1
committed
add condition for no source command if singularity option enabled

Ayan Bhattacharjee
authored and
Pandapip1
committed
semicolon to colon bug fix

Ayan Bhattacharjee
authored and
Pandapip1
committed
another small bug fix with misspelled variable

Ayan Bhattacharjee
authored and
Pandapip1
committed
adding gpu specs to gromax md run commands for nb bonded pme

Ayan Bhattacharjee
authored and
Pandapip1
committed
bug fix in md run command, missed a space

Ayan Bhattacharjee
authored and
Pandapip1
committed
fixed a bug in trjconv commands

Ayan Bhattacharjee
authored and
Pandapip1
committed
bug fix

Ayan Bhattacharjee
authored and
Pandapip1
committed
added center_group to gromax processing, limited support

Ayan Bhattacharjee
authored and
Pandapip1
committed
Move all the fast stuff into src/fast
Pandapip1
committed
Clean up submission wrappers and add mem_per_cpu support
Pandapip1
committed
And then the treewide reformat
Pandapip1
committed
Make analysis/pockets.py not abuse the first index
Pandapip1
committed
Merge the divergent analysis implementations
Pandapip1
committed
Remove hardcoded absolute path in md_gen/upside.py
Pandapip1
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Rewrite gromacs md_gen
Pandapip1
committed
Update project to use pyproject.toml instead of setup.py
Pandapip1
committed
Add enspara to dependencies
Pandapip1
committed

Commits on Aug 22, 2025