[DRAFT] Schrodinger solvation shell extraction#23

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jeevster wants to merge 122 commits intomainfrom schrodinger_solvation_shell_extraction

+2,060-37

Commits on Apr 22, 2024

automated solvation shell extraction workflow
Sanjeev Raja
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Commits on May 15, 2024

begin addressing Daniel comments
Sanjeev Raja
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operate on pairwise distances, account for PBCs
Sanjeev Raja
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switch to kabsch rmsd
Sanjeev Raja
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add pdb file example
Sanjeev Raja
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add dependencies to setup
Sanjeev Raja
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rename from rmse to rmsd
Sanjeev Raja
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random seed for rmsd set instead of always starting at 0, remove reorient function
Sanjeev Raja
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Commits on May 17, 2024

start adding support for multiatom solutes, not working yet
Sanjeev Raja
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fix star import, add al_cl04 test file
Sanjeev Raja
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update extraction script to be the non-working Al_Cl04 one
Sanjeev Raja
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Commits on May 20, 2024

correct charge assignment
Sanjeev Raja
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Commits on May 31, 2024

Commits on Jun 5, 2024

Commits on Jun 6, 2024

Commits on Jun 12, 2024

Commits on Jun 15, 2024

Commits on Jun 17, 2024

remove duplicate "BS"
levineds
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Commits on Jun 18, 2024

Commits on Jun 20, 2024

add slightly more error checking
levineds
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Commits on Jun 25, 2024

more fixes
levineds
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Commits on Jun 26, 2024

function already exists of course
levineds
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Commits on Jun 27, 2024

trying to handle multi-atom solutes, committing before migrating to schrodinger
Sanjeev Raja
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Commits on Jul 1, 2024

start schrodinger workflow
Sanjeev Raja
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can extract shells, now need to loop over solutes, apply pbcs and add charges
Sanjeev Raja
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loop over solutes
Sanjeev Raja
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fix loop nesting
Sanjeev Raja
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add partial charge assignment
Sanjeev Raja
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fix pbc wrapping index error
Sanjeev Raja
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Commits on Jul 2, 2024

append central atom to shell if not already present, have fully running pipeline, need to test
Sanjeev Raja
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cleanup files
Sanjeev Raja
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ignore readme
Sanjeev Raja
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begin solvent-solvent stuff, not working
Sanjeev Raja
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revert to working solvent-solvent interactions, need to implement PBCs
Sanjeev Raja
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uncomment solvent part
Sanjeev Raja
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switch to superimpose version of rmsd
Sanjeev Raja
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make size checking caps hard
Sanjeev Raja
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address some more pr comments - more accurate comments, restructuring solute and solvent resname dictionary construction
Sanjeev Raja
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option to skip solvent centered shells
Sanjeev Raja
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remove equals from dir name
Sanjeev Raja
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assign partial charges once outside loop
Sanjeev Raja
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partial charge assignment once up front
Sanjeev Raja
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remove size filtering function
Sanjeev Raja
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more explicit version of expand shells function
Sanjeev Raja
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fix central solute molecule bug
Sanjeev Raja
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simplify filter solute function
Sanjeev Raja
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Commits on Jul 3, 2024

Commits on Jul 4, 2024

turn off shell expansion if there are no solvents
Sanjeev Raja
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lognormal sampling of max size
Sanjeev Raja
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option to subsample solutes/solvents per frame
Sanjeev Raja
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Commits on Jul 8, 2024

Commits on Jul 9, 2024

Commits on Jul 10, 2024

some logging, restrict to 100 frames for now
levineds
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basic docstrings
levineds
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refactor into separate functions, re-use code
levineds
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refactor bug
levineds
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make solute-free assertion a warning instead
Sanjeev Raja
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add max frames argument
Sanjeev Raja
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arg bug
Sanjeev Raja
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Commits on Jul 15, 2024

Commits on Jul 16, 2024

some more cleanup tools
levineds
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Commits on Jul 17, 2024

there are nitriles...
levineds
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Commits on Jul 18, 2024

Commits on Jul 20, 2024

use absolute path
levineds
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Commits on Jul 22, 2024

ensure ligand chain is present
levineds
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Commits on Jul 26, 2024

Use chain to identify solvent vs. solute
levineds
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Commits on Jul 31, 2024

Commits on Aug 13, 2024

Commits on Aug 23, 2024

refactor and add some comments
Sanjeev Raja
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