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Add ignore_waters option to repack #182

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Merged
mtessmer merged 3 commits into from
Feb 13, 2025
Merged

Add ignore_waters option to repack #182

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5fba823
Bump version
mtessmer Feb 13, 2025
175115e
Add ignore_waters option to mutate.
mtessmer Feb 13, 2025
0c4fcc8
Add missing quote
mtessmer Feb 13, 2025
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2 changes: 1 addition & 1 deletion src/chilife/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,4 +26,4 @@
# SpinLabel = SpinLabel.SpinLabel
# dSpinLabel = dSpinLabel.dSpinLabel

__version__ = '1.1.1'
__version__ = '1.1.2'
19 changes: 12 additions & 7 deletions src/chilife/protein_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -423,6 +423,7 @@ def get_missing_residues(
protein: Union[MDAnalysis.Universe, MDAnalysis.AtomGroup],
ignore: Set[int] = None,
use_H: bool = False,
ignore_waters = True
) -> List:
"""Get a list of RotamerEnsemble objects corresponding to the residues of the provided protein that are missing
heavy atoms.
Expand Down Expand Up @@ -467,6 +468,7 @@ def get_missing_residues(
protein=protein,
chain=res.segid,
use_H=use_H,
ignore_waters=ignore_waters
)
)

Expand All @@ -478,6 +480,7 @@ def mutate(
*ensembles: 'RotamerEnsemble',
add_missing_atoms: bool = True,
rotamer_index: Union[int, str, None] = None,
ignore_waters = True
) -> MDAnalysis.Universe:
"""Create a new Universe where the native residue is replaced with the highest probability rotamer from a
RotamerEnsemble or SpinLabel object.
Expand All @@ -494,7 +497,8 @@ def mutate(
rotamer.
add_missing_atoms : bool
Model side chains missing atoms if they are not present in the provided structure.

ignore_waters : bool
ignore waters when selecting conforers for mutation.
Returns
-------
U : MDAnalysis.Universe
Expand Down Expand Up @@ -524,9 +528,7 @@ def mutate(
else:
use_H = False

missing_residues = get_missing_residues(
protein, ignore={res.site for res in ensembles}, use_H=use_H
)
missing_residues = get_missing_residues(protein, ignore={res.site for res in ensembles}, use_H=use_H, ignore_waters=ignore_waters)
ensembles = list(ensembles) + missing_residues

label_sites = {}
Expand All @@ -537,9 +539,12 @@ def mutate(
else:
label_sites[spin_label.site, spin_label.icode, spin_label.chain] = spin_label

protein = protein.select_atoms(
f'(not altloc B) and (not (byres name OH2 or resname HOH))'
)
# Remove waters if they are being ignored.
if ignore_waters:
protein = protein.select_atoms(f'(not altloc B) and (not (byres name OH2 or resname HOH))')
else:
protein = protein.select_atoms(f'(not altloc B)')

label_selstr = " or ".join([f"({label.selstr})" for label in ensembles])
other_atoms = protein.select_atoms(f"not ({label_selstr})")

Expand Down
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