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Fix can't pickle local object in calcHydrogenBondsTrajectory #2196

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Fix can't pickle local object in calcHydrogenBondsTrajectory #2196

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Copilot Dec 15, 2025
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Copilot Dec 15, 2025
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71 changes: 53 additions & 18 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1702,6 +1702,43 @@ def calcMetalInteractions(atoms, distA=3.0, extraIons=['FE'], excluded_ions=['SO
raise TypeError('An object should contain ions')


def _analyseFrameTrajectory(j0, frame0_coords, atoms_copy, interaction_type,
interactions_dic, start_frame, kwargs):
"""Worker function for trajectory frame analysis (module-level for pickling)."""
LOGGER.info('Frame: {0}'.format(j0))
atoms_copy.setCoords(frame0_coords)
protein = atoms_copy.select('protein')
interactions = interactions_dic[interaction_type](protein, **kwargs)
return interactions


def _analyseFrameTrajectoryWrapper(j0, frame0_coords, atoms_copy, interaction_type,
interactions_dic, start_frame, kwargs, interactions_all):
"""Wrapper for multiprocessing with managed list."""
interactions = _analyseFrameTrajectory(j0, frame0_coords, atoms_copy,
interaction_type, interactions_dic,
start_frame, kwargs)
interactions_all.append(interactions)


def _analyseFrameMultiModel(i, atoms, interaction_type, interactions_dic,
start_frame, kwargs):
"""Worker function for multi-model PDB analysis (module-level for pickling)."""
LOGGER.info('Model: {0}'.format(i+start_frame))
atoms.setACSIndex(i+start_frame)
protein = atoms.select('protein')
interactions = interactions_dic[interaction_type](protein, **kwargs)
return interactions


def _analyseFrameMultiModelWrapper(i, atoms, interaction_type, interactions_dic,
start_frame, kwargs, interactions_all):
"""Wrapper for multiprocessing with managed list."""
interactions = _analyseFrameMultiModel(i, atoms, interaction_type,
interactions_dic, start_frame, kwargs)
interactions_all.append(interactions)


def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs):
"""Compute selected type interactions for DCD trajectory or multi-model PDB
using default parameters or those from kwargs.
Expand Down Expand Up @@ -1750,17 +1787,14 @@ def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs
traj = trajectory[start_frame:stop_frame+1]

atoms_copy = atoms.copy()
def analyseFrame(j0, frame0, interactions_all):
LOGGER.info('Frame: {0}'.format(j0))
atoms_copy.setCoords(frame0.getCoords())
protein = atoms_copy.select('protein')
interactions = interactions_dic[interaction_type](protein, **kwargs)
interactions_all.append(interactions)

if max_proc == 1:
interactions_all = []
for j0, frame0 in enumerate(traj, start=start_frame):
analyseFrame(j0, frame0, interactions_all)
interactions = _analyseFrameTrajectory(j0, frame0.getCoords(),
atoms_copy, interaction_type,
interactions_dic, start_frame, kwargs)
interactions_all.append(interactions)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
Expand All @@ -1771,9 +1805,12 @@ def analyseFrame(j0, frame0, interactions_all):
processes = []
for _ in range(max_proc):
frame0 = traj[j0-start_frame]
frame0_coords = frame0.getCoords()

p = mp.Process(target=analyseFrame, args=(j0, frame0,
interactions_all))
p = mp.Process(target=_analyseFrameTrajectoryWrapper,
args=(j0, frame0_coords, atoms_copy,
interaction_type, interactions_dic,
start_frame, kwargs, interactions_all))
p.start()
processes.append(p)

Expand All @@ -1791,20 +1828,15 @@ def analyseFrame(j0, frame0, interactions_all):

else:
if atoms.numCoordsets() > 1:
def analyseFrame(i, interactions_all):
LOGGER.info('Model: {0}'.format(i+start_frame))
atoms.setACSIndex(i+start_frame)
protein = atoms.select('protein')
interactions = interactions_dic[interaction_type](protein, **kwargs)
interactions_all.append(interactions)

if stop_frame == -1:
stop_frame = atoms.numCoordsets()

if max_proc == 1:
interactions_all = []
for i in range(len(atoms.getCoordsets()[start_frame:stop_frame+1])):
analyseFrame(i, interactions_all)
interactions = _analyseFrameMultiModel(i, atoms, interaction_type,
interactions_dic, start_frame, kwargs)
interactions_all.append(interactions)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
Expand All @@ -1813,7 +1845,10 @@ def analyseFrame(i, interactions_all):
while i < len(atoms.getCoordsets()[start_frame:stop_frame+1]):
processes = []
for _ in range(max_proc):
p = mp.Process(target=analyseFrame, args=(i, interactions_all))
p = mp.Process(target=_analyseFrameMultiModelWrapper,
args=(i, atoms, interaction_type,
interactions_dic, start_frame,
kwargs, interactions_all))
p.start()
processes.append(p)

Expand Down
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