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fixed issue with InSty multiprocessing on Windows and MacOS #2200

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fixed issue with InSty multiprocessing on Windows and MacOS #2200

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90 changes: 36 additions & 54 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1425,7 +1425,7 @@ def calcHydrophobic(atoms, **kwargs):
Additional selection can be added as shown below (with selection that includes
only hydrophobic part):
>>> calcHydrophobic(atoms, non_standard_Hph={'XLE'='noh and not backbone',
'XLI'='noh and not backbone'})
'XLI'='noh and not backbone'})
Predictions for proteins only. To compute protein-ligand interactions use
calcLigandInteractions().
Results can be displayed in VMD by using showVMDinteraction()
Expand Down Expand Up @@ -1702,6 +1702,24 @@ def calcMetalInteractions(atoms, distA=3.0, extraIons=['FE'], excluded_ions=['SO
raise TypeError('An object should contain ions')


def _analyseFrameTrajectory(j0, frame0, interactions_all, atoms_copy, interaction_type, interactions_dic, kwargs):
"""Helper function for calcInteractionsMultipleFrames to handle trajectory frames in parallel."""
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)


def _analyseFrameCoordsets(i, interactions_all, atoms, interaction_type, interactions_dic, start_frame, kwargs):
"""Helper function for calcInteractionsMultipleFrames to handle multi-model PDB models in parallel."""
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)


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 +1768,12 @@ 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)
_analyseFrameTrajectory(j0, frame0, interactions_all, atoms_copy,
interaction_type, interactions_dic, kwargs)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
Expand All @@ -1772,8 +1785,9 @@ def analyseFrame(j0, frame0, interactions_all):
for _ in range(max_proc):
frame0 = traj[j0-start_frame]

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

Expand All @@ -1791,20 +1805,14 @@ 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)
_analyseFrameCoordsets(i, interactions_all, atoms, interaction_type,
interactions_dic, start_frame, kwargs)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
Expand All @@ -1813,7 +1821,9 @@ 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=_analyseFrameCoordsets,
args=(i, interactions_all, atoms, interaction_type,
interactions_dic, start_frame, kwargs))
p.start()
processes.append(p)

Expand Down Expand Up @@ -5304,7 +5314,7 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
trajectory = atoms
else:
LOGGER.info('Include trajectory or use multi-model PDB file.')
return interactions_nb_traj
return None

if isinstance(trajectory, Atomic):
trajectory = Ensemble(trajectory)
Expand Down Expand Up @@ -5341,41 +5351,12 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
atoms_copy = atoms.copy()
protein = atoms_copy.protein

def analyseFrame(j0, frame0, interactions_all, interactions_nb):
LOGGER.info('Frame: {0}'.format(j0))
atoms_copy.setCoords(frame0.getCoords())

ind = j0 - start_frame

hydrogen_bonds = calcHydrogenBonds(protein, **kwargs)
salt_bridges = calcSaltBridges(protein, **kwargs)
RepulsiveIonicBonding = calcRepulsiveIonicBonding(protein, **kwargs)
Pi_stacking = calcPiStacking(protein, **kwargs)
Pi_cation = calcPiCation(protein, **kwargs)
hydrophobic = calcHydrophobic(protein, **kwargs)
Disulfide_Bonds = calcDisulfideBonds(protein, **kwargs)

interactions_all[0][ind].extend(hydrogen_bonds)
interactions_all[1][ind].extend(salt_bridges)
interactions_all[2][ind].extend(RepulsiveIonicBonding)
interactions_all[3][ind].extend(Pi_stacking)
interactions_all[4][ind].extend(Pi_cation)
interactions_all[5][ind].extend(hydrophobic)
interactions_all[6][ind].extend(Disulfide_Bonds)

interactions_nb[0][ind].append(len(hydrogen_bonds))
interactions_nb[1][ind].append(len(salt_bridges))
interactions_nb[2][ind].append(len(RepulsiveIonicBonding))
interactions_nb[3][ind].append(len(Pi_stacking))
interactions_nb[4][ind].append(len(Pi_cation))
interactions_nb[5][ind].append(len(hydrophobic))
interactions_nb[6][ind].append(len(Disulfide_Bonds))

if max_proc == 1:
interactions_all = interactions_traj
interactions_nb = interactions_nb_traj
for j0, frame0 in enumerate(traj, start=start_frame):
analyseFrame(j0, frame0, interactions_all, interactions_nb)
_analyseFrame_Trajectory(j0, frame0, interactions_all, interactions_nb,
atoms_copy, protein, start_frame, **kwargs)
interactions_nb = [[item[0] for item in row] for row in interactions_nb]
else:
with mp.Manager() as manager:
Expand All @@ -5392,9 +5373,10 @@ def analyseFrame(j0, frame0, interactions_all, interactions_nb):
for _ in range(max_proc):
frame0 = traj[j0-start_frame]

p = mp.Process(target=analyseFrame, args=(j0, frame0,
interactions_all,
interactions_nb))
p = mp.Process(target=_analyseFrame_Trajectory,
args=(j0, frame0, interactions_all, interactions_nb,
atoms_copy, protein, start_frame),
kwargs=kwargs)
p.start()
processes.append(p)

Expand Down
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