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simplify calcProteinInteractionsTrajectory
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@jamesmkrieger
jamesmkrieger committed Dec 13, 2024
1 parent 3d68579 commit 3e9568b
Showing 1 changed file with 77 additions and 137 deletions.
214 changes: 77 additions & 137 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5110,7 +5110,7 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
except TypeError:
raise TypeError('coords must be an object '
'with `getCoords` method')

HBs_all = []
SBs_all = []
RIB_all = []
Expand All @@ -5134,153 +5134,93 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
stop_frame = kwargs.pop('stop_frame', -1)
max_proc = kwargs.pop('max_proc', mp.cpu_count()//2)

if trajectory is not None:
if isinstance(trajectory, Atomic):
trajectory = Ensemble(trajectory)

nfi = trajectory._nfi
trajectory.reset()
numFrames = trajectory._n_csets

if stop_frame == -1:
traj = trajectory[start_frame:]
if trajectory is None:
if atoms.numCoordsets() > 1:
trajectory = atoms
else:
traj = trajectory[start_frame:stop_frame+1]
LOGGER.info('Include trajectory or use multi-model PDB file.')
return interactions_nb_traj

atoms_copy = atoms.copy()
protein = atoms_copy.protein
if isinstance(trajectory, Atomic):
trajectory = Ensemble(trajectory)

#nfi = trajectory._nfi
#trajectory.reset()
#numFrames = trajectory._n_csets

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

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].append(hydrogen_bonds)
interactions_all[1].append(salt_bridges)
interactions_all[2].append(RepulsiveIonicBonding)
interactions_all[3].append(Pi_stacking)
interactions_all[4].append(Pi_cation)
interactions_all[5].append(hydrophobic)
interactions_all[6].append(Disulfide_Bonds)
if stop_frame == -1:
traj = trajectory[start_frame:]
else:
traj = trajectory[start_frame:stop_frame+1]

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())

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

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

if max_proc == 1:
interactions_all = []
interactions_all.extend(interactions_traj)
interactions_nb = []
interactions_nb.extend(interactions_nb_traj)
for j0, frame0 in enumerate(traj, start=start_frame):
analyseFrame(j0, frame0, interactions_all, interactions_nb)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
interactions_all.extend([manager.list() for _ in interactions_traj])
if max_proc == 1:
interactions_all = []
interactions_all.extend(interactions_traj)
interactions_nb = []
interactions_nb.extend(interactions_nb_traj)
for j0, frame0 in enumerate(traj, start=start_frame):
analyseFrame(j0, frame0, interactions_all, interactions_nb)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
interactions_all.extend([manager.list() for _ in interactions_traj])

interactions_nb = manager.list()
interactions_nb.extend([manager.list() for _ in interactions_nb_traj])
interactions_nb = manager.list()
interactions_nb.extend([manager.list() for _ in interactions_nb_traj])

j0 = start_frame
while j0 < traj.numConfs()+start_frame:
j0 = start_frame
while j0 < traj.numConfs()+start_frame:

processes = []
for _ in range(max_proc):
frame0 = traj[j0-start_frame]
p = mp.Process(target=analyseFrame, args=(j0, frame0,
interactions_all,
interactions_nb))
p.start()
processes.append(p)
processes = []
for _ in range(max_proc):
frame0 = traj[j0-start_frame]

p = mp.Process(target=analyseFrame, args=(j0, frame0,
interactions_all,
interactions_nb))
p.start()
processes.append(p)

j0 += 1
if j0 >= traj.numConfs()+start_frame:
break
j0 += 1
if j0 >= traj.numConfs()+start_frame:
break

for p in processes:
p.join()
for p in processes:
p.join()

interactions_all = [entry[:] for entry in interactions_all]
interactions_nb = [entry[:] for entry in interactions_nb]
else:
if atoms.numCoordsets() > 1:
def analyseFrame(i, interactions_all, interactions_nb):
LOGGER.info('Model: {0}'.format(i+start_frame))
atoms.setACSIndex(i+start_frame)
protein = atoms.select('protein')

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

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

if max_proc == 1:
interactions_all = []
interactions_all.extend(interactions_traj)
interactions_nb = []
interactions_nb.extend(interactions_nb_traj)
for i in range(len(atoms.getCoordsets()[start_frame:stop_frame])):
analyseFrame(i, interactions_all, interactions_nb)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
interactions_all.extend([manager.list() for _ in interactions_traj])

interactions_nb = manager.list()
interactions_nb.extend([manager.list() for _ in interactions_nb_traj])

i = start_frame
while i < len(atoms.getCoordsets()[start_frame:stop_frame]):
processes = []
for _ in range(max_proc):
p = mp.Process(target=analyseFrame, args=(i, interactions_all,
interactions_nb))
p.start()
processes.append(p)

i += 1
if i >= len(atoms.getCoordsets()[start_frame:stop_frame]):
break

for p in processes:
p.join()

interactions_all = [entry[:] for entry in interactions_all]
interactions_nb = [entry[:] for entry in interactions_nb]
else:
LOGGER.info('Include trajectory or use multi-model PDB file.')
interactions_all = [entry[:] for entry in interactions_all]
interactions_nb = [entry[:] for entry in interactions_nb]

self._atoms = atoms
self._traj = trajectory
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