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Merge branch 'prody:main' into prody-cavifinder-reorg
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@karolamik13
karolamik13 authored Dec 18, 2024
2 parents 56fcbf0 + 9bfeb99 commit 36bff69
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2 changes: 1 addition & 1 deletion README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ ProDy has a modular structure with modules inside various subpackages.

The main ones are:

- :mod:`~prody.atomic`` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`
- :mod:`~prody.atomic` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`

- :mod:`~prody.database` interfaces with databases such as CATH, DALI, UniProt and Pfam

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273 changes: 185 additions & 88 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
from prody.trajectory import TrajBase, Trajectory, Frame
from prody.ensemble import Ensemble

import multiprocessing
import multiprocessing as mp
from .fixer import *
from .compare import *
from prody.measure import calcTransformation, calcDistance, calcRMSD, superpose
Expand All @@ -46,7 +46,7 @@
'calcSASA', 'calcVolume','compareInteractions', 'showInteractionsGraph',
'showInteractionsHist', 'calcLigandInteractions', 'listLigandInteractions',
'showProteinInteractions_VMD', 'showLigandInteraction_VMD',
'calcHydrogenBondsTrajectory', 'calcHydrophobicOverlapingAreas',
'calcHydrophobicOverlapingAreas',
'Interactions', 'InteractionsTrajectory', 'LigandInteractionsTrajectory',
'calcSminaBindingAffinity', 'calcSminaPerAtomInteractions', 'calcSminaTermValues',
'showSminaTermValues', 'showPairEnergy', 'checkNonstandardResidues',
Expand Down Expand Up @@ -1247,7 +1247,7 @@ def calcPiStacking(atoms, **kwargs):
str(sele2.getResnames()[0])+str(sele2.getResnums()[0]), '_'.join(map(str,sele2.getIndices())), str(sele2.getChids()[0])]])

# create a process pool that uses all cpus
with multiprocessing.Pool() as pool:
with mp.Pool() as pool:
# call the function for each item in parallel with multiple arguments
for result in pool.starmap(calcPiStacking_once, items):
if result is not None:
Expand Down Expand Up @@ -1699,7 +1699,12 @@ def calcMetalInteractions(atoms, distA=3.0, extraIons=['FE'], excluded_ions=['SO

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."""
using default parameters or those from kwargs.
:arg max_proc: maximum number of processes to use
default is half of the number of CPUs
:type max_proc: int
"""

try:
coords = getCoords(atoms)
Expand All @@ -1713,6 +1718,7 @@ def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs
interactions_all = []
start_frame = kwargs.pop('start_frame', 0)
stop_frame = kwargs.pop('stop_frame', -1)
max_proc = kwargs.pop('max_proc', mp.cpu_count()//2)

interactions_dic = {
"HBs": calcHydrogenBonds,
Expand All @@ -1738,22 +1744,81 @@ def calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs
traj = trajectory[start_frame:stop_frame+1]

atoms_copy = atoms.copy()
for j0, frame0 in enumerate(traj, start=start_frame):
def analyseFrame(j0, start_frame, 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):
interactions_all.append([])
analyseFrame(j0, start_frame, frame0, interactions_all)
else:
with mp.Manager() as manager:
interactions_all = manager.list()
for j0, frame0 in enumerate(traj, start=start_frame):
interactions_all.append([])

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, start_frame,
frame0,
interactions_all))
p.start()
processes.append(p)

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

for p in processes:
p.join()

interactions_all = interactions_all[:]

trajectory._nfi = nfi

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

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

Expand Down Expand Up @@ -5040,6 +5105,10 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
:arg stop_frame: index of last frame to read
:type stop_frame: int
:arg max_proc: maximum number of processes to use
default is half of the number of CPUs
:type max_proc: int
Selection:
If we want to select interactions for the particular residue or group of residues:
selection='chain A and resid 1 to 50'
Expand All @@ -5055,7 +5124,7 @@ 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 @@ -5072,105 +5141,133 @@ def calcProteinInteractionsTrajectory(self, atoms, trajectory=None, filename=Non
HPh_nb = []
DiBs_nb = []

interactions_traj = [HBs_all, SBs_all, RIB_all, PiStack_all, PiCat_all, HPh_all, DiBs_all]
interactions_nb_traj = [HBs_nb, SBs_nb, RIB_nb, PiStack_nb, PiCat_nb, HPh_nb, DiBs_nb]

start_frame = kwargs.pop('start_frame', 0)
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

for j0, frame0 in enumerate(traj, start=start_frame):
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)

HBs_all.append(hydrogen_bonds)
SBs_all.append(salt_bridges)
RIB_all.append(RepulsiveIonicBonding)
PiStack_all.append(Pi_stacking)
PiCat_all.append(Pi_cation)
HPh_all.append(hydrophobic)
DiBs_all.append(Disulfide_Bonds)

HBs_nb.append(len(hydrogen_bonds))
SBs_nb.append(len(salt_bridges))
RIB_nb.append(len(RepulsiveIonicBonding))
PiStack_nb.append(len(Pi_stacking))
PiCat_nb.append(len(Pi_cation))
HPh_nb.append(len(hydrophobic))
DiBs_nb.append(len(Disulfide_Bonds))

if stop_frame == -1:
traj = trajectory[start_frame:]
else:
if atoms.numCoordsets() > 1:
for i in range(len(atoms.getCoordsets()[start_frame:stop_frame])):
LOGGER.info('Model: {0}'.format(i+start_frame))
atoms.setACSIndex(i+start_frame)
protein = atoms.select('protein')

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

HBs_all.append(hydrogen_bonds)
SBs_all.append(salt_bridges)
RIB_all.append(RepulsiveIonicBonding)
PiStack_all.append(Pi_stacking)
PiCat_all.append(Pi_cation)
HPh_all.append(hydrophobic)
DiBs_all.append(Disulfide_Bonds)
traj = trajectory[start_frame:stop_frame+1]

atoms_copy = atoms.copy()
protein = atoms_copy.protein

def analyseFrame(j0, frame0, interactions_all, interactions_nb, j0_list):
LOGGER.info('Frame: {0}'.format(j0))
atoms_copy.setCoords(frame0.getCoords())

HBs_nb.append(len(hydrogen_bonds))
SBs_nb.append(len(salt_bridges))
RIB_nb.append(len(RepulsiveIonicBonding))
PiStack_nb.append(len(Pi_stacking))
PiCat_nb.append(len(Pi_cation))
HPh_nb.append(len(hydrophobic))
DiBs_nb.append(len(Disulfide_Bonds))
else:
LOGGER.info('Include trajectory or use multi-model PDB file.')
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))

j0_list.append(j0)

if max_proc == 1:
interactions_all = []
interactions_all.extend(interactions_traj)
interactions_nb = []
interactions_nb.extend(interactions_nb_traj)
j0_list = []
for j0, frame0 in enumerate(traj, start=start_frame):
analyseFrame(j0, frame0, interactions_all, interactions_nb,
j0_list)
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])

j0 = start_frame
j0_list = manager.list()
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,
j0_list))
p.start()
processes.append(p)

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

for p in processes:
p.join()

interactions_all = [entry[:] for entry in interactions_all]
interactions_nb = [entry[:] for entry in interactions_nb]
j0_list = [entry for entry in j0_list]

ids = np.argsort(j0_list)
interactions_all = [list(np.array(interactions_type, dtype=object)[ids])
for interactions_type in interactions_all]
interactions_nb = [list(np.array(interactions_type, dtype=object)[ids])
for interactions_type in interactions_nb]

self._atoms = atoms
self._traj = trajectory
self._interactions_traj = [HBs_all, SBs_all, RIB_all, PiStack_all, PiCat_all, HPh_all, DiBs_all]
self._interactions_nb_traj = [HBs_nb, SBs_nb, RIB_nb, PiStack_nb, PiCat_nb, HPh_nb, DiBs_nb]
self._hbs_traj = HBs_all
self._sbs_traj = SBs_all
self._rib_traj = RIB_all
self._piStack_traj = PiStack_all
self._piCat_traj = PiCat_all
self._hps_traj = HPh_all
self._dibs_traj = DiBs_all
self._interactions_traj = interactions_all
self._interactions_nb_traj = interactions_nb
self._hbs_traj = interactions_all[0]
self._sbs_traj = interactions_all[1]
self._rib_traj = interactions_all[2]
self._piStack_traj = interactions_all[3]
self._piCat_traj = interactions_all[4]
self._hps_traj = interactions_all[5]
self._dibs_traj = interactions_all[6]

if filename is not None:
import pickle
with open(str(filename)+'.pkl', 'wb') as f:
pickle.dump(self._interactions_traj, f)
LOGGER.info('File with interactions saved.')

return HBs_nb, SBs_nb, RIB_nb, PiStack_nb, PiCat_nb, HPh_nb, DiBs_nb
return interactions_nb


def getInteractions(self, **kwargs):
Expand Down
6 changes: 4 additions & 2 deletions prody/tests/proteins/test_insty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,8 @@ def testAllInteractionsCalc(self):

if prody.PY3K:
self.INTERACTIONS_ALL = InteractionsTrajectory()
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
self.data_all = np.array(self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS,
stop_frame=13))

try:
assert_equal(self.data_all, self.ALL_INTERACTIONS2,
Expand All @@ -52,7 +53,8 @@ def testAllInteractionsSave(self):
"""Test for saving and loading all types of interactions."""
if prody.PY3K:
self.INTERACTIONS_ALL = InteractionsTrajectory()
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
self.data_all = np.array(self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS,
stop_frame=13))

np.save('test_2k39_all.npy', np.array(self.data_all, dtype=object), allow_pickle=True)

Expand Down

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