Can't pickle local object 'calcInteractionsMultipleFrames.<locals>.analyseFrame'

[houyaxuan634-coder]

I am trying to use insty in Prody 2.6.1
I provide an ensemble pdb file with 40 structures (with hydrogens)
the command is
calcHydrogenBondsTrajectory(atoms)
I get the following error

AttributeError Traceback (most recent call last)
Cell In[6], line 1
----> 1 calcHydrogenBondsTrajectory(atoms)

File ~\anaconda3\envs\prody_env\Lib\site-packages\prody\proteins\interactions.py:1929, in calcHydrogenBondsTrajectory(atoms, trajectory, **kwargs)
1887 def calcHydrogenBondsTrajectory(atoms, trajectory=None, **kwargs):
1888 """Compute hydrogen bonds for DCD trajectory or multi-model PDB using default parameters.
1889
1890 :arg atoms: an Atomic object from which residues are selected
(...) 1926 If we want to study chain-chain interactions:
1927 selection='chain A', selection2='chain B' """
-> 1929 return calcInteractionsMultipleFrames(atoms, 'HBs', trajectory, **kwargs)

File ~\anaconda3\envs\prody_env\Lib\site-packages\prody\proteins\interactions.py:1817, in calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs)
1815 for _ in range(max_proc):
1816 p = mp.Process(target=analyseFrame, args=(i, interactions_all))
-> 1817 p.start()
1818 processes.append(p)
1820 i += 1

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\process.py:121, in BaseProcess.start(self)
118 assert not _current_process._config.get('daemon'),
119 'daemonic processes are not allowed to have children'
120 _cleanup()
--> 121 self._popen = self._Popen(self)
122 self._sentinel = self._popen.sentinel
123 # Avoid a refcycle if the target function holds an indirect
124 # reference to the process object (see bpo-30775)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\context.py:224, in Process._Popen(process_obj)
222 @staticmethod
223 def _Popen(process_obj):
--> 224 return _default_context.get_context().Process._Popen(process_obj)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\context.py:336, in SpawnProcess._Popen(process_obj)
333 @staticmethod
334 def _Popen(process_obj):
335 from .popen_spawn_win32 import Popen
--> 336 return Popen(process_obj)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\popen_spawn_win32.py:95, in Popen.init(self, process_obj)
93 try:
94 reduction.dump(prep_data, to_child)
---> 95 reduction.dump(process_obj, to_child)
96 finally:
97 set_spawning_popen(None)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\reduction.py:60, in dump(obj, file, protocol)
58 def dump(obj, file, protocol=None):
59 '''Replacement for pickle.dump() using ForkingPickler.'''
---> 60 ForkingPickler(file, protocol).dump(obj)

AttributeError: Can't pickle local object 'calcInteractionsMultipleFrames..analyseFrame'

can you please help?
Luke

[AnthonyBogetti]

Hello @houyaxuan634-coder, would you also be able to share the full code you are using? Feel free to share the pdb file as well, but if you don't want to I can substitute my own test file. This will help me reproduce the error and come up with a solution quickly.

[houyaxuan634-coder]

Yeah sure
I was trying to launch the Ensemble PDB analysis function in Insty. So I read through the tutorial on insty (This is the link to the tutorial: http://www.bahargroup.org/prody/tutorials/insty_tutorial/ensemblePDB.html)
I used the PDB I have for the protein which contains 40 model in one PDB, then I follow the tutorial but that error came up when I attempt to run it.
Then I thought the error may be have something to do with my PDB file so I used the exact same command on the tutorial (the 2k39 model) but it does not work as well

The following is my code when I tried to use the 2k39 model
import prody
from prody.proteins.interactions import calcHydrogenBondsTrajectory
from prody import parsePDB
atoms = parsePDB('2k39')
calcHydrogenBondsTrajectory(atoms)

the output is

AttributeError Traceback (most recent call last)
Cell In[5], line 1
----> 1 calcHydrogenBondsTrajectory(atoms)

File ~\anaconda3\envs\prody_env\Lib\site-packages\prody\proteins\interactions.py:1929, in calcHydrogenBondsTrajectory(atoms, trajectory, **kwargs)
1887 def calcHydrogenBondsTrajectory(atoms, trajectory=None, **kwargs):
1888 """Compute hydrogen bonds for DCD trajectory or multi-model PDB using default parameters.
1889
1890 :arg atoms: an Atomic object from which residues are selected
(...) 1926 If we want to study chain-chain interactions:
1927 selection='chain A', selection2='chain B' """
-> 1929 return calcInteractionsMultipleFrames(atoms, 'HBs', trajectory, **kwargs)

File ~\anaconda3\envs\prody_env\Lib\site-packages\prody\proteins\interactions.py:1817, in calcInteractionsMultipleFrames(atoms, interaction_type, trajectory, **kwargs)
1815 for _ in range(max_proc):
1816 p = mp.Process(target=analyseFrame, args=(i, interactions_all))
-> 1817 p.start()
1818 processes.append(p)
1820 i += 1

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\process.py:121, in BaseProcess.start(self)
118 assert not _current_process._config.get('daemon'),
119 'daemonic processes are not allowed to have children'
120 _cleanup()
--> 121 self._popen = self._Popen(self)
122 self._sentinel = self._popen.sentinel
123 # Avoid a refcycle if the target function holds an indirect
124 # reference to the process object (see bpo-30775)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\context.py:224, in Process._Popen(process_obj)
222 @staticmethod
223 def _Popen(process_obj):
--> 224 return _default_context.get_context().Process._Popen(process_obj)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\context.py:336, in SpawnProcess._Popen(process_obj)
333 @staticmethod
334 def _Popen(process_obj):
335 from .popen_spawn_win32 import Popen
--> 336 return Popen(process_obj)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\popen_spawn_win32.py:95, in Popen.init(self, process_obj)
93 try:
94 reduction.dump(prep_data, to_child)
---> 95 reduction.dump(process_obj, to_child)
96 finally:
97 set_spawning_popen(None)

File ~\anaconda3\envs\prody_env\Lib\multiprocessing\reduction.py:60, in dump(obj, file, protocol)
58 def dump(obj, file, protocol=None):
59 '''Replacement for pickle.dump() using ForkingPickler.'''
---> 60 ForkingPickler(file, protocol).dump(obj)

AttributeError: Can't pickle local object 'calcInteractionsMultipleFrames..analyseFrame'

Thank you very much for your reply

[houyaxuan634-coder]

I forgot to mention
Prody version I used is 2.6.1
NumPy version is 1.23.5
scipy is 1.15.3 matplotlib is 3.10.6
I am not sure does the version affect some of the function of prody?