[chimera-dev] Freeing chimera memory after combining two molecules

[Daniel VH]

Thanks a lot!

On Fri, Oct 5, 2018 at 12:51 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Daniel,
> The ‘combine’ function doesn’t add the created Molecule to
> chimera.openModels.  You would have to do that yourself with
> chimera.openModels.add().  Without having added ‘combination' to
> openModels, openModels.remove(combination) is a no-op, and therefore the
> C++ memory being used by the Molecule is not reclaimed.  You either have to
> use openModels.add() or you have to explicitly reclaim the C++ memory with
> combination.destroy().
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Oct 4, 2018, at 6:51 AM, Daniel VH <dviladrich95 at gmail.com> wrote:
>
> Hi, In my python script I'm using the combine() function to merge a
> protein and a molecule into one model and since I'm doing this multiple
> times and only use the combined result to save it with pdbWrite I want to
> free the memory of the object combination right after that, but after the
> instructions chimera.openModels.close(combination), del combination,
> chimera.update.checkForChanges(), gc.collect(), chimera.closeSession() the
> memory is not freed. This is the code that reproduces the problem, it uses
> the molecules in the zipfile I have attatched.
>
> import chimera
> from Combine import combine
> import zipfile
> import time
> import gc
> import os
> #from memory_profiler import profile
>
> for itemnum in range(3):
> #@profile
> def pathmaker(itemnum):
> dirpath = os.path.dirname(os.path.realpath(__file__))
> zippath=dirpath+'/'+'test1_000.zip'
> torsionpath=zipfile.ZipFile(zippath).extract('Pathway_000_Pathway.txt')
> proteinpath=zipfile.ZipFile(zippath).extract('Protein_000_Protein.mol2')
> ligandpath=zipfile.ZipFile(zippath).extract('Ligand_000_Ligand.mol2')
>
> opened = chimera.openModels.open(proteinpath)
> protein = opened[0]
> opened1 = chimera.openModels.open(ligandpath)
> mol=opened1[0]
> combination=combine([mol,protein],protein)
> totalnum=str(itemnum).zfill(3)+'_'+str(i).zfill(3)
> chimera.pdbWrite([combination], chimera.Xform(), 'testpdb%s.pdb' %totalnum)
> print('writing testpdb%s.pdb' %totalnum)
> chimera.openModels.close(combination)
> del combination
> chimera.update.checkForChanges()
> gc.collect()
> chimera.closeSession()
>
>
> for i in range(20):
> pathmaker(itemnum)
> #this stops the code and shows memory increase for each iteration
> print('pause 6 seconds...')
> time.sleep(6)
>
> <testing.py><test1_000.zip>_______________________________________________
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