TypeError: must be string without null bytes, not str
I'm trying to run this code, to run the same command (with little changes) with every frame that I have:
traj.reset()
import os
#os.chdir(outname)
for i, frame in enumerate(traj):
frame.superpose()
comando = "python hollow.py -c constraint -o hollow_%s.pdb urei%s.pdb" % (i, i)
os.system(comando)
pml_cmd = "pymol urei%s.pdb hollow_%s.pdb -c -d 'as cartoon, urei%s;color gray90, urei%s;center chain A;set_view (-0.605158150,0.089404292,0.791067421, .795849979,0.093013920,0.598304033,-0.020089993,0.991641700,-0.127439827, .000000000,0.000000000,-202.017959595,-28.771762848,-7.683309555,10.745590210,-568.485290527,972.520690918,-20.000000000);bg white;as sphere, hollow_%s;color cyan, hollow_%s;ray;save urei%s.png' " % (i, i, i, i, i, i, i)
os.system(pml_cmd)
#remove = "rm urei%s.pdb hollow_%s.pdb" % (i, i)
#os.system(remove)
os.chdir("../")
I run this and I get this error:
TypeError Traceback (most recent call last)
<ipython-input-8-53cd3e7bd107> in <module>()
7 os.system(comando)
8 pml_cmd = "pymol urei%s.pdb hollow_%s.pdb -c -d 'as cartoon, urei%s;color gray90, urei%s;center chain A;set_view (-0.605158150,0.089404292,0.791067421, .795849979,0.093013920,0.598304033,-0.020089993,0.991641700,-0.127439827, .000000000,0.000000000,-202.017959595,-28.771762848,-7.683309555,10.745590210,-568.485290527,972.520690918,-20.000000000);bg white;as sphere, hollow_%s;color cyan, hollow_%s;ray;save urei%s.png' " % (i, i, i, i, i, i, i)
----> 9 os.system(pml_cmd)
10 #remove = "rm urei%s.pdb hollow_%s.pdb" % (i, i)
11 #os.system(remove)
TypeError: must be string without null bytes, not str
I searched in internet, but I can't find a good answer.
The problem is with the char that should either be double escaped, ie changed to "" Or alternatively add an "r" before the string decleration:
pml_cmd = r"pymol urei%s.pdb ..."
You get this particular error since somewhere along the string there is a which is interpreted as a NULL char
I was able to resolve this error by commenting out the print :
for tarfileobj in inputs:
# print(tarfileobj)
tarfileobj.extractall(path=t, members=None)
I could have done print(tarfileobj.split) or printed the repr or removed null bytes, or if its a tarfile, just extract it.