Spyros Charonis wrote:
The problem is that the list (z_coords1) returns as an empty list. I know
the code works (too large to post here)
So you want us to diagnose a problem in code that we can't see? I admire your
confidence in our powers of deduction.
[...]
Short of some intricacy with the scopes of the program I may be missing, I
am not sure why this is happening? Deos anybody have
any ideas? Many thanks for your time.
Your code's indentation is messed up again, which makes it impossible to guess
what it actually does.
Also, it is hard to understand what it *should* do. I'm not sure why you are
writing data to a pickle file, only to read it back in again. You already have
the data in memory, why not just keep it there?
Also, your function serialize_pipeline_model is a misleading name. "Serialize"
in computer science and programming means to take a data structure and turn it
into a format suitable for saving to a file. You are doing the opposite,
taking a file and reading it into a data structure.
Here is my best guess as to what you might need:
def get_zcoords(filename):
"""Read z coordinate data from the named file, and return it as a list."""
f = open(filename, 'r')
zcoords = []
# ... stuff goes here that you don't show
# ... I guess you read from the file and process it somehow
# ...
f.close()
charged_groups = (lys_charged_group + arg_charged_group
+ his_charged_group + asp_charged_group
+ glu_charged_group
)
for group in charged_groups:
zcoords.append(float(group[48:54]))
return zcoords
location = '/Users/spyros/Desktop/3NY8MODELSHUMAN/HomologyModels/'
zdata = []
for filename in os.listdir(location):
zdata.extend(get_zcoords(filename))
print 'Z-VALUES FOR ALL CHARGED RESIDUES'
print zdata
If you need to keep those z coordinates for later use, you can pickle them,
once, at the end of the process, and then later unpickle them.
import pickle
f = open("z_coords1.dat", "wb")
pickle.dump(zdata, f)
f.close()
f = open("z_coords1.dat", "rb")
zdata2 = pickle.load(f)
f.close()
assert zdata == zdata2, "error in pickle/unpickle round trip!"
Does this help?
--
Steven
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