Ben Keshet wrote:
...
I ended up using another method as someone suggested to me. I am still
not sure why the previous version got stuck on empty files, while this
one doesn't:
receptors = ['A' 'B']
*** Alarm bells *** Do you mean ['AB'], or do you mean ['A', 'B']?
...(more code one way) ...
Don't be afraid of defining functions, you are nested too deeply to
easily understand, and hence likely to make mistakes. For similar
reasons, I don't like names like x and i unless there are no better
names. Also, since you don't seem to "really" need to write, I used
print. The comments would be better if I knew the field a bit (or
your code had had better names).
Try something like (obviously I couldn't test it, so untested code):
OUTPUT = 'c:/Linux/Dock_method_validation/%s/validation/pockets.out'
INPUT = ('c:/Linux/Dock_method_validation/%s/validation/'
'ligand_ran_line_%s_%sA_secondary_scored.mol2')
def extract_dist(dest, receptor, line, ligand):
'''Get distances after "PRIMARY" from the appropriate file
'''
source = open(INPUT % (receptor, line, ligand), 'r')
gen = iter(source) # get a name for walking through the file.
try:
# Find the start
for j, text in enumerate(gen):
if 'PRIMARY' in text:
print >>dest, text.strip(),
break
if j == 19: # Stop looking after 20 lines.
return # nothing here, go on to the next one
# copy scores up to TRIPOS
for text in gen:
if 'TRIPOS' in text:
break
print >>dest, text.strip(),
print
print >>dest
finally:
source.close()
for receptor in 'A', 'B':
# open out_file for appending per receptor, close at same level
out_file = open(OUTPUT % receptor, 'a')
for line in range(10):
for ligand in (7, 9, 11, 13, 15, 17):
extract_dist(out_file, receptor, line, ligand)
out_file.close()
--Scott David Daniels
[EMAIL PROTECTED]
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