On 2011-10-12 05:31, lina wrote:
I tried to write one (not working one) as below, so many problems here.
Just some quick remarks:
#!/usr/bin/python3
import os.path
LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}
def sortfile():
for chainid in CHAINID:
sortoneblock(chainid)
def generatedictionary(dictfilename):
You define the function with the parameter "dictfilename" but you'll
never use it.
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
The if-branch is probably wrongly indented (should be inside the for-loop).
def sortoneblock(cID)
text=fetchonefiledata(INFILENAME)
for line in text:
blocks=line.strip().split()
if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] == "cID":
"cID" is a string-variable but you compare block 4 to the literal string
"cID". In "pdbone.pdb" you will never find "cID" so this function will
do nothing. You probably mean "blocks[4] == cID".
valuefromdict[blocks[2]]=mapping[block[2]]
You never fill up "mapping" because you never call your
"generatedictionary"-function. Therefore "mapping" is still an empty
dictionary and this line will raise an exception.
return
Firstly, the indentation is wrong because you would leave "sortoneblock"
after the first processed line. Secondly, as you return nothing, you
don't need this line because you will leave the function anyway.
def fetchonefiledata(infilename):
text=open("infilename").readlines()
Again, "infilename" is a variable, so no need for the quotes.
if os.path.splitext(infilename)[1]=".itp"
return text
if os.path.splitext(infilename)[1]=".pdb"
return text[LINESTOSKIP:]
if __name__=="__main__":
sortfiles()
There is no "sortfiles()" in your script. The function you probably mean
is called "sortfile()"
Bye, Andreas
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