On Wed, Oct 12, 2011 at 3:29 PM, Andreas Perstinger <
andreas.perstin...@gmx.net> wrote:
> 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:
Thanks,
Now the newly-improved one as following: but still the "sort" parts did not
work.
#!/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):
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
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 and
blocks[2] in mapping.keys():
valuefromdict[cID]=mapping[blocks[2]]
print(valuefromdict)
def fetchonefiledata(infilename):
text=open(infilename).readlines()
if os.path.splitext(infilename)[1]==".itp":
return text
if os.path.splitext(infilename)[1]==".pdb":
return text[LINESTOSKIP:]
if __name__=="__main__":
generatedictionary(DICTIONARYFILE)
sortfile()
The result is:
$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
{'C': '3'}
{'C': '2'}
{'C': '1'}
for print(mapping) part, {'O4': '2', 'C19': '3', 'C21': '1'} the value
doesn't keep the 1, 2, 3 order any more.
Thanks for further suggestions.
The relevant files I put it here:
https://docs.google.com/leaf?id=0B93SVRfpVVg3NzkyOGU2ZTUtZTFjNC00ZjE4LThhNmQtOWY1YWFkOWI0NWEw&hl=en_GB
https://docs.google.com/leaf?id=0B93SVRfpVVg3YTEwZjhiOTItN2I2Yi00NTEyLTljODAtYTc2ODI4Njk1YzZl&hl=en_GB
https://docs.google.com/leaf?id=0B93SVRfpVVg3M2Y1MWZiMmEtOTE2Mi00M2VjLTljNjAtYWNlMjhiNzEyODY1&hl=en_GB
>
> #!/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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