CODEWITHSUNDEEP
pythonregex
Macrophage
Macrophage

Reputation: 149

"." wildcard didn't work for me in regex in python?

So I wanted to extract the following amino acid abbreviations from a piece of .pdb format data: ['GLU','PHE',...,'ASN']

ATOM    296  OE2 GLU A  43      18.414  12.323   8.758  1.00 32.23           O  
ATOM    297  N   PHE A  50      18.072  10.668  14.644  1.00 34.68           N  
ATOM    298  CA  PHE A  50      18.038  10.228  16.039  1.00 35.61           C  
ATOM    299  C   PHE A  50      18.501  11.321  17.019  1.00 35.86           C  
ATOM    300  O   PHE A  50      18.018  11.413  18.091  1.00 36.21           O  
ATOM    301  CB  PHE A  50      18.844   8.936  16.226  1.00 35.43           C  
ATOM    302  CG  PHE A  50      18.811   8.386  17.623  1.00 37.33           C  
ATOM    303  CD1 PHE A  50      17.924   7.416  17.982  1.00 36.31           C  
ATOM    304  CD2 PHE A  50      19.659   8.840  18.557  1.00 39.84           C  
ATOM    305  CE1 PHE A  50      17.875   6.922  19.220  1.00 37.80           C  
ATOM    306  CE2 PHE A  50      19.591   8.330  19.833  1.00 40.97           C  
ATOM    307  CZ  PHE A  50      18.709   7.368  20.144  1.00 37.91           C  
ATOM    308  N   ASN A  51      19.462  12.125  16.616  1.00 36.20           N ...

And I used this command in my python script:

residue=re.compile(r"(?<=ATOM...............)+?(?=..............\.)").findall(fpdb)

in hope to extract the target strings based on the format of the file by looking before and after the strings. But I only get an empty list, so I'm confused and need some help badly. Thanks!

Upvotes: 0

Views: 44

Answers (2)

Sunitha
Sunitha

Reputation: 12015

Assuming there are no missing cell values, if you want to extract 3rd column (columns starting from 0) when there are 12 columns,

import re
re.split(r'\s+', fpdb)[3::12]
# ['GLU', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'ASN']

Upvotes: 0

Rakesh
Rakesh

Reputation: 82765

Using str.split()

Ex:

s = """ATOM    296  OE2 GLU A  43      18.414  12.323   8.758  1.00 32.23           O  
ATOM    297  N   PHE A  50      18.072  10.668  14.644  1.00 34.68           N  
ATOM    298  CA  PHE A  50      18.038  10.228  16.039  1.00 35.61           C  
ATOM    299  C   PHE A  50      18.501  11.321  17.019  1.00 35.86           C  
ATOM    300  O   PHE A  50      18.018  11.413  18.091  1.00 36.21           O  
ATOM    301  CB  PHE A  50      18.844   8.936  16.226  1.00 35.43           C  
ATOM    302  CG  PHE A  50      18.811   8.386  17.623  1.00 37.33           C  
ATOM    303  CD1 PHE A  50      17.924   7.416  17.982  1.00 36.31           C  
ATOM    304  CD2 PHE A  50      19.659   8.840  18.557  1.00 39.84           C  
ATOM    305  CE1 PHE A  50      17.875   6.922  19.220  1.00 37.80           C  
ATOM    306  CE2 PHE A  50      19.591   8.330  19.833  1.00 40.97           C  
ATOM    307  CZ  PHE A  50      18.709   7.368  20.144  1.00 37.91           C  
ATOM    308  N   ASN A  51      19.462  12.125  16.616  1.00 36.20           N"""

for i in s.split("\n"):
    print(i.split()[3])

Output:

GLU
PHE
PHE
PHE
PHE
PHE
PHE
PHE
PHE
PHE
PHE
PHE
ASN

Using a list comprehension.

Ex:

data = [i.split()[3] for i in s.split("\n")]
print(data)
#['GLU', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'PHE', 'ASN']

Using Regex

import re
print( re.findall(r"ATOM\s+\d+\s+\w+\s+([A-Z]+)", s) )

Upvotes: 1

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