[Biopython] running naccess
Bala subramanian
bala.biophysics at gmail.com
Wed Jul 21 14:51:07 UTC 2010
Friends,
I am trying to run naccess as follows.
from Bio.PDB.PDBParser import PDBParser
par = PDBParser()
structure = par.get_structure('test','12_25.pdb')
import Bio.PDB.NACCESS as nac
data=nac.run_naccess(structure[0],'12_25.pdb')
It seems that there is an issue with tmp dir creation. I could nt run
naccess even if i define *temp_path='.'* with run_naccess function. Kindly
write me how to resolve the issue.
*I get the following error:*
IOError Traceback (most recent call last)
/tmp/tmpqQLhRl/<ipython console> in <module>()
/apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
56 # get the output, then delete the temp directory
57 rsa_file = tmp_pdb_file[:-4] + '.rsa'
---> 58 rf = open(rsa_file)
59 rsa_data = rf.readlines()
60 rf.close()
IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'
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