getpdb | index /home/orient/pydpi/src/pydpi/protein/getpdb.py

`Created on Sat Jul 13 11:18:26 2013
This module is used for downloading the PDB file from RCSB PDB web and
extract its amino acid sequence.
This is written by Dongsheng Cao
@author: Dongsheng Cao`

Modules

``

ftplib | gzip | os |

Functions

``

GetPDB(pdbidlist=[])
  `Download the PDB file from PDB FTP server by providing a list of pdb id.`

GetSeqFromPDB(pdbfile='')
  `Get the amino acids sequences from pdb file.`

pdbDownload(file_list, hostname='ftp.wwpdb.org', directory='/pub/pdb/data/structures/all/pdb/', prefix='pdb', suffix='.ent.gz')
  `Download all pdb files in file_list and unzip them.`

pdbSeq(pdb, use_atoms=False)
  `Parse the SEQRES entries in a pdb file. If this fails, use the ATOM
  entries. Return dictionary of sequences keyed to chain and type of
  sequence used.`

unZip(some_file, some_output)
  `Unzip some_file using the gzip library and write to some_output.`

Data
`` |  | DIRECTORY = '/pub/pdb/data/structures/all/pdb/' HOSTNAME = 'ftp.wwpdb.org' PREFIX = 'pdb' SUFFIX = '.ent.gz'