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'