ndb_adapter 0.1b2

Adapter for http://ndbserver.rutgers.edu/ created for biologists, bioinformatics etc.

Adapter for easy access to NDB resources directly from python (3.*).

Usage

To get summary of structure, type:

>>> from ndb_adapter import NDB
>>> res = NDB.summary('4Z4B')
>>> res.ndb_id
'4Z4B'
>>> res.title
'2-PYRIDYL HOECHST - A NEW GENERATION DNA-BINDING RADIOPROTECTOR'
>>> res.description
"DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')"
>>> res.get_dict()
{'Molecular Description': "DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')", ...}

As you see some properties are available for result. Full list of them is here. Almost on every result of search you can download related files (.pdb, .cif, .xml etc.) to buffer or save on disc.

>>> res.download() #Pdb is default
"HEADER DNA 01-APR-15 4Z4B ..."

from ndb_adapter import DownloadType
>>> res.download(download_type=DownloadType.Cif)
'data_4Z4B\n# \n_entry.id   4Z4B ...'

>>> res.download(save=True) #saves in current directory
>>> res.download(save=True, target_dir='~/Downloads/') #saves in /Downloads/

To be continued…

Requirements

• python 3.*

• requests

• xlrd

Installation

To install, simply:

$ pip install ndb_adapter

Documentation

Documentation is available at https://michsior14.github.io/ndb_adapter/.