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ndb_adapter 1.3

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

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

Usage

Adapter offers 4 types of search: summary, advanced, dna and rna.

Summary

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 summary result. Full list of them is here.

Structure Download

Almost on every result of search you can download related files (.pdb, .cif, .xml etc.) to buffer or save.

>>> from ndb_adapter import NDB
>>> res = NDB.summary('4Z4B')
>>> 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 = NDB.advanced_search()
>>> res.download(save=True) # saves n files in current directory
>>> res.download(save=True, target_dir='/home/user/Downloads/')  # saves n files in ~/Downloads/

>>> res.report[0].download(save=True) # saves first structure file in current directory

You can also search and download in one line:

>>> from ndb_adapter import NDB
>>> res = NDB.download('4Z4B')   # like above .pdb is default
"HEADER DNA 01-APR-15 4Z4B ..."
# save and target dir is also available

Requirements

Installation

To install, simply:

$ pip install ndb_adapter

Documentation

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

Licence

Software is distributed under the MIT Licence.

 
File Type Py Version Uploaded on Size
ndb_adapter-1.3.zip (md5) Source 2016-06-14 59KB