Skip to main content

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

Project description

https://img.shields.io/pypi/status/ndb_adapter.svg https://img.shields.io/pypi/v/ndb_adapter.svg https://img.shields.io/pypi/dm/ndb_adapter.svg https://img.shields.io/pypi/l/ndb_adapter.svg https://img.shields.io/pypi/pyversions/ndb_adapter.svg

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.

Project details


Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page