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Project Description

The nmrstarlib package is a Python library that facilitates reading and writing NMR-STAR formatted files used by the Biological Magnetic Resonance Data Bank (BMRB) for archival of Nuclear Magnetic Resonance (NMR) data.

The nmrstarlib package provides facilities to convert NMR-STAR formatted files into their equivalent JSONized (JavaScript Object Notation, an open-standard format that uses human-readable text to transmit data objects consisting of attribute-value pairs) representation and vice versa.

In addition, the nmrstarlib package provides methods to visualize chemical shift data.

The nmrstarlib package can be used in several ways:

  • As a library for accessing and manipulating data stored in NMR-STAR format files.
  • As a command-line tool to convert between NMR-STAR format and its equivalent JSONized NMR-STAR format and also to visualize chemical shift data.

Installation

The nmrstarlib package runs under Python 3, use pip to install. Starting with Python 3.4 pip is included by default.

Install on Linux, Mac OS X

python3 -m pip install nmrstarlib

Also make sure that dependencies are installed on the system:

python3 -m pip install docopt
python3 -m pip install graphviz

graphviz Python library requires a working installation of Graphviz (download page).

Install on Windows

py -3 -m pip install nmrstarlib

Also make sure that dependencies are installed on the system:

py -3 -m pip install docopt
py -3 -m pip install graphviz

graphviz Python library requires a working installation of Graphviz (download page).

Quickstart

Import nmrstarlib library and create generator function that will yield nmrstarlib.nmrstarlib.StarFile instance(s):

>>> from nmrstarlib import nmrstarlib
>>>
>>> # "path": path_to_file / path_to_dir / path_to_archive / bmrb_id / file_url
>>> starfile_gen = nmrstarlib.read_files(["path"])
>>>
>>> for starfile in in starfile_gen:
...     print(starfile.bmrbid)         # print BMRB id of StarFile
...     print(starfile.source)         # print source of StarFile
...     print(list(starfile.keys()))   # print StarFile saveframe categories
>>>

Note

Read User Guide and The nmrstarlib Tutorial on ReadTheDocs to learn more and see code examples on using nmrstarlib as a library and as a command-line tool.

License

This package is distributed under the MIT license.

Release History

Release History

1.0.4

This version

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1.0.3

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1.0.2

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1.0.1

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1.0.0

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
nmrstarlib-1.0.4.tar.gz (473.9 kB) Copy SHA256 Checksum SHA256 Source Oct 6, 2016

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