Python library for parsing data from NMR-STAR format files
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.
Links
nmrstarlib @ GitHub
nmrstarlib @ PyPI
Documentation @ ReadTheDocs
Installation
The nmrstarlib package runs under Python 2.7 and Python 3.4+, use pip to install. Starting with Python 3.4 pip is included by default.
Install on Linux, Mac OS X
python3 -m pip install nmrstarlibAlso make sure that dependencies are installed on the system:
python3 -m pip install docopt
python3 -m pip install graphvizgraphviz Python library requires a working installation of Graphviz (download page).
Install on Windows
py -3 -m pip install nmrstarlibAlso make sure that dependencies are installed on the system:
py -3 -m pip install docopt
py -3 -m pip install graphvizgraphviz 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 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
>>>License
This package is distributed under the MIT license.
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