User Guide¶
Description¶
The nmrstarlib
package provides a simple Python interface for parsing and
manipulating data stored in NMR-STAR format files used by Biological Magnetic
Resonance Data Bank (BMRB) for archival of Nuclear Magnetic Resonance (NMR)
experimental 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 visa versa.
The nmrstarlib
package also provides facilities to create simulated peak lists for
different types of standard solution and solid-state NMR experiments from chemical
shifts and assignment information deposited in NMR-STAR files.
In addition, the nmrstarlib
package provides facilities to visualize assigned
chemical shift data.
Installation¶
The nmrstarlib
package runs under Python 2.7 and Python 3.4+.
Starting with Python 3.4, pip is included by default. To install
system-wide with pip run the following:
Install on Linux, Mac OS X¶
python3 -m pip install nmrstarlib
Install on Windows¶
py -3 -m pip install nmrstarlib
Install inside virtualenv¶
For an isolated install, you can run the same inside a virtualenv.
$ virtualenv -p /usr/bin/python3 venv # create virtual environment, use python3 interpreter
$ source venv/bin/activate # activate virtual environment
$ python3 -m pip install nmrstarlib # install nmrstarlib as usually
$ deactivate # if you are done working in the virtual environment
Get the source code¶
Code is available on GitHub: https://github.com/MoseleyBioinformaticsLab/nmrstarlib
You can either clone the public repository:
$ https://github.com/MoseleyBioinformaticsLab/nmrstarlib.git
Or, download the tarball and/or zipball:
$ curl -OL https://github.com/MoseleyBioinformaticsLab/nmrstarlib/tarball/master
$ curl -OL https://github.com/MoseleyBioinformaticsLab/nmrstarlib/zipball/master
Once you have a copy of the source, you can embed it in your own Python package, or install it into your system site-packages easily:
$ python3 setup.py install
Dependencies¶
The nmrstarlib
package depends on several Python libraries, it will install all
dependencies automatically, but if you wish to install them manually run the
following commands:
- docopt for creating
nmrstarlib
command-line interface.
To install docopt run the following:
python3 -m pip install docopt # On Linux, Mac OS X py -3 -m pip install docopt # On Windows
- graphviz for visualizing assigned chemical shift values.
To install the graphviz Python library run the following:
python3 -m pip install graphviz # On Linux, Mac OS X py -3 -m pip install graphviz # On WindowsThe only dependency of the graphviz Python library is a working installation of Graphviz (Graphviz download page).
Optional dependencies¶
- numpy for generating noise values from random distribution during peak list simulation.
Basic usage¶
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:
- Convert from NMR-STAR file format into its equivalent JSON file format and vice versa.
- Create standard solution and solid-state NMR simulated peak lists from chemical shift values and assignment information.
- Visualize (organize) assigned chemical shift values.
Note
Read The nmrstarlib Tutorial to learn more and see code examples on using the nmrstarlib
as a library and as a command-line tool.