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Python library for dealing with metalloprotein structures
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README.rst

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biometal

biometal is a suite of tools for dealing with metalloproteins.

Example

>>> import atomium
>>> import biometal
>>> model = atomium.fetch('1ton').model
>>> zinc = model.atom(element='ZN')
>>> biometal.hydrophobic_contrast(model, *zinc.location, 4)
435.9691187500001

Installing

pip

biometal can be installed using pip:

$ pip3 install biometal

biometal is written for Python 3, and does not support Python 2. It currently requires Python 3.5 and above.

If you get permission errors, try using sudo:

$ sudo pip3 install biometal

Development

The repository for biometal, containing the most recent iteration, can be found here. To clone the biometal repository directly from there, use:

$ git clone git://github.com/samirelanduk/biometal.git

Requirements

biometal relies heavily on atomium - pip will install this automatically when it installs biometal.

Overview

biometal analyses metalloproteins.

Hydrophobic Contrast

biometal can implement the hydrophobic contrast function as implemented in (1990) Where metal ions bind in proteins:

>>> import atomium
>>> import biometal
>>> model = atomium.fetch('1ton').model
>>> zinc = model.atom(element='ZN')
>>> biometal.hydrophobic_contrast(model, *zinc.location, 4)
435.9691187500001

This uses atomic solvation parameters to determine hydrophobicity. To use the square of partial charge instead, use the pc=True argument.

Changelog

Release 0.1.0

17 April 2018

  • Started template generation.
  • Implemented solvation measuring using solvation parameters.
  • Implemented solvation measuring using partial charge.
  • Implemented hydrophobic contrast function.
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