biometal is a suite of tools for dealing with metalloproteins.
>>> import atomium >>> import biometal >>> model = atomium.fetch('1ton').model >>> zinc = model.atom(element='ZN') >>> biometal.hydrophobic_contrast(model, *zinc.location, 4) 435.9691187500001
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
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
biometal relies heavily on atomium - pip will install this automatically when it installs biometal.
biometal analyses metalloproteins.
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.
17 April 2018
- Started template generation.
- Implemented solvation measuring using solvation parameters.
- Implemented solvation measuring using partial charge.
- Implemented hydrophobic contrast function.