/jamber

Wrapping some of AmberTools's programs for Jupyter notebook. Please do not use this yet for your production.

Primary LanguagePythonMIT LicenseMIT

Build Status

Wrapping some of AmberTools's programs for Jupyter notebook. For now, this is only for fun and you should not rely on this unstable API. Hopefully it's still useful.

Install

git clone https://github.com/hainm/jamber
cd jamber
python setup.py install
# If using ambertools
# amber.python setup.py install

Require

  • AmberTools >= 16
  • nglview (optional): For visualization in Jupyter notebook

Example

    from jamber import leap
    command = """
    source leaprc.protein.ff14SB
    seq = sequence {ALA ALA ALA}
    saveamberparm seq seq.prmtop seq.rst7
    """
    leap.run(command)
  • builder
from jamber.builder import build_bdna
build_bdna(seq='AAAAAA')
  • build protein with given secondary structure