interfacea is a Python library written to facilitate the analysis of interfaces of a wide range of biomolecular complexes. The feature list includes:

• Fast and flexible graph-based search of functional groups.
• Identification of several types of atomic interactions (e.g. ionic, hydrogen bonds).
• Rebuilding missing (heavy) atoms and in silico mutagenesis.
• Calculation and decomposition of energetics using OpenMM.
• ...

git clone https://github.com/joaorodrigues/interfacea.git interfacea
cd interfacea
conda env create -f requirements.yml  # create environment with dependencies
python setup.py build && python setup.py install  # install interfacea
conda activate interfacea-install
# Ta-Daa!

1. Loading a molecule and performing energy minimization.

   import interfacea as ia
   
   mol = ia.read('tests/data/mini.pdb')
   mol.prepare(minimize=True)
   
   print(mol.potential_energy)

2. Find ionic interactions in the structure

   import interfacea as ia
   
   mol = ia.read('tests/data/mini.pdb')
   
   analyzer = ia.InteractionAnalyzer(mol)
   analyzer.get_ionic()
   
   print(analyzer.itable._table)  # will obviously change in the future.

3. Find specific functional groups in the structure

   import interfacea as ia
   import interfacea.functional_groups as fgs
   
   mol = ia.read('tests/data/mini.pdb')
   
   # Find phosphate groups in molecule
   
   phosphate = fgs.Phosphate()
   matches = phosphate.search(mol)
   for res, groups in matches.items:
       n_groups = len(groups)
       if n_groups:
           print('Residue {}{} contains {} phosphate(s)'.format(res.name, res.id, n_groups))

interfacea runs on Python 3.6+ only and requires the following packages:

• networkx (https://networkx.github.io)
• pandas (https://http://pandas.pydata.org)
• PDBFixer (https://github.com/pandegroup/pdbfixer)
• OpenMM (http://openmm.org)

Dependencies should be installed via conda using conda env create -f requirements.yml or by following instructions on their websites.