Python 3.11 compatibility

• Add pyproject.toml
• Handle networkx API changes to graph.node -> graph.nodes
• Handle ParmEd API change to take None instead of empty AmberParm()

Dabble

Dabble is a tool for building membrane protein systems. The ultimate goal of the project is to create an easy to use, one stop tool for system construction and parameterization.

Some uses for Dabble:

• Prepare membrane protein systems by inserting them into a membrane
• Prepare solvated proteins by adding water
• Add ions to neutralize and/or to desired concentration
• Parameterize with CHARMM or AMBER parameter sets
• Outputs files for simulation with AMBER or CHARMM
• Automatic detection of post-translational modifications
• Modified amino acids made easy
• Ligands made easy! No more messing with atom names.

Dabble can use CHARMM or AMBER parameters, and generate input files for simulating in NAMD, CHARMM, Anton, or Desmond. While Dabble can be run from the command-line, it also provides a powerful API for building and parameterizing systems.

Dabble's full documentation is available here