Analysis of Null Areas

    ANA input.pdb -c config_file.cfg -d trajectory.nc -f output.pdb 

Precise cavity definition. Flexible tracking. Fast performance. Accurate volume calculation. Ugly output.

Installation

https://anadynamics.netlify.com/docs/install_instructions.html

Usage example

https://anadynamics.netlify.com/docs/quickstart.html

Release History

• 1.0.0

  • Initial release.

• 1.0.1

  • Volume output can be redirected to a file.
  • ANA now appends ".pdb" to output PDB files if the user didn't do it already.

• Road to 2.0.0

  • Major refactoring.
  • Switched to C++ 17.
  • New on Static:
    • New output_wall terminal option to set output filename.
  • New on NDD:
    • No need to input displaced PDBs. ANA will read Amber modes or a raw text file with vectors and move the inpud pdb atoms forward and backwards along those vectors.
    • ANA will output either, the volumes of the perturbed cavities, the numerical derivative, or the flexibility coefficient for that cavity.
    • Default scaling_factors are better adjusted to prevent cavity changes from high frequency modes from being overestimated.
  • Deprecated:
    • Cell filtering by facet area.
  • Deprecations for NDD:
    • No wall residues/atoms output.
    • included area is now mandatory.
    • Fixed to high precision mode.
    • No cavity output.
  • Deprecations for MD:
  • Deprecations for Static:
    • Pymol CGO output.

Contact info

@gpbarletta - pbarletta@gmail.com

License

Distributed under the GPL license.