Introduction

Reproducing molecular ESP from partial charges and more…

This library has been created to aid research in the area of partial charge assignment and molecular electrostatic potential (ESP) fields.

Highlights

The following is a non-exhaustive list of the capabilities of this library alongside the relevant modules:

  • Extracting charges from Gaussian output files (gaussian_format module) and resp input/output files (respin_charges_format module).
  • Parsing and writing Gaussian “cube” files (cube_format module). The extracted values and the associated Mesh object (collection of points in space) are contained in a Field object, an instance of a class central to this library.
  • Parsing ESP field information from the file format generated by Gaussian and saving it to a resp-compatible format (esp_util module). This is a convenient way of obtaining popular fitting meshes, such as MK and CHelpG.
  • Reproducing ESP field at points of a mesh from point charges on atoms and calculating e.g. the difference from or RMS error with respect to the another ESP field (calc_fields module).
  • Creating single-molecule, single-structure input files for the resp program (respin_format module). For common types of fitting, such as two-stage RESP or fitting with equivalencing, running the resp program is conveniently abstracted away (resp_wrapper module). It is also easy to implement customized variations of the fitting (respin_generation module).
  • “A posteriori” averaging of charges according to provided chemical equivalence relations (charge_util module).