factorpol.utilities

This module contains useful functions to use with Factor-Pol model

Functions

calc_rmse(calc, ref)

A function to calculate root mean squared error, RMSE, unit is the same as input data

calc_rrms(calc, ref)

A function to calculate relative root mean squared error, RRMS error, unit less

canonical_ranking(rdmol)

A function to calculte canonical ranking for forced symmetry using RDKit

coulomb_scaling(rdmol[, coulomb14scale])

A function to create scaling matrix for scaling the 1-4 interactions in Coulomb interactions

flatten_a_list(nest_list)

A handy funtion to flatten a nested list

pair_equivalent(pattern)

A function to pair related patterns together for use as constraints

retrieve_records(my_session[, dataset, ...])

A function to retrieve data from the input session and create MoleculeESPRecords for use of polarizability or charge fitting.

smirnoff_labels(offmol, off_forcefield)

A function to label OpenFF molecule objecit with SMIRNOFF patternes specified in the input OpenFF ForceField object.

Classes

BondChargeCorrections([data_source])

A dataclass to read/write bond charge correction parameters for generating AM1-BCC-dPol charges

Polarizability([data_source])

A dataclass to read/write polarizability parameters

StorageHandler([port, url, local_path])

This is a handler to interact with data stored in PostgreSQL database.