Method that applies charge correction to the system. Parameters ---------- system : :obj:`ParaMol.System.system.Para

Method that generates the prior_widths vector. Parameters ---------- method : str, optional Method used

Method that creates an instance of a chosen optimizer. Parameters ---------- settings : dict Dictionary

Method that gets the constraints to be passed into the SciPy optimizer. Parameters ---------- scipy_method : str

Method that computes the RMSD between the old and new set of parameters. Parameters ---------- old_params: list

Method that computes the RMSD between the old and new set of parameters. Parameters ---------- old_params: list

Method that computes the RMSD between the old and new set of parameters. Parameters ---------- old_params: list

Method that accepts or rejects a configuration generated into the QM Markov chain. Parameters ---------- pot_final_q

Method that accepts or rejects a configuration generated into the QM Markov chain. Parameters ---------- pot_final_q

Method that computes the value of the hyperbolic regularization. Parameters ---------- current_parameters : list of

Method that computes the value of the L1 regularization. Parameters ---------- current_parameters : list of floats

Method that computes the value of the L2 regularization. Parameters ---------- current_parameters : list of floats

Method that asserts if the parametrization asked by the user contains the necessary data (coordinates, forces, energies, esp). Param

Method that asserts if the parametrization asked by the user contains the necessary data (coordinates, forces, energies, esp). Param

Method that wraps the functions used to perform the optimization of the parameters. Parameters ---------- settings :

Method that prepares the working directory. Returns ------- None

Method that prepares the working directory. Returns ------- None

Method that initializes the QM engine. qm_engine_name : str Name of the QM engine. Available QM engines are "amb

Method that calculates the derivative of the hyperbolic regularization. Parameters ---------- at_idx : int

Method that calculates the derivative of the L2 regularization. Parameters ---------- at_idx : int Atom

Method that is a parallel version of the ab initio properties calculator. Parameters ---------- system : :obj:`ParaM

Method that performs parametrization. Parameters ---------- settings : dict Dictionary containing global

Method that performs parametrization. Parameters ---------- settings : dict Dictionary containing global

Method that is a a serial version of the ab initio properties calculator. Parameters ---------- system : :obj:`ParaM

Method that sets the force groups of all forces present in the system accordingly to the mapping defined in the forces_groups_dict dictionary

Method that writes the geometry in gen format. Parameters ---------- coords: list or np.array (n_atoms,3

Method that writes the input file necessary to run single-point with forces calculation. Notes ----- It only needs t

Method that adds the torsional terms with `periodicities` to the OpenMM system 'PeriodicTorsionForce' force group. Parameters

Method that appends data to the ParaMol System instance (self). Notes ----- Appends conformations and/or QM energies

Method that returns the angle in radians between vectors 'v1' and 'v2'. Parameters ---------- v1 : list of np.array Vector 1

Method that returns the dihedral angle formed by 4 points using the praxeolitic formula. Parameters ---------- p0 : list of np.array

Method that calculates the distance between two points. Parameters ---------- p0 : list of np.array Point 0 coordinates.

Method that calculates the inverse covariance of the QM forces, i.e., :math:`<F^{QM} * F^{QM}>^{-1}`, where :math:`*` means tensorial multipl

Method that performs the necessary steps to calculate the objective function. Notes ----- This is a shared function

Method that calculates the variance of the QM energies, i.e., :math:`var(E_{QM})=<E^2_{QM}>-<E_{QM}>^2`. Notes ------

Method that checks if the fed files exist. Parameters ---------- files : str or list of str List or str

Method that creates the force field dictionary that contains all the FFTerms of the force field as given by OpenMM. The FFTerms are g

Method that creates the part of the force field regarding OpenMM's force 'HarmonicAngleForce'. Parameters ----------

Method that creates the part of the force field regarding OpenMM's force 'HarmonicBondForce'. Parameters ----------

Method that creates the part of the force field regarding OpenMM's force 'NonbondedForce'. Parameters ---------- opt

Method that creates the Optimizer instance. Parameters ---------- method: `str` Optimizer method.

Method that creates the part of the force field regarding OpenMM's force 'PeriodicTorsionForce'. Parameters ----------

Method that removes configurations for which the energy reference (QM energy) is greater than a given threshold with respect to the l

Method that fits bonded parameters using LLS. Notes ----- Only one ParaMol system is supported at once. Par

Method that explicitly solves RESP equations Parameters ---------- system : :obj:`ParaMol.System.system.ParaMolSyste

Method that reads the output of a gaussian ESP calculation. Notes ----- Energy stored will be the last occurrence of

Method that gets the user-defined charge symmetries . Parameters ---------- force_field_instance : :obj:`ParaMol.For

Method that calculates MM electrostatic potential of the ensemble of configurations contained in the ref_coordinates attribute. Note

Method that gets the number of atoms of the system. Returns ------- n_atoms : n_int Number of atoms of t

Method that is the constructor for the Pool of workers. It Contains a global dictionary with variables shared between threads.

Methods that sets as optimizable all parameters of the torsions contained in the listed passed as an argument. Parameters --

Proposes the next sampling point by optimizing the acquisition function. Args: acquisition: Acquisition function.

Method that reads the force field parameters in the standard format used by ParaMol (usually .ff extension) and creates its ParaMol represent

Method that removes all created directories. Returns ------- created_dirs: list It should be an empty li

Method that performs 1D or 2D torsional scans. Only a scan at a time. Notes ----- Only one ParaMol system is support

Method that calculates ab initio energies and forces and optionally also classical energies and forces. Parameters ---------

Method that performs 1-dimensional torsional scans. Parameters ---------- interface: :obj:`ParaMol.Utils.interface.P

Method that performs 2-dimensional torsional scans. Parameters ---------- interface: :obj:`ParaMol.Utils.interface.P

Method that updates in the OpenMM system the parameters of the terms belonging to the force group 'HarmonicAngleForce'. Parameters

Method that updates in the OpenMM system the parameters of the terms belonging to the force group 'HarmonicBondForce'. Parameters

Method that sets the `charges_initial` attribute by constructing a list with the current ParaMol Force Field charges. Parameters

Method that makes atoms not to be optimized. Notes ----- This is only necessary for the explicit solution case.

Method that updates in the OpenMM system the parameters of the terms belonging to the force group 'PeriodicTorsionForce'. Parameters

Method that sets symmetry constraints. Notes ----- This is only necessary for the explicit solution case. P

Method that writes human-readable scan data to .dat file. Parameters ---------- scan_angles: list List c

Construct a velocity Verlet integrator. Parameters ---------- timestep : np.unit.Quantity compatible with femtoseconds, defau