Defines the print statement to obtain the string representation of a parameter. Returns -------

Method that removes unit from the cell array. Returns ------- cell : np.array(3,3) Array with cell vecto

Method that adds a system to the property. Parameters ---------- system : :obj:`ParaMol.System.system.ParaMolSystem`

Method that adds a system to the property. Parameters ---------- system : :obj:`ParaMol.System.system.ParaMolSystem`

Method that computes the forces term of the objective function. Notes ----- This method should be modified by the us

Method that wraps private regularization methods in order to calculate the regularization term of the objective function. Parameters

Method that calculates the value of the energy property. Notes ----- This method should be modified by the user if a

Method that calculates the variance of the electrostatic potential. Notes ------ The variance will be stored in the

Method that calculates statistics of energies. Parameters ---------- emm : list (n_structures) 1D list c

Computes the EI at points X based on existing samples X_sample and Y_sample using a Gaussian process surrogate model. Args:

Method that may be used as a callback function for the parallel computation of the objective function using CPUs. Parameters

Method that may be used as a callback function for the parallel computation of the objective function using GPUs. Parameters

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

Method that calculates statistics of forces. Parameters ---------- fmm : list (n_structures,n_atoms,3) 3

Method that determines the indices of the hydrogen atoms belonging to methyl or methylene groups. Parameters ----------

Method that retrieves the objective function evaluation counter. Returns ------- int Number of times tha

Parameters ---------- system: :obj:`ParaMol.System.system.ParaMolSystem` ParaMol system instance. torsio

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

Methods that sets a parameter as optimizable if it belongs to a force field term for which at least one of the atoms's indices is greather th

Method that can be used as a callback function for the parallel computation of QM forces and energies. Parameters ---------- conform

Method that resets the objective function evaluation counter. Returns ------- int Number of times that t

Method that perform a single-point calculation with forces. Parameters ---------- coords : np.ndarray, shape=(n_atom

Method that runs a calculation using AMBER's quantum chemisty package sqm. Parameters ---------- coords : list or np

Method that runs a SciPy optimization. Parameters ---------- f: callable Reference to the objective func

Method that performs optimization using the simulated annealing method. Notes ----- Source: #TODO. include s

Method that performs optimization using the Monte Carlo method. Notes ----- Source: 'Developing accurate mol

Method that performs optimization using the gradient descent method. Notes ----- When the number of conformations be

Run the parallel callback function. :return (tuple): fmm_data, emm_data

Method that runs a HMC sampler. Parameters ---------- settings : dict Dictionary containing global ParaM

Method that runs a HMC sampler. Parameters ---------- settings : dict Dictionary containing global ParaM

Method that performs self-consistent parametrization until convergence or maximum number of iterations is achieved. Parameters

Method that performs the standard ParaMol parametrization. Parameters ---------- settings : dict Diction

This method can be used to generate plots of the objective function. Parameters ---------- settings : dict

Method that can be used to perform automatic parametrization of the rotatable (soft) torsions using 1-D scans. "SIMULTANEOUS" is pref

Method that runs a HMC sampler. Parameters ---------- settings : dict Dictionary containing global ParaM

Method that runs a HMC sampler. Parameters ---------- settings : dict Dictionary containing global ParaM

Method that saves the CHARMM parameter file with the current force field parameters of the self._charmm_prm instance Notes -

Method that for the force field term with index `idx` of the force `force_key` set the parameter with name `param_key` to the optimization st

Method that modifies the ForceField of a ParaMol System so that the values of the force constants of torsions for which the inner ato

Test add_torsion_terms.

Test get_atom_list.

Test get_atomic_numbers

Test get_cell.

Test the calculation of MM forces.

Test the calculation of MM energies.

Test the function that calculates the magnitudes of the parameters.

Test the function used to convert the type of the arrays.

Tests the initialization of the OpenMMWrapper by creating systems from AMBER topology format.

Tests the initialization of the OpenMMWrapper by creating systems from XML topology format.

Test the creation of the ParaMol force field.

Test the creation of the QM engines.

Test get rotatable torsions.

Test the filtering function.

Test the function used to get energies of an ensemble of structures.

Test the function used to get forces of an ensemble of structures.

Test the function that obtains the optimizable parameters.

Test get_rdkit_mol_conf

Test get rotatable bonds method.

Test get rotatable torsions.

Test the jacobi preconditioning function.

Test the calculation of the objective function and creation of properties.

Test RESP Task. Fitting point charges to electrostatic potential Charges from ESP fit, RMS= 0.00123 RRMS= 0.10456:

Test the update systems function.