Method that wraps the methods create_force_field_from_openmm/read_ff_file and create_force_field_optimizable in order to ease the procedure o

Method that adds a :obj:`ParaMol.Force_field.force_field_term_parameter.Parameter` with key `param_key` to the parameters dictionary.

Method that runs an ASE calculation. Parameters ---------- coords : np.ndarray, shape=(n_atoms,3), dtype=float

Method that gets the Context positions. Returns ---------- positions : np.array Array containing the pos

Method that, given an array of positions (in nanometers), sets the context atomic positions and computes the potential energy. Param

Method that writes coordinates, reference energies and reference forces to a NetCDF 4 (.nc) file. Parameters ----------

Method that calculates the MM energies of the ensemble of configurations contained in the ref_coordinates attribute. Returns

Method that reads coordinates, reference energies and reference forces from a NetCDF 4 (.nc) file. Parameters ----------

Method that is used when a task is not implemented. Parameters ---------- args : any kwargs : any R

Method that sets the given positions in the given RDKit conformer. Parameters ---------- rdkit_conf : :obj:`rdkit.Ch

Method that writes the force field parameters in the standard format used by ParaMol (usually .ff extension). Parameters ---

Method that writes restart pickle. Parameters ---------- restart_settings: dict Dictionary containing gl

Method (top-level) that creates a QM engine for the system. Parameters ---------- qm_engine_name : str N

Method that defines defines the point of contact with the external world. Parameters ---------- parameters_values :

Method that changes directory. Parameters ---------- args : strings Strings to be joined. absolu

Method that goes back to the base directory. Returns ------- cwd : str Current working directory.

Method that calculates the objective function for a given set of parameters. Parameters ---------- parameters_values

Method that reads restart pickle. Parameters ---------- restart_settings: dict Dictionary containing glo

Method that calculates the weights of every configuration of the ensemble or sets them in case manual weighting is used. Notes

Method that checks the data type of the forces, energies and coordinates data structures and converts them to lists. Parameters

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

Method that creates the optimizable force field dictionary that contains all the optimizable FFTerms. The FFTerms are grouped in list

Method that gets a list of the atom symbols. Returns ------- atom_list : list of str List of the atom sy

Method that, given an array of positions (in nanometers), sets the context atomic positions and computes the forces. Parameters

Method that returns a list with the optimizable parameters to be passed to the optimization. Parameters ---------- s

Method that gets the lists containing all optimizable Parameter instances and parameter values. Parameters ----------

Method that creates and returns a RDKit Conformer instance and a RDKit Molecule instance of the ParaMol system passed as an argument.

Method that gets symmetries with the aid of Parmed. User-defined charge symmetries require the passing of the force_field_instance argument.

Method that wraps the methods set_harmonic_bond_force_parameters, set_harmonic_angle_force_parameters, and set_periodic_torsion_force_paramet

Method that computes the kinetic energy. Returns ------- ekin : float Kinetic energy value in kJ/mol.

A wrapper for subprocess.check_call. Parameters ---------- commands : str or list of str Shell commands

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

Method that sets the Context positions. Parameters ---------- positions : np.array Array containing the

Method that checks if the fed directories exists and if they don't exists it creates them. Parameters ---------- dir

Method that created the ParameterSpace object instance. Parameters ---------- settings : dict Dictionary

Method that initiates OpenMM by creating Parameters ---------- integrator_params : dict Keyword argument

Method that applies Jacobi (diagonal) preconditioning to the parameters that will enter in the optimization. Notes -----

Method that runs an ASE calculation. Parameters ---------- coords : np.ndarray, shape=(n_atoms,3), dtype=float

Method that writes the AMBER, GROMACS, CHARMM, and .mol2 files with the current force field parameters of the self._top_file instance.

Method that updates the non-bonded parameters of the OpenMM system. Parameters ---------- force_field_optimizable :

Method that symmetrizes the ParaMol force field so that it respect atom-type symmetries. Parameters ---------- force

Method that updates the term type parameters in the Parmed AMBER topology object. Notes ----- This method should be

Method that writes the OpenMM system stored in the `system` attribute to an XML file. Parameters ---------- file_nam

Method that calculates the widths of the prior distributions or the scalings constants of the parameters according to different recipes.

Method that calculates the value of the energy property. Parameters ---------- esp_data : np.array Array

Method that calculates the MM forces of the ensemble of configurations contained in the ref_coordinates attribute. Returns -

Method that gets the masses of atoms of the system (in amu). Returns ------- masses : list of floats Mas

Method that determines the indices of the atoms which form rotatable (soft) bonds. Notes ----- Rotatable bond

Method that gets the Context velocities. Returns ---------- velocities : np.array Array containing the v

Method that initializes the variables and calls the functions necessary to perform parallel objective function evaluation. Returns

Method that performs a RESP calculation. Notes ----- Only one ParaMol system is supported at once. Paramete

Method that saves the .frcmod AMBER file with the current force field parameters of the self._amber_prmtop instance. Notes -

Method that sets all non bonded parameters to zero, namely sigma, epsilon and charge to zero. This is done for all the particles and exceptio

Method that writes all stored conformations to a .xyz file. Parameters ---------- output_file_name : str

Method that calculates the prior widths and sets the class attribute self.prior_widths. Parameters ---------- method

Method that calculates the scaling constants and sets the class attribute self.scaling_constants. Parameters ----------

Method that creates the ObjectiveFunction instances Parameters ---------- objective_function_settings : dict

Method that creates the Property instances Parameters ---------- properties_settings : dict Properties se

Method that freezes atoms in atom_list of an OpenMM system. Notes ----- This methods sets the mass of the atoms in a

Method that freezes the torsion_to_freeze torsion of an OpenMM system by adding a restraint to it. Parameters ----------

Method that determines the quartets that form rotatable (soft) torsions. Parameters ---------- system: :obj:`ParaMol

Method that sets the Context positions. Parameters ---------- velocities : np.array Array containing the

Method that updates the value of each Parameter object instance. Parameters ---------- optimizable_parameters_values

Method that adds the regularization part of the A and B matrices. Returns ------- self._A, self._B

Method that adds the symmetrie part of the A and B matrices. Returns ------- self._A, self._B

Method that calculates the auxiliary A matrix. Notes ----- This is only necessary for the explicit solution case.

Method that calculates the A matrix. Parameters ---------- system : :obj:`ParaMol.System.system.ParaMolSystem`

Method that calculates the auxiliary B matrix. Notes ----- This is only necessary for the explicit solution case. :m

Method that calculates the B matrix. Parameters ---------- system : :obj:`ParaMol.System.system.ParaMolSystem`

Method that wraps private regularization derivatives methods in order to calculate the derivative of regularization term. Parameters

Method that generates the scaling constant's vector. Parameters ---------- method : str, optional Method

Method that gets the system's total charge as in the ParaMol ForceField of the ParaMolSystem. Parameters ----------

Method that accepts or rejects a configuration generated by a short MD simulation. Parameters ---------- pot_final :

Method that accepts or rejects a configuration generated by a short MD simulation. Parameters ---------- pot_final :

Method that plots the objective function. Parameters ---------- x : list or np.array x points. y

Method that reconstructs the parameters after the LLS. Parameters ---------- final_parameters : np.array or list

Method that writes objective function plot data to a file. Parameters ---------- data: np.array Returns

Method that calculates the inverse distances (1/rij) between the atomic centre j and the electrostatic point i for every every conformation o

Method that calculates the variance covariance of the QM forces, :math:`var(|F_{i,j}^{QM}|)`. Notes ----- This is us

Method that changes to previous directory. Returns ------- cwd : str Current working directory.

Function that performs conformational sampling on a given ParaMol system and calculated the ab initio properties (energies and forces). Note

Generate random velocities for the solute.

Method that gets a list of the atomic numbers of the system. Returns ------- atom_list : list of str Lis

Method that gets the cell vectors. Returns ------- cell : np.array (3,3) array containing the cell vecto

Method that minimizes the system's energy starting from the state stored at the context attribute. Notes ----- More

Methods that sets as optimizable all parameters of the torsions with the same symmetry groups as the ones contained in the listed passed as a

Method that reads multiple files that correspond to the output of a gaussian ESP calculation. Parameters ----------

Method to run the parameter's optimization per se. Parameters ---------- f : callable Reference to the o

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

Method that sets the initial parameters' values as a private attribute of this instance. Parameters ---------- initi

Method that sets the prior widths of the variables as a private attribute of this instance. Parameters ---------- pr

Method that returns the unit vector of the vector. Parameters ---------- v : list of np.array Vector to normalize. Ret

Method that performs WHAM reweighting. Notes ----- For more info see the source: "Systematic Parametrization