ParaMol's OpenMM wrapper. Parameters ---------- init_openmm : bool, optional, default=False Whether or not to create the Ope

ParaMol representation of a chemical system. Parameters ---------- name : str Name of the system. n_atoms : int

This class defines method that has, for example, moving between and creating new directories, running subprocesses, etc... Parameters --

ParaMol global settings. Attributes ---------- optimizer : dict Dictionary that contains the optimizer settings. paramet

ParaMol parametrization task.

ParaMol representation of a force field term. Parameters ---------- force_group : str Name of the force group as given by Op

ParaMol implementation of torsion scans. Attributes ---------- qm_energies_list : list Array containing the QM energies of t

ParaMol class that implements methods to symmetrize the ParaMol Force Field so that it respects AMBER atom-types. Parameters ----------

ParaMol representation of the set of mathematical parameters that are used in the optimization. This class aggregates information about the P

ParaMol representation of the objective function. Parameters ---------- restart_settings : dict Dictionary containing restar

ParaMol RESP fitting task.

ParaMol implementation of an ASE wrapper. Parameters ---------- system_name : str Name of the system to which this wrapper i

ParaMol representation of the force property. Parameters ---------- systems : list of :obj:`ParaMol.System.system.ParaMolSystem`

ParaMol HMC task.

ParaMol implementation of the algorithm that automatically identifies, scans and parametrizes soft torsions. Attributes ---------- d

ParaMol task that calculates ab initio properties.

ParaMol adaptive parametrization task. Attributes ---------- parameters_generations : List of list of float Parameters of ev

ParaMol representation of the energy property. Parameters ---------- systems : list of :obj:`ParaMol.System.system.ParaMolSystem`

ParaMol wrapper of the QM engines. Notes ----- Available QM engines are "amber", "dftb+" and "ase". Parameters ----------

ParaMol's RESP engine. Parameters ---------- total_charge : int Total charge of the system include_regulatization : bool

ParaMol representation of the regularization property. Parameters ---------- initial_parameters_values : list or np.array of floats

Verlocity Verlet integrator. Notes ----- This integrator is taken verbatim from Peter Eastman's example appearing in the CustomIntegrator

ParaMol's wrapper for the CPU parallel callback function. Attributes ---------- X : list List containing conformations data.

ParaMol representation of the electrostatic potential (ESP) property. Parameters ---------- systems : list of :obj:`ParaMol.System.s

ParaMol representation of a force field. Parameters ---------- openmm_engine : :obj:`ParaMol.MM_engines.openmm.OpenMMEngine`

ParaMol's wrapper for the GPU parallel callback function. Attributes ---------- X : list List containing conformations data.

Linear Least Square Fitting solution. Parameters ---------- parameter_space : :obj:`ParaMol.Parameter_space.parameter_space.Paramete

ParaMol wrapper of the optimization methods. Notes ----- This class is a wrapper for the currently implemented optimization methods,

ParaMol representation of a force field parameter. Parameters ---------- symmetry_group : str Symmetry group of the force fi

Wrapper around the Context OpenMM class. This is necessary to make an OpenMM context pickalable, i.e., serializable. Notes -----

ParaMol implementation of a AMBER SQM wrapper. Parameters ---------- system_name : str Name of the system to which this wrap

ParaMol class that implements methods to symmetrize the ParaMol Force Field so that it respects CHARMM atom-types. Parameters ----------

ParaMol implementation of a DFTB+ wrapper. Parameters ---------- system_name : str Name of the system to which this wrapper

ParaMol implementation of the gradient descent optimizer. Parameters ---------- max_iter : float Maximum number of iteration

ParaMol class that implements methods to symmetrize the ParaMol Force Field so that it respects GROMACS atom-types. Parameters ---------

ParaMol HMC task.

ParaMol Linear Least Square Fitting task.

ParaMol implementation of the Monte Carlo optimizer. Parameters ---------- n_blocks : int Number of iteration (attempted mov

ParaMol task that plots the objective function.

Defines the __setstate__ and __getstate__ methods necessary to convert an object instance into a Pickle.

ParaMol wrapper of the SciPy optimizers. Notes ------ This class is mainly a wrapper around the minimize SciPy function. For mor

ParaMol implementation of the Simulated Annealing optimizer. Parameters ---------- Parameters ---------- n_iter : float

ParaMol bse class that implements methods to symmetrize the ParaMol Force Field. Parameters ---------- top_file : str Topolo

ParaMol Task base class Parameters ---------- task_name : str Name of the task.