molsysmt.molecular_mechanics package#

Submodules#

molsysmt.molecular_mechanics.forcefields module#

molsysmt.molecular_mechanics.get_engine_forcefield module#

molsysmt.molecular_mechanics.get_engine_forcefield.get_engine_forcefield(forcefield, implicit_solvent=None, water_model=None, engine='OpenMM', skip_digestion=False)[source]#

molsysmt.molecular_mechanics.get_forces module#

molsysmt.molecular_mechanics.get_forces.get_forces(molecular_system, element='atom', selection='all', magnitude=False, engine='OpenMM', syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.molecular_mechanics.get_non_bonded_potential_energy module#

Potential Energy#

Methods related with the potential energy of the system. From energy minimization to potential energy contribution of specific set of atoms or interactions.

molsysmt.molecular_mechanics.get_non_bonded_potential_energy.get_non_bonded_potential_energy(molecular_system, selection='all', selection_2=None, platform='CPU', engine='OpenMM', syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.molecular_mechanics.get_num_degrees_of_freedom module#

molsysmt.molecular_mechanics.get_num_degrees_of_freedom.get_degrees_of_freedom(item)[source]#

molsysmt.molecular_mechanics.get_potential_energy module#

Potential Energy#

Methods related with the potential energy of the system. From energy minimization to potential energy contribution of specific set of atoms or interactions.

molsysmt.molecular_mechanics.get_potential_energy.get_potential_energy(molecular_system, selection='all', decomposition=False, platform='CPU', engine='OpenMM', syntax='MolSysMT', skip_digestion=False)[source]#

molsysmt.molecular_mechanics.potential_energy_minimization module#

molsysmt.molecular_mechanics.potential_energy_minimization.potential_energy_minimization(molecular_system, method='L-BFGS', platform='CPU', engine='OpenMM', to_form=None, in_place=False, verbose=False)[source]#

To be written soon…

potential_energy_minimization(molecular_system, …)

A new structure is returned with the molecular model relaxed to the nearest potential energy local minimum.

Parameters:

  • item (molecular model) – Molecular model in any form to be operated by the method.

  • method (str (default "AMBER99SB-ILDN")) – Energy minimization method.

  • method – Forcefield to model the inter-atomic interactions.

  • selection (str, int, list, tuple or numpy array (default None)) – Region to be minimized defined as a selection sentence or atoms indices list. By default None means all atoms and there by the whole molecular model is minized.

  • syntax (str (default "mdtraj")) – Name of the selection syntax used: “mdtraj” or “amber”.

  • engine (str (default "openmm"))

Returns:

item – The result is a new molecular model with coordinates or positions relaxed to the nearest local minimum of the potential energy.

Return type:

molecular model

Examples

Remove chains 0 and 1 from the pdb: 1B3T. >>> import molsysmt as msm >>> system = msm.load(‘pdb:1B3T’) Check the number of chains >>> minimized_system = m3t.molecular_mechanics.potential_energy_minimization(system)

Module contents#