molsysmt.form.openmm_System package#

Submodules#

molsysmt.form.openmm_System.add module#

molsysmt.form.openmm_System.add.add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.openmm_System.append_structures module#

molsysmt.form.openmm_System.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)[source]#

molsysmt.form.openmm_System.attributes module#

molsysmt.form.openmm_System.copy module#

molsysmt.form.openmm_System.copy.copy(item, skip_digestion=False)[source]#

molsysmt.form.openmm_System.extract module#

molsysmt.form.openmm_System.extract.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)[source]#

molsysmt.form.openmm_System.get_structural_attributes module#

molsysmt.form.openmm_System.get_structural_attributes.get_box_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.openmm_System.get_topological_attributes module#

molsysmt.form.openmm_System.get_topological_attributes.get_atom_index_from_atom(item, indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_System.get_topological_attributes.get_n_atoms_from_system(item, skip_digestion=False)[source]#

molsysmt.form.openmm_System.has_attribute module#

molsysmt.form.openmm_System.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#

molsysmt.form.openmm_System.is_form module#

molsysmt.form.openmm_System.is_form.is_form(item)[source]#

molsysmt.form.openmm_System.iterators module#

class molsysmt.form.openmm_System.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, interval=1, stop=None, chunk=1, structure_indices=None, skip_digestion=False)[source]#

Bases: object

class molsysmt.form.openmm_System.iterators.TopologyIterator(molecular_system)[source]#

Bases: object

molsysmt.form.openmm_System.merge module#

molsysmt.form.openmm_System.merge.merge(items, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.openmm_System.set module#

molsysmt.form.openmm_System.to_openmm_Context module#

molsysmt.form.openmm_System.to_openmm_Context.to_openmm_Context(item, atom_indices='all', coordinates=None, integrator='Langevin', temperature='300 kelvin', friction='1.0/picoseconds', time_step='2 femtoseconds', platform='CUDA', skip_digestion=False)[source]#

molsysmt.form.openmm_System.to_openmm_Simulation module#

molsysmt.form.openmm_System.to_openmm_Simulation.to_openmm_Simulation(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.openmm_System.to_openmm_System module#

molsysmt.form.openmm_System.to_openmm_System.to_openmm_System(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)[source]#

Module contents#