molsysmt.form.openmm_Context package#

Submodules#

molsysmt.form.openmm_Context.add module#

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

molsysmt.form.openmm_Context.append_structures module#

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

molsysmt.form.openmm_Context.attributes module#

molsysmt.form.openmm_Context.copy module#

molsysmt.form.openmm_Context.copy.copy(item)[source]#

molsysmt.form.openmm_Context.extract module#

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

molsysmt.form.openmm_Context.get_structural_attributes module#

molsysmt.form.openmm_Context.get_structural_attributes.get_box_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_coordinates_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_coordinates_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_n_structures_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_structure_id_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_time_from_system(item, structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_velocities_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)[source]#
molsysmt.form.openmm_Context.get_structural_attributes.get_velocities_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.openmm_Context.get_topological_attributes module#

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

molsysmt.form.openmm_Context.has_attribute module#

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

molsysmt.form.openmm_Context.is_form module#

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

molsysmt.form.openmm_Context.iterators module#

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

Bases: StructuresIterator

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

Bases: object

molsysmt.form.openmm_Context.merge module#

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

molsysmt.form.openmm_Context.set module#

molsysmt.form.openmm_Context.set.set_coordinates_to_atom(item, indices='all', value=None, skip_digestion=False)[source]#
molsysmt.form.openmm_Context.set.set_coordinates_to_system(item, value=None, skip_digestion=False)[source]#

molsysmt.form.openmm_Context.to_molsysmt_Structures module#

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

molsysmt.form.openmm_Context.to_openmm_Context module#

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

molsysmt.form.openmm_Context.to_openmm_System module#

molsysmt.form.openmm_Context.to_openmm_System.to_openmm_System(item, atom_indices='all', skip_digestion=False)[source]#

Module contents#