molsysmt.form.molsysmt_UniversalJSON package#

Submodules#

molsysmt.form.molsysmt_UniversalJSON.append_structures module#

molsysmt.form.molsysmt_UniversalJSON.append_structures.append_structures(item, items, skip_digestion=False)[source]#: Append structures from other UniversalJSON items.

molsysmt.form.molsysmt_UniversalJSON.attributes module#

molsysmt.form.molsysmt_UniversalJSON.copy module#

molsysmt.form.molsysmt_UniversalJSON.copy.copy(item, skip_digestion=False)[source]#: Deep copy a UniversalJSON object.

molsysmt.form.molsysmt_UniversalJSON.extract module#

molsysmt.form.molsysmt_UniversalJSON.extract.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)[source]#: Extract a subset of atoms/structures from a UniversalJSON.

molsysmt.form.molsysmt_UniversalJSON.get module#

molsysmt.form.molsysmt_UniversalJSON.get.get_atom_id_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_atom_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_atom_name_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_bond_index_from_bond(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_chain_id_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_coordinates_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_entity_id_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_formal_charge_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_group_id_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_group_name_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_n_atoms_from_system(item, skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_n_bonds_from_system(item, skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_n_structures_from_system(item, skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.get.get_time_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.molsysmt_UniversalJSON.has_attribute module#

molsysmt.form.molsysmt_UniversalJSON.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#: Attribute availability for UniversalJSON objects.

molsysmt.form.molsysmt_UniversalJSON.is_form module#

molsysmt.form.molsysmt_UniversalJSON.is_form.is_form(item)[source]#: Check whether item is a molsysmt.native.universal_json.UniversalJSON instance.

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_MolSys module#

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_MolSys.to_molsysmt_MolSys(item, skip_digestion=False)[source]#: Convert a UniversalJSON object into a native MolSys.

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_UniversalJSON module#

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_UniversalJSON.to_molsysmt_UniversalJSON(item, skip_digestion=False)[source]#: Return a deep-copied UniversalJSON (identity conversion).

Module contents#

molsysmt.form.molsysmt_UniversalJSON.append_structures(item, items, skip_digestion=False)[source]#: Append structures from other UniversalJSON items.

molsysmt.form.molsysmt_UniversalJSON.copy(item, skip_digestion=False)[source]#: Deep copy a UniversalJSON object.

molsysmt.form.molsysmt_UniversalJSON.extract(item, atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)[source]#: Extract a subset of atoms/structures from a UniversalJSON.

molsysmt.form.molsysmt_UniversalJSON.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#: Attribute availability for UniversalJSON objects.

molsysmt.form.molsysmt_UniversalJSON.is_form(item)[source]#: Check whether item is a molsysmt.native.universal_json.UniversalJSON instance.

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_MolSys(item, skip_digestion=False)[source]#: Convert a UniversalJSON object into a native MolSys.

molsysmt.form.molsysmt_UniversalJSON.to_molsysmt_UniversalJSON(item, skip_digestion=False)[source]#: Return a deep-copied UniversalJSON (identity conversion).