Index

A

AbstractPotential (class in gmso.abc.abstract_potential) add_connection() (gmso.Topology method) add_site() (gmso.Topology method) add_tag() (gmso.abc.abstract_potential.AbstractPotential method) Angle (class in gmso) angle_type (gmso.Angle property) angle_type_ (gmso.Angle attribute) angle_type_expressions (gmso.Topology attribute) (gmso.Topology property) angle_types (gmso.ForceField attribute) (gmso.Topology attribute) (gmso.Topology property) angles (gmso.Box property) (gmso.Topology attribute) (gmso.Topology property)

AngleType (class in gmso) apply() (in module gmso.parameterization.parameterize) Atom (class in gmso) atom_class_groups (gmso.ForceField property) atom_type (gmso.Atom property) atom_type_ (gmso.Atom attribute) atom_type_expressions (gmso.Topology attribute) (gmso.Topology property) atom_types (gmso.ForceField attribute) (gmso.Topology attribute) (gmso.Topology property) atomclass (gmso.AtomType property) atomclass_ (gmso.AtomType attribute) atomic_number (gmso.Element attribute) AtomType (class in gmso)

B

Bond (class in gmso) bond_order (gmso.Bond property) bond_order_ (gmso.Bond attribute) bond_orders_ (gmso.Improper attribute) bond_type (gmso.Bond property) bond_type_ (gmso.Bond attribute) bond_type_expressions (gmso.Topology attribute) (gmso.Topology property) bond_types (gmso.ForceField attribute) (gmso.Topology attribute) (gmso.Topology property) bonds (gmso.Angle property) (gmso.Dihedral property) (gmso.Improper property) (gmso.Topology attribute) (gmso.Topology property)

bonds_ (gmso.Angle attribute) (gmso.Dihedral attribute) (gmso.Improper attribute) bonds_orders (gmso.Angle property) (gmso.Dihedral property) (gmso.Improper property) BondType (class in gmso) Box (class in gmso) box (gmso.Topology property)

C

charge (gmso.Atom property) (gmso.AtomType property) (gmso.VirtualSite attribute) (gmso.VirtualSite property) (gmso.VirtualType attribute) (gmso.VirtualType property) charge_ (gmso.Atom attribute) (gmso.AtomType attribute) (gmso.VirtualSite attribute) (gmso.VirtualType attribute) clone() (gmso.Atom method) (gmso.AtomType method) (gmso.VirtualType method) combining_rule (gmso.Topology attribute) (gmso.Topology property) Connection (class in gmso.abc.abstract_connection) connection_members (gmso.abc.abstract_connection.Connection property) connection_members_ (gmso.abc.abstract_connection.Connection attribute) (gmso.Angle attribute) (gmso.Bond attribute) (gmso.Dihedral attribute) (gmso.Improper attribute)

connection_type (gmso.Angle property) (gmso.Bond property) (gmso.Dihedral property) (gmso.Improper property) connection_type_expressions (gmso.Topology attribute) (gmso.Topology property) connection_types (gmso.Topology attribute) (gmso.Topology property) connections (gmso.Topology attribute) (gmso.Topology property) connectivity (gmso.Angle attribute) (gmso.Bond attribute) (gmso.Dihedral attribute) (gmso.Improper attribute) convert_potential_styles() (gmso.Topology method) convert_unit_styles() (gmso.Topology method) create_subtop() (gmso.Topology method)

D

definition (gmso.AtomType property) definition_ (gmso.AtomType attribute) delete_tag() (gmso.abc.abstract_potential.AbstractPotential method) description (gmso.AtomType property) description_ (gmso.AtomType attribute) Dihedral (class in gmso) dihedral_type (gmso.Dihedral property) dihedral_type_ (gmso.Dihedral attribute) dihedral_type_expressions (gmso.Topology attribute) (gmso.Topology property)

dihedral_types (gmso.ForceField attribute) (gmso.Topology attribute) (gmso.Topology property) dihedrals (gmso.Topology attribute) (gmso.Topology property) DihedralType (class in gmso) doi (gmso.AtomType property) (gmso.VirtualType property) doi_ (gmso.AtomType attribute) (gmso.VirtualType attribute)

E

Element (class in gmso) element (gmso.Atom property) element_ (gmso.Atom attribute) equivalent_members() (gmso.Angle method) (gmso.Bond method) (gmso.Dihedral method) (gmso.Improper method)

etree() (gmso.VirtualType method) expression (gmso.abc.abstract_potential.AbstractPotential property)

F

ForceField (class in gmso) from_mbuild() (in module gmso.external) from_mbuild_box() (in module gmso.external)

from_networkx() (in module gmso.external) from_parmed() (in module gmso.external) from_xml() (gmso.ForceField class method)

G

get_connection_identifiers() (gmso.abc.abstract_connection.Connection method) get_electrostatics_scale() (gmso.Topology method) get_forcefield() (gmso.Topology method) get_index() (gmso.Topology method) get_lj_scale() (gmso.Topology method) get_parameters() (gmso.ForceField method) (gmso.VirtualType method) get_potential() (gmso.ForceField method) get_scaling_factors() (gmso.Topology method) get_tag() (gmso.abc.abstract_potential.AbstractPotential method) get_unit_vectors() (gmso.Box method), [1]

get_untyped() (gmso.Topology method) get_vectors() (gmso.Box method), [1] GMSOBase (class in gmso.abc.gmso_base) group (gmso.abc.abstract_site.Site property) group_ (gmso.abc.abstract_site.Site attribute) group_angle_types_by_expression() (gmso.ForceField method) group_atom_types_by_expression() (gmso.ForceField method) group_bond_types_by_expression() (gmso.ForceField method) group_dihedral_types_by_expression() (gmso.ForceField method) group_improper_types_by_expression() (gmso.ForceField method) group_pairpotential_types_by_expression() (gmso.ForceField method) group_virtual_types_by_expression() (gmso.ForceField method)

I

identifier (gmso.AngleType property) (gmso.BondType property) (gmso.DihedralType property) (gmso.ImproperType property) (gmso.PairPotentialType property) (gmso.VirtualType property) identifier_ (gmso.AngleType attribute) (gmso.BondType attribute) (gmso.DihedralType attribute) (gmso.ImproperType attribute) (gmso.PairPotentialType attribute) (gmso.VirtualType attribute) identify_connections() (gmso.Topology method) (in module gmso.utils.connectivity) Improper (class in gmso) improper_type (gmso.Improper property) improper_type_ (gmso.Improper attribute) improper_type_expressions (gmso.Topology attribute) (gmso.Topology property)

improper_types (gmso.Topology attribute) (gmso.Topology property) impropers (gmso.Topology attribute) (gmso.Topology property) ImproperType (class in gmso) independent_variables (gmso.abc.abstract_potential.AbstractPotential property) is_fully_typed() (gmso.Topology method) is_typed() (gmso.Topology method) is_valid_charge() (gmso.Atom class method) is_valid_mass() (gmso.Atom class method) is_valid_position() (gmso.abc.abstract_site.Site class method) isrigid (gmso.abc.abstract_site.Molecule property) isrigid_ (gmso.abc.abstract_site.Molecule attribute) iter_connections_by_site() (gmso.Topology method) iter_sites() (gmso.Topology method) iter_sites_and_virtual_sites() (gmso.Topology method) iter_sites_by_molecule() (gmso.Topology method) iter_sites_by_residue() (gmso.Topology method)

J

json_dict() (gmso.abc.gmso_base.GMSOBase method) (gmso.Box method)

L

label (gmso.abc.abstract_site.Site property) label_ (gmso.abc.abstract_site.Site attribute) lengths (gmso.Box property)

load() (gmso.Topology class method) load_json() (in module gmso.formats) LoadersRegistry (in module gmso.formats.formats_registry)

M

mass (gmso.Atom property) (gmso.AtomType property) (gmso.Element attribute) mass_ (gmso.Atom attribute) (gmso.AtomType attribute) member_classes (gmso.abc.abstract_connection.Connection property) (gmso.AngleType property) (gmso.BondType property) (gmso.DihedralType property) (gmso.ImproperType property) (gmso.VirtualType property) member_classes_ (gmso.AngleType attribute) (gmso.BondType attribute) (gmso.DihedralType attribute) (gmso.ImproperType attribute) (gmso.VirtualType attribute), [1] member_types (gmso.abc.abstract_connection.Connection property) (gmso.AngleType property) (gmso.BondType property) (gmso.DihedralType property) (gmso.ImproperType property) (gmso.PairPotentialType property) (gmso.VirtualType property)

member_types_ (gmso.AngleType attribute) (gmso.BondType attribute) (gmso.DihedralType attribute) (gmso.ImproperType attribute) (gmso.PairPotentialType attribute) (gmso.VirtualType attribute), [1] Molecule (class in gmso.abc.abstract_site) molecule (gmso.abc.abstract_site.Site property) (gmso.VirtualSite property) molecule_ (gmso.abc.abstract_site.Site attribute) molecule_scaling_factors (gmso.Topology property)

N

n_angles (gmso.Topology attribute) (gmso.Topology property) n_bonds (gmso.Topology attribute) (gmso.Topology property) n_connections (gmso.Topology attribute) (gmso.Topology property) n_dihedrals (gmso.Topology attribute) (gmso.Topology property) n_impropers (gmso.Topology attribute) (gmso.Topology property) n_sites (gmso.Topology attribute) (gmso.Topology property) n_virtual_sites (gmso.Topology property) name (gmso.abc.abstract_connection.Connection property) (gmso.abc.abstract_potential.AbstractPotential property) (gmso.abc.abstract_site.Molecule property) (gmso.abc.abstract_site.Residue property) (gmso.abc.abstract_site.Site property) (gmso.Element attribute) (gmso.ForceField attribute) (gmso.Topology property) (gmso.VirtualType attribute) (gmso.VirtualType property)

name_ (gmso.abc.abstract_connection.Connection attribute) (gmso.abc.abstract_potential.AbstractPotential attribute) (gmso.abc.abstract_site.Molecule attribute) (gmso.abc.abstract_site.Residue attribute) (gmso.abc.abstract_site.Site attribute) (gmso.VirtualType attribute) non_element_types (gmso.ForceField property) number (gmso.abc.abstract_site.Molecule property) (gmso.abc.abstract_site.Residue property) number_ (gmso.abc.abstract_site.Molecule attribute) (gmso.abc.abstract_site.Residue attribute)

O

overrides (gmso.AtomType property)

overrides_ (gmso.AtomType attribute)

P

pairpotential_type_expressions (gmso.Topology attribute) (gmso.Topology property) pairpotential_types (gmso.Topology attribute) (gmso.Topology property) PairPotentialType (class in gmso) parent_sites (gmso.VirtualSite attribute) (gmso.VirtualSite property) parent_sites_ (gmso.VirtualSite attribute) parse_molecule() (gmso.abc.abstract_site.Site class method) parse_name() (gmso.abc.abstract_site.Site class method)

parse_residue() (gmso.abc.abstract_site.Site class method) pop_tag() (gmso.abc.abstract_potential.AbstractPotential method) position (gmso.abc.abstract_site.Site property) position() (gmso.VirtualSite method) position_ (gmso.abc.abstract_site.Site attribute) (gmso.VirtualSite attribute) (gmso.VirtualType attribute) positions (gmso.Topology property) potential_expression (gmso.abc.abstract_potential.AbstractPotential property) potential_expression_ (gmso.abc.abstract_potential.AbstractPotential attribute)

R

read_gro() (in module gmso.formats) read_lammpsdata() (in module gmso.formats) read_mol2() (in module gmso.formats) read_xyz() (in module gmso.formats) remove_connection() (gmso.Topology method) remove_pairpotentialtype() (gmso.Topology method) remove_site() (gmso.Topology method) Residue (class in gmso.abc.abstract_site) residue (gmso.abc.abstract_site.Site property)

residue_ (gmso.abc.abstract_site.Site attribute) restraint (gmso.Angle property) (gmso.Atom property) (gmso.Bond property) (gmso.Dihedral property) restraint_ (gmso.Angle attribute) (gmso.Atom attribute) (gmso.Bond attribute) (gmso.Dihedral attribute)

S

save() (gmso.Topology method) SaversRegistry (in module gmso.formats.formats_registry) scaling_factors (gmso.ForceField attribute) (gmso.Topology attribute) (gmso.Topology property) serialize_charge() (gmso.Atom method) (gmso.AtomType method) (gmso.VirtualType method) serialize_expression() (gmso.abc.abstract_potential.AbstractPotential method) serialize_mass() (gmso.Atom method) (gmso.AtomType method) (gmso.Element method)

serialize_position() (gmso.abc.abstract_site.Site method) serialize_restraint() (gmso.Atom method) serialize_tags() (gmso.abc.abstract_potential.AbstractPotential method) set_dependent_value_default() (gmso.Angle class method) (gmso.Dihedral class method) (gmso.Improper class method) set_electrostatics_scale() (gmso.Topology method) set_lj_scale() (gmso.Topology method) set_rigid() (gmso.Topology method) set_scaling_factors() (gmso.Topology method) Site (class in gmso.abc.abstract_site) sites (gmso.Topology property) symbol (gmso.Element attribute)

T

tag_names (gmso.abc.abstract_potential.AbstractPotential property) tag_names_iter (gmso.abc.abstract_potential.AbstractPotential property) tags (gmso.abc.abstract_potential.AbstractPotential property) tags_ (gmso.abc.abstract_potential.AbstractPotential attribute) to_dataframe() (gmso.Topology method) to_gsd_snapshot() (in module gmso.external) to_hoomd_forcefield() (in module gmso.external) to_hoomd_snapshot() (in module gmso.external)

to_mbuild() (in module gmso.external) to_networkx() (in module gmso.external) to_openmm() (in module gmso.external) to_parmed() (in module gmso.external) to_xml() (gmso.ForceField method) Topology (class in gmso) total_charge (gmso.Topology property) typed (gmso.Topology attribute) (gmso.Topology property)

U

unique_site_labels() (gmso.Topology method) unit_system (gmso.Topology property) units (gmso.ForceField attribute) update_angle_types() (gmso.Topology method) update_atom_types() (gmso.Topology method)

update_bond_types() (gmso.Topology method) update_connection_types() (gmso.Topology method) update_dihedral_types() (gmso.Topology method) update_improper_types() (gmso.Topology method) update_topology() (gmso.Topology method)

V

validate() (gmso.abc.gmso_base.GMSOBase class method) validate_charge() (gmso.AtomType class method) (gmso.VirtualType class method) validate_fields() (gmso.abc.abstract_connection.Connection class method) validate_mass() (gmso.AtomType class method) validate_potential_expression() (gmso.abc.abstract_potential.AbstractPotential class method) version (gmso.ForceField attribute) virtual_position (gmso.VirtualType attribute) (gmso.VirtualType property)

virtual_position_ (gmso.VirtualType attribute) virtual_potential (gmso.VirtualType attribute) (gmso.VirtualType property) virtual_potential_ (gmso.VirtualType attribute) virtual_sites (gmso.Topology property) virtual_type (gmso.VirtualSite attribute) (gmso.VirtualSite property) virtual_type_ (gmso.VirtualSite attribute) VirtualSite (class in gmso) VirtualType (class in gmso)

W

write_forcefield() (gmso.Topology method) write_gro() (in module gmso.formats) write_gsd() (in module gmso.formats) write_json() (in module gmso.formats)

write_lammpsdata() (in module gmso.formats) write_mcf() (in module gmso.formats) write_mol2() (in module gmso.formats) write_top() (in module gmso.formats) write_xyz() (in module gmso.formats)

X

xml_from_forcefield_utilities() (gmso.ForceField class method)