Topology

Methods for querying or modifying the topology of a molecule, which consists of all defined atoms, bonds, angles, dihedrals, and impropers, for applicable topology formats (usually NAMD).

Not all molecular file formats will explicitly define these terms. Carefully check if these methods are applicable to your file.

Editing individual terms

addangle	Add an angle between three atoms with given indices.
addbond	Add a bond between two atoms with given indices.
adddihedral	Add a dihedral between four atoms with the given indices.
addimproper	Add an improper dihedral between four atoms with the given indices.
delangle	Delete an angle between atoms with the given indices.
delbond	Delete a bond between atoms with the given indices.
deldihedral	Delete a dihedral angle between atoms with the given indices.
delimproper	Delete an improper dihedral angle between atoms with the given indices.

Per-molecule functions

angles	Get all unique angles within a specified molecule.
bonds	Get all unique bonds within a specified molecule.
dihedrals	Get all unique dihedrals within a specified molecule.
impropers	Get all unique impropers within a specified molecule.
delallangles	Delete all angles in a given molecule
delallbonds	Delete all bonds in a given molecule
delalldihedrals	Delete all dihedrals in a given molecule
delallimpropers	Delete all improper dihedrals in a given molecule

Forcefield parameters

angletypes	Get all angle types defined in the molecule.
bondtypes	Get all bond types defined in the molecule.
dihedraltypes	Get all dihedral types defined in the molecule.
impropertypes	Get all improper dihedral types defined in the molecule.