An introductory tutorial on how to score biomolecules using Rosetta can be found here. This page is intended to be broadly useful for understanding how Rosetta scores macromolecule conformations.
An energy method is the workhorse of scoring in Rosetta.
EnergyGraph: Stores the inter-residue energies for interacting residue pairs.
EnergyEdge: Each edge stores interactions for an individual pair of residues
EnergyMap: Maps score types to their values
ScoreFunction: The main class responsible for scoring a Pose.
One-body energies: Intra-residue energies. These are stored separately from the EnergyGraph.
Two-body energies: Inter-residue energies evaluated between pairs of residues. These are stored in the EnergyGraph.
Whole structure energies: These energies apply to (you guessed it) the whole structure.
Context dependent: The energy for a residue or pair of residues depends on the conformation of surrounding residues. For example, the strength of a hydrogen bond between two residues depends on the number of neighbors each residue has.
Context independent: The energy for a residue or residue pair does not depend on the surroundings (e.g. the Lennard-Jones energy).
Short range: There is some distance cutoff beyond which this energy is considered to be zero (i.e. the energy is not evaluated between two residues unless they are within this distance cutoff). For example, hydrogen bonds energies are short range.
Long range: There is no distance cutoff; the energy is evaluated for all applicable pairs of residues. They are typically only evaluated between certain pairs of residues (e.g. AtomPairConstraints