# Glossary
Terms used in the {doc}`quickstart` and API. The diagrams show how scores
and coordinate changes relate; the {doc}`playground` gives a working example.
(glossary-score-function)=
## Score function and score terms
A score function combines weighted contributions from atomic interactions and
molecular geometry. Lower totals are favored during minimization and packing.
Individual terms show which interactions contribute to a change.
```{raw} html
↳
Attraction, short-range repulsion, and electrostatics depend on the relative positions of atoms.
```
`sum_terms=False` returns weighted contributions in `sfxn.all_score_types()`
order. `apply_weights=False` returns unweighted values instead.
See {doc}`score terms ` for individual definitions.
(glossary-posestack)=
## Pose, block, and PoseStack
A **pose** is one molecular system. A **block** is a typed chemical unit, such
as an amino acid, nucleotide, or ligand fragment. A **PoseStack** batches poses
as padded tensors on a single PyTorch device.
```text
PoseStack
pose 0 [ALA]—[PHE]—[GLY]—[SER]
pose 1 [LEU]—[TYR] ··· ··· ← padding, not atoms
```
Use atom and block masks to distinguish real entries from padding. Group
similarly sized poses to limit padding; see {doc}`tensor layouts `.
(glossary-repacking)=
## Torsions, rotamers, and repacking
A **torsion** is a rotation around a bond, described by four atoms. Protein
backbone angles include φ and ψ; side-chain angles are called χ1, χ2, and so on.
A **rotamer** is a candidate side-chain conformation.
**Repacking** chooses conformations for a fixed sequence. It considers how
neighboring choices interact. **Design** also permits residue identities to
change, according to the packer task.
The {doc}`playground` isolates two side-chain angles. The
{doc}`scoring and optimization notebook ` runs a full
repacking calculation with residue-specific conformer samplers.
## Gradients and minimization
A coordinate gradient tells you how the score changes as an atom moves.
Minimization uses these derivatives to improve a conformation continuously.
Repacking searches discrete candidates; minimization can refine their geometry.
**Cartesian minimization** changes atom coordinates. **Kinematic minimization**
changes selected internal coordinates and rigid-body jumps. The allowed moves
come from a coordinate mask or a `MoveMap`, respectively.
(glossary-foldforest)=
## Fold tree, fold forest, and jumps
A **fold tree** is a rooted, acyclic description of how coordinates are built
for one pose. A **fold forest** stores these trees across a batch. A **jump**
defines a rigid-body connection in that coordinate model; it is not a chemical
bond. Polymer and chemical edges describe other kinematic connections.
In this schematic, orange nodes move downstream of the selected edge.
The two poses remain independent.
```{raw} html
A backbone torsion along A1 → A2 moves downstream A2 and A3. Chain B is attached through A1, so this move leaves it fixed.
```
Chemical connectivity and the kinematic tree are distinct. A cyclic molecule
needs a cut in its kinematic representation even though its chemical bond
remains. Choose the tree and allowed moves together; see the
{doc}`fold-forest notebook `.
## MoveMap and constraints
A **MoveMap** selects torsions and jumps for kinematic movement. Creating one
does not enable movement: set its flags or masks explicitly. A
**CartesianMoveMap** selects atom coordinates for Cartesian FastRelax.
A **constraint** adds a score penalty, such as a restraint to a target position.
It affects optimization only when attached to the pose and given a nonzero
score-function weight. A frozen degree of freedom cannot move; a restrained
one may move at a scoring cost.
(glossary-fastrelax)=
## FastRelax
FastRelax alternates repacking with minimization. Early stages soften steric
repulsion so side chains can rearrange; later stages restore its full weight.
The protocol retains the best conformation for each pose under the acceptance
score. Lower repulsion during a stage does not itself mean the structure improved.
Select a stage to see the default repulsion-weight fractions:
```{raw} html
Repack 4.0%→Minimize 5.1%→Next stage
Stage 1: repack, then minimize at the indicated fractions of the full repulsion weight.
```
The default protocol uses Cartesian minimization and repeats the four-stage
schedule twice. See the {doc}`scoring and optimization notebook ` to run
it and compare structures.
## Parameters and prepared chemistry
**ParameterDatabase** holds chemical definitions and scoring parameters.
**PackedBlockTypes** holds the block types and their device-resident setup data;
it does not cache conformation energies.
Preparing a ligand may extend the parameter database. Use the returned
`context.parameter_database` to score that pose. Check termini, protonation,
disulfides, and built atoms when preparing inputs. `no_optH=True` skips polar
hydrogen optimization; it does not freeze those atoms in later optimization.
## Rendered scorer
Rendering builds a scoring module for a particular pose layout. Reuse it while
coordinates change. Render a new scorer after changing block types, atom counts,
connectivity, or batch layout, including after packing.
```{toctree}
:hidden:
playground
```