CodeEntropy.levels.dihedrals.topology module

Dihedral topology discovery for conformational state analysis.

This module contains the static molecule/residue dihedral discovery logic used by conformational entropy calculations. The methods here identify which dihedrals should be analysed; they do not inspect trajectory frames.

class CodeEntropy.levels.dihedrals.topology.DihedralTopologyDiscovery[source]

Bases: object

Discover molecule-level dihedral definitions for conformational analysis.

class CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology(group_id: int, molecule_id: Any, molecule_order: int, num_residues: int, ua_dihedrals_by_residue: dict[int, list[Any]], residue_dihedrals: list[Any])[source]

Bases: object

Static conformational dihedral topology for one molecule.

Variables:

  • group_id (int) – Molecule group id.

  • molecule_id (Any) – Molecule id.

  • molecule_order (int) – Position of the molecule within its group.

  • num_residues (int) – Number of residues in the molecule.

  • ua_dihedrals_by_residue (dict[int, list[Any]]) – United-atom dihedrals by residue index.

  • residue_dihedrals (list[Any]) – Residue-level dihedrals for the molecule.

group_id: int
molecule_id: Any
molecule_order: int
num_residues: int
residue_dihedrals: list[Any]
ua_dihedrals_by_residue: dict[int, list[Any]]