Geometry Restraints

Geometry restraints maintain chemically reasonable geometry during refinement.

Overview

The Restraints class handles:

Bond length restraints
Bond angle restraints
Torsion angle restraints
Planarity restraints

Restraint Setup

Restraints are automatically generated from the monomer library:

from torchref.restraints import Restraints

# Automatic setup from model
restraints = Restraints(model, cif_file=None, verbose=1)

# Or with custom CIF file for ligands
restraints = Restraints(model, cif_file="ligand.cif", verbose=1)

Restraint Storage

Restraints are stored in a nested dictionary structure. We store the indices needed to access the atoms involved, along with ideal values and sigma values.

restraints.restraints = {
    'bond': {
        'intra': {
            'indices': Tensor of shape (N_bonds, 2),
            'ideal_values': Tensor of shape (N_bonds,),
            'weights': Tensor of shape (N_bonds,),
        },
        'inter': { ... },
    },
    'angle': {
        'intra': { ... },
        'inter': { ... },
    },
    'torsion': { ... },
    'planarity': { ... },
}

Restraint Types

Bond Restraints

Penalize deviations from ideal bond lengths:

\[E_{bond} = \sum_i w_i \left( d_i - d_i^{ideal} \right)^2\]

where \(d_i\) is the observed distance and \(d_i^{ideal}\) is the target.

Angle Restraints

Penalize deviations from ideal bond angles:

\[E_{angle} = \sum_i w_i \left( \theta_i - \theta_i^{ideal} \right)^2\]

Torsion Restraints

Periodic restraints for dihedral angles.

Planarity Restraints

Restrain groups of atoms to lie in a plane (aromatic rings, peptide bonds).

Accessing Restraint Statistics

# RMSD values
bond_rmsd = restraints.get_bond_rmsd()
angle_rmsd = restraints.get_angle_rmsd()

# Number of restraints
n_bonds = len(restraints.bond_restraints)
n_angles = len(restraints.angle_restraints)