TemplateMatchEnergy

Definition

The template match energy measures the structural deviation from a reference template. It supports two modes: RMSD mode (default, distogram_separation=False):

E_{\mathrm{RMSD}} = \mathrm{RMSD}(\mathbf{X}_G, \mathbf{X}_{\mathrm{template}})

Distogram mode (distogram_separation=True):

E_{\mathrm{distogram}} = \frac{1}{N_{\mathrm{pairs}}} \sum_{\alpha,\beta \in G} \left| d_{\alpha\beta} - d_{\alpha\beta}^{\mathrm{template}} \right|

$\mathbf{X}_G$ are the atom positions of the selected residues after optimal superposition
$\mathbf{X}_{\mathrm{template}}$ are the template atom positions
$d_{\alpha\beta}$ and $d_{\alpha\beta}^{\mathrm{template}}$ are pairwise distances in the structure and template, respectively

Parameters

Oracle

required

The oracle to use for the energy term.

AtomArray

required

An array of atoms that specify the desired positions of the structure.

list[Residue]

required

Which residues in the structure to compare to the template.

bool

default:"False"

Whether to only consider backbone atoms in the template and structure. Considers all atoms by default.

bool

default:"False"

Whether structure - template separation is measured by taking the root mean square of the difference between the two pairwise distance matrices. By default, the root mean square of the difference in positions is used instead.

float

default:"1.0"

The weight of the energy term.

str | None

default:"None"

Optional name to append to the energy term name.

Methods

compute

Parameters

OraclesResultDict

required

Example

import bagel as bg
import biotite.structure.io as strucio

# Load a template structure from a PDB file
template_atoms = strucio.load_structure("template.pdb")

# Create the folding oracle
esmfold = bg.oracles.ESMFold()

# RMSD mode (default): minimize positional deviation from template
rmsd_energy = bg.energies.TemplateMatchEnergy(
    oracle=esmfold,
    template_atoms=template_atoms,
    residues=residues,
    backbone_only=True,
    weight=1.0,
)

# Distogram mode: minimize pairwise-distance deviation from template
distogram_energy = bg.energies.TemplateMatchEnergy(
    oracle=esmfold,
    template_atoms=template_atoms,
    residues=residues,
    distogram_separation=True,
    weight=1.0,
)

# Add to a state
state = bg.State(
    chains=[chain],
    energy_terms=[rmsd_energy],
    name="my_state",
)

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TemplateMatchEnergy

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example