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EnergyTerms can be inheritable, which is only relevant for bagel.mutation.GrandCanonical. In that type of simulation when adding a new residues, the “inheritable” attribute decides whether or not the new residue will be added to the residues for which this term is calculated. In general, a new residue inherits all energy terms of one of its neighbours (chosen randomly to be the left or right neighbour), if these terms are inheritable.

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Definition

The total energy of a state is the weighted sum of all its energy terms: ES=∑jNSwjs ϵjs({C}S)E_{S} = \sum_{j}^{N_S} w_{js}\,\epsilon_{js}(\{C\}_S)
  • ESE_S is the energy of state SS
  • wjsw_{js} is the weight of energy term jj in state SS
  • ϵjs\epsilon_{js} is the unweighted energy of term jj
  • {C}S\{C\}_S is the set of chains in state SS

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Parameters

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name
str
required
The name of the energy term.
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oracle
Oracle
required
The oracle to use for the energy term.
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inheritable
bool
required
Whether the energy term is inheritable.
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weight
float
default:"1.0"
The weight of the energy term.

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Methods

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compute

Calculates the EnergyTerm’s energy given information about the folded structure. The result is returned and stored as an internal attribute (.value). Parameters
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oracles_result
OraclesResultDict
required
Dictionary mapping oracles to their results. This is used to get the relevant information for the energy term.
Returns
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return
(unweighted_energy, weighted_energy) : tuple[float, float]
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return
float
How well the structure satisfies the given criteria. Where possible, this number should be between 0 and 1.
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return
float
The unweighted energy multiplied by the energy term’s weight.

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shift_residues_indices_after_removal

Shifts internally stored res_indices on a given chain to reflect a residue has been removed from the chain. Parameters
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chain_id
str
required
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res_index
int
required

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shift_residues_indices_before_addition

Shifts internally stored res_indices on a given chain to reflect a residue has been added. Parameters
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chain_id
str
required
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res_index
int
required

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remove_residue

Remove residue from this energy term’s calculations. Parameters
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chain_id
str
required
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res_index
int
required

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add_residue

Adds residue to this energy term’s calculations, in the same group as its parent residue. Parameters
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chain_id
str
required
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res_index
int
required
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parent_res_index
int
required

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get_residue_mask

Creates residue mask from residue group. Structure used to find unique residues in state Parameters
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structure
AtomArray
required
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residue_group_index
int
required

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get_atom_mask

Creates atom mask from residue group. Structure used to find unique atoms in state Parameters
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structure
AtomArray
required
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residue_group_index
int
required