Design Mutator

DesignMutator(p_mut::AbstractFloat, grammar::LGrammar, selection::Opt{AbstractSelection}; [searchable_aminoacids::Dict{Char, Bool} = Peptides.available_aminoacids])

Return a DesignMutator instance. This AbstractMutator is a functor, called with the following signature:

(design_mutator::DesignMutator)(pose::Pose)

The DesignMutator AbstractMutator loops through all Atom instances in the given Pose and applies a mutation (using the mutate! method) if a random number (rand()) is bellow a given probability of mutation p_mut. A different mutation is attempted for each Atom instance looped over (therefore, for a single attempt at a mutation per Residue, unique Atom names should be selected, as an"CA", for example). If an AbstractSelection selection is provided, only Atom instances marked as true in this selection are considered for mutation. The applied mutation is sampled from the given searchable_aminoacids dictionary (only for entries marked as true), and uses the given LGrammar grammar to perform the mutation. If no searchable_aminoacids dictionary is provided, will use the default Peptides.available_aminoacids dictionary (contains all aminoacids set as true). Note that the DesignMutator syncs any pending cartesian to internal coordinate conversion (using the c2i! method). Requests internal to cartesian coordinates conversion (using the request_i2c! method). Does not sync! the given Pose afterwards.

The DesignMutator AbstractMutator can also be optionally called using the following signature, in which case only the provided list of Atom instances will be considered for the application of this AbstractMutator.

(design_mutator::DesignMutator)(pose::Pose, atoms::Vector{Atom})

Fields

• p_mut::AbtractFloat - Compared against a rand() call, applies this Mutator to Atom instances where rand() < p_mut;
• grammar::LGrammar - The LGrammar instance with the aminoacid templates;
• selection::Opt{AbstractSelection} - If given, this Mutator will only loop over the selected Atom instances;
• searchable_aminoacids::Dict{Char, Bool} - The dictionary of available aminoacids, where each entry sets the availability of that aminoacid type to be the result of the mutation.

See also

RotamerMutator

Examples

julia> dm = ProtoSyn.Peptides.Mutators.DesignMutator(1.0, res_lib, an"CA")
⚯  Design Mutator:
+----------------------------------------------------------------------+
| Index | Field                       | Value                          |
+----------------------------------------------------------------------+
| 1     | grammar                     | Set ✓                          |
| 2     | p_mut                       | 1.000                          |
+----------------------------------------------------------------------+
 ● Searchable aminoacids: M 🗹 | K 🗹 | P 🗹 | N 🗹 | I 🗹 | H 🗹 | E 🗹 | W 🗹 | S 🗹 | T 🗹 | C 🗹 | D 🗹 | A 🗹 | L 🗹 | Y 🗹 | V 🗹 | R 🗹 | G 🗹 | Q 🗹 | F 🗹 
 ● Selection: Set
 └── FieldSelection › Atom.name = CA