Crankshaft Mutator

CrankshaftMutator(angle_sampler::Function, p_mut::AbstractFloat, step_size::AbstractFloat, selection::Opt{AbstractSelection}, inc_last_res::Opt{AbstractSelection})

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

(crankshaft_mutator::CrankshaftMutator)(pose::Pose)

The CrankshaftMutator AbstractMutator loops through all pairs of two atoms possible, in the given Pose. For each pair, if a random number (rand()) is bellow a given probability of mutation p_mut, both atoms are selected for a crankshaft movement (therefore a higher p_mut value applies a larger number of crankshaft movements per call). A crankshaft movement is a concerted rotation around a virtual axis formed between the two selected atoms, by a certain angle given by the angle_sampler function and multiplied by the step_size value. The rotation is applied to the region between the two atoms, by travelling the Pose Graph (See travel_graph), by calculating and applying a rotation matrix (See rotation_matrix_from_axis_angle). Note that a new angle for the crankshaft movement is sampled for each selected pair of Atom instances. If an AbstractSelection selection is provided, only the selected Atom instances are looped over. If an AbstractSelection selection is provided, only the selected Atom instances are looped over. If the given AbstractSelection selection is not of selection type Atom, it will be promoted to this type (using promote with default aggregator any). If an AbstractSelection inc_last_res is provided, all atoms in this AbstractSelection and in the last residue considered for the crankshaft movement will be included in the rotation. As an example, for a correct crankshaft movement in peptidic structures, the sidechain of the last residue should also be included in the rotation. In this example, inc_last_res should be !(an"^CA$|^N$|^C$|^H$|^O$"r). Note that the CrankshaftMutator syncs any pending internal to cartesian coordinate conversion (using the i2c! method). Requests cartesian to internal coordinates conversion (using request_c2i! method). Does not sync! the given Pose afterwards.

The CrankshaftMutator 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.

(crankshaft_mutator::CrankshaftMutator)(pose::Pose, atoms::Vector{Atom})

Fields

• angle_sampler::Function - Should return a Float angle value (in radians). Is called with no input arguments;
• p_mut::AbtractFloat - Compared against a rand() call, applies this Mutator to Atom instance pairs where rand() < p_mut;
• step_size::AbstractFloat - Multiplies the sampled angle by this value;
• selection::Opt{AbstractSelection} - If given, this Mutator will only loop over the selected Atom instances;
• inc_last_res::Opt{AbstractSelection} - If given, all atoms in this Mutator and in the last residue considered for the crankshaft movement will be included in the rotation.

See also

DihedralMutator

Examples

julia> ProtoSyn.Mutators.CrankshaftMutator(randn, 1.0, 1.0, nothing, nothing)
⚯  Crankshaft Mutator:
+----------------------------------------------------------------------+
| Index | Field                       | Value                          |
+----------------------------------------------------------------------+
| 1     | angle_sampler               | Function randn                 |
| 2     | p_mut                       | 1.0000                         |
| 3     | step_size                   | 1.0000                         |
+----------------------------------------------------------------------+
 ○  Selection: Not Set
 ○  Include on last residue: Not Set

julia> ProtoSyn.Mutators.CrankshaftMutator(randn, 0.01, 1.0, an"CA", !(an"^CA$|^N$|^C$|^H$|^O$"r))
⚯  Crankshaft Mutator:
+----------------------------------------------------------------------+
| Index | Field                       | Value                          |
+----------------------------------------------------------------------+
| 1     | angle_sampler               | Function randn                 |
| 2     | p_mut                       | 0.0100                         |
| 3     | step_size                   | 1.0000                         |
+----------------------------------------------------------------------+
 ● Selection: Set
 └── FieldSelection › Atom.name = CA
 ● Include on last residue: Set
 └── UnarySelection ❯ ! "not" (Atom)
      └── FieldSelection › Atom.name = r"^CA$|^N$|^C$|^H$|^O$"