Dihedral Mutator

A DihedralMutator instance changes a Pose State by introducing one or more dihedral rotations.

ProtoSyn.Mutators.DihedralMutator — Type

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

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

(dihedral_mutator::DihedralMutator)(pose::Pose)

The DihedralMutator AbstractMutator loops through all the Atom instances in a given Pose and applies a new dihedral angle if a random number (rand()) is bellow a given probability of mutation p_mut (therefore a higher p_mut value applies a larger number of dihedral rotations per call). The applied rotation is an angle value (in radians), sampled by calling angle_sampler and multiplied by the step_size value. The resulting value is then added to the selected Atom.Δϕ. Note that a new dihedral rotation is sampled for each selected Atom instance. 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). Note that the DihedralMutator syncs any pending cartesian to internal coordinate conversion (using the c2i! method). Requests internal to cartesian coordinates conversion (using request_i2c! method). Does not sync! the given Pose afterwards.

The DihedralMutator 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.

(dihedral_mutator::DihedralMutator)(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 instances 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.

See also

CrankshaftMutator

Examples

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

julia> ProtoSyn.Mutators.DihedralMutator(randn, 0.05, 1.0, an"CA$|C$"r)
⚯  Dihedral Mutator:
+----------------------------------------------------------------------+
| Index | Field                       | Value                          |
+----------------------------------------------------------------------+
| 1     | angle_sampler               | Function randn                 |
| 2     | p_mut                       | 0.0500                         |
| 3     | step_size                   | 1.0000                         |
+----------------------------------------------------------------------+
 ● Selection: Set
 └── FieldSelection › Atom.name = r"CA$|C$"

source

ProtoSyn Dihedral Mutator

Figure 1 | A schematic representation of a DihedralMutator instance. In this example, the selection an"C$"r selects only the carbon atoms of the backbone of the peptide, excluding the alpha carbons. The :Δϕ field in this AtomState instance applies a given dihedral rotation to all children Atom instances, therefore setting, in this case, the psi dihedral angle of the backbone of this Residue. As such, by providing the DihedralMutator with this selection, only the psi dihedral angles are being sampled for rotation. Each of the selected Atom instances is looped over and one or more instances can be designated for dihedral angle sampling. This is performed by comparing a random number (by calling rand()) against the DihedralMutator.p_mut field, for each of the looped Atom instances. If the random number is lower, the current Atom instance is selected. A high value for p_mut therefore translates into a higher number of dihedral rotations in a single call to the DihedralMutator. As a general rule, using a p_mut value of 1/N will result in 1 rotation per call of the DihedralMutator, on average (where N is the number of atoms in the Pose or number of selected atoms by selection). To sample a new dihedral angle, the DihedralMutatorangle_sampler is called (with no input arguments) and multiplied by the DihedralMutator.step_size field. This value is added to the selected AtomState.Δϕ.