Caterpillar Solvation

ProtoSyn.Peptides.Calculators.Caterpillar.neighbour_count([::A], pose::Pose, selection::Opt{AbstractSelection}, [update_forces::Bool = false]; [identification_curve::Function = null_identification_curve], [hydrophobicity_weight::Function = null_hydrophobicity_weight], [rmax::T = 9.0], [sc::T = 1.0], [Ω::Union{Int, T} = 750.0], [hydrophobicity_map::Dict{String, T} = ProtoSyn.Peptides.doolitle_hydrophobicity]) where {A, T <: AbstractFloat}

Calculate the given Pose pose caterpillar solvation energy using the Neighbour Count (NC) algorithm (see this article). If an AbstractSelection selection is provided, consider only the selected Atom instances (any given selection will be promoted to be of Atom type, see ProtoSyn.promote). In this model, the burial degree Ωi of each atom is equal to the number (count) of neighbouring Atom instances (within the defined rmax cut-off, in Angstrom Å) multiplied by a w1 weight, provided by the identification_curve Function. This Function receives the distance between each pair of neighbouring atoms (as a float), the rmax value and, optionally, a slope control sc value, and return a weight w1 (as a float). The identification_curve signature is as follows:

identification_curve(distance::T; rmax::T = 9.0, sc::T = 1.0) where {T <: AbstractFloat}

In order to use pre-defined identification_curve Function instances defined in ProtoSyn, check linear and sigmoid.

Note that: - Shorter rmax value identify buried residues in the local environment (i.e.: in the scale of the secondary structure, recommended) while a larger rmax value identifies buried residues in the global scale (i.e.: in comparison with the whole structure). - The slope control sc value only has effect in sigmoid identification_curve Function instances. A smaller value augments the prevalence of distance information in the w1 weight calculation, while a larger value defines a more strict cut-off (recommended);

An Atom is, therefore, considered buried if the number of neighbors (multiplied by w1) is over a defined cut-off value Ω. Buried hydrophobic aminoacids receive an energetic reward, while exposed hydrophobic Residue instances receive a penalty (and vice-versa for hydrophylic aminoacids), defined in the provided hydrophobicity_map (hydrophobicity map examples can be found in Peptides.constants.jl) and multiplied by w2, calculated by the hydrophobicity_weight Function. This Function receives the neighbor count Ωi, the hydrophobicity_map_value and the cut-off value Ω, returning a w2 weight (as a float). The hydrophobicity_weight signature is as follows:

hydrophobicity_weight(Ωi::Union{Int, T}; hydrophobicity_map_value::T = 0.0, Ω::Union{Int, T} = 0.0) where {T <: AbstractFloat}

In order to use pre-defined hydrophobicity_weight Function instances defined in ProtoSyn, check nc_scalling_exposed_only, nc_non_scalling_exposed_only, nc_scalling_all_contributions (recommended) and nc_non_scalling_all_contributions.

The optional A parameter defines the acceleration mode used (SISD0, SIMD1 or CUDA2). If left undefined the default ProtoSyn.acceleration.active mode will be used. This function does not calculate forces (not applicable), and therefore the `updateforces` flag serves solely for uniformization with other energy-calculating functions.

See also

neighbour_vector

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.neighbour_count(pose, false)
(0.0, nothing)

ProtoSyn.Peptides.Calculators.Caterpillar.neighbour_vector([::A], pose::Pose, selection::Opt{AbstractSelection}, [update_forces::Bool = false]; [identification_curve::Function = null_identification_curve], [hydrophobicity_weight::Function = null_hydrophobicity_weight], [rmax::T = 9.0], [sc::T = 1.0], [Ω::Union{Int, T} = 750.0], [hydrophobicity_map::Dict{String, T} = ProtoSyn.Peptides.doolitle_hydrophobicity]) where {A, T <: AbstractFloat}

Calculate the given Pose pose caterpillar solvation energy using the Neighbour Vector (NV) algorithm (see this article). If an AbstractSelection selection is provided, consider only the selected Atom instances (any given selection will be promoted to be of Atom type, see ProtoSyn.promote). In this model, vectors ωi are defined between an Atom and all neighbouring Atom instances (within the defined rmax cut-off (in Angstrom Å)). Note that only the selected atoms by the selection are considered. A resulting vector Ωi is calculated by suming all ωi vectors, multiplied by a w1 weight, provided by the identification_curve Function. This Function receives the distance between each pair of neighbouring atoms (as a float), the rmax value and, optionally, a slope control sc value, and return a weight w1 (as a float). The identification_curve signature is as follows:

identification_curve(distance::T; rmax::T = 9.0, sc::T = 1.0) where {T <: AbstractFloat}

In order to use pre-defined identification_curve Function instances defined in ProtoSyn, check linear, sigmoid and sigmoid_normalized.

Note that:

• Shorter rmax value identify buried residues in the local environment (i.e.:

in the scale of the secondary structure, recommended) while a larger rmax value identifies buried residues in the global scale (i.e.: in comparison with the whole structure).

• The slope control sc value only has effect in sigmoid

identification_curve Function instances. A smaller value augments the prevalence of distance information in the w1 weight calculation, while a larger value defines a more strict cut-off (recommended);

An Atom is, therefore, considered buried if the magnitude of the resulting vector from the sum of the ωi (multiplied by w1) is within a defined cut-off value Ω. Buried hydrophobic aminoacids receive an energetic reward, while exposed hydrophobic Residue instances receive a penalty (and vice-versa for hydrophylic aminoacids), defined in the provided hydrophobicity_map (hydrophobicity map examples can be found in Peptides.constants.jl) and multiplied by w2, calculated by the hydrophobicity_weight Function. This Function receives the vector magnitude Ωi, the hydrophobicity_map_value and the cut-off value Ω, returning a w2 (as a float). The hydrophobicity_weight signature is as follows:

hydrophobicity_weight(Ωi::Union{Int, T}; hydrophobicity_map_value::T = 0.0, Ω::Union{Int, T} = 0.0) where {T <: AbstractFloat}

In order to use pre-defined hydrophobicity_weight Function instances defined in ProtoSyn, check nv_scalling_exposed_only, nv_non_scalling_exposed_only, nv_scalling_all_contributions (recommended) and nv_non_scalling_all_contributions.

The optional A parameter defines the acceleration mode used (SISD0, SIMD1 or CUDA2). If left undefined the default ProtoSyn.acceleration.active mode will be used. This function does not calculate forces (not applicable), and therefore the `updateforces` flag serves solely for uniformization with other energy-calculating functions.

See also

neighbour_count

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.neighbour_vector(pose, false)
(0.0, nothing)

linear(distance::T; rmax::T = 9.0, sc::T = 1.0) where {T <: AbstractFloat}

Returns the linear identification curve weight w1 (max at distance 0.0, linearly decreasing until rmax). Note that slope control sc has no effect.

See also

sigmoid sigmoid_normalized

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.linear(10.0, rmax = 20.0)
0.5

sigmoid(distance::T; rmax::T = 9.0, sc::T = 1.0) where {T <: AbstractFloat}

Returns the sigmoid identification curve weight w1 (max at distance 0.0, min at distance rmax). The slope control sc defines how sharp the sigmoid curve is.

See also

linear sigmoid_normalized

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.sigmoid(10.0, rmax = 20.0)
0.9999546021312976

sigmoid_normalized(distance::T; rmax::T = 9.0, sc::T = 1.0) where {T <: AbstractFloat}

Returns the sigmoid identification curve weight w1 (max at distance 0.0, min at distance rmax), normalized by the given distance (should only be applied in Neighbor Vector (NV) algorithms). The slope control sc defines how sharp the sigmoid curve is.

See also

linear sigmoid

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.sigmoid_normalized(10.0, rmax = 20.0)
0.09999546021312976

get_default_caterpillar_solvation_energy(;[α::T = 1.0]) where {T <: AbstractFloat}

Return the default Caterpillar solvation energy energy EnergyFunctionComponent. α sets the component weight (on an EnergyFunction instance, 1.0 by default). This function employs neighbour_vector as the :calc function.

Settings

• hydrophobicity_weight::Function - Returns the hydrophobicity weight of a given burial degree based on a hydrophobicity map value and default buried state;
• identification_curve::Function - Returns the burial degree weight given an inter-atomic distance, rmax and slope control value;
• Ω::Union{Int, T} - The default buried state (the average, buried degrees above this value are considered buried);
• sc::T = 1.0 - Slope control, used in sigmoid identification curves to control how sharp to consider an interaction as buried or not.
• hydrophobicity_map::Dict{String, T} - A 1-on-1 map between Residue types and hydrophobicity indexes;
• rmax::T - The cutoff value to consider some inter-atomic interaction as buriable;

Examples

julia> ProtoSyn.Peptides.Calculators.Caterpillar.get_default_caterpillar_solvation_energy()
🞧  Energy Function Component:
+---------------------------------------------------+
| Name           | Caterpillar_Solv                 |
| Alpha (α)      | 1.0                              |
| Update forces  | false                            |
| Calculator     | neighbour_vector                 |
+---------------------------------------------------+
 |    +----------------------------------------------------------------------------------+
 ├──  ● Settings                      | Value                                            |
 |    +----------------------------------------------------------------------------------+
 |    | hydrophobicity_weight         | nv_scalling_all_contributions                    |
 |    | identification_curve          | sigmoid                                          |
 |    | Ω                             | 24.0                                             |
 |    | sc                            | 1.0                                              |
 |    | hydrophobicity_map            | Dict{String, Float64}(21 components)             |
 |    | rmax                          | 9.0                                              |
 |    +----------------------------------------------------------------------------------+
 |    
 └──  ●  Selection:
      └── BinarySelection ❯  | "or" (Atom)
           ├── FieldSelection › Atom.name = CB
           └── BinarySelection ❯  & "and" (Atom)
                ├── FieldSelection › Atom.name = HA2
                └── FieldSelection › Residue.name = GLY