Selections

The Selections is a submodule of ProtoSyn.Peptides module. As such, the following section introduces both new types and methods that work together, in a generally independent way from the rest of the module, and require an unique exploratory section on their own.

As an expansion of the Core module Selections, this submodule introduces some protein specific AbstractSelection types:

ProteinSelection
PolarSelection
SidechainSelection
SecondaryStructureSelection
PhiSelection
PsiSelection
OmegaSelection
ChiSelection

ProtoSyn.ProteinSelection — Type

ProteinSelection()

A ProteinSelection outputs a Mask of Residue instances where the protein aminoacids are marked as true. A known aminoacid is defined as having an entry both in ProtoSyn.three_2_one dictionary and in the default Peptides LGrammar.

State mode

The state mode of ProteinSelection M is forced to be Stateless

Selection type

The selection type of ProteinSelection T is forced to be Residue.

Note:

This selection does not have a short syntax version.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> ProteinSelection()
ProteinSelection › (Residue)

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ProtoSyn.PolarSelection — Type

PolarSelection()

A PolarSelection outputs a Mask of Residue instances where the polar aminoacids are marked as true (as defined in ProtoSyn.Peptides.polar_residues).

State mode

The state mode of PolarSelection M is forced to be Stateless

Selection type

The selection type of PolarSelection T is forced to be Residue.

Note:

This selection does not have a short syntax version.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> PolarSelection()
PolarSelection › (Residue)

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ProtoSyn Polar Selection

Figure 1 | An example of a PolarSelection application.

ProtoSyn.SidechainSelection — Type

SidechainSelection()

A SidechainSelection outputs a Mask of Atom instances where the sidechain atoms are marked as true (all atoms not named C, H, CA, N or O - marks caps as true).

State mode

The state mode of SidechainSelection M is forced to be Stateless

Selection type

The selection type of SidechainSelection T is forced to be Atom.

Note:

This selection does not have a short syntax version.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> SidechainSelection()
SidechainSelection › (Atom)

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ProtoSyn Sidechain Selection

Figure 2 | An example of a SidechainSelection application.

ProtoSyn.SecondaryStructureSelection — Type

SecondaryStructureSelection(ss::Symbol, [threshold::Float64 = 0.87])

A SecondaryStructureSelection outputs a Mask of Residue instances where the residues are marked as true if the current phi and psi dihedrals are within the threshold angular distance (in radians, 50° by default) of the reference values for the requested ss SecondaryStructure type.

State mode

The state mode of SidechainSelection M is forced to be Stateful.

Selection type

The selection type of SidechainSelection T is forced to be Residue.

Short syntax

ss"helix" = Helix secondary structure
ss"parallel_sheet" = Parallel beta sheet secondary structure
ss"antiparallel_sheet" = Antiparallel beta sheet secondary structure
ss"linear" = Linear secondary structure

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> SecondaryStructureSelection(:parallel_sheet, deg2rad(20))
SecondaryStructureSelection › parallel_sheet (± 20.0°)

julia> ss"helix"
SecondaryStructureSelection › helix (± 50.0°)

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ProtoSyn SS Selection

Figure 3 | An example of a SecondaryStructureSelection application.

ProtoSyn.PhiSelection — Type

PhiSelection()

A PhiSelection outputs a Mask of Atom instances where the phi-controlling atoms are marked as true. Phi-controlling atoms are non upstream-terminal Atom instances named "C". (make sure the IUPAC naming conventions are respected, consider using assign_default_atom_names!) for renaming peptide structures into the default atom names).

State mode

The state mode of PhiSelection M is forced to be Stateless

Selection type

The selection type of PhiSelection T is forced to be Atom.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> PhiSelection()
PhiSelection › (Atom)

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ProtoSyn.PsiSelection — Type

PsiSelection()

A PsiSelection outputs a Mask of Atom instances where the psi-controlling atoms are marked as true. Psi-controlling atoms are non downstream-terminal Atom instances named "N". (make sure the IUPAC naming conventions are respected, consider using assign_default_atom_names!) for renaming peptide structures into the default atom names).

State mode

The state mode of PsiSelection M is forced to be Stateless

Selection type

The selection type of PsiSelection T is forced to be Atom.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> PsiSelection()
PsiSelection › (Atom)

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ProtoSyn.OmegaSelection — Type

OmegaSelection()

An OmegaSelection outputs a Mask of Atom instances where the omega-controlling atoms are marked as true. Omega-controlling atoms are non upstream-terminal Atom instances named "CA". (make sure the IUPAC naming conventions are respected, consider using assign_default_atom_names!) for renaming peptide structures into the default atom names).

State mode

The state mode of OmegaSelection M is forced to be Stateless

Selection type

The selection type of OmegaSelection T is forced to be Atom.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> PsiSelection()
PsiSelection › (Atom)

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ProtoSyn.ChiSelection — Type

ChiSelection(n::Union{Int, Vector{Int}})

A ChiSelection outputs a Mask of Atom instances where the chi-controlling Atom instances of sidechain are marked as true (all atoms defined in Peptides.chi_dict, by name - make sure the IUPAC naming conventions are respected, consider using assign_default_atom_names!) for renaming peptide structures into the default atom names). this AbstractSelection selects the n-chi dihedral angles (chi1, chi2, chi3 or chi4). Optionally, a Vector{Int} can be provided, in wich case multiple chi-angles can be selected simultaneously.

State mode

The state mode of ChiSelection M is forced to be Stateless.

Selection type

The selection type of ChiSelection T is forced to be Atom.

Short syntax

chi"..." = Chi angle

Note:

Using the short version syntax, it's possible to select multiple chi angles by using the 'r' flasg, as such: chi"1|2|3|4"r.

Note:

This selection is provided by the Peptides module but registered under ProtoSyn Core module, in order to directly accessible and merged with other AbstractSelection instances.

Examples

julia> ChiSelection(1)
ChiSelection (chi-1) › (Atom)


julia> ChiSelection([1, 2])
ChiSelection (chi-1 and chi-2) › (Atom)


julia> chi"1"
ChiSelection (chi-1) › (Atom)


julia> chi"1|2|3|4"r
ChiSelection (chi-1, chi-2, chi-3 and chi-4) › (Atom)

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