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Builder

The Builder 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 Builder, this submodule introduces the peptidic LGrammar type, as well as the necessary methods to append and insert Fragment instances from a derivation, organized in the following topics:

Loading the default Peptides Stochastic L-Grammar

The default Peptides grammar is loaded when ProtoSyn is loaded, and can be accessed at Peptides.grammar.

ProtoSyn.Peptides.load_default_grammar — Function
load_default_grammar([::Type{T}])

Load the default Peptides LGrammar (from the default resources/Peptides/ directory, types as T <: AbstractFloat, if not provided will use ProtoSyn.Units.defaultFloat).

Note:

The default Peptides LGrammar is automatically loaded when using ProtoSyn. It can be found at Peptides.grammar.

Examples

julia> ProtoSyn.Peptides.load_default_grammar()
LGrammar{Float64, String, Vector{String}}:
 (...)
source
ProtoSyn.Peptides.load_grammar_from_file — Function
load_grammar_from_file([::Type{T}], filename::AbstractString, key::String) where {T <: AbstractFloat}

Load a LGrammar from the given filename (this should in .yml format, only loads the given key), typed to be of type T <: AbstractFloat. If not provided, will use ProtoSyn.Units.defaultFloat.

See also

load_grammar_from_file!

Examples

julia> ProtoSyn.Peptides.load_grammar_from_file("grammars.yml", "default")
LGrammar{Float64, String, Vector{String}}:
 (...)
source
ProtoSyn.Peptides.load_grammar_from_file! — Function
load_grammar_from_file!([::Type{T}], grammar::LGrammar{T, K, V}, filename::AbstractString, key::String) where {T <: AbstractFloat, K, V}

Load a LGrammar from the given filename (this should in .yml format, only loads the given key), typed to be of type T <: AbstractFloat. If not provided, will use ProtoSyn.Units.defaultFloat. Automatically add the loaded LGrammar instance to the given grammar (using the join_grammars! method).

See also

load_grammar_from_file

Examples

julia> g1 = ProtoSyn.Peptides.load_grammar_from_file("grammars.yml", "default");

julia> g2 = ProtoSyn.Peptides.load_grammar_from_file!(g1, "grammars.yml", "ncaa")
LGrammar{Float64, String, Vector{String}}:
 (...)
source
ProtoSyn.Peptides.join_grammars! — Function
join_grammars!(g1::LGrammar{T, K, V}, g2::LGrammar{T, K, V}) where {T <: AbstractFloat, K, V}

Add LGrammar g2 rules, variables and operators to LGrammar g1, joining both instances.

Examples

julia> g1 = ProtoSyn.Peptides.load_grammar_from_file("grammars.yml", "default");

julia> g2 = ProtoSyn.Peptides.load_grammar_from_file("grammars.yml", "ncaa");

julia> ProtoSyn.Peptides.join_grammars!(g1, g2)
LGrammar{Float64, String, Vector{String}}:
 (...)
source
ProtoSyn.Peptides.load_grammar_extras_from_file! — Function
load_grammar_extras_from_file!([::Type{T}], filename::AbstractString, key::String) where {T <: AbstractFloat}

Fill missing information in the following ProtoSyn constants with extra details from the loaded LGrammar .yml filename (under the key entry, typed as T <: AbstractFloat, if not provided will use ProtoSyn.Units.defaultFloat):

  • ProtoSyn.Peptides.chi_dict
  • ProtoSyn.Peptides.available_aminoacids
  • ProtoSyn.three_2_one
  • ProtoSyn.one_2_three

See also

load_grammar_from_file

Examples

julia> ProtoSyn.Peptides.load_grammar_extras_from_file!("grammars.yml", "default")
source

Building a molecular structure

ProtoSyn.Peptides.build — Method
build(grammar::LGrammar{T}, derivation, ss::NTuple{3,Number} = SecondaryStructure[:linear]) where {T <: AbstractFloat}

Build a Pose using the given derivation sequence on the provided grammar instructions. If an ss is provided, automatically apply it to the built pose (linear secondary structure, by default).

Note:

This function is an extension of ProtoSyn.build.

See also

setss!

Examples

julia> pose = ProtoSyn.Peptides.build(res_lib, seq"QQQ")
Pose{Topology}(Topology{/UNK:1}, State{Float64}:
 Size: 51
 i2c: false | c2i: false
 Energy: Dict(:Total => Inf)
)
source

Manipulating a molecular structure by adding new residues from templates

ProtoSyn.Peptides.append_fragment! — Method
append_fragment!(pose::Pose{Topology}, residue::Residue, grammar::LGrammar, derivation; [ss::Opt{SecondaryStructureTemplate} = nothing], [op = "α"])

Add the a Fragment built from the given derivation to the provided Pose pose, appending it after the given Residue residue. This residue and the new Fragment frag will be connected using operation op ("α" by default) of the given LGrammar grammar. If given, a SecondaryStructureTemplate ss can be applied to the new appendage (using the setss! method). In either case, the C=O bond position is re-calculated and set (in the anchor for the first residue of the appendage). Request internal to cartesian coordinate conversion and return the altered Pose pose.

Note:

This function is an extension of ProtoSyn.append_fragment!.

See also

insert_fragment!

Examples

julia> ProtoSyn.Peptides.append_fragment!(pose, pose.graph[1][end], res_lib, seq"AAA")
Pose{Topology}(Topology{/UNK:1}, State{Float64}:
 Size: 373
 i2c: true | c2i: false
 Energy: Dict(:Total => Inf)
)
source
ProtoSyn.Peptides.insert_fragment! — Method
insert_fragment!(pose::Pose{Topology}, residue::Residue, grammar::LGrammar, derivation; ss::Opt{SecondaryStructureTemplate} = nothing, op = "α")

Insert the Fragment built from the given derivation in the provided pose, on the position of the provided Residue instance residue (the residue gets shifted downstream). This first downstream Residue and the new Fragment will be connected using operation op ("α" by default) from [LGrammar] grammar. Also connects to the upstream Residue instance, using the same operation. If given, a SecondaryStructureTemplate ss can be applied to the new appendage (using the setss! method). If the appendage is not being inserted at the root, the C=O bond position is re-calculated and set (in the anchor for the first residue of the appendage). If the appendage is being inserted at the root, perform a soft uncap of the terminal hydrogen atoms (removes "H2" and "H3", leaves "H1", renames it to "H") and recalculate the N-H bond position (at the first downstream Residue). Request internal to cartesian coordinate conversion and return the altered Pose pose.

Note:

This function is an extension of ProtoSyn.insert_fragment!.

See also

append_fragment!

Examples

julia> ProtoSyn.Peptides.insert_fragment!(pose, pose.graph[1][1], res_lib, seq"AAA")
Pose{Topology}(Topology{/UNK:1}, State{Float64}:
 Size: 373
 i2c: true | c2i: false
 Energy: Dict(:Total => Inf)
)
source