BioJulia/BioStructures.jl

Multiple selection and Merge Selection

Wang-Lin-boop opened this issue · 5 comments

Wang-Lin-boop commented

can we use collectresidues to select multiple region of protein? such as :

domain = collectresidues(chain, res -> (13 <= resnumber(res) <= 436) || (504 <= resnumber(res) <= 534), allselector)

or try to merge different selections to a new selection?

jgreener64 commented

Yes you can do it as you have by using || in the selector. You can merge selections by defining them as functions:

selector1(res) = 13  <= resnumber(res) <= 436
selector2(res) = 504 <= resnumber(res) <= 534
combinedselector(res) = selector1(res) || selector2(res)
domain = collectresidues(chain, combinedselector)

I deleted the allselector as it doesn't do anything here.

Wang-Lin-boop commented

yeah, I have found this method about || .

and I wanna select many fragments and merge them into one domain.

firstly, I test it in REPL:

image

        for domain_range in split(domain_vec,",")
            frag_N = parse(Int64,split(domain_range,"-")[1])
            frag_C = parse(Int64,split(domain_range,"-")[2])
            ( length(domain_selection) == 0 ) && (domain_selection = "($frag_N <= resnumber(res) <= $frag_C)" )
            ( length(domain_selection) == 0 ) || (domain_selection = "$(domain_selection) || ( $frag_N <= resnumber(res) <= $frag_C)" )
        end
        println(domain_selection)
# (13 <= resnumber(res) <= 436) || ( 13 <= resnumber(res) <= 436) || ( 504 <= resnumber(res) <= 534) || ( 655 <= resnumber(res) <= 682)
        domain_str = collectresidues(chain, res -> ("$(domain_selection)"), allselector)
        writepdb("$output_dir/$pdb_name-$model_num-$chain_id-$domain_id.pdb", domain_str)

however, an error occured that:
nested task error: TypeError: non-boolean (var"#12#13") used in boolean context

image

I think that it may be caused by the inappropriate statement construction. Even after I replace the res -> ("$(domain_selection)") to Meta.parse("res -> (\"$(domain_selection)\")") |> eval or res -> ( eval(domain_selection) ), it still doesn't work....

jgreener64 commented

I would just form a Vector or Set of all residue numbers in the domain (domain_res) and then do:

domain_selector(res) = resnumber(res) in domain_res
Wang-Lin-boop commented

wow, a great idea!

Wang-Lin-boop commented 
    for domain_ddd in readlines("$index_dir/$pdb_name-$model_num-$chain_id-domain.info")
        domain_id = split(domain_ddd,":")[1]
        domain_vec = split(domain_ddd,":")[2]
        com_id = 0
        domain_selection = []
        for domain_range in split(domain_vec,",")
            frag_N = parse(Int64,split(domain_range,"-")[1])
            frag_C = parse(Int64,split(domain_range,"-")[2])
            for resi in frag_N:frag_C
                push!(domain_selection, resi)
            end
        end
        domain_str = collectresidues(chain, res -> resnumber(res) in domain_selection , allselector)
        writepdb("$output_dir/$pdb_name-$model_num-$chain_id-$domain_id.pdb", domain_str)
    end

It works now! Thanks, Greener~

  • 👍1