### A Pluto.jl notebook ###
# v0.18.2

using Markdown
using InteractiveUtils

# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
    quote
        local iv = try
            Base.loaded_modules[Base.PkgId(
                Base.UUID("6e696c72-6542-2067-7265-42206c756150"),
                "AbstractPlutoDingetjes"
            )].Bonds.initial_value
        catch
            b -> missing
        end
        local el = $(esc(element))
        global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
        el
    end
end

# ╔═╡ 6c1969e0-02f5-11eb-3fa2-09931a63b1ac
begin
    using PoreMatMod, PlutoUI, Bio3DView
    HOME = joinpath(homedir(), ".PoreMatModGO")
    rc[:paths][:crystals] = HOME
    rc[:paths][:moieties] = HOME
    if !isdir(HOME)
        mkdir(HOME)
    end
    cd(HOME)
    md"""
    # 💠 PoreMatModGO 🚀

    This notebook interactively substitutes moieties within a crystal using a modified implementation of Ullmann's algorithm to perform substructure searches and applying singular value decomposition to align fragments of the generated materials. Read the docs [here](SimonEnsemble.github.io/PoreMatMod.jl).

    See the original publication on PoreMatMod.jl here: [(article)](https://doi.org/10.33774/chemrxiv-2021-vx5r3) [(GitHub)](https://github.com/SimonEnsemble/PoreMatMod.jl)
    """
end

# ╔═╡ 5dc43a20-10b8-11eb-26dc-7fb98e9aeb1a
md"""
Adrian Henle, [Simon Ensemble](http://simonensemble.github.io), 2021

$(Resource("https://simonensemble.github.io/osu_logo.jpg", :width => 250))
"""

# ╔═╡ 90696d20-10b7-11eb-20b5-6174faeaf613
@bind load_inputs Button("Reset")

# ╔═╡ 50269ffe-02ef-11eb-0614-f11975d991fe
begin
    load_inputs
    # input fields: query, replacement, xtal
    md"""
    ##### Input Files

    Parent Crystal $(@bind parent_crystal FilePicker())

    Search Moiety $(@bind search_moiety FilePicker())

    Replace Moiety $(@bind replace_moiety FilePicker())
    """
end

# ╔═╡ 33b1fb50-0f73-11eb-2ab2-9d2cb6c5a533
# write file input strings to files in temp directory
begin
    # dict for tracking load status of inputs
    isloaded = Dict([:replacement => false, :query => false, :parent => false])
    # replacement loader
    if !isnothing(replace_moiety)
        write("replacement.xyz", replace_moiety["data"])
        replacement = moiety("replacement.xyz")
        isloaded[:replacement] = true
    end
    # query loader
    if !isnothing(search_moiety)
        write("query.xyz", search_moiety["data"])
        query = moiety("query.xyz")
        isloaded[:query] = true
    end
    # xtal loader
    if !isnothing(parent_crystal)
        write("parent.cif", parent_crystal["data"])
        xtal = Crystal("parent.cif"; check_overlap=false)
        Xtals.strip_numbers_from_atom_labels!(xtal)
        infer_bonds!(xtal, true)
        isloaded[:parent] = true
    end
    # run search and display terminal message
    if isloaded[:query] && isloaded[:parent]
        search = query ∈ xtal
        with_terminal() do
            @info "Search Results" isomorphisms = nb_isomorphisms(search) locations =
                nb_locations(search)
        end
    end
end

# ╔═╡ 415e9210-0f71-11eb-15c8-e7484b5be309
# choose replacement type
if all(values(isloaded))
    md"""
    ### Find/Replace Options

    Mode $(@bind replace_mode Select(["", "random replacement at each location", "random replacement at n random locations", "random replacement at specific locations", "specific replacements"]))
    """
end

# ╔═╡ 3997c4d0-0f75-11eb-2976-c161879b8d0c
# options populated w/ conditional logic based on mode selection
if all(values(isloaded))
    local output = nothing
    x = ["$(x)" for x in 1:nb_locations(search)]
    if replace_mode == "random replacement at each location"
        output = nothing
    elseif replace_mode == "random replacement at n random locations"
        output = md"Number of locations $(@bind nb_loc Slider(1:nb_locations(search)))"
    elseif replace_mode == "random replacement at specific locations"
        output = md"Locations $(@bind loc MultiSelect(x))"
    elseif replace_mode == "specific replacements"
        output = md"""
       Locations $(@bind loc MultiSelect(x))

       Orientations $(@bind ori TextField())
       """
    end
    output
end

# ╔═╡ 69edca20-0f94-11eb-13ba-334438ca2406
if all(values(isloaded))
    new_xtal_flag = true
    if replace_mode == "random replacement at each location"
        new_xtal = substructure_replace(search, replacement)
    elseif replace_mode == "random replacement at n random locations" && nb_loc > 0
        new_xtal = substructure_replace(search, replacement; nb_loc=nb_loc)
    elseif replace_mode == "random replacement at specific locations" && loc ≠ []
        new_xtal =
            substructure_replace(search, replacement; loc=[parse(Int, x) for x in loc])
    elseif replace_mode == "specific replacements"
        if loc ≠ [] && ori ≠ "" && length(loc) == length(split(ori, ","))
            new_xtal = substructure_replace(
                search,
                replacement;
                loc=[parse(Int, x) for x in loc],
                ori=[parse(Int, x) for x in split(ori, ",")]
            )
        else
            new_xtal_flag = false
        end
    else
        new_xtal_flag = false
    end
    if new_xtal_flag
        with_terminal() do
            if replace_mode == "random replacement at each location"
                @info replace_mode new_xtal
            elseif replace_mode == "random replacement at n random locations"
                @info replace_mode nb_loc new_xtal
            elseif replace_mode == "random replacement at specific locations"
                @info replace_mode loc new_xtal
            elseif replace_mode == "specific replacements"
                @info replace_mode loc ori new_xtal
            end
        end
    end
end;

# ╔═╡ 5918f770-103d-11eb-0537-81036bd3e675
if all(values(isloaded)) && new_xtal_flag
    write_cif(new_xtal, "crystal.cif")
    write_xyz(new_xtal, "atoms.xyz")
    write_vtk(new_xtal.box, "unit_cell.vtk")
    write_bond_information(new_xtal, "bonds.vtk")
    no_pb = deepcopy(new_xtal)
    drop_cross_pb_bonds!(no_pb)
    write_mol2(new_xtal; filename="crystal.mol2")
    write_mol2(no_pb; filename="view.mol2")
    viewfile("view.mol2", "mol2"; vtkcell="unit_cell.vtk", axes=Axes(4, 0.25))
end

# ╔═╡ 31832e30-1054-11eb-24ed-219fd3e236a1
if all(values(isloaded)) && new_xtal_flag
    download_cif = DownloadButton(read("crystal.cif"), "crystal.cif")
    download_box = DownloadButton(read("unit_cell.vtk"), "unit_cell.vtk")
    download_xyz = DownloadButton(read("atoms.xyz"), "atoms.xyz")
    download_bonds = DownloadButton(read("bonds.vtk"), "bonds.vtk")
    download_mol2 = DownloadButton(read("crystal.mol2"), "crystal.mol2")
    md"""
    ### Output Files
    Complete Crystal $download_mol2 $download_cif

    Components $download_xyz $download_bonds $download_box
    """
end

# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
Bio3DView = "99c8bb3a-9d13-5280-9740-b4880ed9c598"
PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
PoreMatMod = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"

[compat]
Bio3DView = "~0.1.3"
PlutoUI = "~0.7.14"
PoreMatMod = "~0.2.0"
"""

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[[MsgPack]]
deps = ["Serialization"]
git-tree-sha1 = "a8cbf066b54d793b9a48c5daa5d586cf2b5bd43d"
uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671"
version = "1.1.0"

[[NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"

[[OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"

[[OrderedCollections]]
git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.4.1"

[[Parsers]]
deps = ["Dates"]
git-tree-sha1 = "bfd7d8c7fd87f04543810d9cbd3995972236ba1b"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "1.1.2"

[[Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[[Pluto]]
deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "InteractiveUtils", "Logging", "Markdown", "MsgPack", "Pkg", "REPL", "Sockets", "TableIOInterface", "Tables", "UUIDs"]
git-tree-sha1 = "a5b3fee95de0c0a324bab53a03911395936d15d9"
uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
version = "0.17.2"

[[PlutoSliderServer]]
deps = ["Base64", "Configurations", "Distributed", "FromFile", "GitHubActions", "HTTP", "Logging", "Pkg", "Pluto", "SHA", "Sockets", "TOML", "UUIDs"]
git-tree-sha1 = "ed9660bb2c9eee9d389601bd80a10cee3dd64f0b"
uuid = "2fc8631c-6f24-4c5b-bca7-cbb509c42db4"
version = "0.2.7"

[[PlutoUI]]
deps = ["AbstractPlutoDingetjes", "Base64", "Dates", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "Markdown", "Random", "Reexport", "UUIDs"]
git-tree-sha1 = "b68904528fd538f1cb6a3fbc44d2abdc498f9e8e"
uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
version = "0.7.21"

[[PooledArrays]]
deps = ["DataAPI", "Future"]
git-tree-sha1 = "db3a23166af8aebf4db5ef87ac5b00d36eb771e2"
uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
version = "1.4.0"

[[PoreMatMod]]
deps = ["Bio3DView", "CSV", "DataFrames", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
git-tree-sha1 = "e4b40bedba7a4aadefe93b52b809de10539bc915"
uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
version = "0.2.6"

[[PrettyTables]]
deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
git-tree-sha1 = "574a6b3ea95f04e8757c0280bb9c29f1a5e35138"
uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
version = "0.11.1"

[[Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[PyCall]]
deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"]
git-tree-sha1 = "4ba3651d33ef76e24fef6a598b63ffd1c5e1cd17"
uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
version = "1.92.5"

[[REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[Random]]
deps = ["SHA", "Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[Reexport]]
git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
uuid = "189a3867-3050-52da-a836-e630ba90ab69"
version = "1.2.2"

[[Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "1.1.3"

[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

[[SentinelArrays]]
deps = ["Dates", "Random"]
git-tree-sha1 = "f45b34656397a1f6e729901dc9ef679610bd12b5"
uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
version = "1.3.8"

[[Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"

[[SimpleTraits]]
deps = ["InteractiveUtils", "MacroTools"]
git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231"
uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
version = "0.9.4"

[[Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[SortingAlgorithms]]
deps = ["DataStructures", "Random", "Test"]
git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "0.3.1"

[[SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.2.13"

[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[[StatsAPI]]
git-tree-sha1 = "0f2aa8e32d511f758a2ce49208181f7733a0936a"
uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
version = "1.1.0"

[[StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
git-tree-sha1 = "2bb0cb32026a66037360606510fca5984ccc6b75"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.33.13"

[[StructTypes]]
deps = ["Dates", "UUIDs"]
git-tree-sha1 = "d24a825a95a6d98c385001212dc9020d609f2d4f"
uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
version = "1.8.1"

[[TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

[[TableIOInterface]]
git-tree-sha1 = "9a0d3ab8afd14f33a35af7391491ff3104401a35"
uuid = "d1efa939-5518-4425-949f-ab857e148477"
version = "0.1.6"

[[TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.6.0"

[[Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"

[[Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.6"

[[URIs]]
git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.3.0"

[[UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[VersionParsing]]
git-tree-sha1 = "e575cf85535c7c3292b4d89d89cc29e8c3098e47"
uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
version = "1.2.1"

[[Xtals]]
deps = ["Bio3DView", "CSV", "DataFrames", "Documenter", "Graphs", "JLD2", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
git-tree-sha1 = "3147503cd35c4f2b3744fe36301c7de3efee98c5"
uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
version = "0.3.9"

[[Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

[[libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"

[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

[[p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
"""

# ╔═╡ Cell order:
# ╟─6c1969e0-02f5-11eb-3fa2-09931a63b1ac
# ╟─50269ffe-02ef-11eb-0614-f11975d991fe
# ╟─33b1fb50-0f73-11eb-2ab2-9d2cb6c5a533
# ╟─415e9210-0f71-11eb-15c8-e7484b5be309
# ╟─3997c4d0-0f75-11eb-2976-c161879b8d0c
# ╟─69edca20-0f94-11eb-13ba-334438ca2406
# ╟─5918f770-103d-11eb-0537-81036bd3e675
# ╟─31832e30-1054-11eb-24ed-219fd3e236a1
# ╟─5dc43a20-10b8-11eb-26dc-7fb98e9aeb1a
# ╟─90696d20-10b7-11eb-20b5-6174faeaf613
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002