Module:SMILES2IUPAC

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Usage

{{#invoke:SMILES2IUPAC|main}}

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Subpages of this module.

local Parser = require('Module:SMILES2IUPAC/Parser')
local Alkanes = require('Module:SMILES2IUPAC/Alkanes')
local Alkenes = require('Module:SMILES2IUPAC/Alkenes')
local Dienes = require('Module:SMILES2IUPAC/Dienes')
local Alkynes = require('Module:SMILES2IUPAC/Alkynes')
local Enynes = require('Module:SMILES2IUPAC/Enynes')
local Functional = require('Module:SMILES2IUPAC/Functional')

local p = {}

local namingSubmodules = {
	{ name = 'Functional', tryName = Functional.name },
	{ name = 'Enynes', tryName = Enynes.name },
	{ name = 'Dienes', tryName = Dienes.name },
	{ name = 'Alkenes', tryName = Alkenes.name },
	{ name = 'Alkynes', tryName = Alkynes.name },
	{ name = 'Alkanes', tryName = Alkanes.name },
}


--- Converts a SMILES string into an IUPAC name.
-- @param smiles string
-- @return name string on success, or nil, errorMessage on failure.
function p.nameFromSmiles(smiles)
	local graph, parseErr = Parser.parse(smiles)
	if not graph then
		return nil, 'could not parse SMILES: ' .. parseErr
	end

	local lastErr
	for _, submodule in ipairs(namingSubmodules) do
		local name, err = submodule.tryName(graph)
		if name then
			return name
		end
		lastErr = submodule.name .. ': ' .. tostring(err)
	end

	return nil, 'no naming rule could handle this molecule yet (' .. tostring(lastErr) .. ')'
end

--- {{#invoke:SMILES2IUPAC|main|<smiles>}} entry point.
function p.main(frame)
	local args = frame.args
	if args.smiles == nil and args[1] == nil and frame:getParent() then
		args = frame:getParent().args
	end
	local smiles = args.smiles or args[1]
	if not smiles or smiles == '' then
		return 'Error: no SMILES string given'
	end

	local ok, nameOrErr, err = pcall(p.nameFromSmiles, smiles)
	if not ok then
		return 'Error: internal error while naming SMILES (' .. tostring(nameOrErr) .. ')'
	end
	if not nameOrErr then
		return 'Error: ' .. tostring(err)
	end
	return nameOrErr
end
function p.testParser(frame)
    local smiles = frame.args[1] or frame.args.smiles
    local graph, err = Parser.parse(smiles)

    if not graph then
        return 'ERROR: ' .. err
    end

    local out = {}

    table.insert(out, 'Atoms:')
    for i, atom in ipairs(graph.atoms) do
        table.insert(out, i .. ': ' .. atom.element)
    end

    table.insert(out, 'Bonds:')
    for _, bond in ipairs(graph.bonds) do
        table.insert(
            out,
            bond.a .. ' -- ' .. bond.b .. ' (order=' .. bond.order .. ')'
        )
    end

    return table.concat(out, '\n')
end

function p.debugName(frame)

	local smiles =
		frame.args[1]
		or frame.args.smiles

	if not smiles or smiles == '' then
		return 'Error: no SMILES supplied'
	end

	local graph, parseErr =
		Parser.parse(smiles)

	if not graph then
		return 'Parser: ' .. tostring(parseErr)
	end

	local out = {}

	for _, submodule in ipairs(namingSubmodules) do

		local ok, name, err =
			pcall(
				submodule.tryName,
				graph
			)

		if not ok then

			table.insert(
				out,
				submodule.name
				.. ': CRASH: '
				.. tostring(name)
			)

		elseif name then

			table.insert(
				out,
				submodule.name
				.. ': PASS -> '
				.. tostring(name)
			)

		else

			table.insert(
				out,
				submodule.name
				.. ': FAIL -> '
				.. tostring(err)
			)
		end
	end

	return table.concat(out, '\n')
end
function p.debugGraph(frame)

	local smiles =
		frame.args[1]
		or frame.args.smiles

	if not smiles or smiles == '' then
		return 'Error: no SMILES supplied'
	end

	local graph, err =
		Parser.parse(smiles)

	if not graph then
		return 'Parser ERROR: ' .. tostring(err)
	end

	local out = {}

	table.insert(
		out,
		'SMILES: ' .. smiles
	)

	table.insert(
		out,
		'Atoms:'
	)

	for i, atom in ipairs(graph.atoms) do
		table.insert(
			out,
			string.format(
				'%d: %s',
				i,
				atom.element
			)
		)
	end

	table.insert(
		out,
		'Bonds:'
	)

	for i, bond in ipairs(graph.bonds) do
		table.insert(
			out,
			string.format(
				'%d: %d -- %d (order=%d)',
				i,
				bond.a,
				bond.b,
				bond.order
			)
		)
	end

	return table.concat(
		out,
		'\n'
	)
end
function p.debugAlkene(frame)

	local smiles =
		frame.args[1]
		or frame.args.smiles

	if not smiles or smiles == '' then
		return 'Error: no SMILES'
	end

	local graph, err =
		Parser.parse(smiles)

	if not graph then
		return 'Parser: ' .. tostring(err)
	end

	local ok, result =
		pcall(
			Alkenes.debugChains,
			graph
		)

	if not ok then
		return 'Alkenes ERROR: ' .. tostring(result)
	end

	return result
end
return p