-- -- This is file `pgfmolbio.domains.lua', -- generated with the docstrip utility. -- -- The original source files were: -- -- pgfmolbio.dtx (with options: `pmb-dom-lua') -- -- Copyright (C) 2013 by Wolfgang Skala -- -- This work may be distributed and/or modified under the -- conditions of the LaTeX Project Public License, either version 1.3 -- of this license or (at your option) any later version. -- The latest version of this license is in -- http://www.latex-project.org/lppl.txt -- and version 1.3 or later is part of all distributions of LaTeX -- version 2005/12/01 or later. -- module("pgfmolbio.domains", package.seeall) if luatexbase then luatexbase.provides_module({ name = "pgfmolbio.domains", version = 0.2, date = "2012/10/01", description = "Domain graphs", author = "Wolfgang Skala", copyright = "Wolfgang Skala", license = "LPPL", }) end local stringToDim = pgfmolbio.stringToDim local dimToString = pgfmolbio.dimToString local packageError = pgfmolbio.packageError local packageWarning = pgfmolbio.packageWarning local getRange = pgfmolbio.getRange function printSequenceFeature(feature, xLeft, xRight, yMid, xUnit, yUnit) xLeft = xLeft + 0.5 for currResidue in feature.sequence:gmatch(".") do tex.sprint("\n\t\t\\def\\xMid{" .. dimToString(xLeft * xUnit) .. "}") tex.sprint("\n\t\t\\def\\yMid{" .. dimToString(yMid * yUnit) .. "}") tex.sprint("\n\t\t\\def\\currentResidue{" .. currResidue .. "}") tex.sprint("\n\t\t\\pmbdomdrawfeature{other/sequence}") xLeft = xLeft + 1 end end function printHelixFeature(feature, xLeft, xRight, yMid, xUnit, yUnit) local residuesLeft, currX tex.sprint("\n\t\t\\pgfmolbioset[domains]{current style}") residuesLeft = feature.stop - feature.start + 1 currX = xLeft tex.sprint("\n\t\t\\def\\xLeft{" .. dimToString(currX * xUnit) .. "}") tex.sprint("\n\t\t\\def\\yMid{" .. dimToString(yMid * yUnit) .. "}") tex.sprint("\n\t\t\\pmbdomdrawfeature{helix/half upper back}") residuesLeft = residuesLeft - 2 currX = currX + 2.5 while residuesLeft > 0 do if residuesLeft == 1 then tex.sprint( "\n\t\t\\def\\xRight{" .. dimToString((currX + 0.5) * xUnit) .. "}" ) tex.sprint("\n\t\t\\def\\yMid{" .. dimToString(yMid * yUnit) .. "}") tex.sprint("\n\t\t\\pmbdomdrawfeature{helix/half lower back}") else tex.sprint("\n\t\t\\def\\xMid{" .. dimToString(currX * xUnit) .. "}") tex.sprint( "\n\t\t\\def\\yLower{" .. dimToString(yMid * yUnit - 1.5 * xUnit) .. "}" ) tex.sprint("\n\t\t\\pmbdomdrawfeature{helix/full back}") end residuesLeft = residuesLeft - 2 currX = currX + 2 end residuesLeft = feature.stop - feature.start currX = xLeft + 1.5 while residuesLeft > 0 do if residuesLeft == 1 then tex.sprint( "\n\t\t\\def\\xRight{" .. dimToString((currX + 0.5) * xUnit) .. "}" ) tex.sprint("\n\t\t\\def\\yMid{" .. dimToString(yMid * yUnit) .. "}") tex.sprint("\n\t\t\\pmbdomdrawfeature{helix/half upper front}") else tex.sprint("\n\t\t\\def\\xMid{" .. dimToString(currX * xUnit) .. "}") tex.sprint( "\n\t\t\\def\\yLower{" .. dimToString(yMid * yUnit - 1.5 * xUnit) .. "}" ) tex.sprint("\n\t\t\\pmbdomdrawfeature{helix/full front}") end residuesLeft = residuesLeft - 2 currX = currX + 2 end end SpecialKeys = {} function SpecialKeys:new(parms) parms = parms or {} local newSpecialKeys = { disulfideKeys = {}, featureStyles = {}, printFunctions = {} } for keyList, listContents in pairs(parms) do for key, value in pairs(listContents) do newSpecialKeys[keyList][key] = value end end setmetatable(newSpecialKeys, self) self.__index = self return newSpecialKeys end function SpecialKeys:setKeys(keylist, keys, value) for key in keys:gmatch("([^,]+)") do key = key:trim() self[keylist][key] = value end end function SpecialKeys:setFeatureStyle(key, style) local newStyleList, styleCycles, styleContents newStyleList = {} while style ~= "" do styleCycles = 1 if style:sub(1,1) == "{" then styleContents = style:match("%b{}") style = style:match("%b{}(.*)") elseif style:sub(1,1) == "*" then styleCycles, styleContents = style:match("%*(%d*)(%b{})") if styleCycles == "" then styleCycles = 1 end style = style:match("%*%d*%b{}(.*)") elseif style:sub(1,1) == "," or style:sub(1,1) == " " then style = style:match("[,%s]+(.*)") styleCycles, styleContents = nil, nil else styleContents = style:match("([^,]+),") if not styleContents then styleContents = style style = "" else style = style:match("[^,]+,(.*)") end end if styleCycles then table.insert( newStyleList, {cycles = styleCycles, style = styleContents} ) end end self.featureStyles[key] = newStyleList end function SpecialKeys:aliasFeatureStyle(newKey, oldKey) self.featureStyles[newKey] = {alias = oldKey} end function SpecialKeys:getBaseKey(key) if self.featureStyles[key] then if self.featureStyles[key].alias then return self.featureStyles[key].alias end end return key end function SpecialKeys:clearKeys(keylist) self[keylist] = {} end function SpecialKeys:selectStyleFromList(key, styleID) local styleList if not self.featureStyles[key] then packageWarning( "Feature style `" .. key .. "' unknown, using `default'." ) styleList = self.featureStyles.default elseif self.featureStyles[key].alias then styleList = self.featureStyles[self.featureStyles[key].alias] else styleList = self.featureStyles[key] end while true do for _, v in ipairs(styleList) do styleID = styleID - v.cycles if styleID < 1 then return v.style end end end end Protein = {} function Protein:new() local newProtein = { name = "", sequenceLength = -1, ft = {}, sequence = "", xUnit = stringToDim("0.5mm"), yUnit = stringToDim("6mm"), residuesPerLine = 250, residueRangeMin = 1, residueRangeMax = 100, residueNumbering = {}, revResidueNumbering = {}, baselineSkip = 3, rulerRange = {}, defaultRulerStepSize = 50, showRuler = true, currentStyle = {}, specialKeys = SpecialKeys:new() } setmetatable(newProtein, self) self.__index = self return newProtein end function Protein:toAbsoluteResidueNumber(value) local result = value:match("%b()") if result then result = tonumber(result:sub(2, -2)) else result = self.revResidueNumbering[(value:gsub("[<>%?]", ""))] end if not result then packageError("Bad or missing start/end point value: " .. value) end return result end function Protein:readUniprotFile(filename) local uniprotFile, errorMsg = io.open(filename, "r") if not uniprotFile then packageError(errorMsg) end local sequence = {} local inSequence = false local featureTable = {} for currLine in uniprotFile:lines() do local lineCode = currLine:sub(1, 2) local lineContents = currLine:sub(3) if lineCode == "ID" then local name, sequenceLength = lineContents:match("%s*(%S+)%s*%a+;%s*(%d+)%s*AA%.") self.name = name self.sequenceLength = tonumber(sequenceLength) self.residueRangeMax = self.sequenceLength elseif lineCode == "FT" then local key = currLine:sub(6, 13):trim() local start, stop, description = currLine:sub(15, 20), currLine:sub(22, 27), currLine:sub(35, 75) if key ~= "" then table.insert(featureTable, { key = key, start = "(" .. start .. ")", stop = "(" .. stop .. ")", description = description, style = "", kvList = "" }) else featureTable[#featureTable].description = featureTable[#featureTable].description .. description end elseif lineCode == "SQ" then inSequence = true elseif lineCode == " " and inSequence then table.insert(sequence, (lineContents:gsub("%s+", ""))) elseif lineCode == "\\\\" then break end end uniprotFile:close() if next(sequence) then self.sequence = table.concat(sequence) end for _, v in ipairs(featureTable) do self:addFeature(v) end end function Protein:readGffFile(filename) local gffFile, errorMsg = io.open(filename, "r") local lineContents, fields, lineNumber if not gffFile then packageError(errorMsg) end lineNumber = 1 for currLine in gffFile:lines() do lineContents = currLine:gsub("#.*$", "") fields = {} if lineContents ~= "" then for currField in lineContents:gmatch("([^\t]+)") do table.insert(fields, currField) end if not fields[5] then packageError("Bad line (" .. lineNumber .. ") in gff file '" .. filename .. "':\n" .. currLine) break end self:addFeature{ key = fields[3], start = "(" .. fields[4] .. ")", stop = "(" .. fields[5] .. ")", description = fields[9] or "", style = "", kvList = "" } end lineNumber = lineNumber + 1 end gffFile:close() end function Protein:getParameters() tex.sprint( "\\pgfmolbioset[domains]{name={" .. self.name .. "},sequence={" .. self.sequence .. "},sequence length=" .. self.sequenceLength .. "}" ) end function Protein:setParameters(newParms) local keyHash = { sequenceLength = function(v) v = tonumber(v) if not v then return self.sequenceLength end if v < 1 then packageError("Sequence length must be larger than zero.") end return v end, residueNumbering = function(v) local ranges = {} local start, startNumber, startLetter, stop self.revResidueNumbering = {} if v:trim() == "auto" then for i = 1, self.sequenceLength do table.insert(ranges, tostring(i)) end else --example list: `1-4,5,6A-D' for _, value in ipairs(v:explode(",+")) do value = value:trim() start, stop = value:match("(%w*)%s*%-%s*(%w*)$") if not start then start = value:match("(%w*)") end if not start or start == "" then --invalid range packageError("Unknown residue numbering range: " .. value) end if stop then if tonumber(start) and tonumber(stop) then --process range `1-4' for currNumber = tonumber(start), tonumber(stop) do table.insert(ranges, tostring(currNumber)) end else --process range `6A-D' startNumber, startLetter = start:match("(%d*)(%a)") stop = stop:match("(%a)") for currLetter = startLetter:byte(), stop:byte() do table.insert(ranges, startNumber .. string.char(currLetter)) end end else --process range `5' table.insert(ranges, start) end end end for i, value in ipairs(ranges) do if self.revResidueNumbering[value] then packageError("The range value " .. value .. " appears more than once.") else self.revResidueNumbering[value] = i end end return ranges end, residueRange = function(v) local num local residueRangeMin, residueRangeMax = getRange(v:trim(), "^([%w%(%)]+)%s*%-", "%-%s*([%w%(%)]+)$") if residueRangeMin == "auto" then self.residueRangeMin = 1 else num = residueRangeMin:match("%b()") if num then self.residueRangeMin = tonumber(num:sub(2, -2)) elseif self.revResidueNumbering[residueRangeMin] then self.residueRangeMin = self.revResidueNumbering[residueRangeMin] else packageError("Invalid residue range: " .. residueRangeMin) end end if residueRangeMax == "auto" then self.residueRangeMax = self.sequenceLength else num = residueRangeMax:match("%b()") if num then self.residueRangeMax = tonumber(num:sub(2, -2)) elseif self.revResidueNumbering[residueRangeMax] then self.residueRangeMax = self.revResidueNumbering[residueRangeMax] else packageError("Invalid residue range: " .. residueRangeMax) end end if self.residueRangeMin >= self.residueRangeMax then packageError("Residue range is smaller than 1.") end end, defaultRulerStepSize = tonumber, name = tostring, sequence = tostring, xUnit = stringToDim, yUnit = stringToDim, residuesPerLine = tonumber, baselineSkip = tonumber, rulerRange = function(v) local num local ranges = {} local rulerRangeMin, rulerRangeMax, rulerRangeStep for _, value in ipairs(v:explode(",+")) do rulerRangeMin, rulerRangeMax, rulerRangeStep = getRange(value:trim(), "^([%w%(%)]+)", "%-%s*([%w%(%)]+)", "step%s*(%d+)$") if rulerRangeMin == "auto" then rulerRangeMin = self.residueRangeMin else num = rulerRangeMin:match("%b()") if num then rulerRangeMin = tonumber(num:sub(2, -2)) elseif self.revResidueNumbering[rulerRangeMin] then rulerRangeMin = self.revResidueNumbering[rulerRangeMin] else packageError("Invalid lower ruler range: " .. rulerRangeMin) end end if rulerRangeMax then if rulerRangeMax == "auto" then rulerRangeMax = self.residueRangeMax else num = rulerRangeMax:match("%b()") if num then rulerRangeMax = tonumber(num:sub(2, -2)) elseif self.revResidueNumbering[rulerRangeMax] then rulerRangeMax = self.revResidueNumbering[rulerRangeMax] else packageError("Invalid upper ruler range: " .. rulerRangeMax) end end if rulerRangeMin >= rulerRangeMax then packageError("Ruler range is smaller than 1.") end if rulerRangeMin < self.residueRangeMin then rulerRangeMin = self.residueRangeMin packageWarning( "Lower ruler range is smaller than" .. "lower residue range. It was adjusted to " .. rulerRangeMin .. "." ) end if rulerRangeMax > self.residueRangeMax then rulerRangeMax = self.residueRangeMax packageWarning( "Upper ruler range exceeds" .. "upper residue range. It was adjusted to " .. rulerRangeMax .. "." ) end else rulerRangeMax = rulerRangeMin end rulerRangeStep = tonumber(rulerRangeStep) or self.defaultRulerStepSize for i = rulerRangeMin, rulerRangeMax, rulerRangeStep do table.insert( ranges, {pos = i, number = self.residueNumbering[i]} ) end end return ranges end, showRuler = function(v) if v == "true" then return true else return false end end } for key, value in pairs(newParms) do if keyHash[key] then self[key] = keyHash[key](value) if pgfmolbio.errorCatched then return end end end end function Protein:addFeature(newFeature) local baseKey, ftEntry baseKey = self.specialKeys:getBaseKey(newFeature.key) if self.currentStyle[baseKey] then self.currentStyle[baseKey] = self.currentStyle[baseKey] + 1 else self.currentStyle[baseKey] = 1 end ftEntry = { key = newFeature.key, start = self:toAbsoluteResidueNumber(newFeature.start), stop = self:toAbsoluteResidueNumber(newFeature.stop), kvList = "style={" .. self.specialKeys:selectStyleFromList(baseKey, self.currentStyle[baseKey]) .. "}", level = newFeature.level or nil } if newFeature.kvList ~= "" then ftEntry.kvList = ftEntry.kvList .. "," .. newFeature.kvList end if newFeature.description then ftEntry.kvList = ftEntry.kvList .. ",description={" .. newFeature.description .. "}" ftEntry.description = newFeature.description end table.insert(self.ft, newFeature.layer or #self.ft + 1, ftEntry) end function Protein:calculateDisulfideLevels() if pgfmolbio.errorCatched then return end local disulfideGrid, currLevel, levelFree disulfideGrid = {} for i, v in ipairs(self.ft) do if self.specialKeys.disulfideKeys[v.key] then if v.level then if not disulfideGrid[v.level] then disulfideGrid[v.level] = {} end for currPos = v.start, v.stop do disulfideGrid[v.level][currPos] = true end else currLevel = 1 repeat levelFree = true if disulfideGrid[currLevel] then for currPos = v.start, v.stop do levelFree = levelFree and not disulfideGrid[currLevel][currPos] end if levelFree then self.ft[i].level = currLevel for currPos = v.start, v.stop do disulfideGrid[currLevel][currPos] = true end end else self.ft[i].level = currLevel disulfideGrid[currLevel] = {} for currPos = v.start, v.stop do disulfideGrid[currLevel][currPos] = true end levelFree = true end currLevel = currLevel + 1 until levelFree == true end end end end function Protein:printTikzDomains() if pgfmolbio.errorCatched then return end local xLeft, xMid, xRight, yMid, xLeftClip, xRightClip, currLine, residuesLeft, currStyle for _, currFeature in ipairs(self.ft) do currLine = 0 xLeft = currFeature.start - self.residueRangeMin - currLine * self.residuesPerLine + 1 while xLeft > self.residuesPerLine do xLeft = xLeft - self.residuesPerLine currLine = currLine + 1 end xLeft = xLeft - 1 xRight = currFeature.stop - self.residueRangeMin - currLine * self.residuesPerLine + 1 residuesLeft = self.residueRangeMax - self.residueRangeMin - currLine * self.residuesPerLine + 1 xLeftClip = stringToDim("-5cm") xRightClip = self.residuesPerLine * self.xUnit if currFeature.start <= self.residueRangeMax and currFeature.stop >= self.residueRangeMin then repeat if residuesLeft <= self.residuesPerLine then if residuesLeft < xRight then xRightClip = residuesLeft * self.xUnit else xRightClip = xRight * self.xUnit + stringToDim("5cm") end else if xRight <= self.residuesPerLine then xRightClip = xRight * self.xUnit + stringToDim("5cm") end end if xLeft < 0 then xLeftClip = stringToDim("0cm") end xMid = (xLeft + xRight) / 2 yMid = -currLine * self.baselineSkip if currFeature.level then currFeature.kvList = currFeature.kvList .. ",level=" .. currFeature.level end currFeature.sequence = self.sequence:sub(currFeature.start, currFeature.stop) tex.sprint("\n\t\\begin{scope}\\begin{pgfinterruptboundingbox}") tex.sprint("\n\t\t\\def\\xLeft{" .. dimToString(xLeft * self.xUnit) .. "}") tex.sprint("\n\t\t\\def\\xMid{" .. dimToString(xMid * self.xUnit) .. "}") tex.sprint("\n\t\t\\def\\xRight{" .. dimToString(xRight * self.xUnit) .. "}") tex.sprint("\n\t\t\\def\\yMid{" .. dimToString(yMid * self.yUnit) .. "}") tex.sprint("\n\t\t\\def\\featureSequence{" .. currFeature.sequence .. "}") tex.sprint( "\n\t\t\\clip (" .. dimToString(xLeftClip) .. ", \\yMid + " .. dimToString(stringToDim("10cm")) .. ") rectangle (" .. dimToString(xRightClip) .. ", \\yMid - " .. dimToString(stringToDim("10cm")) .. ");" ) tex.sprint( "\n\t\t\\pgfmolbioset[domains]{" .. currFeature.kvList .. "}" ) if self.specialKeys.printFunctions[currFeature.key] then self.specialKeys.printFunctions[currFeature.key]( currFeature, xLeft, xRight, yMid, self.xUnit, self.yUnit) else tex.sprint("\n\t\t\\pmbdomdrawfeature{" .. currFeature.key .. "}") end tex.sprint("\n\t\\end{pgfinterruptboundingbox}\\end{scope}") currLine = currLine + 1 xLeft = xLeft - self.residuesPerLine xRight = xRight - self.residuesPerLine residuesLeft = residuesLeft - self.residuesPerLine until xRight < 1 or residuesLeft < 1 end end if self.showRuler then currStyle = 1 tex.sprint("\n\t\\begin{scope}") for _, currRuler in ipairs(self.rulerRange) do currLine = 0 xMid = currRuler.pos - self.residueRangeMin - currLine * self.residuesPerLine + 1 while xMid > self.residuesPerLine do xMid = xMid - self.residuesPerLine currLine = currLine + 1 end xMid = xMid - 0.5 yMid = -currLine * self.baselineSkip tex.sprint( "\n\t\t\\pgfmolbioset[domains]{current style/.style={" .. self.specialKeys:selectStyleFromList("other/ruler", currStyle) .. "}}" ) tex.sprint("\n\t\t\t\\def\\xMid{" .. dimToString(xMid * self.xUnit) .. "}") tex.sprint("\n\t\t\t\\let\\xLeft\\xMid\\let\\xRight\\xMid") tex.sprint("\n\t\t\t\\def\\yMid{" .. dimToString(yMid * self.yUnit) .. "}") tex.sprint("\n\t\t\t\\def\\residueNumber{" .. currRuler.number .. "}") tex.sprint("\n\t\t\t\\pmbdomdrawfeature{other/ruler}") currStyle = currStyle + 1 end tex.sprint("\n\t\\end{scope}") end xMid = math.min( self.residuesPerLine, self.residueRangeMax - self.residueRangeMin + 1 ) / 2 tex.sprint("\n\t\\begin{scope}") tex.sprint( "\n\t\t\\pgfmolbioset[domains]{current style/.style={" .. self.specialKeys:selectStyleFromList("other/name", 1) .. "}}" ) tex.sprint("\n\t\t\\def\\xLeft{0mm}") tex.sprint("\n\t\t\\def\\xMid{" .. dimToString(xMid * self.xUnit) .. "}") tex.sprint("\n\t\t\\def\\xRight{" .. dimToString(self.residuesPerLine * self.xUnit) .. "}") tex.sprint("\n\t\t\\def\\yMid{0mm}") tex.sprint("\n\t\t\\pmbdomdrawfeature{other/name}") tex.sprint("\n\t\\end{scope}") tex.sprint( "\n\t\\pmbprotocolsizes{" .. "\\pmbdomvalueof{enlarge left}}{\\pmbdomvalueof{enlarge top}}" ) currLine = math.ceil( (self.residueRangeMax - self.residueRangeMin + 1) / self.residuesPerLine ) - 1 xRight = math.min( self.residuesPerLine, self.residueRangeMax - self.residueRangeMin + 1 ) tex.sprint( "\n\t\\pmbprotocolsizes{" .. dimToString(xRight * self.xUnit) .. " + \\pmbdomvalueof{enlarge right}}{" .. dimToString(-currLine * self.baselineSkip * self.yUnit) .. " + \\pmbdomvalueof{enlarge bottom}}" ) end function Protein:__tostring() local result = {} local currLine currLine = "\\begin{pmbdomains}\n\t\t[name={" .. self.name .. "}" if self.sequence ~= "" then currLine = currLine .. ",\n\t\tsequence=" .. self.sequence end currLine = currLine .. "]{" .. self.sequenceLength .. "}" table.insert(result, currLine) for i, v in ipairs(self.ft) do if v.key ~= "other/main chain" then currLine = "\t\\addfeature" if self.includeDescription and v.description then currLine = currLine .. "[description={" .. v.description .. "}]" end currLine = currLine .. "{" .. v.key .. "}{" .. v.start .. "}{" .. v.stop .. "}" table.insert(result, currLine) end end table.insert(result, "\\end{pmbdomains}" ) return table.concat(result, "\n") end -- -- End of file `pgfmolbio.domains.lua'.