if not modules then modules = { } end modules ['chem-str'] = { version = 1.001, comment = "companion to chem-str.mkiv", author = "Hans Hagen and Alan Braslau", copyright = "PRAGMA ADE / ConTeXt Development Team", license = "see context related readme files" } -- The original \PPCHTEX\ code was written in pure \TEX\, although later we made -- the move from \PICTEX\ to \METAPOST\. The current implementation is a mix between -- \TEX\, \LUA\ and \METAPOST. Although the first objective is to get a compatible -- but better implementation, later versions might provide more. -- -- Well, the later version has arrived as Alan took it upon him to make the code -- deviate even further from the original implementation. The original (early \MKII) -- variant operated within the boundaries of \PICTEX\ and as it supported MetaPost as -- alternative output. As a consequence it still used a stepwise graphic construction -- approach. As we used \TEX\ for parsing, the syntax was more rigid than it is now. -- This new variant uses a more mathematical and metapostisch approach. In the process -- more rendering variants have been added and alignment has been automated.. As a result -- the current user interface is slightly different from the old one but hopefully users -- will like the added value. -- directive_strictorder: one might set this to off when associated texts are disordered too local trace_structure = false trackers .register("chemistry.structure", function(v) trace_structure = v end) local trace_metapost = false trackers .register("chemistry.metapost", function(v) trace_metapost = v end) local trace_textstack = false trackers .register("chemistry.textstack", function(v) trace_textstack = v end) local directive_strictorder = true directives.register("chemistry.strictorder", function(v) directive_strictorder = v end) local directive_strictindex = false directives.register("chemistry.strictindex", function(v) directive_strictindex = v end) local report_chemistry = logs.reporter("chemistry") local format, gmatch, match, lower, gsub = string.format, string.gmatch, string.match, string.lower, string.gsub local concat, insert, remove, unique, sorted = table.concat, table.insert, table.remove, table.unique, table.sorted local processor_tostring = typesetters and typesetters.processors.tostring local settings_to_array = utilities.parsers.settings_to_array local settings_to_array_with_repeat = utilities.parsers.settings_to_array_with_repeat local lpegmatch = lpeg.match local P, R, S, C, Cs, Ct, Cc, Cmt = lpeg.P, lpeg.R, lpeg.S, lpeg.C, lpeg.Cs, lpeg.Ct, lpeg.Cc, lpeg.Cmt local variables = interfaces and interfaces.variables local context = context local formatters = string.formatters local v_default = variables.default local v_small = variables.small local v_medium = variables.medium local v_big = variables.big local v_normal = variables.normal local v_fit = variables.fit local v_on = variables.on local mpnamedcolor = attributes.colors.mpnamedcolor local topoints = number.topoints local todimen = string.todimen chemistry = chemistry or { } local chemistry = chemistry chemistry.instance = "chemistry" chemistry.format = "metafun" chemistry.structures = 0 local common_keys = { b = "line", r = "line", sb = "line", sr = "line", rd = "line", rh = "line", rb = "line", rbd = "line", cc = "line", ccd = "line", line = "line", dash = "line", arrow = "line", c = "fixed", cd = "fixed", z = "text", zt = "text", zlt = "text", zrt = "text", rz = "text", rt = "text", lrt = "text", rrt = "text", label = "text", zln = "number", zrn = "number", rn = "number", lrn = "number", rrn = "number", zn = "number", number = "number", mov = "transform", mark = "transform", move = "transform", diff = "transform", off = "transform", adj = "transform", sub = "transform", } local front_keys = { bb = "line", eb = "line", rr = "line", lr = "line", lsr = "line", rsr = "line", lrd = "line", rrd = "line", lrh = "line", rrh = "line", lrbd = "line", rrbd = "line", lrb = "line", rrb = "line", lrz = "text", rrz = "text", lsub = "transform", rsub = "transform", } local one_keys = { db = "line", tb = "line", bb = "line", dr = "line", hb = "line", bd = "line", bw = "line", oe = "line", sd = "line", rdb = "line", ldb = "line", ldd = "line", rdd = "line", ep = "line", es = "line", ed = "line", et = "line", cz = "text", rot = "transform", dir = "transform", rm = "transform", mir = "transform", } local ring_keys = { db = "line", br = "line", lr = "line", rr = "line", lsr = "line", rsr = "line", lrd = "line", rrd = "line", lrb = "line", rrb = "line", lrh = "line", rrh = "line", lrbd = "line", rrbd = "line", dr = "line", eb = "line", er = "line", ed = "line", au = "line", ad = "line", s = "line", ss = "line", mid = "line", mids = "line", midz = "text", lrz = "text", rrz = "text", crz = "text", rot = "transform", mir = "transform", adj = "transform", lsub = "transform", rsub = "transform", rm = "transform", } -- table.setmetatableindex(front_keys,common_keys) -- table.setmetatableindex(one_keys,common_keys) -- table.setmetatableindex(ring_keys,common_keys) -- or (faster but not needed here): front_keys = table.merged(front_keys,common_keys) one_keys = table.merged(one_keys,common_keys) ring_keys = table.merged(ring_keys,common_keys) local syntax = { carbon = { max = 4, keys = one_keys, }, alkyl = { max = 4, keys = one_keys, }, newmanstagger = { max = 6, keys = one_keys, }, newmaneclipsed = { max = 6, keys = one_keys, }, one = { max = 8, keys = one_keys, }, three = { max = 3, keys = ring_keys, }, four = { max = 4, keys = ring_keys, }, five = { max = 5, keys = ring_keys, }, six = { max = 6, keys = ring_keys, }, seven = { max = 7, keys = ring_keys, }, eight = { max = 8, keys = ring_keys, }, nine = { max = 9, keys = ring_keys, }, fivefront = { max = 5, keys = front_keys, }, sixfront = { max = 6, keys = front_keys, }, chair = { max = 6, keys = front_keys, }, boat = { max = 6, keys = front_keys, }, pb = { direct = 'chem_pb ;' }, pe = { direct = 'chem_pe ;' }, save = { direct = 'chem_save ;' }, restore = { direct = 'chem_restore ;' }, chem = { direct = 'chem_symbol("\\chemicaltext{%s}") ;', arguments = 1 }, space = { direct = 'chem_symbol("\\chemicalsymbol[space]") ;' }, plus = { direct = 'chem_symbol("\\chemicalsymbol[plus]") ;' }, minus = { direct = 'chem_symbol("\\chemicalsymbol[minus]") ;' }, gives = { direct = 'chem_symbol("\\chemicalsymbol[gives]{%s}{%s}") ;', arguments = 2 }, equilibrium = { direct = 'chem_symbol("\\chemicalsymbol[equilibrium]{%s}{%s}") ;', arguments = 2 }, mesomeric = { direct = 'chem_symbol("\\chemicalsymbol[mesomeric]{%s}{%s}") ;', arguments = 2 }, opencomplex = { direct = 'chem_symbol("\\chemicalsymbol[opencomplex]") ;' }, closecomplex = { direct = 'chem_symbol("\\chemicalsymbol[closecomplex]") ;' }, reset = { direct = 'chem_reset ;' }, mp = { direct = '%s', arguments = 1 }, -- backdoor MP code - dangerous! } chemistry.definitions = chemistry.definitions or { } local definitions = chemistry.definitions storage.register("chemistry/definitions",definitions,"chemistry.definitions") function chemistry.undefine(name) definitions[lower(name)] = nil end function chemistry.define(name,spec,text) name = lower(name) local dn = definitions[name] if not dn then dn = { } definitions[name] = dn end dn[#dn+1] = { spec = settings_to_array_with_repeat(spec,true), text = settings_to_array_with_repeat(text,true), } end local metacode, variant, keys, max, txt, pstack, sstack, align local molecule = chemistry.molecule -- or use lpegmatch(chemistry.moleculeparser,...) local function fetch(txt) local st = stack[txt] local t = st.text[st.n] -- inspect(stack) while not t and txt > 1 do txt = txt - 1 st = stack[txt] t = st.text[st.n] end if t then if trace_textstack then report_chemistry("fetching from stack %s slot %s: %s",txt,st.n,t) end st.n = st.n + 1 end return txt, t end local remapper = { ["+"] = "p", ["-"] = "m", } local dchrs = R("09") local sign = S("+-") local digit = dchrs / tonumber local amount = (sign^-1 * (dchrs^0 * P('.'))^-1 * dchrs^1) / tonumber local single = digit local range = digit * P("..") * digit local set = Ct(digit^2) local colon = P(":") local equal = P("=") local other = 1 - digit - colon - equal local remapped = sign / remapper local operation = Cs(other^1) local special = (colon * C(other^1)) + Cc("") local text = (equal * C(P(1)^0)) + Cc(false) local pattern = (amount + Cc(1)) * (remapped + Cc("")) * Cs(operation/lower) * Cs(special/lower) * ( range * Cc(false) * text + Cc(false) * Cc(false) * set * text + single * Cc(false) * Cc(false) * text + Cc(false) * Cc(false) * Cc(false) * text ) -- local n, operation, index, upto, set, text = lpegmatch(pattern,"RZ1357") -- print(lpegmatch(pattern,"RZ=x")) -- 1 RZ false false false x -- print(lpegmatch(pattern,"RZ1=x")) -- 1 RZ 1 false false x -- print(lpegmatch(pattern,"RZ1..3=x")) -- 1 RZ 1 3 false x -- print(lpegmatch(pattern,"RZ13=x")) -- 1 RZ false false table x local f_initialize = formatters['if unknown context_chem : input mp-chem.mpiv ; fi ;'] local f_start_structure = formatters['chem_start_structure(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s);'] local f_stop_structure = formatters['chem_stop_structure;'] local f_start_component = formatters['chem_start_component;'] local f_stop_component = formatters['chem_stop_component;'] local f_line = formatters['chem_%s%s(%s,%s,%s,%s,%s);'] local f_set = formatters['chem_set(%s);'] local f_number = formatters['chem_%s%s(%s,%s,"\\chemicaltext{%s}");'] local f_text = f_number local f_empty_normal = formatters['chem_%s(%s,%s,"");'] local f_empty_center = formatters['chem_c%s(%s,%s,"");'] local f_transform = formatters['chem_%s(%s,%s,%s);'] local prepareMPvariable = commands and commands.prepareMPvariable local function process(level,spec,text,n,rulethickness,rulecolor,offset,default_variant) insert(stack,{ spec = spec, text = text, n = n }) local txt = #stack local m = #metacode local saved_rulethickness = rulethickness local saved_rulecolor = rulecolor local saved_align = align local current_variant = default_variant or "six" for i=1,#spec do local step = spec[i] local s = lower(step) local n = current_variant .. ":" .. s local d = definitions[n] if not d then n = s d = definitions[n] end if d then if trace_structure then report_chemistry("%s > %s => definition: %s (%s snippets)",level,step,n,#d) end for i=1,#d do local di = d[i] current_variant = process(level+1,di.spec,di.text,1,rulethickness,rulecolor,offset,current_variant) -- offset? end else local factor, osign, operation, special, index, upto, set, text = lpegmatch(pattern,step) if trace_structure then local set = set and concat(set," ") or "-" report_chemistry("%s > %s => factor: %s, osign: %s operation: %s, special: %s, index: %s, upto: %s, set: %s, text: %s", level,step,factor or "",osign or "",operation or "-",special and special ~= "" or "-",index or "-",upto or "-",set or "-",text or "-") end if operation == "rulecolor" then local t = text if not t then txt, t = fetch(txt) end if t == v_default or t == v_normal or t == "" then rulecolor = saved_rulecolor elseif t then rulecolor = mpnamedcolor(t) end elseif operation == "rulethickness" then local t = text if not t then txt, t = fetch(txt) end if t == v_default or t == v_normal or t == t_medium or t == "" then rulethickness = saved_rulethickness elseif t == v_small then rulethickness = topoints(1/1.2 * todimen(saved_rulethickness)) elseif t == v_big then rulethickness = topoints(1.2 * todimen(saved_rulethickness)) elseif t then -- rulethickness = topoints(todimen(t)) -- mp can't handle sp rulethickness = topoints(tonumber(t) * todimen(saved_rulethickness)) end elseif operation == "symalign" then local t = text if not t then txt, t = fetch(txt) end if t == v_default or t == v_normal then align = saved_align elseif t and t ~= "" then align = "." .. t end elseif operation == "pb" then insert(pstack,variant) m = m + 1 ; metacode[m] = syntax.pb.direct if keys[special] == "text" and index then if keys["c"..special] == "text" then -- can be option: auto ... m = m + 1 ; metacode[m] = f_empty_center(special,variant,index) else m = m + 1 ; metacode[m] = f_empty_normal(special,variant,index) end end elseif operation == "pe" then variant = remove(pstack) local ss = syntax[variant] keys, max = ss.keys, ss.max m = m + 1 ; metacode[m] = syntax[operation].direct m = m + 1 ; metacode[m] = f_set(variant) current_variant = variant elseif operation == "save" then insert(sstack,variant) m = m + 1 ; metacode[m] = syntax.save.direct elseif operation == "restore" then variant = remove(sstack) local ss = syntax[variant] keys, max = ss.keys, ss.max m = m + 1 ; metacode[m] = syntax[operation].direct m = m + 1 ; metacode[m] = f_set(variant) current_variant = variant elseif operation then local ss = syntax[operation] local what = keys[operation] local ns = 0 if set then local sv = syntax[current_variant] local ms = sv and sv.max set = unique(set) ns = #set if directive_strictorder then if what == "line" then set = sorted(set) end if directive_strictindex and ms then for i=ns,1,-1 do local si = set[i] if si > ms then report_chemistry("%s > operation %s: limited to %s steps, ignoring %s", level,operation,ms,si) set[i] = nil ns = ns - 1 else break end end end else if directive_strictindex and ms then local t, nt = { }, 0 for i=1,ns do local si = set[i] if si > ms then report_chemistry("%s > operation %s: limited to %s steps, ignoring %s", level,operation,ms,si) set[i] = nil else nt = nt + 1 t[nt] = si end end ns = nt set = t end end end if ss then local ds = ss.direct if ds then local sa = ss.arguments if sa == 1 then local one ; txt, one = fetch(txt) m = m + 1 ; metacode[m] = format(ds,one or "") elseif sa == 2 then local one ; txt, one = fetch(txt) local two ; txt, two = fetch(txt) m = m + 1 ; metacode[m] = format(ds,one or "",two or "") else m = m + 1 ; metacode[m] = ds end elseif ss.keys then variant, keys, max = s, ss.keys, ss.max m = m + 1 ; metacode[m] = f_set(variant) current_variant = variant end elseif what == "line" then local s = osign if s ~= "" then s = "." .. s end if set then -- condense consecutive numbers in a set to a range local sf, st = set[1] for i=1,ns do if i > 1 and set[i] ~= set[i-1]+1 then m = m + 1 ; metacode[m] = f_line(operation,s,variant,sf,st,rulethickness,rulecolor) sf = set[i] end st = set[i] end m = m + 1 ; metacode[m] = f_line(operation,s,variant,sf,st,rulethickness,rulecolor) elseif upto then m = m + 1 ; metacode[m] = f_line(operation,s,variant,index,upto,rulethickness,rulecolor) elseif index then m = m + 1 ; metacode[m] = f_line(operation,s,variant,index,index,rulethickness,rulecolor) else m = m + 1 ; metacode[m] = f_line(operation,s,variant,1,max,rulethickness,rulecolor) end elseif what == "number" then if set then for i=1,ns do local si = set[i] m = m + 1 ; metacode[m] = f_number(operation,align,variant,si,si) end elseif upto then for i=index,upto do local si = set[i] m = m + 1 ; metacode[m] = f_number(operation,align,variant,si,si) end elseif index then m = m + 1 ; metacode[m] = f_number(operation,align,variant,index,index) else for i=1,max do m = m + 1 ; metacode[m] = f_number(operation,align,variant,i,i) end end elseif what == "text" then if set then for i=1,ns do local si = set[i] local t = text if not t then txt, t = fetch(txt) end if t then t = molecule(processor_tostring(t)) m = m + 1 ; metacode[m] = f_text(operation,align,variant,si,t) end end elseif upto then for i=index,upto do local t = text if not t then txt, t = fetch(txt) end if t then t = molecule(processor_tostring(t)) m = m + 1 ; metacode[m] = f_text(operation,align,variant,i,t) end end elseif index == 0 then local t = text if not t then txt, t = fetch(txt) end if t then t = molecule(processor_tostring(t)) m = m + 1 ; metacode[m] = f_text(operation,align,variant,index,t) end elseif index then local t = text if not t then txt, t = fetch(txt) end if t then t = molecule(processor_tostring(t)) m = m + 1 ; metacode[m] = f_text(operation,align,variant,index,t) end else for i=1,max do local t = text if not t then txt, t = fetch(txt) end if t then t = molecule(processor_tostring(t)) m = m + 1 ; metacode[m] = f_text(operation,align,variant,i,t) end end end elseif what == "transform" then if osign == "m" then factor = -factor end if set then for i=1,ns do local si = set[i] m = m + 1 ; metacode[m] = f_transform(operation,variant,si,factor) end elseif upto then for i=index,upto do m = m + 1 ; metacode[m] = f_transform(operation,variant,i,factor) end else m = m + 1 ; metacode[m] = f_transform(operation,variant,index or 1,factor) end elseif what == "fixed" then m = m + 1 ; metacode[m] = f_transform(operation,variant,rulethickness,rulecolor) elseif trace_structure then report_chemistry("%s > warning: undefined operation %s ignored here", level, operation or "") end end end end remove(stack) return current_variant end -- the size related values are somewhat special but we want to be -- compatible -- -- rulethickness in points function chemistry.start(settings) chemistry.structures = chemistry.structures + 1 local emwidth, rulethickness, rulecolor, axiscolor = settings.emwidth, settings.rulethickness, settings.rulecolor, settings.framecolor local width, height, scale, rotation, offset = settings.width or 0, settings.height or 0, settings.scale or "normal", settings.rotation or 0, settings.offset or 0 local l, r, t, b = settings.left or 0, settings.right or 0, settings.top or 0, settings.bottom or 0 -- metacode = { } -- align = settings.symalign or "auto" if trace_structure then report_chemistry("scale: %s, rotation: %s, width: %s, height: %s, l: %s, r: %s, t: %s, b: %s", scale, rotation, width, height, l, r, t, b) report_chemistry("symalign: %s", align) end if align ~= "" then align = "." .. align end if scale == v_small then scale = 1/1.2 elseif scale == v_normal or scale == v_medium or scale == 0 then scale = 1 elseif scale == v_big then scale = 1.2 else scale = tonumber(scale) if not scale or scale == 0 then scale = 1 elseif scale >= 10 then scale = scale / 1000 elseif scale < .01 then scale = .01 end end if width == v_fit then width = true else width = tonumber(width) or 0 if width >= 10 then width = width / 1000 end if l == 0 then if r == 0 then l = width == 0 and 2 or width/2 r = l elseif width ~= 0 then if r > 10 or r < -10 then r = r / 1000 end l = width - r end elseif r == 0 and width ~= 0 then if l > 10 or l < -10 then l = l / 1000 end r = width - l end width = false end if height == v_fit then height = true else height = tonumber(height) or 0 if height >= 10 then height = height / 1000 end if t == 0 then if b == 0 then t = height == 0 and 2 or height/2 b = t elseif height ~= 0 then if b > 10 or b < -10 then b = b / 1000 end t = height - b end elseif b == 0 and height ~= 0 then if t > 10 or t < -10 then t = t / 1000 end b = height - t end height = false end rotation = tonumber(rotation) or 0 -- metacode[#metacode+1] = f_start_structure( chemistry.structures, l, r, t, b, scale, rotation, tostring(width), tostring(height), tostring(emwidth), tostring(offset), tostring(settings.axis == v_on), tostring(rulethickness), tostring(axiscolor) ) -- variant, keys, stack, pstack, sstack = "one", { }, { }, { }, { } end function chemistry.stop() metacode[#metacode+1] = f_stop_structure() local mpcode = concat(metacode,"\n") if trace_metapost then report_chemistry("metapost code:\n%s", mpcode) end if metapost.instance(chemistry.instance) then f_initialize = nil end metapost.graphic { instance = chemistry.instance, format = chemistry.format, data = mpcode, definitions = f_initialize and f_initialize(), } t_initialize = "" metacode = nil end function chemistry.component(spec,text,settings) rulethickness, rulecolor, offset = settings.rulethickness, settings.rulecolor local spec = settings_to_array_with_repeat(spec,true) -- no lower? local text = settings_to_array_with_repeat(text,true) -- inspect(spec) metacode[#metacode+1] = f_start_component() process(1,spec,text,1,rulethickness,rulecolor) -- offset? metacode[#metacode+1] = f_stop_component() end statistics.register("chemical formulas", function() if chemistry.structures > 0 then return format("%s chemical structure formulas",chemistry.structures) -- no timing needed, part of metapost end end) -- interfaces commands.undefinechemical = chemistry.undefine commands.definechemical = chemistry.define commands.startchemical = chemistry.start commands.stopchemical = chemistry.stop commands.chemicalcomponent = chemistry.component -- todo: top / bottom -- maybe add "=" for double and "≡" for triple? local inline = { ["single"] = "\\chemicalsinglebond", ["-"] = "\\chemicalsinglebond", ["double"] = "\\chemicaldoublebond", ["--"] = "\\chemicaldoublebond", ["triple"] = "\\chemicaltriplebond", ["---"] = "\\chemicaltriplebond", ["gives"] = "\\chemicalgives", ["->"] = "\\chemicalgives", ["equilibrium"] = "\\chemicalequilibrium", ["<->"] = "\\chemicalequilibrium", ["mesomeric"] = "\\chemicalmesomeric", ["<>"] = "\\chemicalmesomeric", ["plus"] = "\\chemicalplus", ["+"] = "\\chemicalplus", ["minus"] = "\\chemicalminus", ["space"] = "\\chemicalspace", } function commands.inlinechemical(spec) local spec = settings_to_array_with_repeat(spec,true) for i=1,#spec do local s = spec[i] local inl = inline[lower(s)] if inl then context(inl) -- could be a fast context.sprint else context.chemicalinline(molecule(s)) end end end