stable 2010-05-24 13:10

1 files changed, 490 insertions, 0 deletions

diff --git a/tex/context/base/chem-str.lua b/tex/context/base/chem-str.lua
new file mode 100644
index 000000000..ad4cc6c1b
--- /dev/null
+++ b/tex/context/base/chem-str.lua
@@ -0,0 +1,490 @@
+if not modules then modules = { } end modules ['chem-str'] = {
+    version   = 1.001,
+    comment   = "companion to chem-str.mkiv",
+    author    = "Hans Hagen, PRAGMA-ADE, Hasselt NL",
+    copyright = "PRAGMA ADE / ConTeXt Development Team",
+    license   = "see context related readme files"
+}
+
+-- This module in incomplete and experimental.
+
+-- We can push snippets into an mp instance.
+
+local trace_structure = false  trackers.register("chemistry.structure",  function(v) trace_structure = v end)
+local trace_textstack = false  trackers.register("chemistry.textstack",  function(v) trace_textstack = v end)
+
+local format, gmatch, match, lower, gsub = string.format, string.gmatch, string.match, string.lower, string.gsub
+local concat, insert, remove = table.concat, table.insert, table.remove
+local apply = structure.processors.apply
+local texsprint, ctxcatcodes = tex.sprint, tex.ctxcatcodes
+local lpegmatch = lpeg.match
+
+local variables = interfaces.variables
+
+chemicals = chemicals or { }
+
+chemicals.instance   = "metafun" -- "ppchtex"
+chemicals.format     = "metafun"
+chemicals.structures = 0
+
+local remapper = {
+    ["+"] = "p",
+    ["-"] = "m",
+}
+
+local common_keys = {
+    b = "line", eb = "line", db = "line", er = "line", dr = "line", br = "line",
+    sb = "line", msb = "line", psb = "line",
+    r = "line", pr = "line", mr = "line",
+    au = "line", ad = "line",
+    rb = "line", mrb = "line", prb = "line",
+    rd = "line", mrd = "line", prd = "line",
+    sr = "line", msr = "line", psr = "line",
+    c = "line", cc = "line", cd = "line", ccd = "line",
+    rn = "number", rtn = "number", rbn = "number",
+    s = "line", ss = "line",  pss = "line", mss = "line",
+    mid = "fixed", mids = "fixed", midz = "text",
+    z = "text", rz = "text", mrz = "text", prz = "text", crz = "text",
+    rt = "text", rtt = "text", rbt = "text", zt = "text", zn = "number",
+    mov = "transform", rot = "transform", adj = "transform", dir = "transform", sub = "transform",
+}
+
+local front_keys = {
+    b = "line", bb= "line",
+    sb = "line", msb = "line", psb = "line",
+    r = "line", pr = "line", mr = "line",
+    z = "text", mrz = "text", prz = "text",
+}
+
+local one_keys = {
+    sb = "line", db = "line", tb = "line",
+    ep = "line", es = "line", ed = "line", et = "line",
+    sd = "line", ldd = "line", rdd = "line",
+    hb = "line", bb = "line", oe = "line", bd = "line", bw = "line",
+    z = "text", cz = "text", zt = "text", zn = "number",
+    zbt = "text", zbn = "number", ztt = "text", ztn = "number",
+    mov = "transform", sub = "transform", dir = "transform", off = "transform",
+}
+
+local front_align = {
+    mrz = { { "b","b","b","b","b","b" } },
+    prz = { { "t","t","t","t","t","t" } },
+}
+
+local syntax = {
+    one = {
+        n = 1, max = 8, keys = one_keys,
+        align = {
+            z = { { "r", "r_b", "b", "l_b", "l", "l_t", "t", "r_t" } },
+--~             z = { { "r", "r", "b", "l", "l", "l", "t", "r" } },
+        }
+    },
+    three = {
+        n = 3, max = 3, keys = common_keys,
+        align = {
+            mrz = { { "r","b","l" }, { "b","l","t" }, { "l","t","r" }, { "t","r","b" } },
+            rz  = { { "r","l_b","l_t" }, { "b","l_t","r_t" }, { "l","r_t","r_b" }, { "t","r_b","l_b" } },
+            prz = { { "r","l","t" }, { "b","t","r" }, { "l","r","b" }, { "t","b","l" } },
+        }
+    },
+    four = {
+        n = 4, max = 4, keys = common_keys,
+        align = {
+            mrz = { { "t","r","b","l" }, { "r","b","l","t" }, { "b","l","t","r" }, { "l","t","r","b" } },
+            rz  = { { "r_t","r_b","l_b","l_t" }, { "r_b","l_b","l_t","r_t" }, { "l_b","l_t","r_t","r_b" }, { "l_t","r_t","r_b","l_b" } },
+            prz = { { "r","b","l","t" }, { "b","l","t","r" }, { "l","t","r","b" }, { "t","r","b","l" } },
+        }
+    },
+    five = {
+        n = 5, max = 5, keys = common_keys,
+        align = {
+            mrz = { { "t","r","b","b","l" }, { "r","b","l","l","t" }, { "b","l","t","r","r" }, { "l","t","r","r","b" } },
+            rz  = { { "r","r","b","l","t" }, { "b","b","l","t","r" }, { "l","l","t","r","b" }, { "t","t","r","b","l" } },
+            prz = { { "r","b","l","t","t" }, { "b","l","t","r","r" }, { "l","t","r","b","b" }, { "t","r","b","l","l" } },
+        }
+    },
+    six  = {
+        n = 6, max = 6, keys = common_keys,
+        align = {
+            mrz = { { "t","t","r","b","b","l" }, { "r","b","b","l","t","t" }, { "b","b","l","t","t","r" }, { "l","t","t","r","b","b" } },
+            rz  = { { "r","r","b","l","l","t" }, { "b","b","l","t","t","r" }, { "l","l","t","r","r","b" }, { "t","t","r","b","b","l" } },
+            prz = { { "r","b","l","l","t","r" }, { "b","l","t","t","r","b" }, { "l","t","r","r","b","l" }, { "t","r","b","b","l","t" } },
+        }
+    },
+    eight = {
+        n = 8, max = 8, keys = common_keys,
+        align = { -- todo
+            mrz = { { "t","r","r","b","b","l","l","t" }, { "r","b","b","l","l","t","t","r" }, { "b","l","l","t","t","r","r","b" }, { "l","t","t","r","r","b","b","l" } },
+            rz  = { { "r","r","b","b","l","l","t","t" }, { "b","b","l","l","t","t","r","r" }, { "l","l","t","t","r","r","b","b" }, { "t","t","r","r","b","b","l","l" } },
+            prz = { { "r","b","b","l","l","t","t","r" }, { "b","l","l","t","t","r","r","b" }, { "l","t","t","r","r","b","b","l" }, { "t","r","r","b","b","l","l","t" } },
+        }
+    },
+    five_front = {
+        n = -5, max = 5, keys = front_keys, align = front_align,
+    },
+    six_front = {
+        n = -6, max = 6, keys = front_keys, align = front_align,
+    },
+    pb           = { direct = 'chem_pb ;' },
+    pe           = { direct = 'chem_pe ;' },
+    save         = { direct = 'chem_save ;' },
+    restore      = { direct = 'chem_restore ;' },
+    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]") ;' },
+}
+
+local definitions = { }
+
+function chemicals.undefine(name)
+    definitions[lower(name)] = nil
+end
+
+function chemicals.define(name,spec,text)
+    name = lower(name)
+    local dn = definitions[name]
+    if not dn then dn = { } definitions[name] = dn end
+    dn[#dn+1] = {
+        spec = aux.settings_to_array(lower(spec)),
+        text = aux.settings_to_array(text),
+    }
+end
+
+local metacode, kind, keys, bonds, max, txt, textsize, rot, pstack
+local molecule = chemicals.molecule -- or use lpegmatch(chemicals.moleculeparser,...)
+
+local function fetch(txt)
+    local st = stack[txt]
+    local t = st.text[st.n]
+--~ st.n = st.n + 1
+    while not t and txt > 1 do
+        txt = txt - 1
+        st = stack[txt]
+        t = st.text[st.n]
+--~ st.n = st.n + 1
+    end
+    if t then
+        if trace_textstack then
+            logs.report("chemical", "fetching from stack %s slot %s: %s",txt,st.n,t)
+        end
+st.n = st.n + 1
+    end
+    return txt, t
+end
+
+local digit     = lpeg.R("09")/tonumber
+local colon     = lpeg.P(":")
+local equal     = lpeg.P("=")
+local other     = 1 - digit - colon - equal
+local remapped  = lpeg.S("+-") / remapper
+local operation = lpeg.Cs((remapped^0 * other)^1)
+local amount    = digit
+local single    = digit
+local special   = (colon * lpeg.C(other^1)) + lpeg.Cc("")
+local range     = digit * lpeg.P("..") * digit
+local set       = lpeg.Ct(digit^2)
+local text      = (equal * lpeg.C(lpeg.P(1)^0)) + lpeg.Cc(false)
+local pattern   =
+    (amount + lpeg.Cc(1)) *
+    operation *
+    special * (
+        range * lpeg.Cc(false) * text +
+        lpeg.Cc(false) * lpeg.Cc(false) * set * text +
+        single * lpeg.Cc(false) * lpeg.Cc(false) * text +
+        lpeg.Cc(false) * lpeg.Cc(false) * lpeg.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 function process(spec,text,n,rulethickness,rulecolor,offset)
+    insert(stack,{ spec=spec, text=text, n=n })
+    local txt = #stack
+    for i=1,#spec do
+        local s = spec[i]
+        local d = definitions[s]
+        if d then
+            for i=1,#d do
+                local di = d[i]
+                process(di.spec,di.text,1,rulethickness,rulecolor)
+            end
+        else
+            local rep, operation, special, index, upto, set, text = lpegmatch(pattern,s)
+            if operation == "pb" then
+                insert(pstack,kind)
+                metacode[#metacode+1] = syntax.pb.direct
+                if keys[special] == "text" and index then
+                    if keys["c"..special] == "text" then -- can be option: auto ...
+                        metacode[#metacode+1] = format('chem_c%s(%s,%s,"");',special,bonds,index)
+                    else
+                        metacode[#metacode+1] = format('chem_%s(%s,%s,"");',special,bonds,index)
+                    end
+                end
+            elseif operation == "save" then
+                insert(pstack,kind)
+                metacode[#metacode+1] = syntax.save.direct
+            elseif operation == "pe" or operation == "restore" then
+                kind = remove(pstack)
+                local ss = syntax[kind]
+                local prev = bonds or 6
+                keys, bonds, max, rot = ss.keys, ss.n, ss.max, 1
+                metacode[#metacode+1] = syntax[operation].direct
+                metacode[#metacode+1] = format("chem_set(%s,%s) ;",prev,bonds)
+            elseif operation == "front" then
+                if syntax[kind .. "_front"] then
+                    kind = kind .. "_front"
+                    local ss = syntax[kind]
+                    local prev = bonds or 6
+                    keys, bonds, max, rot = ss.keys, ss.n, ss.max, 1
+                    metacode[#metacode+1] = format("chem_set(%s,%s) ;",prev,bonds)
+                end
+            elseif operation then
+                local ss = syntax[operation]
+                if ss then
+                    local ds = ss.direct
+                    if ds then
+                        local sa = ss.arguments
+                        if sa == 1 then
+                            local one ; txt, one = fetch(txt)
+                            metacode[#metacode+1] = format(ds,one or "")
+                        elseif sa ==2 then
+                            local one ; txt, one = fetch(txt)
+                            local two ; txt, two = fetch(txt)
+                            metacode[#metacode+1] = format(ds,one or "",two or "")
+                        else
+                            metacode[#metacode+1] = ds
+                        end
+                    elseif ss.keys then
+                        local prev = bonds or 6
+                        kind, keys, bonds, max, rot = s, ss.keys, ss.n, ss.max, 1
+                        metacode[#metacode+1] = format("chem_set(%s,%s) ;",prev,bonds)
+                    end
+                else
+                    local what = keys[operation]
+                    if what == "line" then
+                        if set then
+                            for i=1,#set do
+                                local si = set[i]
+                                metacode[#metacode+1] = format("chem_%s(%s,%s,%s,%s,%s);",operation,bonds,si,si,rulethickness,rulecolor)
+                            end
+                        elseif upto then
+                            metacode[#metacode+1] = format("chem_%s(%s,%s,%s,%s,%s);",operation,bonds,index,upto,rulethickness,rulecolor)
+                        elseif index then
+                            metacode[#metacode+1] = format("chem_%s(%s,%s,%s,%s,%s);",operation,bonds,index,index,rulethickness,rulecolor)
+                        else
+                            metacode[#metacode+1] = format("chem_%s(%s,%s,%s,%s,%s);",operation,bonds,1,max,rulethickness,rulecolor)
+                        end
+                    elseif what == "number" then
+                        if set then
+                            for i=1,#set do
+                                local si = set[i]
+                                metacode[#metacode+1] = format('chem_%s(%s,%s,"\\dochemicaltext{%s}");',operation,bonds,si,si)
+                            end
+                        elseif upto then
+                            for i=index,upto do
+                                local si = set[i]
+                                metacode[#metacode+1] = format('chem_%s(%s,%s,"\\dochemicaltext{%s}");',operation,bonds,si,si)
+                            end
+                        elseif index then
+                            metacode[#metacode+1] = format('chem_%s(%s,%s,"\\dochemicaltext{%s}");',operation,bonds,index,index)
+                        else
+                            for i=1,max do
+                                metacode[#metacode+1] = format('chem_%s(%s,%s,"\\dochemicaltext{%s}");',operation,bonds,i,i)
+                            end
+                        end
+                    elseif what == "text" then
+                        local align = syntax[kind].align
+                        align = align and align[operation]
+                        align = align and align[rot]
+                        if set then
+                            for i=1,#set do
+                                local si = set[i]
+                                local t = text
+                                if not t then txt, t = fetch(txt) end
+                                if t then
+                                    local a = align and align[si]
+                                    if a then a = "." .. a else a = "" end
+                                    metacode[#metacode+1] = format('chem_%s%s(%s,%s,"\\dochemicaltext{%s}");',operation,a,bonds,si,molecule(apply(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
+                                    local s = align and align[i]
+                                    if s then s = "." .. s else s = "" end
+                                    metacode[#metacode+1] = format('chem_%s%s(%s,%s,"\\dochemicaltext{%s}");',operation,s,bonds,i,molecule(apply(t)))
+                                end
+                            end
+                        elseif index == 0 then
+                            local t = text
+                            if not t then txt, t = fetch(txt) end
+                            if t then
+                                metacode[#metacode+1] = format('chem_%s_zero("\\dochemicaltext{%s}");',operation,molecule(apply(t)))
+                            end
+                        elseif index then
+                            local t = text
+                            if not t then txt, t = fetch(txt) end
+                            if t then
+                                local s = align and align[index]
+                                if s then s = "." .. s else s = "" end
+                                metacode[#metacode+1] = format('chem_%s%s(%s,%s,"\\dochemicaltext{%s}");',operation,s,bonds,index,molecule(apply(t)))
+                            end
+                        else
+                            for i=1,max do
+                                local t = text
+                                if not t then txt, t = fetch(txt) end
+                                if t then
+                                    local s = align and align[i]
+                                    if s then s = "." .. s else s = "" end
+                                    metacode[#metacode+1] = format('chem_%s%s(%s,%s,"\\dochemicaltext{%s}");',operation,s,bonds,i,molecule(apply(t)))
+                                end
+                            end
+                        end
+                    elseif what == "transform" then
+                        if index then
+                            for r=1,rep do
+                                metacode[#metacode+1] = format('chem_%s(%s,%s);',operation,bonds,index)
+                            end
+                            if operation == "rot" then
+                                rot = index
+                            end
+                        end
+                    elseif what == "fixed" then
+                        metacode[#metacode+1] = format("chem_%s(%s,%s,%s);",operation,bonds,rulethickness,rulecolor)
+                    end
+                end
+            end
+        end
+    end
+    remove(stack)
+end
+
+-- the size related values are somewhat special but we want to be
+-- compatible
+--
+-- maybe we should default to fit
+--
+-- rulethickness in points
+
+function chemicals.start(settings)
+    chemicals.structures = chemicals.structures + 1
+    local textsize, rulethickness, rulecolor = settings.size, settings.rulethickness, settings.rulecolor
+    local width, height, scale, offset = settings.width or 0, settings.height or 0, settings.scale or "medium", 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
+    if scale == variables.small then
+        scale = 500
+    elseif scale == variables.medium or scale == 0 then
+        scale = 625
+    elseif scale == variables.big then
+        scale = 750
+    else
+        scale = tonumber(scale)
+        if not scale or scale == 0 then
+            scale = 750
+        elseif scale < 500 then
+            scale = 500
+        end
+    end
+    if width == variables.fit then
+        width = true
+    else
+        width = tonumber(width) or 0
+        if l == 0 then
+            if r == 0 then
+                l = (width == 0 and 2000) or width/2
+                r = l
+            elseif width ~= 0 then
+                l = width - r
+            end
+        elseif r == 0 and width ~= 0 then
+            r = width - l
+        end
+        width = false
+    end
+    if height == variables.fit then
+        height = true
+    else
+        height = tonumber(height) or 0
+        if t == 0 then
+            if b == 0 then
+                t = (height == 0 and 2000) or height/2
+                b = t
+            elseif height ~= 0 then
+                t = height - b
+            end
+        elseif b == 0 and height ~= 0 then
+            b = height - t
+        end
+        height = false
+    end
+    scale = 0.75 * scale/625
+    metacode = { format("chem_start_structure(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s) ;",
+        chemicals.structures,
+        l/25, r/25, t/25, b/25, scale,
+        tostring(settings.axis == variables.on), tostring(width), tostring(height), tostring(offset)
+    ) }
+    kind, keys, bonds, stack, rot, pstack = "six", { }, 6, { }, 1, { }
+end
+
+function chemicals.stop()
+    metacode[#metacode+1] = "chem_stop_structure ;"
+    local mpcode = concat(metacode,"\n")
+    if trace_structure then
+        logs.report("chemical", "metapost code:\n%s", mpcode)
+    end
+    metapost.graphic(chemicals.instance,chemicals.format,mpcode)
+    metacode = nil
+end
+
+function chemicals.component(spec,text,settings)
+    rulethickness, rulecolor, offset = settings.rulethickness, settings.rulecolor
+    local spec = aux.settings_to_array(lower(spec))
+    local text = aux.settings_to_array(text)
+    metacode[#metacode+1] = "chem_start_component ;"
+    process(spec,text,1,rulethickness,rulecolor)
+    metacode[#metacode+1] = "chem_stop_component ;"
+end
+
+local inline = {
+    ["single"]      = "\\chemicalsinglebond",  ["-"]   = "\\chemicalsinglebond",
+    ["double"]      = "\\chemicaldoublebond",  ["--"]  = "\\chemicaldoublebond",
+    ["triple"]      = "\\chemicaltriplebond",  ["---"] = "\\chemicaltriplebond",
+    ["gives"]       = "\\chemicalgives",       ["->"]  = "\\chemicalgives",
+    ["equilibrium"] = "\\chemicalequilibrium", ["<->"] = "\\chemicalequilibrium",
+    ["mesomeric"]   = "\\chemicalmesomeric",   ["<>"]  = "\\chemicalmesomeric",
+    ["plus"]        = "\\chemicalsplus",       ["+"]   = "\\chemicalsplus",
+    ["minus"]       = "\\chemicalsminus",
+    ["space"]       = "\\chemicalsspace",
+}
+
+-- todo: top / bottom
+
+function chemicals.inline(spec)
+    local spec = aux.settings_to_array(spec)
+    for i=1,#spec do
+        local s = spec[i]
+        local inl = inline[lower(s)]
+        if inl then
+            texsprint(ctxcatcodes,inl)
+        else
+            texsprint(ctxcatcodes,format("\\chemicalinline{%s}",molecule(s)))
+        end
+    end
+end
+
+statistics.register("chemical formulas", function()
+    if chemicals.structures > 0 then
+        return format("%s chemical structure formulas",chemicals.structures) -- no timing needed, part of metapost
+    end
+end)