2016-01-12 16:26:00

1 files changed, 882 insertions, 0 deletions

diff --git a/tex/context/base/mkiv/chem-str.lua b/tex/context/base/mkiv/chem-str.lua
new file mode 100644
index 000000000..d724394bb
--- /dev/null
+++ b/tex/context/base/mkiv/chem-str.lua
@@ -0,0 +1,882 @@
+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_boundingbox     = false  trackers  .register("chemistry.boundingbox",   function(v) trace_boundingbox     = 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 commands     = commands
+local context      = context
+local implement    = interfaces.implement
+
+local formatters   = string.formatters
+local texgetcount  = tex.getcount
+
+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 v_none       = variables.none
+
+local mpnamedcolor = attributes.colors.mpnamedcolor
+local topoints     = number.topoints
+local todimen      = string.todimen
+
+local trialtypesetting = context.trialtypesetting
+
+chemistry = chemistry or { }
+local chemistry = chemistry
+
+chemistry.instance   = "chemistry"
+chemistry.format     = "metafun"
+chemistry.method     = "double"
+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",
+    au    = "line",
+    ad    = "line",
+    cz    = "text",
+    rot   = "transform",
+    dir   = "transform",
+    rm    = "transform",
+    mir   = "transform",
+}
+
+local ring_keys = {
+    db    = "line",
+    hb    = "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 = formatters['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 = formatters['chem_symbol("\\chemicalsymbol[gives]{%s}{%s}");'], arguments = 2 },
+    equilibrium    = { direct = formatters['chem_symbol("\\chemicalsymbol[equilibrium]{%s}{%s}");'], arguments = 2 },
+    mesomeric      = { direct = formatters['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 = formatters['%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]
+    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 %a, slot %a, data %a",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       = '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);']
+local f_set_trace_bounds = formatters['chem_trace_boundingbox := %l ;']
+local f_stop_structure   = 'chem_stop_structure;'
+local f_start_component  = 'chem_start_component;'
+local f_stop_component   = '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("level %a, step %a, definition %a, snippets %a",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("level %a, step %a, factor %a, osign %a, operation %a, special %a, index %a, upto %a, set %a, text %a",
+                    level,step,factor,osign,operation,special,index,upto,set,text)
+            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.pe.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
+                if #sstack > 0 then
+                    variant = remove(sstack)
+                else
+                    report_chemistry("restore without save")
+                end
+                local ss = syntax[variant]
+                keys, max = ss.keys, ss.max
+                m = m + 1 ; metacode[m] = syntax.restore.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("level %a, operation %a, max nofsteps %a, ignoring %a",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("level %a, operation %a, max nofsteps %a, ignoring %a",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] = ds(one or "")
+                        elseif sa == 2 then
+                            local one ; txt, one = fetch(txt)
+                            local two ; txt, two = fetch(txt)
+                            m = m + 1 ; metacode[m] = 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))
+-- local p, t = processors.split(t)
+-- m = m + 1 ; metacode[m] = f_text(operation,p or align,variant,si,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("level %a, ignoring undefined operation %s",level,operation)
+                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
+
+local function checked(d,bondlength,unit,scale)
+    if d == v_none then
+        return 0
+    end
+    local n = tonumber(d)
+    if not n then
+        -- assume dimen
+    elseif n >= 10 or n <= -10 then
+        return bondlength * unit * n / 1000
+    else
+        return bondlength * unit * n
+    end
+    local n = todimen(d)
+    if n then
+        return scale * n
+    else
+        return v_fit
+    end
+end
+
+local function calculated(height,bottom,top,bondlength,unit,scale)
+    local scaled = 0
+    if height == v_none then
+        -- this always wins
+        height = "0pt"
+        bottom = "0pt"
+        top    = "0pt"
+    elseif height == v_fit then
+        height = "true"
+        bottom = bottom == v_fit and "true" or topoints(checked(bottom,bondlength,unit,scale))
+        top    = top    == v_fit and "true" or topoints(checked(top,   bondlength,unit,scale))
+    else
+        height = checked(height,bondlength,unit,scale)
+        if bottom == v_fit then
+            if top == v_fit then
+                bottom  = height / 2
+                top     = bottom
+            else
+                top     = checked(top,bondlength,unit,scale)
+                bottom  = height - top
+            end
+        elseif top == v_fit then
+            bottom = checked(bottom,bondlength,unit,scale)
+            top    = height - bottom
+        else
+            bottom  = checked(bottom,bondlength,unit,scale)
+            top     = checked(top,   bondlength,unit,scale)
+            local ratio = height / (bottom+top)
+            bottom  = bottom  * ratio
+            top     = top     * ratio
+        end
+        scaled = height
+        top    = topoints(top)
+        bottom = topoints(bottom)
+        height = topoints(height)
+    end
+    return height, bottom, top, scaled
+end
+
+function chemistry.start(settings)
+    --
+    local width          = settings.width         or v_fit
+    local height         = settings.height        or v_fit
+    local unit           = settings.unit          or 655360
+    local bondlength     = settings.factor        or 3
+    local rulethickness  = settings.rulethickness or 65536
+    local rulecolor      = settings.rulecolor     or ""
+    local axiscolor      = settings.framecolor    or ""
+    local scale          = settings.scale         or "normal"
+    local rotation       = settings.rotation      or 0
+    local offset         = settings.offset        or 0
+    local left           = settings.left          or v_fit
+    local right          = settings.right         or v_fit
+    local top            = settings.top           or v_fit
+    local bottom         = settings.bottom        or v_fit
+    --
+    align = settings.symalign or "auto"
+    if trace_structure then
+        report_chemistry("unit %p, bondlength %s, symalign %s",unit,bondlength,align)
+    end
+    if align ~= "" then
+        align = "." .. align
+    end
+    if trace_structure then
+        report_chemistry("%s scale %a, rotation %a, width %s, height %s, left %s, right %s, top %s, bottom %s","asked",scale,rotation,width,height,left,right,top,bottom)
+    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
+    --
+    unit = scale * unit
+    --
+    local sp_width  = 0
+    local sp_height = 0
+    --
+    width,  left,   right, sp_width  = calculated(width, left,  right,bondlength,unit,scale)
+    height, bottom, top,   sp_height = calculated(height,bottom,top,  bondlength,unit,scale)
+    --
+    if width ~= "true" and height ~= "true" and trialtypesetting() then
+        if trace_structure then
+            report_chemistry("skipping trial run")
+        end
+        context.hrule(sp_width,sp_height,0) -- maybe depth
+        return
+    end
+    --
+    chemistry.structures = chemistry.structures + 1
+    --
+    rotation = tonumber(rotation) or 0
+    --
+    metacode = { }
+    --
+    if trace_structure then
+        report_chemistry("%s scale %a, rotation %a, width %s, height %s, left %s, right %s, top %s, bottom %s","used",scale,rotation,width,height,left,right,top,bottom)
+    end
+    metacode[#metacode+1] = f_start_structure(
+        chemistry.structures,
+        left, right, top, bottom,
+        rotation, topoints(unit), bondlength, scale, topoints(offset),
+        tostring(settings.axis == v_on), topoints(rulethickness), tostring(axiscolor)
+    )
+    metacode[#metacode+1] = f_set_trace_bounds(trace_boundingbox) ;
+    --
+    variant, keys, stack, pstack, sstack = "one", { }, { }, { }, { }
+end
+
+function chemistry.stop()
+    if metacode then
+        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,
+            method      = chemistry.method,
+            data        = mpcode,
+            definitions = f_initialize,
+        }
+        t_initialize = ""
+        metacode = nil
+    end
+end
+
+function chemistry.component(spec,text,rulethickness,rulecolor)
+    if metacode then
+        local spec = settings_to_array_with_repeat(spec,true) -- no lower?
+        local text = settings_to_array_with_repeat(text,true)
+        metacode[#metacode+1] = f_start_component
+        process(1,spec,text,1,rulethickness,rulecolor)
+        metacode[#metacode+1] = f_stop_component
+    end
+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
+
+implement {
+    name      = "undefinechemical",
+    actions   = chemistry.undefine,
+    arguments = "string"
+}
+
+implement {
+    name      = "definechemical",
+    actions   = chemistry.define,
+    arguments = { "string", "string", "string" }
+}
+
+implement {
+    name      = "startchemical",
+    actions   = chemistry.start,
+    arguments = {
+        {
+            { "width" },
+            { "height" },
+            { "left" },
+            { "right" },
+            { "top" },
+            { "bottom" },
+            { "scale" },
+            { "rotation" },
+            { "symalign" },
+            { "axis" },
+            { "framecolor" },
+            { "rulethickness" },
+            { "offset" },
+            { "unit" },
+            { "factor" }
+        }
+    }
+}
+
+implement {
+    name      = "stopchemical",
+    actions   = chemistry.stop,
+}
+
+implement {
+    name      = "chemicalcomponent",
+    actions   = chemistry.component,
+    arguments = { "string", "string", "string", "string" }
+}
+
+-- 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",
+}
+
+local ctx_chemicalinline = context.chemicalinline
+
+function chemistry.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
+            ctx_chemicalinline(molecule(s))
+        end
+    end
+end
+
+implement {
+    name      = "inlinechemical",
+    actions   = chemistry.inlinechemical,
+    arguments = "string"
+}