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-rw-r--r--tex/context/base/chem-str.lua1640
1 files changed, 820 insertions, 820 deletions
diff --git a/tex/context/base/chem-str.lua b/tex/context/base/chem-str.lua
index dfcf0a3e1..679314e2d 100644
--- a/tex/context/base/chem-str.lua
+++ b/tex/context/base/chem-str.lua
@@ -1,820 +1,820 @@
-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 formatters = string.formatters
-
-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 texcount = tex.count
-
-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
-
-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 = 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);']
-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
- variant = remove(sstack)
- 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))
- 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,factor,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 factor * unit * n / 1000
- else
- return factor * 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,factor,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,factor,unit,scale))
- top = top == v_fit and "true" or topoints(checked(top, factor,unit,scale))
- else
- height = checked(height,factor,unit,scale)
- if bottom == v_fit then
- if top == v_fit then
- bottom = height / 2
- top = bottom
- else
- top = checked(top,factor,unit,scale)
- bottom = height - top
- end
- elseif top == v_fit then
- bottom = checked(bottom,factor,unit,scale)
- top = height - bottom
- else
- bottom = checked(bottom,factor,unit,scale)
- top = checked(top, factor,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 factor = 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, factor %s, symalign %s",unit,factor,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,factor,unit,scale)
- height, bottom, top, sp_height = calculated(height,bottom,top, factor,unit,scale)
- --
- if width ~= "true" and height ~= "true" and texcount["@@trialtypesetting"] ~= 0 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), factor, 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,
- data = mpcode,
- definitions = f_initialize,
- }
- t_initialize = ""
- metacode = nil
- end
-end
-
-function chemistry.component(spec,text,settings)
- if metacode then
- 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
-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
+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 formatters = string.formatters
+
+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 texcount = tex.count
+
+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
+
+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 = 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);']
+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
+ variant = remove(sstack)
+ 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))
+ 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,factor,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 factor * unit * n / 1000
+ else
+ return factor * 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,factor,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,factor,unit,scale))
+ top = top == v_fit and "true" or topoints(checked(top, factor,unit,scale))
+ else
+ height = checked(height,factor,unit,scale)
+ if bottom == v_fit then
+ if top == v_fit then
+ bottom = height / 2
+ top = bottom
+ else
+ top = checked(top,factor,unit,scale)
+ bottom = height - top
+ end
+ elseif top == v_fit then
+ bottom = checked(bottom,factor,unit,scale)
+ top = height - bottom
+ else
+ bottom = checked(bottom,factor,unit,scale)
+ top = checked(top, factor,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 factor = 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, factor %s, symalign %s",unit,factor,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,factor,unit,scale)
+ height, bottom, top, sp_height = calculated(height,bottom,top, factor,unit,scale)
+ --
+ if width ~= "true" and height ~= "true" and texcount["@@trialtypesetting"] ~= 0 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), factor, 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,
+ data = mpcode,
+ definitions = f_initialize,
+ }
+ t_initialize = ""
+ metacode = nil
+ end
+end
+
+function chemistry.component(spec,text,settings)
+ if metacode then
+ 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
+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
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-01 21:27:53 +0000