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|
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.
local trace_structure = false trackers.register("chemistry.structure", function(v) trace_structure = v end)
local trace_metapost = false trackers.register("chemistry.metapost", function(v) trace_metapost = v end)
local trace_textstack = false trackers.register("chemistry.textstack", function(v) trace_textstack = v end)
local 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 = table.concat, table.insert, table.remove
local processor_tostring = typesetters and typesetters.processors.tostring
local settings_to_array = utilities.parsers.settings_to_array
local lpegmatch = lpeg.match
local P, R, S, C, Cs, Ct, Cc = lpeg.P, lpeg.R, lpeg.S, lpeg.C, lpeg.Cs, lpeg.Ct, lpeg.Cc
local variables = interfaces and interfaces.variables
local context = context
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",
cc = "line",
ccd = "line",
line = "line",
dash = "line",
arrow = "line",
c = "fixed",
cd = "fixed",
z = "text",
zt = "text",
zn = "number",
mov = "transform",
mark = "transform",
off = "transform",
adj = "transform",
}
local front_keys = {
bb = "line",
rr = "line",
lr = "line",
lsr = "line",
rsr = "line",
lrz = "text",
rrz = "text",
-- rz = "text", -- no
lsub = "transform",
rsub = "transform",
}
local one_keys = {
db = "line",
tb = "line",
bb = "line",
rb = "line",
dr = "line",
hb = "line",
bd = "line",
bw = "line",
oe = "line",
sd = "line",
ld = "line",
rd = "line",
ldd = "line",
rdd = "line",
ep = "line",
es = "line",
ed = "line",
et = "line",
zlt = "text",
zln = "number",
zrt = "text",
zrn = "number",
rz = "text",
cz = "text",
rot = "transform",
dir = "transform",
rm = "transform",
mir = "transform",
sub = "transform",
}
local ring_keys = {
db = "line",
br = "line",
lr = "line",
rr = "line",
lsr = "line",
rsr = "line",
lrd = "line",
rrd = "line",
rb = "line",
lrb = "line",
rrb = "line",
dr = "line",
eb = "line",
er = "line",
ed = "line",
au = "line",
ad = "line",
s = "line",
ss = "line",
mid = "line",
mids = "line",
midz = "text",
zlt = "text",
zln = "number",
zrt = "text",
zrn = "number",
rz = "text",
lrz = "text",
rrz = "text",
crz = "text",
rt = "text",
lrt = "text",
rrt = "text",
rn = "number",
lrn = "number",
rrn = "number",
rot = "transform",
mir = "transform",
adj = "transform",
sub = "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, },
fivefront = { max = 5, keys = front_keys, },
sixfront = { max = 6, keys = front_keys, },
chair = { max = 6, keys = front_keys, },
boat = { max = 6, keys = front_keys, },
pb = { direct = 'chem_pb ;' },
pe = { direct = 'chem_pe ;' },
save = { direct = 'chem_save ;' },
restore = { direct = 'chem_restore ;' },
chem = { direct = 'chem_symbol("\\chemicaltext{%s}") ;', arguments = 1 },
space = { direct = 'chem_symbol("\\chemicalsymbol[space]") ;' },
plus = { direct = 'chem_symbol("\\chemicalsymbol[plus]") ;' },
minus = { direct = 'chem_symbol("\\chemicalsymbol[minus]") ;' },
gives = { direct = 'chem_symbol("\\chemicalsymbol[gives]{%s}{%s}") ;', arguments = 2 },
equilibrium = { direct = 'chem_symbol("\\chemicalsymbol[equilibrium]{%s}{%s}") ;', arguments = 2 },
mesomeric = { direct = 'chem_symbol("\\chemicalsymbol[mesomeric]{%s}{%s}") ;', arguments = 2 },
opencomplex = { direct = 'chem_symbol("\\chemicalsymbol[opencomplex]") ;' },
closecomplex = { direct = 'chem_symbol("\\chemicalsymbol[closecomplex]") ;' },
reset = { direct = 'chem_reset ;' },
mp = { direct = '%s', arguments = 1 }, -- backdoor MP code - dangerous!
}
local 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(lower(spec)),
text = settings_to_array(text),
}
end
local metacode, variant, keys, max, txt, pstack, sstack
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 %s slot %s: %s",txt,st.n,t)
end
st.n = st.n + 1
end
return txt, t
end
local remapper = {
["+"] = "p",
["-"] = "m",
}
local dchrs = R("09")
local sign = S("+-")
local digit = dchrs / tonumber
local amount = (sign^-1 * (dchrs^0 * P('.'))^-1 * dchrs^1) / tonumber
local single = digit
local range = digit * P("..") * digit
local set = Ct(digit^2)
local colon = P(":")
local equal = P("=")
local other = 1 - digit - colon - equal
local remapped = sign / remapper
local operation = Cs(other^1)
local special = (colon * C(other^1)) + Cc("")
local text = (equal * C(P(1)^0)) + Cc(false)
local pattern =
(amount + Cc(1)) *
(remapped + Cc("")) *
Cs(operation/lower) *
Cs(special/lower) * (
range * Cc(false) * text +
Cc(false) * Cc(false) * set * text +
single * Cc(false) * Cc(false) * text +
Cc(false) * Cc(false) * Cc(false) * text
)
-- local n, operation, index, upto, set, text = lpegmatch(pattern,"RZ1357")
-- print(lpegmatch(pattern,"RZ=x")) -- 1 RZ false false false x
-- print(lpegmatch(pattern,"RZ1=x")) -- 1 RZ 1 false false x
-- print(lpegmatch(pattern,"RZ1..3=x")) -- 1 RZ 1 3 false x
-- print(lpegmatch(pattern,"RZ13=x")) -- 1 RZ false false table x
local t_initialize = 'if unknown context_chem : input mp-chem.mpiv ; fi ;'
local t_start_structure = 'chem_start_structure(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s);'
local t_stop_structure = 'chem_stop_structure;'
local t_start_component = 'chem_start_component;'
local t_stop_component = 'chem_stop_component;'
local t_line = 'chem_%s%s(%s,%s,%s,%s,%s);'
local t_set = 'chem_set(%s);'
local t_number = 'chem_%s(%s,%s,"\\chemicaltext{%s}");'
local t_text = t_number
local t_empty_normal = 'chem_%s(%s,%s,"");'
local t_empty_center = 'chem_c%s(%s,%s,"");'
local t_transform = 'chem_%s(%s,%s,%s);'
local function process(spec,text,n,rulethickness,rulecolor,offset)
insert(stack,{ spec=spec, text=text, n=n })
local txt = #stack
local m = #metacode
for i=1,#spec do
local step = spec[i]
local s = lower(step)
local d = definitions[s]
if d then
if trace_structure then
report_chemistry("%s => definition: %s",step,s)
end
for i=1,#d do
local di = d[i]
process(di.spec,di.text,1,rulethickness,rulecolor) -- offset?
end
else
--~local rep, operation, special, index, upto, set, text = lpegmatch(pattern,step)
local factor, osign, operation, special, index, upto, set, text = lpegmatch(pattern,step)
if trace_structure then
local set = set and concat(set," ") or "-"
report_chemistry("%s => factor: %s, osign: %s operation: %s, special: %s, index: %s, upto: %s, set: %s, text: %s",
step,factor or "",osign or "",operation or "-",special and special ~= "" or "-",index or "-",upto or "-",set or "-",text or "-")
end
if 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] = format(t_empty_center,special,variant,index)
else
m = m + 1 ; metacode[m] = format(t_empty_normal,special,variant,index)
end
end
elseif operation == "pe" then
variant = remove(pstack)
local ss = syntax[variant]
keys, max = ss.keys, ss.max
m = m + 1 ; metacode[m] = syntax[operation].direct
m = m + 1 ; metacode[m] = format(t_set,variant)
elseif operation == "save" then
insert(sstack,variant)
m = m + 1 ; metacode[m] = syntax.save.direct
elseif operation == "restore" then
variant = remove(sstack)
if variant and #sstack == 0 then
insert(sstack,variant) -- allow multiple restores at the bottom of the stack.
end
local ss = syntax[variant]
keys, max = ss.keys, ss.max
m = m + 1 ; metacode[m] = syntax[operation].direct
m = m + 1 ; metacode[m] = format(t_set,variant)
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)
m = m + 1 ; metacode[m] = format(ds,one or "")
elseif sa ==2 then
local one ; txt, one = fetch(txt)
local two ; txt, two = fetch(txt)
m = m + 1 ; metacode[m] = format(ds,one or "",two or "")
else
m = m + 1 ; metacode[m] = ds
end
elseif ss.keys then
variant, keys, max = s, ss.keys, ss.max
m = m + 1 ; metacode[m] = format(t_set,variant)
end
else
local what = keys[operation]
if what == "line" then
local s = osign
if s ~= "" then s = "." .. s end
if set then
-- condense consecutive numbers in a set to a range
-- (numbers modulo max are currently not dealt with...)
table.sort(set)
local sf, st = set[1]
for i=1,#set do
if i > 1 and set[i] ~= set[i-1]+1 then
m = m + 1 ; metacode[m] = format(t_line,operation,s,variant,sf,st,rulethickness,rulecolor)
sf = set[i]
end
st = set[i]
end
m = m + 1 ; metacode[m] = format(t_line,operation,s,variant,sf,st,rulethickness,rulecolor)
elseif upto then
m = m + 1 ; metacode[m] = format(t_line,operation,s,variant,index,upto,rulethickness,rulecolor)
elseif index then
m = m + 1 ; metacode[m] = format(t_line,operation,s,variant,index,index,rulethickness,rulecolor)
else
m = m + 1 ; metacode[m] = format(t_line,operation,s,variant,1,max,rulethickness,rulecolor)
end
elseif what == "number" then
if set then
for i=1,#set do
local si = set[i]
m = m + 1 ; metacode[m] = format(t_number,operation,variant,si,si)
end
elseif upto then
for i=index,upto do
local si = set[i]
m = m + 1 ; metacode[m] = format(t_number,operation,variant,si,si)
end
elseif index then
m = m + 1 ; metacode[m] = format(t_number,operation,variant,index,index)
else
for i=1,max do
m = m + 1 ; metacode[m] = format(t_number,operation,variant,i,i)
end
end
elseif what == "text" then
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
t = molecule(processor_tostring(t))
m = m + 1 ; metacode[m] = format(t_text,operation,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] = format(t_text,operation,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] = format(t_text,operation,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] = format(t_text,operation,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] = format(t_text,operation,variant,i,t)
end
end
end
elseif what == "transform" then
if osign == "m" then factor = -factor end
if set then
for i=1,#set do
local si = set[i]
m = m + 1 ; metacode[m] = format(t_transform,operation,variant,si,factor)
end
elseif upto then
for i=index,upto do
m = m + 1 ; metacode[m] = format(t_transform,operation,variant,i,factor)
end
else
m = m + 1 ; metacode[m] = format(t_transform,operation,variant,index or 1,factor)
end
elseif what == "fixed" then
m = m + 1 ; metacode[m] = format(t_transform,operation,variant,rulethickness,rulecolor)
elseif trace_structure then
report_chemistry("warning: undefined operation %s ignored here", operation or "")
end
end
end
end
end
remove(stack)
end
-- the size related values are somewhat special but we want to be
-- compatible
--
-- rulethickness in points
function chemistry.start(settings)
chemistry.structures = chemistry.structures + 1
local emwidth, rulethickness, rulecolor, axiscolor = settings.emwidth, settings.rulethickness, settings.rulecolor, settings.framecolor
local width, height, scale, offset = settings.width or 0, settings.height or 0, settings.scale or "normal", settings.offset or 0
local l, r, t, b = settings.left or 0, settings.right or 0, settings.top or 0, settings.bottom or 0
--
metacode = { }
--
if trace_structure then
report_chemistry("scale: %s, width: %s, height: %s, l: %s, r: %s, t: %s, b: %s", scale, width, height, l, r, t, b)
end
if scale == variables.small then
scale = 1/1.2
elseif scale == variables.normal or scale == variables.medium or scale == 0 then
scale = 1
elseif scale == variables.big then
scale = 1.2
else
scale = tonumber(scale)
if not scale or scale == 0 then
scale = 1
elseif scale >= 10 then
scale = scale / 1000
elseif scale < .01 then
scale = .01
end
end
if width == variables.fit then
width = true
else
width = tonumber(width) or 0
if width >= 10 then
width = width / 1000
end
if l == 0 then
if r == 0 then
l = width == 0 and 2 or width/2
r = l
elseif width ~= 0 then
if r > 10 or r < -10 then
r = r / 1000
end
l = width - r
end
elseif r == 0 and width ~= 0 then
if l > 10 or l < -10 then
l = l / 1000
end
r = width - l
end
width = false
end
if height == variables.fit then
height = true
else
height = tonumber(height) or 0
if height >= 10 then
height = height / 1000
end
if t == 0 then
if b == 0 then
t = height == 0 and 2 or height/2
b = t
elseif height ~= 0 then
if b > 10 or b < -10 then
b = b / 1000
end
t = height - b
end
elseif b == 0 and height ~= 0 then
if t > 10 or t < -10 then
t = t / 1000
end
b = height - t
end
height = false
end
--
metacode[#metacode+1] = format(t_start_structure,
chemistry.structures,
l, r, t, b, scale,
tostring(width), tostring(height), tostring(emwidth), tostring(offset),
tostring(settings.axis == variables.on), tostring(rulethickness), tostring(axiscolor)
)
--
variant, keys, stack, pstack, sstack = "one", { }, { }, { }, { }
end
function chemistry.stop()
metacode[#metacode+1] = t_stop_structure
local mpcode = concat(metacode,"\n")
if trace_metapost then
report_chemistry("metapost code:\n%s", mpcode)
end
metapost.graphic(chemistry.instance,chemistry.format,mpcode,"","",t_initialize)
metacode = nil
end
function chemistry.component(spec,text,settings)
rulethickness, rulecolor, offset = settings.rulethickness, settings.rulecolor
local spec = settings_to_array(spec)
local text = settings_to_array(text)
metacode[#metacode+1] = t_start_component
process(spec,text,1,rulethickness,rulecolor) -- offset?
metacode[#metacode+1] = t_stop_component
end
statistics.register("chemical formulas", function()
if chemistry.structures > 0 then
return format("%s chemical structure formulas",chemistry.structures) -- no timing needed, part of metapost
end
end)
-- interfaces
commands.undefinechemical = chemistry.undefine
commands.definechemical = chemistry.define
commands.startchemical = chemistry.start
commands.stopchemical = chemistry.stop
commands.chemicalcomponent = chemistry.component
-- todo: top / bottom
-- maybe add "=" for double and "≡" for triple?
local inline = {
["single"] = "\\chemicalsinglebond", ["-"] = "\\chemicalsinglebond",
["double"] = "\\chemicaldoublebond", ["--"] = "\\chemicaldoublebond",
["triple"] = "\\chemicaltriplebond", ["---"] = "\\chemicaltriplebond",
["gives"] = "\\chemicalgives", ["->"] = "\\chemicalgives",
["equilibrium"] = "\\chemicalequilibrium", ["<->"] = "\\chemicalequilibrium",
["mesomeric"] = "\\chemicalmesomeric", ["<>"] = "\\chemicalmesomeric",
["plus"] = "\\chemicalplus", ["+"] = "\\chemicalplus",
["minus"] = "\\chemicalminus",
["space"] = "\\chemicalspace",
}
function commands.inlinechemical(spec)
local spec = settings_to_array(spec)
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
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