path: root/metapost/context/base/mpiv/mp-chem.mpiv

%D \module
%D   [       file=mp-chem.mpiv,
%D        version=2009.05.13,
%D          title=\CONTEXT\ \METAPOST\ graphics,
%D       subtitle=chemicals,
%D         author=Hans Hagen \& Alan Braslau,
%D           date=\currentdate,
%D      copyright={PRAGMA ADE \& \CONTEXT\ Development Team}]
%C
%C This module is part of the \CONTEXT\ macro||package and is
%C therefore copyrighted by \PRAGMA. See licen-en.pdf for
%C details.

%D This module is incomplete and experimental. Okay, it's not that bad but we do need
%D some disclaimer.

% either consistent setting or not

if known context_chem : endinput ; fi ;

boolean context_chem ; context_chem := true ;

numeric
    chem_num[], % scratch
    chem_text_min, chem_text_max,
    chem_rotation, chem_adjacent, chem_stack_n,
    chem_substituent, chem_substituent.lft, chem_substituent.rt,
    chem_setting_offset, chem_text_offset,
    chem_center_offset, chem_dbl_offset,
    chem_bb_angle, chem_axis_rulethickness,
    chem_setting_l, chem_setting_r, chem_setting_t, chem_setting_b,
    chem_setting_rotation, chem_emwidth, chem_b_length,
    chem_front_b[] ;

boolean
    chem_setting_axis,
    chem_doing_pb, chem_bd_wedge,
    chem_star[], chem_front[], chem_stacked[], chem_tetra[] ;

string
    chem_previous ;

path
    chem_path[], % scratch
    chem_b_path[], chem_c_path[],
    chem_r_path[], chem_r_path.lft[], chem_r_path.rt[] ;

pair
    chem_origin, chem_mirror,
    chem_pair[], % scratch
    chem_sb_pair, chem_sb_pair.m, chem_sb_pair.mm, chem_sb_pair.p, chem_sb_pair.pp, chem_sb_pair.b ;

picture
    chem_pic; % scratch
    % The use of dashpattern is found to dot the starting point with chem_sb_dash.m...
    %chem_sb_dash, chem_sb_dash.m, chem_sb_dash.p, chem_sb_dash.b,

% nice hack but now redone
%
% picture chem_axis_color ;
%
% chem_axis_color := image(draw origin withcolor axiscolor) ; % so we handle all color models
%
% withpen pencircle scaled chem_axis_rulethickness withcolor colorpart(chem_axis_color) ;

string
    chem_axis_color ;

transform
    chem_t ; % scratch

% debugging

boolean chem_trace_nesting     ; chem_trace_nesting     := false ;
boolean chem_trace_text        ; chem_trace_text        := false ;
boolean chem_trace_boundingbox ; chem_trace_boundingbox := false ;

chem_axis_color         := "lightblue" ;
chem_setting_axis       := false ;
chem_axis_rulethickness := 1pt ;
chem_emwidth            := 10pt ; % EmWidth or \the\emwidth does not work...
chem_b_length           := 3  chem_emwidth ;
chem_text_offset        := -.3chem_emwidth ; % -.71chem_emwidth ; % 1/sqrt(2)
chem_center_offset      :=  .5chem_emwidth ;
chem_dbl_offset         := .05 ;
chem_bb_angle           := angle(1,2chem_dbl_offset) ;
chem_text_min           := 0.75 ;
chem_text_max           := 1.25 ;
chem_dot_factor         := 2 ; % *linewidth
chem_sb_pair            := (0.25,0.75) ; %chem_sb_dash   := dashpattern(off 0.25 on 0.5 off 0.25) ;
chem_sb_pair.m          := (0.25,1   ) ; %chem_sb_dash.m := dashpattern(off 0.25 on 0.75) ;
chem_sb_pair.mm         := (0.50,1   ) ; %chem_sb_dash.m := dashpattern(off 0.25 on 0.75) ;
chem_sb_pair.p          := (0   ,0.75) ; %chem_sb_dash.p := dashpattern(on  0.75 off 0.25) ;
chem_sb_pair.pp         := (0   ,0.50) ; %chem_sb_dash.p := dashpattern(on  0.75 off 0.25) ;
chem_sb_pair.b          := (0   ,1   ) ; %chem_sb_dash.b := dashpattern(on  1) ;

chem_bd_wedge           := true ; % according to IUPAC 2005

def chem_reset =
    chem_rotation         := 0 ;
    chem_mirror           := origin ;
    chem_adjacent         := 0 ;
    chem_substituent      := 0 ;
    chem_substituent.lft  := 0 ;
    chem_substituent.rt   := 0 ;
    chem_stack_n          := 0 ;
    chem_doing_pb         := false ;
    chem_origin           := origin ;
    chem_previous         := "one" ;
    pair chem_mark_pair[] ;
enddef ;

chem_reset ;

newinternal numeric
    one, carbon, alkyl, newmanstagger, newmaneclipsed,
    three, four, five, six, seven, eight, nine,
    fivefront, sixfront, chair, boat ;

vardef chem_init_some (suffix $) (expr e) =
    if not known chem_star[$]    : chem_star[$]    := false ; fi
    if not known chem_front[$]   : chem_front[$]   := false ; fi
    if not known chem_stacked[$] : chem_stacked[$] := false ; fi
    if not known chem_tetra[$]   : chem_tetra[$]   := false ; fi

    % We define all paths as closed, so that they may be indexed mod length.
    if path(e) :
        chem_b_path[$] := e if not cycle(e) : -- cycle fi ;
        chem_num0 := length(chem_b_path[$]) ;
    else : % polygon
        chem_num0 := e ;
        chem_num1 := 360/chem_num0 ;
        chem_b_path[$] :=
            (
                for i=0 upto chem_num0-1 :
                    dir(if chem_star[$] : -i else : (.5-i) fi *chem_num1) --
                endfor
                cycle
            )
            if chem_front[$] :
                rotated (chem_num1-90)
            fi
            if not chem_star[$] :
                scaled (.5/(sind .5chem_num1))
                % carbon-carbon benzene bond length
                scaled (1.4/1.54)
            fi ;
    fi ;

    if chem_front[$] and (not known chem_front_b[$]) :
        chem_front_b[$] := floor(.5(length chem_b_path[$])) + 1 ;
    fi

    chem_num2 := 0 ;
    chem_c_path[$] :=
        reverse(fullcircle) rotated angle(point 0 of chem_b_path[$])
        if not chem_star[$] :
             hide (for i=0 upto chem_num0-1:
                       if abs(point i+.5 of chem_b_path[$]) <
                          abs(point chem_num2+.5 of chem_b_path[$]) :
                           chem_num2 := i ;
                       fi
                   endfor)
             scaled (2*(abs(point chem_num2+.5 of chem_b_path[$]) - 2chem_dbl_offset))
        fi ;

    chem_r_path[$] :=
        if chem_star[$] :
            chem_b_path[$]
        else :
            (
                for i=0 upto chem_num0-1 :
                    (unitvector point i of chem_b_path[$])
                    shifted point i of chem_b_path[$] --
                endfor
                cycle
            )
        fi ;

    chem_r_path.lft[$] :=
        (
        for i=0 upto chem_num0-1 :
            if chem_front[$] :
                up
                scaled .5
                shifted point i of chem_b_path[$]
            elseif chem_star[$] :
                point i   of chem_b_path[$]
            else :
                point i+1 of chem_b_path[$]
                rotatedabout(point i of chem_b_path[$],180)
            fi --
        endfor
        cycle
        ) ;
    chem_r_path.rt[$] :=
        (
        for i=0 upto chem_num0-1 :
            if chem_front[$] :
                down
                scaled .5
                shifted point i of chem_b_path[$]
            elseif chem_star[$] :
                point i+2 of chem_b_path[$]
            else :
                point i-1 of chem_b_path[$]
                rotatedabout(point i of chem_b_path[$],180)
            fi --
        endfor
        cycle
        ) ;

enddef ;

% The following is used only once:
def chem_init_all =
begingroup
    save a, b, c, d, e ; numeric a, b, c, d, e ;
    save lft, rt ; path lft, rt ;

    % tetrahedrial angle
    a := 2angle(1,sqrt 2) ;

    % solve for chair
    2b = 180 - .5a ;
    4c = 180 - .5a ;
    d + e = 360 - 2a ;
    d = 5e ; % this is the one tunable parameter which fixes the perspective.
    z2 = z1 shifted dir(90+a+d) ;
    z3 = z2 shifted dir(270-a) ;
    z4 = z3 shifted dir(90+a) ;
    z6 = z1 shifted dir(90+a) ;
    z5 = z6 shifted dir(270-a) ;
    z4 = z1 xyscaled (-1,-1) ;
    z5 = z2 xyscaled (-1,-1) ;

    save indx ; numeric indx ; indx = 2 ; % starting value doesn't matter, really.
    % polygons
    three          := incr indx ; % 3 (these numbers don't matter - they are just indices)
    four           := incr indx ; % 4
    five           := incr indx ; % 5
    six            := incr indx ; % 6
    seven          := incr indx ; % 7
    eight          := incr indx ; % 8
    nine           := incr indx ; % 9

    chem_init_some(three,3) ;
    chem_init_some(four, 4) ;
    chem_init_some(five, 5) ;
    chem_init_some(six,  6) ;
    chem_init_some(seven,7) ;
    chem_init_some(eight,8) ;
    chem_init_some(nine, 9) ;

    % star-form
    one            := incr indx ; % 10
    carbon         := incr indx ; % 11
    alkyl          := incr indx ; % 12
    newmanstagger  := incr indx ; % 13
    newmaneclipsed := incr indx ; % 14

    chem_star[one]            := true ;
    chem_star[carbon]         := true ; chem_tetra[carbon]         := true ;
    chem_star[alkyl]          := true ; chem_tetra[alkyl]          := true ;
    chem_star[newmanstagger]  := true ; chem_tetra[newmanstagger]  := true ;
    chem_star[newmaneclipsed] := true ; chem_tetra[newmaneclipsed] := true ;
    chem_stacked[newmanstagger]  := true ;
    chem_stacked[newmaneclipsed] := true ;
    chem_init_some(one,            8) ;
    chem_init_some(carbon,         dir(0)--dir(360-a)--dir(180-.5a+b)--dir(180-.5a)) ;
    chem_init_some(alkyl,          dir(0)--dir(360-a)--dir(360-a-90)--dir(90)) ;
    chem_init_some(newmanstagger,  dir(30)--dir(270)--dir(150)--dir(330)--dir(210)--dir(90)) ;
    chem_init_some(newmaneclipsed, dir(30)--dir(270)--dir(150)--dir(0)--dir(240)--dir(120)) ;

    % front views
    fivefront      := incr indx ; % 15
    sixfront       := incr indx ; % 16
    chair          := incr indx ; % 17
    boat           := incr indx ; % 18

    chem_front[fivefront]    := true ; chem_front_b[fivefront] := 3 ;
    chem_front[sixfront]     := true ; chem_front_b[sixfront]  := 3 ;
    chem_init_some(fivefront,5) ;
    chem_init_some(sixfront, 6) ;
    % chair
    chem_front[chair]        := true ; chem_front_b[chair]     := 4 ;
    chem_init_some(chair,          z1--z2--z3--z4--z5--z6) ;
    lft := dir(90-a)--down--dir(90+a+d)--down--dir(90+a)--down ;
    rt  := up--dir(270+a)--up--dir(270-a)--up--dir(90+e) ;
    chem_r_path.lft[chair] :=
        for i=0 upto 5 : point i of lft shifted point i of chem_b_path[chair] -- endfor
        cycle ;
    chem_r_path.rt[chair] :=
        for i=0 upto 5 : point i of rt shifted point i of chem_b_path[chair] -- endfor
        cycle ;
    % boat
    chem_front[boat]         := true ; chem_front_b[boat]      := 4 ;
    chem_init_some(boat,
        for i=1 upto 4 : point i-1 of chem_b_path[sixfront] -- endfor
        point 2 of chem_b_path[sixfront] yscaled .5 --
        point 1 of chem_b_path[sixfront] yscaled .5
    ) ;
    lft := dir(30+.5a)--dir(330+.5a)--dir(210-.5a)--dir(150-.5a)--dir(120)--dir(60) ;
    rt  := dir(30-.5a)--dir(330-.5a)--dir(210+.5a)--dir(150+.5a)--dir(120+a)--dir(60-a) ;
    chem_r_path.lft[boat] :=
        for i=0 upto 5 : point i of lft shifted point i of chem_b_path[boat] -- endfor
        cycle ;
    chem_r_path.rt[boat] :=
        for i=0 upto 5 : point i of rt shifted point i of chem_b_path[boat] -- endfor
        cycle ;
endgroup
enddef ;

chem_init_all ; % WHY does this not work unless defined and then called?

% Like most often in ConTeXt, we will trap but then silently ignore mistaken use,
% unless of course the error be too harmful...

% \startchemical

def chem_start_structure(expr i, l, r, t, b, rotation, unit, bond, scale, offset, axis, rulethickness, axiscolor) =
    save chem_setting_l, chem_setting_r, chem_setting_t, chem_setting_b ;

    chem_emwidth            := unit ; % dynamically set for each structure.
    chem_text_offset        := -.3chem_emwidth ; % -.71chem_emwidth ; % 1/sqrt(2)
    chem_center_offset      :=  .5chem_emwidth ;
    chem_b_length           :=    chem_emwidth * bond * scale ;
    % scale (normally 1) scales the structure but not the text.

    if numeric l :
        chem_setting_l      := -l ;
    fi
    if numeric r :
        chem_setting_r      := r ;
    fi
    if numeric t :
        chem_setting_t      := t ;
    fi
    if numeric b  :
        chem_setting_b      := -b ;
    fi
    chem_setting_rotation   := rotation ;
    chem_setting_offset     := offset ;
    chem_setting_axis       := if boolean axis : axis else : (axis<>0) fi ;
    chem_axis_rulethickness := .75*(rulethickness) ; % axis 50% thinner than frame and bonds.
    chem_axis_color         := axiscolor ;

    chem_reset ;
enddef ;

% \stopchemical

vardef chem_stop_structure =
    % Make sure that all of the saved stack has been restored... (this was a gotcha!)
    forever :
        exitif chem_stack_n=0 ;
        chem_restore ;
    endfor

    currentpicture := (currentpicture shifted -chem_origin) rotated chem_setting_rotation ;

    save l, r, b, t ;
    l := min(xpart llcorner currentpicture, xpart lrcorner currentpicture) ;
    r := max(xpart llcorner currentpicture, xpart lrcorner currentpicture) ;
    b := min(ypart llcorner currentpicture, ypart ulcorner currentpicture) ;
    t := max(ypart llcorner currentpicture, ypart ulcorner currentpicture) ;

    if unknown chem_setting_l : chem_setting_l := l ; fi
    if unknown chem_setting_r : chem_setting_r := r ; fi
    if unknown chem_setting_b : chem_setting_b := b ; fi
    if unknown chem_setting_t : chem_setting_t := t ; fi

    if chem_setting_axis : % put it behind the picture
        chem_pic := currentpicture ; currentpicture := nullpicture ;
        chem_num0 := .5chem_b_length ;
        chem_num1 := .2chem_num0 ;
        % draw the axes to the bounding box of the entire structure,
        % not necessarily the bounding box of the final figure
        draw (l,0) -- (r,0)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        draw (0,b) -- (0,t)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        for i = 0 step  chem_num0 until r :
            draw (i,-chem_num1) -- (i,chem_num1)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        endfor
        for i = 0 step -chem_num0 until l :
            draw (i,-chem_num1) -- (i,chem_num1)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        endfor
        for i = 0 step  chem_num0 until t :
            draw (-chem_num1,i) -- (chem_num1,i)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        endfor
        for i = 0 step -chem_num0 until b :
            draw (-chem_num1,i) -- (chem_num1,i)
            withpen pencircle scaled chem_axis_rulethickness withcolor chem_axis_color ;
        endfor
        addto currentpicture also chem_pic ;
    fi ;
    if chem_trace_boundingbox :
        fill boundingbox currentpicture withcolor blue withtransparency(1,.25) ;
    fi ;
    setbounds currentpicture to
        ((chem_setting_l,chem_setting_b) -- (chem_setting_r,chem_setting_b) --
         (chem_setting_r,chem_setting_t) -- (chem_setting_l,chem_setting_t) -- cycle) ;
    if chem_trace_boundingbox :
        fill boundingbox currentpicture withcolor red withtransparency(1,.25) ;
    fi ;
enddef ;

% \chemical

vardef chem_start_component = enddef ;
vardef chem_stop_component  = enddef ;

vardef chem_pb = % PB :
    if chem_trace_nesting :
        draw boundingbox currentpicture withpen pencircle scaled 1mm withcolor chem_axis_color ;
        draw origin withpen pencircle scaled 2mm withcolor chem_axis_color ;
    fi ;
    chem_doing_pb := true ;
enddef ;

vardef chem_pe = % PE
    if chem_trace_nesting :
        draw boundingbox currentpicture withpen pencircle scaled .5mm withcolor red ;
        draw origin withpen pencircle scaled 1mm withcolor red ;
    fi ;
    currentpicture := currentpicture shifted -chem_origin ;
    if chem_trace_nesting :
        draw origin withpen pencircle scaled .5mm withcolor green ;
    fi ;
    chem_origin := origin ;
    chem_doing_pb := false ;
enddef ;

vardef chem_do (expr pos) =
    if (unknown chem_doing_pb) or (not chem_doing_pb) :
        pos
    else :
        chem_doing_pb := false ;
        currentpicture := currentpicture shifted -pos ;
        chem_origin    := chem_origin    shifted -pos ;
        origin %  nullpicture
    fi
enddef ;


picture chem_stack_p[] ;
pair    chem_stack_origin[], chem_stack_mirror[] ;
numeric chem_stack_rotation[] ;
string  chem_stack_previous[] ;

vardef chem_save = % SAVE
    chem_stack_p       [incr chem_stack_n] := currentpicture ;
    chem_stack_origin  [     chem_stack_n] := chem_origin ; chem_origin := origin ;
    chem_stack_rotation[     chem_stack_n] := chem_rotation ;
    chem_stack_mirror  [     chem_stack_n] := chem_mirror ;
    chem_stack_previous[     chem_stack_n] := chem_previous ;
    currentpicture := nullpicture ;
enddef ;

vardef chem_restore = % RESTORE
    if chem_stack_n>0 :
        currentpicture := currentpicture shifted -chem_origin ;
        addto             chem_stack_p       [chem_stack_n] also currentpicture ;
        currentpicture := chem_stack_p       [chem_stack_n] ;
        chem_stack_p[chem_stack_n] := nullpicture ;
        chem_origin    := chem_stack_origin  [chem_stack_n] ;
        chem_rotation  := chem_stack_rotation[chem_stack_n] ;
        chem_mirror    := chem_stack_mirror  [chem_stack_n] ;
        chem_previous  := chem_stack_previous[chem_stack_n] ;
        chem_stack_n := chem_stack_n - 1 ;
    fi ;
enddef ;

% chem_adj and chem_sub are to be followed by chem_set(n) which does all the work...

vardef chem_adj (suffix $) (expr d, s) = % ADJ
    % scale s is ignored (for now?)
    if not chem_front[$] :
        chem_substituent     := 0 ;
        chem_substituent.lft := 0 ;
        chem_substituent.rt  := 0 ;
        chem_adjacent := d ;
    fi
enddef ;

vardef chem_lsub (suffix $) (expr d, s) =  % LSUB
    chem_sub.lft($,d,s) ;
enddef ;

vardef chem_rsub (suffix $) (expr d, s) =  % RSUB
    chem_sub.rt ($,d,s) ;
enddef ;

vardef chem_sub@# (suffix $) (expr d, s) = % SUB
    % scale s is ignored (for now?)
    chem_adjacent        := 0 ;
    chem_substituent     := 0 ;
    chem_substituent.lft := 0 ;
    chem_substituent.rt  := 0 ;
    % then :
    chem_substituent@#   := d ;
enddef ;

def chem_transformed (suffix $) = % not vardef!
    scaled chem_b_length
    if not chem_front[$] :
        if chem_mirror<>origin : reflectedabout(origin,chem_mirror) fi
        rotated chem_rotation
    fi
enddef ;

% vardef chem_draw (expr what, r, c) (text extra) =
%     draw what
%         withpen pencircle scaled r
%         withcolor c
%         extra ;
% enddef ;

vardef chem_draw (expr what, r, c) (text extra) =
    draw what
        withpen pencircle scaled r
        if string c :
            if c <> "" : withcolor c fi
        else :
            withcolor c
        fi
        extra ;
enddef ;

vardef chem_fill (expr what, r, c) (text extra) =
    fill what
        withpen pencircle scaled r
        withcolor c
        extra ;
enddef ;

vardef chem_drawarrow (expr what, r, c) (text extra) =
    drawarrow what
        withpen pencircle scaled r
        withcolor c
        extra ;
enddef ;

vardef chem_set (suffix $) =
    forsuffixes P = scantokens chem_previous :

    % This is a fairly complicated optimization and ajustement. It took some
    % thinking to get right, so beware!

    % And then even more time fixing a bug of a rotation +- half the symmetry
    % angle of a structure depending on the scale and/or the font size
    % (through chem_b_length).

    % first save the symmetry angle of the structure (as in chem_rot):
    chem_num0 := if chem_stacked[$] : 3 else : 0 fi ;
    chem_num9 := if chem_tetra[$] : 360 else :
                 abs(angle(point 0+chem_num0 of chem_b_path[$]) -
                     angle(point 1+chem_num0 of chem_b_path[$]))
                 fi ;

    if (chem_adjacent<>0) and chem_star[P] and chem_star[$] :
        % nop
        chem_adjacent := 0 ;
    elseif (chem_adjacent<>0) and (chem_front[P] or chem_front[$]) :
        % not allowed for FRONT
        chem_adjacent := 0 ;
    elseif chem_adjacent<>0 :
        chem_substituent     := 0 ;
        chem_substituent.lft := 0 ;
        chem_substituent.rt  := 0 ;
        % move to the bond midpoint of the first structure
        chem_pair0 := center (
            if chem_star[P] :
                origin -- point (chem_adjacent-1)
            else :
                subpath (chem_adjacent-1,chem_adjacent)
            fi
            of chem_b_path[P]
        ) chem_transformed(P) ;
        % find the closest opposite bond of the second structure
        chem_pair1 := chem_pair0 rotated if chem_star[P] : 90 else : 180 fi ;
        chem_num0 := abs(chem_pair1) ;
        chem_num1 := if chem_tetra[$] : 1 else : length chem_b_path[$] fi ;
        % only consider even indices (cardinal points) for ONE
        chem_num2 := if chem_star[$] and not chem_tetra[$] : 2 else : 1 fi ;
        for i=0 step chem_num2 until chem_num1 :
            chem_pair2 := (
                (
                    unitvector
                    center (
                        if chem_star[$] :
                            origin -- point i
                        else :
                            subpath (i,i+1)
                        fi
                        of chem_b_path[$])
                    )
                    scaled chem_num0
                ) chem_transformed($) ;
            if i=0 :
                chem_pair3 := chem_pair2 ;
                chem_num3 := 0 ;
            elseif (abs(chem_pair1 shifted -chem_pair2)) < (abs(chem_pair1 shifted -chem_pair3)) :
                chem_pair3 := chem_pair2 ;
                chem_num3 := i ;
            fi
        endfor
        if chem_star[$] :
            chem_pair4 := chem_pair0 shifted
                          -((point (chem_adjacent-1) of chem_b_path[P]) chem_transformed(P)) ;
        fi
        % adjust the bond angles
        chem_num4 := (angle(chem_pair1)-angle(chem_pair3)) zmod chem_num9 ;
        chem_rotation := chem_rotation + chem_num4 ;
        if not chem_star[$] :
            chem_pair4 :=
                if chem_star[P] :
                    (point chem_num3
                else :
                    center(subpath (chem_num3,chem_num3+1)
                fi
                of chem_b_path[$])
                chem_transformed($) ;
        fi
        if not chem_star[P] :
            chem_pair4 := chem_pair4 shifted -chem_pair0 ;
        fi
        currentpicture := currentpicture shifted chem_pair4 ;
        chem_origin    := chem_origin    shifted chem_pair4 ;
        chem_adjacent  := 0 ;
    fi ;

    % Insure that only one, if any, will be nonzero
    if ((chem_substituent     <> 0) and (chem_substituent.lft <> 0)) or
       ((chem_substituent     <> 0) and (chem_substituent.rt  <> 0)) or
       ((chem_substituent.lft <> 0) and (chem_substituent.rt  <> 0)) :
        chem_substituent     := 0 ;
        chem_substituent.lft := 0 ;
        chem_substituent.rt  := 0 ;
    fi
    if (chem_substituent <> 0) or (chem_substituent.lft <> 0) or (chem_substituent.rt <> 0) :
        % move origin to radical endpoint of the first structure
        if chem_substituent.lft > 0 :
            chem_pair0 := point chem_substituent.lft-1 of chem_r_path.lft[P] ;
            chem_substituent := chem_substituent.lft ;
            chem_substituent.lft := 0 ;
        elseif chem_substituent.rt > 0 :
            chem_pair0 := point chem_substituent.rt-1 of chem_r_path.rt[P] ;
            chem_substituent := chem_substituent.rt ;
            chem_substituent.rt := 0 ;
        else :
            chem_pair0 := point chem_substituent-1 of chem_r_path[P] ;
        fi
        chem_pair1 := chem_pair0 if not chem_star[P] :
                                 shifted -(point chem_substituent-1 of chem_b_path[P]) fi ;
        chem_t := identity chem_transformed(P) ;
        chem_pair0 := chem_pair0 transformed chem_t ; % radical
        chem_pair1 := chem_pair1 transformed chem_t ; % recentered (see below)
        currentpicture := currentpicture shifted -chem_pair0 ;
        chem_origin    := chem_origin    shifted -chem_pair0 ;
        if (not (chem_star[P] and chem_star[$])) or chem_tetra[P] or chem_tetra[$] :
            if chem_tetra[P] and chem_tetra[$] and ((chem_substituent=1) or (chem_substituent=2)):
                chem_rotation := (chem_rotation + 180) mod 360 ; % trans-alkane
                chem_pair2 := (point .5 of chem_b_path[$]) ; % bisector, not chem_transformed
                if chem_mirror=origin :
                    chem_mirror := chem_pair2 ;
                else :
                    chem_num0 := angle(chem_mirror)-angle(chem_pair2) ;
                    if (chem_num0>0) and (chem_num0> 180) :
                        chem_num0 :=  360 - chem_num0 ;
                    elseif (chem_num0<0) and (chem_num0<-180) :
                        chem_num0 := -360 - chem_num0 ;
                    fi
                    chem_rotation := (chem_rotation + 2chem_num0) mod 360 ;
                    chem_mirror := origin ;
                fi
            fi
            chem_t := identity chem_transformed($) ;
            chem_pair1 := chem_pair1 rotated 180 ; % opposite direction of radical bond
            % find the closest node
            chem_num0 := abs(chem_pair1) ;         % distance
            % search to find the nearest node of $; only consider 1 and 2 for CARBON,ALKYL
            chem_num1 := if chem_tetra[$] : 1 else : length chem_b_path[$] fi ;
            % only consider even indices (cardinal points) for ONE
            chem_num2 := if chem_star[$] and not chem_tetra[$] : 2 else : 1 fi ;
            for i=0 step chem_num2 until chem_num1 :
                chem_pair2 := (unitvector(point i of chem_b_path[$]) scaled chem_num0)
                              transformed chem_t ;
                if i=0 :
                    chem_pair3 := chem_pair2 ;
                    chem_num3  := 0 ;
                elseif (abs(chem_pair1 shifted -chem_pair2)) <
                       (abs(chem_pair1 shifted -chem_pair3)) :
                    chem_pair3 := chem_pair2 ;
                    chem_num3  := i ;
                fi
            endfor
            if not chem_front[$] : % adjust rotation
                chem_num4 := angle(chem_pair1)-angle(chem_pair3) ;
                chem_rotation := (chem_rotation + chem_num4) mod 360 ;
            fi ;
            chem_t := identity chem_transformed($) ;
            chem_pair4 := (point chem_num3 of chem_b_path[$]) transformed chem_t ;
            if not chem_star[$] :
                currentpicture := currentpicture shifted chem_pair4 ;
                chem_origin    := chem_origin    shifted chem_pair4 ;
            fi
            if not chem_front[$] : % adjust rotation
                chem_rotation := chem_rotation zmod chem_num9 ;
            fi
        fi
        chem_substituent := 0 ;
    fi ;
    endfor
    chem_previous := str $ ;
enddef ;

% line (f_rom, t_o, r_ule, c_olor)

vardef chem_b@# (suffix $) (expr f,     t,   r,     c) = % B
    if chem_star[$] :
        chem_r@#($,f,t,r,c) ;
    elseif length(str @#)>0 :
        chem_sb@#($,f,t,r,c) ;
    else :
        chem_draw(
            (subpath (f-1,t) of chem_b_path[$]) chem_transformed($),
            r,c,) ;
    fi
enddef ;

vardef chem_sb@# (suffix $) (expr f, t, r, c) = % SB
    if chem_star[$] :
        chem_sr@#($,f,t,r,c) ;
    else :
        %chem_draw(
        %    (subpath (f-1,t) of chem_b_path[$]) chem_transformed($),
        %    r,c,dashed chem_sb_dash@# scaled chem_b_length) ;
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$])
                transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_sd@# (suffix $) (expr f, t, r, c) = % SD
    if chem_star[$] :
        chem_rd@#($,f,t,r,c) ;
    else :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$])
                transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_r_fragment@# (suffix $) (expr i) =
    (
        if chem_star[$] :
             origin
        else :
             point i-1 of chem_b_path[$]
        fi --
        point i-1 of chem_r_path@#[$]
    ) % no ;
enddef ;

vardef chem_r@# (suffix $) (expr f, t, r, c) = % R
    if length(str @#)>0 :
        chem_sr@#($,f,t,r,c) ;
    else :
        chem_sr.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_er@# (suffix $) (expr f, t, r, c) = % ER
    if length(str @#)>0:
        chem_dr@#($,f,t,r,c) ;
    else :
        chem_dr.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_dr@# (suffix $) (expr f, t, r, c) = % DR
    if not chem_front[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := (subpath chem_sb_pair@# of chem_r_fragment($,i)) ;
            chem_draw(
                (chem_path0 paralleled  chem_dbl_offset) transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled -chem_dbl_offset) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_lr@# (suffix $) (expr f, t, r, c) = % LR
    if length(str @#)>0 :
        chem_lsr@#($,f,t,r,c) ;
    else :
        chem_lsr.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_rr@# (suffix $) (expr f, t, r, c) = % RR
    if length(str @#)>0 :
        chem_rsr@#($,f,t,r,c) ;
    else :
        chem_rsr.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_eb@# (suffix $) (expr f, t, r, c) = % EB
    if not chem_star[$] :
        %chem_draw(
        %    ((subpath (f-1,t) of chem_b_path[$]) paralleled -2chem_dbl_offset)
        %    chem_transformed($),
        %    r,c,dashed chem_sb_dash scaled chem_b_length) ;
        for i=f upto t :
            chem_t := identity chem_transformed($) ;
            chem_draw(
                ((subpath (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$])
                paralleled -2chem_dbl_offset) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_ad@# (suffix $) (expr f, t, r, c) = % AD
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_drawarrow(
            (
            (subpath
            if chem_star[$] :
                 chem_sb_pair@#                    of chem_r_fragment($,i)
                ) paralleled 5chem_dbl_offset
             else :
                (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$]
                ) paralleled 2chem_dbl_offset
             fi
            ) transformed chem_t,
            r,c,) ;
    endfor
enddef ;

vardef chem_au@# (suffix $) (expr f, t, r, c) = % AU
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_drawarrow(
             ((reverse
               subpath
             if chem_star[$] :
                 chem_sb_pair@#                    of chem_r_fragment($,i)
                ) paralleled -5chem_dbl_offset
             else :
                (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$]
                ) paralleled -2chem_dbl_offset
             fi
            ) transformed chem_t,
            r,c,) ;
    endfor
enddef ;

vardef chem_es@# (suffix $) (expr f, t, r, c) = % ES
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                ((point i-1 of chem_r_path[$]) scaled (xpart chem_sb_pair)) transformed chem_t,
                chem_dot_factor*r,c,) ;
        endfor
    fi
enddef ;

vardef chem_ed@# (suffix $) (expr f, t, r, c) = % ED
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        if chem_star[$] :
            chem_path0 := subpath chem_sb_pair of chem_r_fragment($,i) ;
            chem_draw(
                (point 0 of (chem_path0 paralleled -chem_dbl_offset)) transformed chem_t,
                chem_dot_factor*r,c,) ;
            chem_draw(
                (point 0 of (chem_path0 paralleled  chem_dbl_offset)) transformed chem_t,
                chem_dot_factor*r,c,) ;
        else :
            chem_draw(
                ((subpath (chem_sb_pair shifted (i-1,i-1)) of chem_b_path[$])
                paralleled -2chem_dbl_offset) transformed chem_t,
                r,c,dashed evenly) ;
        fi
    endfor
enddef ;

vardef chem_ep@# (suffix $) (expr f, t, r, c) = % EP
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair of chem_r_fragment($,i) ;
            chem_draw(
                (point 0 of (chem_path0 paralleled -chem_dbl_offset) --
                 point 0 of (chem_path0 paralleled  chem_dbl_offset)) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_et@# (suffix $) (expr f, t, r, c) = % ET
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair of chem_r_fragment($,i) ;
            chem_draw(
                (point 0 of (chem_path0 paralleled -2chem_dbl_offset)) transformed chem_t,
                chem_dot_factor*r,c,) ;
            chem_draw(
                (point 0 of chem_path0) transformed chem_t,
                chem_dot_factor*r,c,) ;
            chem_draw(
                (point 0 of (chem_path0 paralleled  2chem_dbl_offset)) transformed chem_t,
                chem_dot_factor*r,c,) ;
        endfor
    fi
enddef ;

vardef chem_db@# (suffix $) (expr f, t, r, c) = % DB
    if chem_star[$] :
        chem_dr@#($,f,t,r,c) ;
    elseif not chem_front[$] :
        chem_t := identity chem_transformed($) ;
        %chem_draw(
        %    ((subpath (f-1,t) of chem_b_path[$]) paralleled -chem_dbl_offset)
        %    transformed chem_t,
        %    r,c,dashed chem_sb_dash@# scaled chem_b_length) ;
        %chem_draw(
        %    ((subpath (f-1,t) of chem_b_path[$]) paralleled  chem_dbl_offset)
        %    transformed chem_t,
        %    r,c,dashed chem_sb_dash@# scaled chem_b_length) ;
        for i=f upto t :
            chem_path0 := subpath (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$] ;
            chem_draw(
                (chem_path0 paralleled -chem_dbl_offset) transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled  chem_dbl_offset) transformed chem_t,
                r,c,) ;
            % todo : this should be cut-off where it overlaps a neighboring standard bond.
        endfor
    fi
enddef ;

vardef chem_tb@# (suffix $) (expr f, t, r, c) = % TB
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_draw(
                (chem_path0 paralleled -2chem_dbl_offset) transformed chem_t,
                r,c,) ;
            chem_draw(
                chem_path0 transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled  2chem_dbl_offset) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_sr@# (suffix $) (expr f, t, r, c) = % SR
    chem_t := identity chem_transformed($) ;
    if chem_stacked[$] :
        chem_num0 := length chem_b_path[$] ; chem_num1 := floor(.5chem_num0) ;
        for i=f upto t :
            chem_draw(
                (subpath (if i>chem_num1: .5,ypart fi chem_sb_pair@#) of chem_r_fragment($,i))
                transformed chem_t,
                r,c,) ;
        endfor
    else :
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment($,i))
                transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_rd@# (suffix $) (expr f, t, r, c) = % RD
    chem_t := identity chem_transformed($) ;
    if chem_stacked[$] :
        chem_num0 := length chem_b_path[$] ; chem_num1 := floor(.5chem_num0) ;
        for i=f upto t :
            chem_draw(
                (subpath (if i>chem_num1: .5,ypart fi chem_sb_pair@#) of chem_r_fragment($,i))
                transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    else :
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment($,i))
                transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_rh@# (suffix $) (expr f, t, r, c) = % RH
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_draw(
            (subpath chem_sb_pair@# of chem_r_fragment($,i))
            transformed chem_t,
            chem_dot_factor*r,c,dashed withdots scaled ((.5chem_b_length/3)/5bp)) ;
            % not symmetric - needs to be tweaked...
    endfor
enddef ;

vardef chem_lrh@# (suffix $) (expr f, t, r, c) = % LRH
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_draw(
            (subpath chem_sb_pair@# of chem_r_fragment.lft($,i))
            transformed chem_t,
            chem_dot_factor*r,c,dashed withdots scaled ((.5chem_b_length/3)/5bp)) ;
            % not symmetric - needs to be tweaked...
    endfor
enddef ;

vardef chem_rrh@# (suffix $) (expr f, t, r, c) = % RRH
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_draw(
            (subpath chem_sb_pair@# of chem_r_fragment.rt($,i))
            transformed chem_t,
            chem_dot_factor*r,c,dashed withdots scaled ((.5chem_b_length/3)/5bp)) ;
            % not symmetric - needs to be tweaked...
    endfor
enddef ;

vardef chem_hb@# (suffix $) (expr f, t, r, c) = % HB
    if chem_star[$] :
        chem_rh@#($,f,t,r,c)
    else :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath (chem_sb_pair@# shifted (i-1,i-1)) of chem_b_path[$])
                transformed chem_t,
                chem_dot_factor*r,c,dashed withdots scaled ((.5chem_b_length/3)/5bp)) ;
                % not symmetric - needs to be tweaked...
        endfor
    fi
enddef ;

vardef chem_bb@# (suffix $) (expr f, t, r, c) = % BB
    if chem_star[$] :
        chem_rb@#($,f,t,r,c) ;
    elseif chem_front[$] :
        chem_t := identity chem_transformed($) ;
        chem_draw(
            (subpath (f-1,t) of chem_b_path[$]) transformed chem_t,
            r,c,) ;
        chem_num0 := length chem_b_path[$] ; % total number of bonds
        chem_num1 := chem_front_b[$] ;       % number of bonds to be made bold
        % bold bonds within f and t
        chem_num2 := if f<0 :((f+1) mod chem_num0) + chem_num0 else : ((f-1) mod chem_num0) + 1 fi ;
        chem_num3 := if t<0 :((t+1) mod chem_num0) + chem_num0 else : ((t-1) mod chem_num0) + 1 fi ;
        if chem_num3<chem_num2 :
            chem_num4 := chem_num3 ;
            chem_num3 := chem_num2 ;
            chem_num2 := chem_num4 ;
        fi
        if chem_num2<chem_num1 : % Are there any bonds to be made bold?
            if chem_num2=1 :     % Skip the first bold bond.
                chem_fill(
                    (point chem_num2-1 of chem_b_path[$] --
                     point chem_num2   of chem_b_path[$] shifted (0,-chem_dbl_offset) --
                     point chem_num2   of chem_b_path[$] shifted (0, chem_dbl_offset) --
                     cycle) transformed chem_t,
                    r,c,) ;
            fi
            if (chem_num2<=chem_num1-1) and (chem_num3>1) :
                chem_path0 := subpath (if chem_num2>2 :         chem_num2-1 else : 1 fi,
                                       if chem_num3<chem_num1 : chem_num3   else : chem_num1-1 fi)
                    of chem_b_path[$] ;
                chem_fill(
                    (chem_path0          paralleled -chem_dbl_offset --
                     reverse(chem_path0) paralleled -chem_dbl_offset --
                    cycle) transformed chem_t,
                    r,c,) ;
            fi
            if chem_num3>=chem_num1 :
                chem_fill(
                    (point chem_num1 of chem_b_path[$] --
                     point chem_num1-1 of chem_b_path[$] shifted (0,-chem_dbl_offset) --
                     point chem_num1-1 of chem_b_path[$] shifted (0, chem_dbl_offset) --
                     cycle) transformed chem_t,
                    r,c,) ;
            fi
        fi
    fi
enddef ;

vardef chem_rb@# (suffix $) (expr f, t, r, c) = % RB
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
        chem_fill(
            (point 0 of chem_path0 --
             point 1 of chem_path0
                 rotatedaround(point 0 of chem_path0, -chem_bb_angle) --
             point 1 of chem_path0
                 rotatedaround(point 0 of chem_path0,  chem_bb_angle) --
             cycle) transformed chem_t,
            r,c,) ;
    endfor
enddef ;

vardef chem_lrb@# (suffix $) (expr f, t, r, c) = % LRB
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment.lft($,i) ;
            chem_fill(
                (point 0 of chem_path0 --
                 point 1 of chem_path0
                     rotatedaround(point 0 of chem_path0, -chem_bb_angle) --
                 point 1 of chem_path0
                     rotatedaround(point 0 of chem_path0,  chem_bb_angle) --
                 cycle) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_rrb@# (suffix $) (expr f, t, r, c) = % RRB
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment.rt($,i) ;
            chem_fill(
                (point 0 of chem_path0 --
                 point 1 of chem_path0
                     rotatedaround(point 0 of chem_path0, -chem_bb_angle) --
                 point 1 of chem_path0
                     rotatedaround(point 0 of chem_path0,  chem_bb_angle) --
                 cycle) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_lsr@# (suffix $) (expr f, t, r, c) = % LSR
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment.lft($,i)) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_rsr@# (suffix $) (expr f, t, r, c) = % RSR
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment.rt($,i)) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_lrd@# (suffix $) (expr f, t, r, c) = % LRD
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment.lft($,i)) transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_rrd@# (suffix $) (expr f, t, r, c) = % RRD
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of chem_r_fragment.rt($,i)) transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_s@# (suffix $) (expr f, t, r, c) = % S
    if length(str @#)>0 :
       chem_ss@#($,f,t,r,c) ;
    else :
       chem_ss.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_ss@# (suffix $) (expr f, t, r, c) = % SS
    if not (chem_star[$] or chem_front[$]) :
        chem_draw(
            subpath chem_sb_pair@# of (point f-2 of chem_b_path[$] -- point t of chem_b_path[$])
            chem_transformed($),
            r,c,) ;
    fi
enddef ;

vardef chem_mid@# (suffix $) (expr f, t, r, c) = % MID
    if length(str @#)>0 :
        chem_mids@#($,f,t,r,c) ;
    else :
        chem_mids.b($,f,t,r,c) ;
    fi
enddef ;

vardef chem_mids@# (suffix $) (expr f, t, r, c) = % MIDS
    if not (chem_star[$] or chem_front[$]) :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_draw(
                (subpath chem_sb_pair@# of (origin -- point i-1 of chem_b_path[$]))
                transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_cd  (suffix $) (expr r, c) =  % CD
    chem_draw(
        chem_c_path[$] chem_transformed($),
        r,c,dashed evenly) ;
enddef ;

vardef chem_c (suffix $) (expr r, c) = % C
    chem_draw(
        chem_c_path[$] chem_transformed($),
        r,c,) ;
enddef ;

vardef chem_ccd  (suffix $) (expr f, t, r, c) = % CCD
    chem_num0 := ypart((origin--center(subpath (f-2,f-1) of chem_b_path[$]))
               intersectiontimes chem_c_path[$]) ;
    chem_num1 := ypart((origin--center(subpath (t-1,t)   of chem_b_path[$]))
               intersectiontimes chem_c_path[$]) ;
    if chem_num1>chem_num0 :
        chem_num0 := chem_num0 + length chem_c_path[$] ;
    fi
    chem_draw(
        subpath (chem_num1,chem_num0) of chem_c_path[$] chem_transformed($),
        r,c,dashed evenly) ;
enddef ;

vardef chem_cc (suffix $) (expr f, t, r, c) = % CC
    chem_num0 := ypart((origin--center(subpath (f-2,f-1) of chem_b_path[$]))
               intersectiontimes chem_c_path[$]) ;
    chem_num1 := ypart((origin--center(subpath (t-1,t)   of chem_b_path[$]))
               intersectiontimes chem_c_path[$]) ;
    if chem_num1>chem_num0 :
        chem_num0 := chem_num0 + length chem_c_path[$] ;
    fi
    chem_draw(
        subpath (chem_num1,chem_num0) of chem_c_path[$] chem_transformed($),
        r,c,) ;
enddef ;

vardef chem_ldb@# (suffix $) (expr f, t, r, c) = % LD
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_draw(
                chem_path0 transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled  2chem_dbl_offset) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_rdb@# (suffix $) (expr f, t, r, c) = % LD
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_draw(
                chem_path0 transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled -2chem_dbl_offset) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_ldd@# (suffix $) (expr f, t, r, c) = % LDD
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_draw(
                chem_path0 transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled  2chem_dbl_offset) transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_rdd@# (suffix $) (expr f, t, r, c) = % RDD
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_draw(
                chem_path0 transformed chem_t,
                r,c,) ;
            chem_draw(
                (chem_path0 paralleled -2chem_dbl_offset) transformed chem_t,
                r,c,dashed evenly) ;
        endfor
    fi
enddef ;

vardef chem_oe@# (suffix $) (expr f, t, r, c) = % OE
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_path1 := chem_path0 paralleled -.5chem_dbl_offset ;
            chem_path2 := chem_path0 paralleled  .5chem_dbl_offset ;
            chem_draw(
                (  point 0 of chem_path0 --
                .2[point 0 of chem_path0, point infinity of chem_path0]..
                .3[point 0 of chem_path1, point infinity of chem_path1]..
                .4[point 0 of chem_path0, point infinity of chem_path0]..
                .5[point 0 of chem_path2, point infinity of chem_path2]..
                .6[point 0 of chem_path0, point infinity of chem_path0]..
                .7[point 0 of chem_path1, point infinity of chem_path1]..
                .8[point 0 of chem_path0, point infinity of chem_path0]--
                   point infinity of chem_path0) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_bw@# (suffix $) (expr f, t, r, c) = % BW
    if chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
            chem_path1 := chem_path0 paralleled -.5chem_dbl_offset ;
            chem_path2 := chem_path0 paralleled  .5chem_dbl_offset ;
            chem_draw(
                (  point 0 of chem_path0..
                .1[point 0 of chem_path1, point infinity of chem_path1]..
                .2[point 0 of chem_path0, point infinity of chem_path0]..
                .3[point 0 of chem_path2, point infinity of chem_path2]..
                .4[point 0 of chem_path0, point infinity of chem_path0]..
                .5[point 0 of chem_path1, point infinity of chem_path1]..
                .6[point 0 of chem_path0, point infinity of chem_path0]..
                .7[point 0 of chem_path2, point infinity of chem_path2]..
                .8[point 0 of chem_path0, point infinity of chem_path0]..
                .9[point 0 of chem_path1, point infinity of chem_path1]..
                   point infinity of chem_path0) transformed chem_t,
                r,c,) ;
        endfor
    fi
enddef ;

vardef chem_bd@# (suffix $) (expr f, t, r, c) = % BD
    if chem_star[$] : chem_rbd@#($,f,t,r,c) ; fi
enddef ;

vardef chem_rbd@# (suffix $) (expr f, t, r, c) = % RBD
    chem_t := identity chem_transformed($) ;
    for i=f upto t :
        chem_path0 := subpath chem_sb_pair@# of chem_r_fragment($,i) ;
        if chem_bd_wedge :
            chem_path1 := chem_path0 rotated -chem_bb_angle ;
            chem_path2 := chem_path0 rotated  chem_bb_angle ;
        else :
            chem_path1 := chem_path0 paralleled -chem_dbl_offset ;
            chem_path2 := chem_path0 paralleled  chem_dbl_offset ;
        fi
        for j=0 upto 3 :
            chem_draw(
                (point (j/3) of chem_path1 -- point (j/3) of chem_path2) transformed chem_t,
                2r,c,) ;
        endfor
    endfor
enddef ;

vardef chem_lrbd@# (suffix $) (expr f, t, r, c) = % LRBD
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment.lft($,i) ;
            if chem_bd_wedge :
                chem_path1 := chem_path0 rotated -chem_bb_angle ;
                chem_path2 := chem_path0 rotated  chem_bb_angle ;
            else :
                chem_path1 := chem_path0 paralleled -.5chem_dbl_offset ;
                chem_path2 := chem_path0 paralleled  .5chem_dbl_offset ;
            fi
            for j=0 upto 3 :
                chem_draw(
                    (point (j/3) of chem_path1 -- point (j/3) of chem_path2) transformed chem_t,
                    2r,c,) ;
            endfor
        endfor
    fi
enddef ;

vardef chem_rrbd@# (suffix $) (expr f, t, r, c) = % RRBD
    if not chem_star[$] :
        chem_t := identity chem_transformed($) ;
        for i=f upto t :
            chem_path0 := subpath chem_sb_pair@# of chem_r_fragment.rt($,i) ;
            if chem_bd_wedge :
                chem_path1 := chem_path0 rotated -chem_bb_angle ;
                chem_path2 := chem_path0 rotated  chem_bb_angle ;
            else :
                chem_path1 := chem_path0 paralleled -.5chem_dbl_offset ;
                chem_path2 := chem_path0 paralleled  .5chem_dbl_offset ;
            fi
            for j=0 upto 3 :
                chem_draw(
                    (point (j/3) of chem_path1 -- point (j/3) of chem_path2) transformed chem_t,
                    2r,c,) ;
            endfor
        endfor
    fi
enddef ;

% text, number (no alignment on number);

vardef chem_z@#(suffix $) (expr p) (text t) = % Z
    draw chem_text@#
        (t,chem_do(
            if p=0 :
                origin
            else :
                (point p-1 of chem_b_path[$]) chem_transformed($)
            fi
        )) ;
enddef ;

vardef chem_cz@#(suffix $) (expr p) (text t) = chem_z@#($,p,t) ; enddef ; % CZ ?

vardef chem_midz@#(suffix $) (expr p) (text t) = % MIDZ
    if not (chem_star[$] or chem_front[$]) :
        draw chem_text@#
            (t,chem_do(
                (xpart chem_sb_pair, 0) scaled (xpart point 0 of chem_b_path[$])
                chem_transformed($)
            )) ;
    fi
enddef ;

vardef chem_rz@#(suffix $) (expr p) (text t) = % RZ
     draw chem_text@#
         (t, chem_do((point p-1 of chem_r_path[$]) chem_transformed($))) ;
enddef ;

vardef chem_lrz@#(suffix $) (expr p) (text t) = % LRZ
    if not chem_star[$] :
        draw chem_text@#
            (t,
             chem_do((point p-1 of chem_r_path.lft[$]) chem_transformed($))) ;
    fi
enddef ;

vardef chem_rrz@#(suffix $) (expr p) (text t) = % RRZ
    if not chem_star[$] :
        draw chem_text@#
            (t, chem_do((point p-1 of chem_r_path.rt[$]) chem_transformed($))) ;
    fi
enddef ;

vardef chem_zn@#(suffix $) (expr p) (text t) =  % ZN
    chem_zt($,p,t) ;
enddef ;

vardef chem_zt@#(suffix $) (expr p) (text t) = % ZT
    draw chem_text@#(t,chem_do ((point p-1 of chem_b_path[$]) chem_transformed($)
                                 scaled chem_text_min)) ;
enddef ;

vardef chem_zln@#(suffix $) (expr p) (text t) = % ZLN
    chem_zlt($,p,t) ;
enddef ;

vardef chem_zlt@#(suffix $) (expr p) (text t) = % ZLT
    draw chem_text@#(t, chem_do((point p-1.5 of chem_b_path[$]) chem_transformed($)
                                scaled chem_text_min)) ;
enddef ;

vardef chem_zrn@#(suffix $) (expr p) (text t) = % ZRN
    chem_zrt($,p,t) ;
enddef ;

vardef chem_zrt@#(suffix $) (expr p) (text t) = % ZRT
    draw chem_text@#(t, chem_do((point p-0.5 of chem_b_path[$]) chem_transformed($)
                                 scaled chem_text_min)) ;
enddef ;

vardef chem_crz@#(suffix $) (expr p) (text t) = % CRZ ????
    if chem_star[$] :
        draw chem_text@#(t, chem_do((point p-1 of chem_b_path[$] enlonged chem_center_offset)
                                   chem_transformed($))) ;
    fi
enddef ;

vardef chem_rn@#(suffix $) (expr i, t) =  % RN
    chem_rt($,i,t) ;
enddef ;

vardef chem_rt@#(suffix $) (expr p) (text t) = % RT
    draw chem_text@#(t, chem_do((center chem_r_fragment($,p)) chem_transformed($))) ;
enddef ;

vardef chem_lrn@#(suffix $) (expr i, t) = % LRN
    chem_lrt($,i,t) ;
enddef ;

vardef chem_lrt@#(suffix $) (expr p) (text t) = % LRT
    draw chem_text@#(t, chem_do((center chem_r_fragment.lft($,p)) chem_transformed($))) ;
enddef ;

vardef chem_rrn@# (suffix $) (expr i, t) = % RRN
    chem_rrt($,i,t) ;
enddef ;

vardef chem_rrt@#(suffix $) (expr p) (text t) = % RRT
    draw chem_text@#(t, chem_do((center chem_r_fragment.rt($,p)) chem_transformed($))) ;
enddef ;

vardef chem_symbol(expr t) = draw textext(t) ; enddef ;

vardef chem_align@#(expr pic) =
    pic
        if (mfun_labtype@# >= 10) :
            shifted (0,ypart center pic)
        fi
        shifted (-(mfun_labxf@#*lrcorner pic + mfun_labyf@#*ulcorner pic + (1-mfun_labxf@#-mfun_labyf@#)*llcorner pic))
enddef ;

vardef chem_text@#(expr txt, z) =
    chem_pic := textext(txt) ;
        if length(str @#)=0 :
            chem_pic := chem_align(chem_pic) ;
        elseif (str @#) = "auto" :
            if z<>origin :
                chem_num0 := abs(angle(z rotated chem_setting_rotation)) ;
                if chem_num0<=60 :
                    chem_pic := chem_align.rt (chem_pic) xshifted  chem_text_offset ;
                elseif chem_num0>=120 :
                    chem_pic := chem_align.lft(chem_pic) xshifted -chem_text_offset ;
                else :
                    chem_pic := chem_align    (chem_pic) ;
                fi
            else :
                    chem_pic := chem_align    (chem_pic) ;
            fi
        else :
            chem_pic := chem_align@#(chem_pic) shifted (chem_text_offset*mfun_laboff@#) ;
        fi
    chem_pic := (chem_pic rotated -chem_setting_rotation) shifted z ;

    if chem_trace_text :
        draw z                    withpen pencircle scaled 2pt withcolor red ;
        draw boundingbox chem_pic withpen pencircle scaled 1pt withcolor red ;
    fi

    chem_pic
enddef ;

% transform

% rotations and reflections

vardef chem_rot (suffix $) (expr d, s) = % ROT
    if not chem_front[$] :
        if d=0 :
            chem_rotation := 0
        else :
            chem_num0 := if chem_stacked[$] : 3 else : 0 fi ;
            chem_num1 := .5(angle(point d+chem_num0   of chem_b_path[$]) -
                            angle(point d+chem_num0-1 of chem_b_path[$])) ;
            chem_rotation := (chem_rotation + s*chem_num1) zmod 360 ;
        fi
    fi
enddef ;

vardef chem_mir (suffix $) (expr d, s)  = % MIR
    % We take the scale factor s to multiply the rotation, but only ONCE.
    % For example: CARBON,.5MIR12 will give a rotation by 104°
    if not chem_front[$] :
        if d=0 : % inversion
            if chem_mirror=origin :
                chem_rotation := (chem_rotation + 180*s) zmod 360 ;
            else :
                chem_mirror := chem_mirror rotated 90 ;
            fi
        else :
            chem_pair0 := (point d-1 of chem_b_path[$]) scaled s ; % not chem_transformed
            if chem_mirror=origin :
                chem_mirror := chem_pair0 ;
            else :
                chem_num0 := angle(chem_mirror)-angle(chem_pair0) ;
                if (chem_num0>0) and (chem_num0> 180) :
                    chem_num0 :=  360 - chem_num0 ;
                elseif (chem_num0<0) and (chem_num0<-180) :
                    chem_num0 := -360 - chem_num0 ;
                fi
                chem_num0 := chem_num0 * s ;
                chem_rotation := (chem_rotation + 2chem_num0) zmod 360 ;
                chem_mirror := origin ;
            fi
        fi
    fi
enddef ;

% translations

vardef chem_dir (suffix $) (expr d, s) = % DIR (same as MOV(d-1)MOV(d+1))
    if not chem_front[$] :
        if d=0 :
            currentpicture := currentpicture shifted -chem_origin ;
            chem_origin    := origin ;
        else :
            chem_pair0 :=
                 (((point d-2 of chem_b_path[$]) shifted (point d of chem_b_path[$])) scaled s)
                 chem_transformed($) ;
            currentpicture := currentpicture shifted -chem_pair0 ;
            chem_origin    := chem_origin    shifted -chem_pair0 ;
        fi
   fi
enddef ;

vardef chem_mov (suffix $) (expr d, s) = % MOV
    if d=0 :
        currentpicture := currentpicture shifted -chem_origin ;
        chem_origin    := origin ;
    else :
        chem_pair0 := ((point d-1 of chem_b_path[$]) scaled s) chem_transformed($) ;
        currentpicture := currentpicture shifted -chem_pair0 ;
        chem_origin    := chem_origin    shifted -chem_pair0 ;
    fi ;
enddef ;

vardef chem_mark (suffix $) (expr d, s) = % MARK
    % scale s is ignored
    if d<>0 :
        chem_mark_pair[d] := -chem_origin ;
    fi
enddef ;

vardef chem_marked (expr d) =
    if d=0 :
        chem_origin
    elseif known chem_mark_pair[d] :
        chem_mark_pair[d] shifted chem_origin
    else :
        origin
    fi
enddef ;

vardef chem_number@#(suffix $) (expr p) (text t) = chem_label@#($,p,t) enddef ; % NUMBER
vardef chem_label@# (suffix $) (expr p) (text t) = % LABEL
    draw chem_text@#(t,chem_do(chem_marked(p))) ;
enddef ;

vardef chem_move (suffix $) (expr d, s) = % MOVE
    chem_pair0 := chem_marked(d) scaled s ;
    currentpicture := currentpicture shifted -chem_pair0 ;
    chem_origin    := chem_origin    shifted -chem_pair0 ;
enddef ;

vardef chem_diff (suffix $) (expr d, s) = % DIFF
    chem_pair0 := (chem_marked(d) shifted -chem_origin) scaled s ;
    currentpicture := currentpicture shifted -chem_pair0 ;
    chem_origin    := chem_origin    shifted -chem_pair0 ;
enddef ;

vardef chem_line (suffix $) (expr f, t, r, c) = % LINE
    draw if f=t : origin else : chem_marked(f) fi -- chem_marked(t)
        % no chem_transformed
        withpen pencircle scaled r
        withcolor c
enddef ;

vardef chem_dash (suffix $) (expr f, t, r, c) = % DASH
    draw if f=t : origin else : chem_marked(f) fi -- chem_marked(t)
        % no chem_transformed
        withpen pencircle scaled r
        withcolor c
        dashed evenly ;
enddef ;

vardef chem_arrow (suffix $) (expr f, t, r, c) = % ARROW
    drawarrow if f=t : origin else : chem_marked(f) fi -- chem_marked(t)
        % no chem_transformed
        withpen pencircle scaled r
        withcolor c
enddef ;


vardef chem_rm (suffix $) (expr d, s) = % RM
    if (not chem_front[$]) and (d<>0) :
        chem_pair0 := ((point d-1 of chem_r_path[$]) scaled s) chem_transformed($) ;
        currentpicture := currentpicture shifted -chem_pair0 ;
        chem_origin    := chem_origin    shifted -chem_pair0 ;
    fi ;
enddef ;

vardef chem_off (suffix $) (expr d, s) = % OFF
    if d=0 :
        currentpicture := currentpicture shifted -chem_origin ;
        chem_origin    := origin ;
    else :
        chem_pair0 := (unitvector(point d-1 of chem_b_path[one])) scaled chem_setting_offset*s ;
        % not chem_transformed
        currentpicture := currentpicture shifted -chem_pair0 ;
        chem_origin    := chem_origin    shifted -chem_pair0 ;
    fi ;
enddef ;