%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  Molecular Coding Format manual     by  Akira Yamaji 2015.7.25
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[dvipdfmx]{graphicx}
%%%%\usepackage[pdftex]{graphicx}
%%%%\usepackage{epstopdf}
\pagestyle{empty}
\topmargin=-17mm
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\textwidth=18cm
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\makeatletter
%----------------------------------------------------------------------------
\newcount \fontnum%
\newcount \tempnum%
\fontnum=0%
\tempnum=1%
%----------------------------------------------------------------------------
\font\@strufont=mcf_man_soc\relax%
%----------------------------------------------------------------------------
\def\MCFtitle#1{\framebox{\bf No.\the\tempnum}\hspace{2mm}#1}
%----------------------------------------------------------------------------
\def\MCFstructure{%
 \makebox(75,0)[t]{\frame{\makebox(70,35){\@strufont\char\fontnum}}}
 \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
}%
%----------------------------------------------------------------------------
\begin{document}
\noindent%
\begin{picture}(180,0)
 \put(35,12){{\LARGE Molecular Coding Format manual}\hspace{10mm}
 by Akira Yamaji 2015.7.25}
\end{picture}\vspace{-6mm}\\
%----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain (1)}
\begin{verbatim}
plus(+):anticlockwize,minus(-)clockwize
bold arrow is default angle and position

  ^^30,-60,60,-60,60,-60,60
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%1----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain (2)}
\begin{verbatim}
!,!!: take 60 or -60 depend on 
      current angle and enviroment

  !6 (!!6)

  ** !!6: !,!,!,!,!,!
     !6:  {,!!6,}
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Ring}
\begin{verbatim}
six membered ring

  ?6 (??6)

  ** ??6 :^^-120,60,60,60,60,60,&(-5)
     ?6 : {,??6,}

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{rotate}
\begin{verbatim}
^^angle:rotate current angle

   ^^30,!4,^^30,?6
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change bond (1)}
\begin{verbatim}
~bond change bond 
  dm:double,dl:double(left),dr:double(right),
  wf:wedge forward,wb:wedge backward,
  zf:wedge dotted,zb:wedge dotted backward

  ^^30,!~dm,!~dl,!~dr,!~wf,!~wb,!~zf,!~zb
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change bond (2)}
\begin{verbatim}
 Bn=bond : change bond 
  vf:vector forward, vb:vector backward,
  tm:triple, wv:waved, bd:broad single,
  ov:over line

  ^^30,!9,1=vf,2=vb,3=tm,4=dt,5=wv,
  @(7~bd^-45`2,9~ov^45`2)/Me
\end{verbatim}
\end{minipage}
\MCFstructure
\newpage
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change bond length (1)}
\begin{verbatim}
B`length : change bond length of B

  ^^30,!2,!2`1.2,!
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change bond length (2)}
\begin{verbatim}
``length : change all bond length after

  ^^30,!2,``1.2,!2,!
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change chain length (3)}
\begin{verbatim}
?n`length : change ring length

  ^^30,?6,3\,?6`1.2,4=??6
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (1)}
\begin{verbatim}
Insert hetero atom

  ^^30,!2,O,!2
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (2)}
\begin{verbatim}
2:O : change A2 C to O
@(3,5)N : change  A3,A5 C to N

  ^^30,!6,2:O,@(3,5)N
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (3)}
\begin{verbatim}
2:N : change A2(brock ahead) C to N

  ?6,4\,?6,2:N
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (4)}
\begin{verbatim}
2:N : change A2(brock ahead) C to N
??6 is not brock
  ?6,4\,??6,2:N

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (5)}
\begin{verbatim}
#2:N : change A#2 C to N

  ?6,4\,?6,#2:N
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom (6)}
\begin{verbatim}
-2:N : change A(-2) C to N

  ?6,4\,?6,-2:N
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (1)}
\begin{verbatim}
?6,3=?6 : fuse ?6 at B3

  ?6,3=?6

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (2)}
\begin{verbatim}

  ?6,$(3,3,3)??6       NG
  ?6,$(3,9,14)??6      OK
  ?6,$(-4,-3,-3)??6    OK
  ?6,$(#3,#9,#14)??6   OK

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (3)}
\begin{verbatim}

  ?6,$(3,3,3)?6        OK
  ?6,$(3,9,14)?6       NG
  ?6,$(-4,-3,-3)?6     OK
  ?6,$(#3,#9,#14)?6    OK

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (4)}
\begin{verbatim}
(4,11)=??6[4]  : fuse 4/6 ring to B4 ..B11
(16,17)=??6[3] : fuse 3/6 ring to B16..B17
(20,5)=??4[2]  : fuse 2/4 ring to B20.. B5

  ^^30,?6,$(3,9)??6,(4,11)=??6[4],
      (16,17)=??6[3],(20,5)=??4[2]

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (5)}
\begin{verbatim}
(20,5)=??5[3]  : fuse 3/5 ring to B20..B5
(16,17)=??5[2] : fuse 2/5 ring to B16..B17

  ^^30,?6,$(3,9)??6,(4,11)=??6[4],
      (20,5)=??5[3],(16,17)=??5[2]
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Spiro ring}
\begin{verbatim}
4*,?5 : add ?5(5 membered ring) to A4

  ^^30,!6,4*,?5
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Branch (1)}
\begin{verbatim}
/ : branch bond
/ : process at last
 
 ^^30,!3,/!2,!3
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Branch (2)}
\begin{verbatim}
4\ : branch bond at A4

  ^^30,!6,4\,!2
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Substituent (1)}
\begin{verbatim}
/  : single          // : double
*/ : wedge forward   /* : wedge backward
** : direct

  ^^30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,!
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Substituent (2)}
\begin{verbatim}
Insert substituent

  ^^30,!,/Me,!,/Et,!3,/Pr,!,/iPr,!3,/tBu,!
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Substituent (3)}
\begin{verbatim}
Add substituent

  ^^30,!10,2:/Me,3:/Et,6:/Pr,7:/iPr,10:/tBu

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Substituent (4)}
\begin{verbatim}
~,^,`,> : change type,angle,length,enviroment
          of substituent

  ^^30,?6,
  @(3`2^30,3~wf,4~zf,6~wf^-30,6~zf^30)/H
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Substituent (5)}
\begin{verbatim}
~,^,`,> : change type,angle,length,enviroment
          of substituent

  ^^30,!7`1,
  @(2,3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change atom and Substituent}
\begin{verbatim}
NH,SOO : inset hetero atom and substituent
         simultaneously

  ^^30,!3,NH,!,SOO,!3

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain strech direction environment (1)}
\begin{verbatim}
>hz : horizontal enviroment (default)
>vt : vertical enviroment

  ?4,
  @(3^-90,3^-30,3^90)/'(!3,"{>hz}")>hz,
  @(1^-60,1`1.5,1^60)/'(!2,"{>vt}")>vt

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain strech direction environment (2)}
\begin{verbatim}
>lr : left-right enviroment
>rl : right-left enviroment

  ^^30,!6,
  @(3^-30,3,3^30)/'(!3,"{>lr}")>lr,
  @(5^-30,5,5^30)/'(!3,"{>rl}")>rl

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain strech direction environment (3)}
\begin{verbatim}
>45 : fixed angle enviroment
>'(-90,90,-90) : multi angle enviroment

  ^^-30,!6,@(2>45)/'(!3,"{>45}"),
  @(6>'(-90,90,-90))/'(!2,"{>(-90,90,-90)}")
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Change color}
\begin{verbatim}
@(5)green : change color of A5 green
$(3)red :   change color of B3 red

  ^^30,Ph,@(2,5)N,
          2:red,5:blue,3=green

\end{verbatim}
\end{minipage}
%%%%\MCFstructure   % for Metafont
\makebox(75,0)[t]{\frame{\makebox(70,35)%
{\includegraphics{mcf_man_soc-032.eps}}}}%  for dvipdfmx
%%%%{\includegraphics[width=30mm]{mcf_man_soc-030.png}}}}%   for pdfLaTeX
\advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Chain start multiple characters}
\begin{verbatim}
Use !0 instead of !,
if begin with multi charactor string

  ^^30,COOH,!0,!,/OH^-30,/COOH^30,!2,COOH
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{User definition}
\begin{verbatim}
iBuOH : user defined substructure

 iBuOH:='(!,/Me,!,OH)
 MCf(^^30,?6,@(4,6)/iBuOH)

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Inline definition}
\begin{verbatim}
Insert user defined substructure
 
 ^^30,!3,/'(!,/Me,!,OH),!3

\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch Start Vector}
\begin{verbatim}

  MCd(.8,.8)( 0, 0)(^^30,Ph,4:/Cl,3:/F)
  sw_start_vector:=1;
  MCd(.8,.8)( 1, 1)(^^30,Ph,4:/Cl,3:/F)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch NumberingA}
\begin{verbatim}

  sw_numberA:=1;
  MCf(^^30,
      Ph,-4=Ph1,-3\,!,Ph,10:/Et)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch NumberingB}
\begin{verbatim}

  sw_numberB:=1;
  MCf(^^30,
      Ph,-4=Ph1,-3\,!,Ph,10:/Et)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch Frame}
\begin{verbatim}

  MCd(.8,.8)(0,0)(^^30,Ph,4:/Cl,3:/F)
  sw_frame:=1;
  MCd(.8,.8)(1,1)(^^30,Ph,4:/Cl,3:/F)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch Solid ratio}
\begin{verbatim}

  MCd(.8,.8)( 0, 0)(^^30,Ph,4:/Cl,3:/F)
  sw_solid:=1; ratio_bond_width:=0.08;
  MCd(.8,.8)( 1, 1)(^^30,Ph,4:/Cl,3:/F)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Switch Expand}
\begin{verbatim}

  MCd(.6,.6)(0,0)(^^30,Ph,4:/COOH,3:/NH2)
  sw_expand:=1;
  MCd(.6,.6)(1,1)(^^30,Ph,4:/COOH,3:/NH2)
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(1) Ampicillin}
\begin{verbatim}

 ^^45,
  ?4,2:N,2=??5,-1:S,
  @(3^45,4^-45)/*H,1://O^15,
  5:/*COOH^-18,@(6^35,6^-35)/Me,
  4\^75,NH,!,//O,!,NH,!,Ph
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(2) Cholesterol}
\begin{verbatim}

  ^^30,
  ?6,$(-4,-2)??6,-4=??5,7=dl,
  1:*/OH,@(4,12)*/Me^60,9:*/H^60,
  10:/*H^180,@(11,-1)/*H^-60,
  -1\^17,/*Me,!4,/Me,!,
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(3) alfa-Tocopherol}
\begin{verbatim}

  ^^30,
  Ph,3=??6,
  7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH,
  8\,!12,@(4,8)/*Me,12:/Me
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(4) Caffeine}
\begin{verbatim}

  ^^30,
  ?6,-4=??5,$(3,8)dl,@(2,6,7,9)N,
  @(2,6,9)/Me,@(1,5)//O
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(5) Lycorine}
\begin{verbatim}

  ^^30,
  Ph,-4=??6,-2=??6,6=??5,(9,12)=??5[3],
  13=dl,8:N,@(15,17)O,
  9:/*H^180,10:*/H^60,13:*/OH,14:/*OH
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(6) Gibberellin}
\begin{verbatim}

  ^^12,
  ?6`1.3,3=??5,9=??7,12\^160`1.6,&8,
  4\^155~zf`-1.2,O,55,//O^180`1,&2~zb,
  3=dr,11=wf,13=wb,7:/COOH,11://Me,1:*/OH,
  12:/*OH,2:*/Me,@(3^-60,9^60)*/H
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\end{document}
