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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Molecular Coding Format manual by Akira Yamaji 2015.7
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\documentclass[a4paper]{article}
+\usepackage{graphicx}
+\pagestyle{empty}
+\topmargin=-17mm
+\textheight=27.5cm
+\textwidth=18cm
+\oddsidemargin=-9mm
+\parindent=0mm
+\unitlength=1mm%
+\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%
+}%
+%----------------------------------------------------------------------------
+\def\MCFstructureEPS{%
+ \makebox(75,0)[t]%
+ {\frame{\makebox(70,35){%
+ \ifnum\fontnum<10\includegraphics{mcf_man_soc-00\the\fontnum}%
+ \else\ifnum\fontnum<100\includegraphics{mcf_man_soc-0\the\fontnum}\fi\fi}}}%
+ \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
+}%
+%----------------------------------------------------------------------------
+\begin{document}
+\noindent%
+\begin{picture}(180,0)
+ \put(50,12){{\LARGE Molecular coding format manual}\hspace{20mm}
+ by Akira Yamaji 2015.7}
+\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
+ dm:double,dl:double(left),dr:double(right),
+ wf:wedge forward,wb:wedge backward,
+ zf:wedge dotted,zb:wedge dotted backward
+
+ ^^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,!3,!`1.2,!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,!3,``1.2,!3
+\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,$(3,3,3)??6 NG
+ ?6,$(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 (2)}
+\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 (3)}
+\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,$(3,9)??6,(4,11)=??6[4],
+ (16,17)=??6[3],(20,5)=??4[2]
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Fused ring (4)}
+\begin{verbatim}
+(20,5)=??5[3] : fuse 3/5 ring to B20..B5
+(16,17)=??5[2] : fuse 2/5 ring to B16..B17
+
+ ^^30,?6,$(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,{,``1,!7,},
+ @(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,?6,@(2,5)N,
+ 2:red,5:green,3=red
+
+\end{verbatim}
+\end{minipage}
+\MCFstructureEPS
+\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}\\
+%-----------------------------------------------------------------------------
+\end{document}