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-rw-r--r--graphics/mcf2graph/mcf_manual.tex179
1 files changed, 87 insertions, 92 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex
index 8ae6c12536..aaf2017799 100644
--- a/graphics/mcf2graph/mcf_manual.tex
+++ b/graphics/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2020.01.26
+% Molecular Coding Format manual by Akira Yamaji 2020.07.07
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\documentclass[a4paper,twoside]{article}
@@ -138,7 +138,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
real number plus (+): Counterclockwize
real number minus(-): Clockwize
- <10,-30,45,-45,30,-30,60
+ <-10,-30,45,-45,30,-30,60
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -147,8 +147,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
current angle and enviroment
!6 : !,!,!,!,!,!
- <30,!,!,!,!,!,!
- <30,!6
+ <-30,!,!,!,!,!,!
+ <-30,!6
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -157,14 +157,14 @@ pk font,PNG,SVG,EPS or MDL MOL file.
n:@ : Jump to An
** An: atom number(-999<=n<=4095)
- <30,!6,3:@,0,!,5:@,-30
+ <-30,!6,3:@,0,!,5:@,-30
\end{verbatim}
\MCFgraph
%------------------------------------
\begin{verbatim}
3:\ : 3:@,0
- <30,!6,3:\,!
+ <-30,!6,3:\,!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -182,7 +182,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\MCFgraph
%-----------------------------------------------------------------------------
\begin{verbatim}
- <-30,!6,
+ <30,!6,
2:\~dr,!, : 2:@,0~dr,!
4:\`1.5,-90, : 4:@,0`1.5,-90
6:\^15,-60 : 6:@,0^15,-60
@@ -194,7 +194,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
n:# : Connect to An
n1@#n2 : n1:@,n2:#
- <30,!6,3:\,!3,6:#~bd,9@#4~bz
+ <-30,!6,3:\,!3,6:#~bd,9@#4~bz
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -225,8 +225,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
tm : triple
!! : !~db / !!! : !~tm
- <30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm
- <30,!~dm,!,!~dl,!,!~dr,!! ,!! ,!,!!!
+ <-30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm
+ <-30,!~dm,!,!~dl,!,!~dr,!! ,!! ,!,!!!
\end{verbatim}
\MCFgraph
\vspace{-3mm}%
@@ -240,7 +240,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
zf : wedge dotted
zb : wedge dotted backward
- <30,!~wf,!,!~wb,!,!~zf,!,!~zb
+ <-30,!~wf,!,!~wb,!,!~zf,!,!~zb
\end{verbatim}
\MCFgraph
\vspace{-3mm}%
@@ -252,7 +252,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\begin{verbatim}
vf:vector forward / vb:vector backward
- <30,!~vf,!,!~vb
+ <-30,!~vf,!,!~vb
\end{verbatim}
\MCFgraph
\vspace{-3mm}%
@@ -266,7 +266,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
dt : dotted / wv : wave
bd : broad / bz : broad dotted
- <30,!7,1=dt,3=wv,5=bd,7=bz
+ <-30,!7,1=dt,3=wv,5=bd,7=bz
\end{verbatim}
\MCFgraph
\vspace{-3mm}%
@@ -289,7 +289,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
wb_ : wedge backward over line
bd_ : broad over line
- <-30,!8,!,60,90`8,
+ <30,!8,!,60,90`8,
{2~si_,4~wf_,6~wb_,8~bd_}:/_`2
\end{verbatim}
\MCFgraph
@@ -299,7 +299,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\begin{verbatim}
(!,!n)`length : change length of !,!n
- <30,!2,!2`1.2,!2
+ <-30,!2,!2`1.2,!2
** !2`1.2 : '`1.2,!2
\end{verbatim}
@@ -308,7 +308,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\begin{verbatim}
``length : change all bond length after
- <30,!2,``1.2,!4
+ <-30,!2,``1.2,!4
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -325,7 +325,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\begin{verbatim}
Insert hetero atom
- <30,!2,O,!2,N,!2
+ <-30,!2,O,!2,N,!2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -474,7 +474,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\subsubsection{Insert group}
\begin{verbatim}
/ : single
- <30,!,/Me,!,/Et,!3,/Pr,!,/iPr,
+ <-30,!,/Me,!,/Et,!3,/Pr,!,/iPr,
!3,/tBu,!,/Ph^-30,!
** Me:methyl(/_) Et:ethyl(/!)
@@ -505,14 +505,14 @@ pk font,PNG,SVG,EPS or MDL MOL file.
` : change length
> : change enviroment
- <30,``1,!,
+ <-30,``1,!,
/_`2^30,!2,/!2>lr,!2,/!2>rl,!)
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Add group}
\begin{verbatim}
- <-30,!17,2:/_,4:/!,6:/!2,
+ <30,!17,2:/_,4:/!,6:/!2,
10:/iPr,14:/tBu,16:/Ph^-60
\end{verbatim}
\MCFgraph
@@ -521,7 +521,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\begin{verbatim}
~,^,` : change type,angle,length
- <-30,!6,
+ <30,!6,
{2~wf,4~zf,6^-30}:/_
\end{verbatim}
\MCFgraph
@@ -530,7 +530,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
^,`,> : change angle,length,environment
- <30,!7`1,
+ <-30,!7`1,
3:/_`2^30,5:/!2>lr,7:/!2>rl
\end{verbatim}
\MCFgraph
@@ -551,7 +551,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
>lr : left-right enviroment
>rl : right-left enviroment
- <30,!6,
+ <-30,!6,
{3^-30,3,3^30}:/'(!3,"{lr}")>lr,
{5^-30,5,5^30}:/'(!3,"{rl}")>rl
\end{verbatim}
@@ -562,20 +562,20 @@ pk font,PNG,SVG,EPS or MDL MOL file.
>45 : fixed angle enviroment
>'(-90,90,-90) : multi angle enviroment
- <-30,!6,2>45:/'(!3,"{45}"),
+ <30,!6,2>45:/'(!3,"{45}"),
{6>'(-90,90,-90)}:/'(!3,"{(-90,90,-90)}")
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Miscellaneous}
%-----------------------------------------------------------------------------
-\subsubsection{Change atom and Group}
+\subsubsection{Change atom and add group}
\begin{verbatim}
NH,SO,SOO :
inset hetero atom and group
simultaneously
- <30,!2,NH,!,SO,!,SOO,!
+ <-30,!2,NH,!,SO,!,SOO,!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -602,21 +602,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
>| : end brock
|=n, bond length=n ,=|
- <30,!2,|<,``1.2,!2,>|,!2
- <30,!2,|=1.2,!2,=|,!2
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsubsection{Chain start multiple characters}
-\begin{verbatim}
- if chain start multi charactor string,
- use !0 instead of !
-
- MC(<30,COOH,!0,!3,COOH)
-\end{verbatim}
-\MCFgraph
-\begin{verbatim}
- MC(<30,COOH,!4,COOH)
+ <-30,!2,|<,``1.2,!2,>|,!2
+ <-30,!2,|=1.2,!2,=|,!2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -959,7 +946,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\subsubsection{Atom frame}
\begin{verbatim}
sw_aframe=1 ** default: sw_aframe=0
- MC(<30,COOH,!0,COOH)
+ MC(<30,COOH,!,COOH)
\end{verbatim}
\MCFgraph
\newpage
@@ -1095,6 +1082,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
beginfont()
fsize:=(60mm,20mm);
msize:=(1,0.85);
+ %---------------------------------------
MCat(0,0)(<30,Ph,3=dl,4:/NH2)
add(
labeloffset:=.7aw;
@@ -1104,6 +1092,7 @@ beginfont()
drawarrow B3m..A3+B2up**1.5aw
..{A3down}A3;
)
+ %---------------------------------------
MCat(1,0)(<30,?6,{1,5}=dl,4://NH2)
add(
labeloffset:=.7aw;
@@ -1112,6 +1101,7 @@ beginfont()
label(lonepair A3ang,A3+A3up**.7aw);
)
ext(drawdblarrow (.4w,.4h)..(.55w,.4h);)
+ %---------------------------------------
endfont
\end{verbatim}
\MCFgraph
@@ -1134,12 +1124,11 @@ endfont
h[m]: molecular height
ratio_thickness_char:
pen thickness / char width
-
-%========================================
-ext(label(inf_EN,(.5w,0));) => all font
-%========================================
+%----------------------------------------
beginfont()
- fsize:=(70mm,30mm;); blength:=0.065;
+ fsize:=(70mm,30mm;);
+ blength:=0.065;
+ %---------------------------------------
MCat(0.1,0.5)
(<-210,60`1,60`1,60`1,{1,3}=dl,
1:/R1,4:/R2^-60)
@@ -1151,6 +1140,7 @@ beginfont()
label.bot("Dienophile",p0+(.5w,0));)
MCat(0.9,0.5)
(<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1)
+ %---------------------------------------
ext(
drawarrow (.52w,.5h)..(.6w,.5h);
defaultscale:=0.7;
@@ -1164,39 +1154,60 @@ endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\newpage
-\section{MCF example}
-%-----------------------------------------------------------------------------
-\subsection{Acetamiprid}
+\subsection{Local ext() setting}
\begin{verbatim}
- <30,Ph,2:N,1:/Cl,
- 4:\,!,N,/_,!,/_,!!,N,!,CN
+beginfont("EN:?3")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(<30,?3)
+endfont
+beginfont("EN:?4")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?4)
+ %-------------------------------
+ ext(label.top(inf_EN,(0.5w,0));)
+ %-------------------------------
+endfont
+beginfont("EN:?5")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?5)
+endfont
+beginfont("EN:?5")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?6)
+endfont
\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Fenitrothion}
+\MCFgraph\MCFgraph\MCFgraph\MCFgraph
+\subsection{Global ext() setting}
\begin{verbatim}
- <30,!,O,!,P,//S,/O!^160,!,O,!,
- |,Ph,3:/_,4:/NO2
+ext_clear: reset global ext()
+
+beginfont("EN:?3")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(<30,?3)
+endfont
+%-------------------------------
+ext(label.top(inf_EN,(0.5w,0));)
+%-------------------------------
+beginfont("EN:?4")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?4)
+endfont
+beginfont("EN:?5")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?5)
+endfont
+%---------
+ext_clear;
+%---------
+beginfont("EN:?6")
+ fsize:=(12mm,15mm);
+ MCat(0.5,1)(?6)
+endfont
\end{verbatim}
-\MCFgraph
+\MCFgraph\MCFgraph\MCFgraph\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Permethrin}
-\begin{verbatim}
- <-30,?3,2^-35:*/_,2^35:/*_,
- 1:\,!!,/Cl,!,Cl,
- 3:\,//O,!,O,!2,Ph,
- -4:\,O,-60,Ph
-\end{verbatim}
-\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Endosulfan}
-\begin{verbatim}
- <26,?7,7=?6[13],11:@,208~wf`1.45,8~wb:#,
- 10=d,{3,5}:O,4:S,4://O,
- {8,9,10,11,12^-210,12^-150}:/Cl
-\end{verbatim}
-\MCFgraph
+\section{MCF example}
%-----------------------------------------------------------------------------
\subsection{Luciferin}
\begin{verbatim}
@@ -1206,14 +1217,6 @@ endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Warfarin}
-\begin{verbatim}
- <30,Ph,3=?6,8=dl,
- 10:O,7:/OH,9://O,
- 8:\,/Ph`1,60,!,//O,!
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
\subsection{Limonin}
\begin{verbatim}
<30,?6,{-3,-4}=?6,-5=?3,
@@ -1278,7 +1281,7 @@ endfont
\subsection{Atoropin}
\begin{verbatim}
<-30,O,!,//O,!,!,Ph,
- $1:@,-120~zb,
+ $1:@,-60~zb,
|,?7,6:*\^190`1.02,N,/_,3~wb:#,
$3:*\*,!,OH
\end{verbatim}
@@ -1301,14 +1304,6 @@ endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Validamycin}
-\begin{verbatim}
- <30,?6,{5,6}:/OH,3:/!OH>rl,
- $4:\,O,-60,|,?6,2:O,{3,4,5}:/OH,6:/!OH,
- $1:\,NH,!,|,?6,2=dl,{4,5,6}:/OH,3:/!OH
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
\subsection{Paclitaxel}
\begin{verbatim}
?6,5=d,3:@,|=1,36,45,45,45,45,=|,$5:#,
@@ -1329,7 +1324,7 @@ endfont
%-------------------------------------------------------------------------
input mcf2graph.mf; % input macro
%-------------------------------------------------------------------------
-sw_aux_out:=1; % aux(information) file output on > Gloval setting
+sw_aux_out:=1; % aux(information) file output on > Global setting
fsize:=(60mm,40mm); % (font width,font height) >
var3:="cal_MW"; tag3:="cMW"; > AUX file table
var4:="cal_FM"; tag4:="cFM"; >