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-rw-r--r--graphics/mcf2graph/mcf_manual.tex78
1 files changed, 44 insertions, 34 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex
index f879fd6ab7..2573d33c6d 100644
--- a/graphics/mcf2graph/mcf_manual.tex
+++ b/graphics/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2020.12.12
+% Molecular Coding Format manual by Akira Yamaji 2021.01.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\documentclass[a4paper,twoside]{article}
@@ -485,12 +485,12 @@ exact mass, molecular formula.
\subsubsection{Insert group}
\begin{verbatim}
/ : single
- <-30,!,/Me,!,/Et,!3,/Pr,!,/iPr,
- !3,/tBu,!,/Ph^-30,!
+ <-30,!,/_,!,/!,!3,/!2,!,/?!,
+ !3,/??!,!,/Ph^-30,!
- ** Me:methyl(/_) Et:ethyl(/!)
- Pr:propyl(/!2) iPr:isopropyl
- tBu:tertial buthyl Ph:phenyl
+ ** /_ : methyl /! : ethyl
+ /!2 : propyl /?! : isopropyl
+ /??! : tert-butyl /Ph : phenyl
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -533,7 +533,7 @@ exact mass, molecular formula.
\subsubsection{Add group}
\begin{verbatim}
<30,!17,2:/_,4:/!,6:/!2,
- 10:/iPr,14:/tBu,16:/Ph^-60
+ 10:/?!,14:/??!,16:/Ph^-60
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -585,9 +585,12 @@ exact mass, molecular formula.
\subsubsection{Fixed rotate angle}
\index{\textgreater}%
\begin{verbatim}
- >45 : rotate 45
+ >n : rotate n
+
+ <30,!4,
+ 2:/!6>30, % 2:\,30,30,30,30,30,30
+ 4:/!4>-45 % 4:\,-45,-45,-45,-45
- <30,!6,6>45:/!3
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -601,28 +604,38 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Miscellaneous}
%-----------------------------------------------------------------------------
-\subsubsection{}
+\subsubsection{Abbreviated parts}
+\index{N!}%
+\begin{verbatim}
+ NH : N,/H~nl
+ N! : N,/_
+ N!2 : N,/!
+ SO : S,//O
+ SOO : S,//O^35,//^-35
+
+ <-30,!2,NH,!2,N!,!2,N!2,SO,!2,SOO,!
+\end{verbatim}
+\MCFgraph
+\index{?!}%
+\index{??}%
\begin{verbatim}
- NH,SO,SOO :
- insert hetero atom and group
- simultaneously
+ ?! : /_,!
+ ?? : /_^35,/_-35
+ /?! : isopropyl
+ /??! : tert-butyl
+ /N?! : dimethylamino
- <-30,!2,NH,!,SO,!,SOO,!
- <-30,!4,3:NH,5:SO,7:SOO
+ <30,!9`1,?!,!,??,!,
+ 2:??,4:/??,6:/??!,8:/N?!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Make block}
-\index{\textbar\textless \textgreater\textbar}% |<
\index{\textbar= =\textbar}% |=
\begin{verbatim}
- |< : start brock
- >| : end brock
-
|= : start brock / bond length=n
=| : end brock
- <-30,!2,|<,``1.2,!4,>|,!2
<-30,!2,|=1.2,!4,=|,!2
\end{verbatim}
\MCFgraph
@@ -641,8 +654,7 @@ exact mass, molecular formula.
<30,!, /'(!,/_,!,OH),
!4,/'(!,/_,!,OH),!3
- <30,!8,
- {2,6}:/'(!,/_,!,OH)
+ <30,!8,{2,6}:/'(!,/_,!,OH)
\end{verbatim}
\MCFgraph
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -1366,8 +1378,7 @@ beginfont("EN:Paclitaxel","MW:853.91")
1:\,O,!,//O,!,*/OH,!,/Ph,
60~wf,NH,-60,//O,60,Ph,
7:\*,O,-45,//O,60,Ph,
- 11:*\,O,-60,//O,60,
- 12:\*^-15,O,60,//O,-60
+ 11:*/OCO!>rl,12:/*OCO!^-15>lr
)
endfont
\end{verbatim}
@@ -1408,13 +1419,13 @@ beginfont("EN:Quinine","MW:324.42")
MC(
<30,Ph,3=Ph,7:N,6:/O!,
10:\,*/OH,/H~zf^-60,!,
- |,?6,2:N,1:*/H^60,4:*\,!!,
+ |,?6,2:N,1:*/H^60,4:*/!!,
2:@,165~zf,60,5~zb:#
)
endfont
\end{verbatim}
\MCFgraph
-%-----------------------------------------------------------------------------
+%------------------------------------------------------------------------
\onecolumn
\section{Example to use mcf2graph}
\subsection{Molecular definition file}
@@ -1436,8 +1447,7 @@ outputtemplate:="%j-%3c.png"; >
%-------------------------------------------------------------------------
beginfont("N:1","EN:Ampicillin") > begin font(information)
MC(<45,?4,2:N,2=?5,-1:S, > begin MCF (1)
- {3^45,4^-45}:/*H,1://O^15,5:/*COOH^-18, >
- {6^35,6^-35}:/_, >
+ {3^45,4^-45}:/*H,1://O^15,5:/*COOH^-18,6:??, >
4:@,75,NH,!,//O,!,/*NH,!,Ph) > end MCF
endfont > end font
%------------------------------------------------------------------------
@@ -1445,7 +1455,7 @@ beginfont("N:2","EN:Cholesterol") > begin font(information)
MC(<30,?6,{-4,-2}=?6,-4=?5,7=dl, > begin MCF (2)
1:*/OH,{4,12}:*/_^60,9:*/H^60, >
10:/*H^180,{11,-1}:/*H^-60, >
- -1:@,17,/*_,!4,/_,!) > end MCF
+ -1:@,17,/*_,!4,?!) > end MCF
endfont > end font
%------------------------------------------------------------------------
beginfont("N:3","EN:Limonin") > begin font(information)
@@ -1461,7 +1471,7 @@ beginfont("N:4","EN:beta-carotene) > begin font(information)
MC(<30,?6,3=dl,{3,5^35,5^-35}:/_, > begin MCF (4)
4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr, >
{3,7,12,16}:/_, >
- |,?6,6=dl,{6,2^35,2^-35}:/_) > end MCF
+ |,?6,6=dl,2:??,6:/_) > end MCF
endfont > end font
%------------------------------------------------------------------------
bye
@@ -1735,15 +1745,15 @@ endfont;
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\INFO{F:mcf_man_soc,C:139,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:140,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:140,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:141,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}%
%############################################################################
%------------------------------------------------------------------------
-\INFO{F:mcf_man_soc,C:139,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:140,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:140,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:141,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}%
%------------------------------------------------------------------------
\printindex
%------------------------------------------------------------------------