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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex137
1 files changed, 61 insertions, 76 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index f8678eb7167..ef6c9b124f8 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2021.01.31
+% Molecular Coding Format manual by Akira Yamaji 2021.02.11
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[pdftex]{graphicx}
@@ -124,19 +124,19 @@ exact mass, molecular formula.
\subsubsection{Jump to atom}
\index{"@}%
\begin{verbatim}
- n:@ : Jump to An
+ @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
%------------------------------------
\subsubsection{Branch bond}
\index{\textbackslash}%
\begin{verbatim}
- 3:\ : 3:@,0
+ \ : 0
- <-30,!6,3:\,!
+ <-30,!6,@3,\,!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -146,14 +146,14 @@ exact mass, molecular formula.
\index{\textbackslash\textbackslash}%
\index{*\textbackslash*}%
\begin{verbatim}
- 2:\ : 2:@,0
- 4:*\ : 4:@,0~wf
- 6:\* : 6:@,0~zf
- 8:\\ : 8:@,0~dm
- 10:*\* : 10:@,0~wv
+ \ : 0
+ *\ : 0~wf
+ \* : 0~zf
+ \\ : 0~dm
+ *\* : 0~wv
<30,!8,
- 2:\,!,4:*\,!,6:\*,!,8:\\,!,10:*\*,!
+ @2,\,!,@4,*\,!,@6,\*,!,@8,\\,!,@10,*\*,!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -162,20 +162,18 @@ exact mass, molecular formula.
\index{`}%
\begin{verbatim}
<30,!6,
- 2:\~dr,!, : 2:@,0~dr,!
- 4:\`1.5,-90, : 4:@,0`1.5,-90
- 6:\^15,-60 : 6:@,0^15,-60
+ \~dr,!, : 0~dr,!
+ \`1.5,-90 : 0`1.5,-90
+ \^15,-60 : 0^15,-60
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Connect atom}
-\index{\#}%
-\index{"@\#}%
+\index{\&}%
\begin{verbatim}
- n:# : Connect to An
- n1@#n2 : n1:@,n2:#
+ &n : Connect to An
- <-30,!6,3:\,!3,6:#~bd,9@#4~bz
+ <-30,!6,@3,\,!3,&6~bd,@9,&4~bz
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -183,7 +181,7 @@ exact mass, molecular formula.
\index{?}%
\begin{verbatim}
?n : n membered ring(3<=n<=20)
- ?6 : <-120,60,60,60,60,60,1:#
+ ?6 : <-120,60,60,60,60,60,&1
?6
\end{verbatim}
\MCFgraph
@@ -318,17 +316,17 @@ exact mass, molecular formula.
\begin{verbatim}
(!,!n)`length : change length of !,!n
- <-30,!2,!2`1.2,!2
-
- ** !2`1.2 : !`1.2,!`1.2
+ <-30,!2,!4`1.2,!2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\index{``}%
+\index{\#}%
+\index{\#\#}%
\begin{verbatim}
-``length : change all bond length after
+ #n : bond length=n
+ ## : reset bond length
- <-30,!2,``1.2,!4
+ <-30,!2,#1.2,!4,##,!2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -336,7 +334,7 @@ exact mass, molecular formula.
\begin{verbatim}
?n`length : change ring length
- ?6,4:\,?6`1.2
+ ?6,@4,\,?6`1.2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -364,7 +362,7 @@ exact mass, molecular formula.
\begin{verbatim}
| : divide brock
- ?6,4:\,|,?6,2:O
+ ?6,@4,\,|,?6,2:O
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -373,35 +371,33 @@ exact mass, molecular formula.
\begin{verbatim}
|| : reset brock adress
- ?6,4:\,|,?6,||,2:N
+ ?6,@4,\,|,?6,||,2:N
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Absolute address}
\index{\$}% $
\begin{verbatim}
- $2:N : change A$2 C to N
- ** $n : (1<=n<=3095)
+ $2:N : change A$2 C to N **1<=n<=3095
- ?6,4:\,|,?6,$2:N
+ ?6,@4,\,|,?6,$2:N
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Relative address}
\begin{verbatim}
- -2:N : change A(-2) C to N
- ** -n : (1<=n<=999)
+ -2:N : change A(-2) C to N **-999<=n<=-1
- ?6,4:\,?6,-2:N
+ ?6,@4,\,?6,-2:N
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Charged atom}
\begin{verbatim}
- N[1]:N+ / O[-1]:O- / A,&"c":A+c
+ "+" : positive / "-" : negative
- <-30,!2,N[1],!2,O[-1],
- !2,&"-",!2,N,&"+"^180,!
+<-30,!2,N,??,"+",!2,S,"-"^180,
+!6,7:N,7:??,9:S,7:"+",9:"-"^180
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -419,7 +415,7 @@ exact mass, molecular formula.
** fused ring size depend on
attached bond length
- ?6,4:\,?6`1.2,5=?6,11=?6
+ ?6,@4,\,?6`1.2,5=?6,11=?6
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -482,11 +478,11 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsubsection{Spiro ring}
\begin{verbatim}
- 4:@,?5 : add ?5 at A4
+ @4,?5 : add ?5 at A4
- <30,!6,4:@,?5
+ <30,!6,@4,?5
- An:@ : jump to An
+ @An : jump to An
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -648,17 +644,6 @@ exact mass, molecular formula.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Make block}
-\index{\textbar=}% |=
-\index{=\textbar}% =|
-\begin{verbatim}
- |= : start brock / bond length=n
- =| : end brock
-
- <-30,!2,|=1.2,!4,=|,!2
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
\subsubsection{Parts definition}
\begin{verbatim}
'(..) : user defined parts
@@ -1399,7 +1384,7 @@ endfont
beginfont("EN:Luciferin","MW:280.33")
fsize:=(60mm,20mm);
MC(
- <30,Ph,3=?5,8:\,?5,{9,16}=dl,
+ <30,Ph,3=?5,@8,\,?5,{9,16}=dl,
{9,14}:N,{7,11}:S,1:/OH,-2:*/COOH
)
endfont
@@ -1414,7 +1399,7 @@ beginfont("EN:Colchicine","MW:385.41")
<30,Ph,{1,2,6}:/O!,-4=?7,
-5=?7,{-1,-4,-6}=dl,
-2://O,-3:/O!,
- 9:\,NH,!,//O,!
+ @9,\,NH,!,//O,!
)
endfont
\end{verbatim}
@@ -1424,14 +1409,14 @@ endfont
\begin{verbatim}
beginfont("EN:Paclitaxel","MW:853.91")
MC(
- ?6,5=dl,3:@,|=1,36,45,45,45,45,=|,
- $5:#,-4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
+ ?6,5=dl,@3,#1,36,45,45,45,45,##,
+ &.$5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
{4^35,4^-35,6}:/_,{3^-60,15}:*/OH,
8:/*H^-60,9:*/_^60,10://O,
- 1:\,O,!,//O,!,*/OH,!,/Ph,
+ @1,\,O,!,//O,!,*/OH,!,/Ph,
60~wf,NH,-60,//O,60,Ph,
- 7:\*,O,-45,//O,60,Ph,
- 11:*/OCO!>rl,12:/*OCO!^-15>lr
+ @7,\*,O,-45,//O,60,Ph,
+ @11,*/OCO!>rl,12:/*OCO!^-15>lr
)
endfont
\end{verbatim}
@@ -1455,9 +1440,9 @@ endfont
beginfont("EN:Gibberellin","MW:346.37");
fsize:=(60mm,20mm);
MC(
- <18,?5,3=?7,5=?6[12],8:@,160`1.3,3:#,
+ <18,?5,3=?7,5=?6[12],@8,160`1.3,&3,
13=dl,6=wf,8=wb,
- 5:@,40~zf`1,O,50,//O^180,14~zb:#,
+ @5,40~zf`1,O,50,//O^180,&14~zb,
2:/COOH,7://_,13:*/OH,8:/*OH,
14:*/_,{1,4}:*/H^60
)
@@ -1471,9 +1456,9 @@ beginfont("EN:Quinine","MW:324.42")
fsize:=(60mm,25mm);
MC(
<30,Ph,3=Ph,7:N,6:/O!,
- 10:\,*/OH,/H~zf^-60,!,
+ @10,\,*/OH,/H~zf^-60,!,
|,?6,2:N,1:*/H^60,4:*/!!,
- 2:@,165~zf,60,5~zb:#
+ @2,165~zf,60,&5~zb
)
endfont
\end{verbatim}
@@ -1504,14 +1489,14 @@ 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:??, >
- 4:@,75,NH,!,//O,!,/*NH,!,Ph) > end MCF
+ @4,75,NH,!,//O,!,/*NH,!,Ph) > end MCF
endfont > end font
%------------------------------------------------------------------------
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)
@@ -1520,12 +1505,12 @@ beginfont("N:3","EN:Limonin") > begin font(information)
{13,15,17,20}:O,{3,12,21}://O, >
{4~wf^60,8~zf^60,18^35,18^-35}:/_, >
{1^60,5^180,16^60}:/*H, >
- 14:\*,|,?5,{1,4}=dl,3:O) > end MCF
+ @14,\*,|,?5,{1,4}=dl,3:O) > end MCF
endfont > end font
%------------------------------------------------------------------------
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, >
+ @4,\,|,!18,{1,3,5,7,9,11,13,15,17}=dr, >
{3,7,12,16}:/_, >
|,?6,6=dl,2:??,6:/_) > end MCF
endfont > end font
@@ -1756,7 +1741,7 @@ M END
{13,15,17,20}:O,{3,12,21}://O,
{4~wf^60,8~zf^60,18^35,18^-35}:/_,
{1^60,5^180,16^60}:/*H,
- 14:\*,|,?5,{1,4}=dl,3:O
+ @14,\*,|,?5,{1,4}=dl,3:O
)
endfont
\end{mplibcode}\\
@@ -1766,7 +1751,7 @@ M END
beginfont("NO:2","EN:beta-carotene","MW:536.87")
MC(<30,
?6,3=dl,{3,5^35,5^-35}:/_,
- 4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr,
+ @4,\,|,!18,{1,3,5,7,9,11,13,15,17}=dr,
{3,7,12,16}:/_,
|,?6,6=dl,{6,2^35,2^-35}:/_
)
@@ -1777,8 +1762,8 @@ M END
fsize:=(50mm,50mm);
beginfont("NO:3","EN:Gibberellin A3","MW:346.37");
MC(<18,?5,3=?7,5=?6[12],
- 8:@,160`1.3,3:#,13=dl,6=wf,8=wb,
- 5:@,40~zf`1,O,60,//O^180,14~zb:#,
+ @8,160`1.3,&3,13=dl,6=wf,8=wb,
+ @5,40~zf`1,O,60,//O^180,&14~zb,
2:/COOH,7://_,13:*/OH,8:/*OH,
14:*/_,{1^60,4^60}:*/H
)
@@ -1816,15 +1801,15 @@ endfont;
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\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}%
+\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}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}%
%############################################################################
%------------------------------------------------------------------------
-\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}%
+\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}%
%------------------------------------------------------------------------
\printindex
%------------------------------------------------------------------------