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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex395
1 files changed, 274 insertions, 121 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index d48fed43a5b..3500652d6c7 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 2016.02.06
+% Molecular Coding Format manual by Akira Yamaji 2016.02.11
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[dvipdfmx]{graphicx}
@@ -43,16 +43,27 @@
pk font,PNG,SVG,EPS or MDL MOL file(V2000). \\
\end{minipage}\vspace{3mm}\\
\linethickness{0.08mm}%
-%----------------------------------------------------------------------------
\noindent%
+%----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Chain}
+\MCFtitle{Chain(1)}
\begin{verbatim}
plus(+):anticlockwize,minus(-):clockwize
-! : take value depend on
- current angle and enviroment
<30,-60,60,-60,60,-60,60
+
+ ** bold arrow is default angle and position
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Chain(2)}
+\begin{verbatim}
+! : take value(60 or -60) depend on
+ current angle and enviroment
+
<30,!,!,!,!,!,!
\end{verbatim}
@@ -61,6 +72,54 @@ plus(+):anticlockwize,minus(-):clockwize
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Chain(3)}
+\begin{verbatim}
+!6 : !,!,!,!, !,!
+
+ <30,!6
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Jump to atom}
+\begin{verbatim}
+3* : Jump to A3
+
+ <30,!6,3*,0,!
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Jump to atom and branch bond}
+\begin{verbatim}
+3\ : 3*,0
+
+ <30,!6,3\,!
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Connect bond}
+\begin{verbatim}
+&5 : Connect to A5
+
+ <30,!6,3\,!,&5
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
\MCFtitle{Ring}
\begin{verbatim}
six membered ring
@@ -68,7 +127,6 @@ six membered ring
?6
** ?6 : <-120,60,60,60,60,60,&1
- ** &1 : make bond connect to A1
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -81,8 +139,6 @@ six membered ring
<30,!4,<30,?6
- ** !4: !,!,!,!
- ** bold arrow is default angle and position
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -140,7 +196,7 @@ Bn`length : change bond length at Bn
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Change chain length (3)}
+\MCFtitle{Change ring length}
\begin{verbatim}
?n`length : change ring length
@@ -169,7 +225,7 @@ Insert hetero atom
<30,!6,2:O,@(3,5)N
-An(-999<=n<=4095): atom number
+** An(-999<=n<=4095): atom number
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -187,27 +243,35 @@ An(-999<=n<=4095): atom number
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Change atom (brock address)}
+\MCFtitle{Change atom (brock address 1)}
\begin{verbatim}
-2:N : change A2(brock address) C to N
-
-?6,4\,|,?6,2:N,||,@(2,6)O
-
| : divide brock
+
+?6,4\,|,?6,2:N,
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Change atom (brock address 2)}
+\begin{verbatim}
|| : reset brock adress
+
+?6,4\,|,?6,||,2:N
\end{verbatim}
\end{minipage}
\MCFstructure
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Change atoma (absolute address)}
+\MCFtitle{Change atom (absolute address)}
\begin{verbatim}
#2:N : change A#2 C to N
?6,4\,|,?6,#2:N
-#n : (1<=n<=3095)
+** #n : (1<=n<=3095)
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -220,7 +284,7 @@ An(-999<=n<=4095): atom number
?6,4\,?6,-2:N
--n : (1<=n<=999)
+** -n : (1<=n<=999)
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -233,7 +297,7 @@ An(-999<=n<=4095): atom number
?6,3=?5
-Bn(n:-999<=n<=4095): bond number
+** Bn(n:-999<=n<=4095): bond number
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -363,12 +427,10 @@ MCf(<30,!`1,/Me~zf`2^30,!`1,/Me~zf`2^30,
\begin{minipage}[t][38mm]{90mm}
\MCFtitle{Add substituent(1)}
\begin{verbatim}
-sw_numberA:=1; numberA_end:=_skeletonA_end;
+sw_numberA:=1; numberA_end:=12;
MCf(<30,!11,
2:/Me,3:/Et,6:/Pr,7:/iPr,10:/tBu,11:/Ph^-30)
-** _skeletonA_end :
- end number of molecular skeleton atom
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -407,8 +469,8 @@ MCF(<30,!7`1,
>vt : vertical enviroment
?4,
- @(3^-90,3^-30,3^90)/'(!3,"{>hz}")>hz,
- @(1^-60,1`2,1^60)/'(!2,"{>vt}")>vt
+ @(3^-90,3^-30,3^90)/'(!3,"{hz}")>hz,
+ @(1^-60,1`2,1^60)/'(!2,"{vt}")>vt
\end{verbatim}
\end{minipage}
@@ -422,8 +484,8 @@ MCF(<30,!7`1,
>rl : right-left enviroment
<30,!6,
- @(3^-30,3,3^30)/'(!3,"{>lr}")>lr,
- @(5^-30,5,5^30)/'(!3,"{>rl}")>rl
+ @(3^-30,3,3^30)/'(!3,"{lr}")>lr,
+ @(5^-30,5,5^30)/'(!3,"{rl}")>rl
\end{verbatim}
\end{minipage}
@@ -436,8 +498,8 @@ MCF(<30,!7`1,
>45 : fixed angle enviroment
>'(-90,90,-90) : multi angle enviroment
- <-30,!6,@(2>45)/'(!3,"{>45}"),
- @(6>'(-90,90,-90))/'(!3,"{>(-90,90,-90)}")
+ <-30,!6,@(2>45)/'(!3,"{45}"),
+ @(6>'(-90,90,-90))/'(!3,"{(-90,90,-90)}")
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -465,6 +527,7 @@ $(3)red : change color of B3 red
<30,Ph,@(2,5)N,
2:red,5:blue,3=green
+** METAFONT ignore color command
\end{verbatim}
\end{minipage}
%%%%\MCFstructure % for Metafont
@@ -514,81 +577,6 @@ Insert user defined substructure
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Example(1) Ampicillin}
-\begin{verbatim}
-
- <45,?4,2:N,2=?5,-1:S,
- @(3^45,4^-45)/*H,1://O^15,
- 5:/*COOH^-18,@(6^35,6^-35)/Me,
- 4\^75,NH,!,//O,!,NH,!,Ph
-\end{verbatim}
-\end{minipage}
-\MCFstructure
-\vspace{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Example(2) Cholesterol}
-\begin{verbatim}
-
- <30,?6,$(-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{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
-\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{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
-\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{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
-\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{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
-\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,
- 5=dl,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{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
\MCFtitle{Font size}
\begin{verbatim}
beginfont("EN:Caffeine")
@@ -815,18 +803,6 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
-\MCFtitle{Switch Start Vector}
-\begin{verbatim}
-
- MCd(1,.6)( 0,0.5)(<30,Ph,4:/Cl,3:/F)
- sw_start_vector:=1;
- MCd(1,.6)( 1,0.5)(<30,Ph,4:/Cl,3:/F)
-\end{verbatim}
-\end{minipage}
-\MCFstructure
-\vspace{5mm}\\
-%-----------------------------------------------------------------------------
-\begin{minipage}[t][38mm]{90mm}
\MCFtitle{Switch Numbering atom}
\begin{verbatim}
numberA_start:=3; numberA_end:=8;
@@ -857,11 +833,54 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
\vspace{5mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Switch substituent off}
+\begin{verbatim}
+
+ MCd(1,.6)( 0,0.5)(<30,Ph,4:/Cl,3:/F)
+ sw_subst_off:=1;
+ MCd(1,.6)( 1,0.5)(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_subst_off=0
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Switch all bond single}
+\begin{verbatim}
+
+ MCd(1,.6)( 0,0.5)(<30,Ph,4:/Cl,3:/F)
+ sw_bond_single:=1;
+ MCd(1,.6)( 1,0.5)(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_bond_single=0
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Switch start vector}
+\begin{verbatim}
+ sw_start_vector:=1;
+
+ MCf(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_start_vector=0
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
\MCFtitle{Switch font frame}
\begin{verbatim}
sw_font_frame:=1;
MCf(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_font_frame=0
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -874,6 +893,8 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
MCd(1,.6)(0,0.5)(<30,Ph,4:/Cl,3:/F)
sw_mol_frame:=1;
MCd(1,.6)(1,0.5)(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_mol_frame=0
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -886,6 +907,8 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
sw_atom_frame:=1;
MCf(<30,Ph,4:/COOH,3:/OH)
+
+ ** default: sw_atom_frame=0
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -898,6 +921,8 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
MCd(1,.8)( 0,0.5)(<30,Ph,4:/Cl,3:/F)
sw_solid:=1; ratio_bond_width:=0.08;
MCd(1,.8)( 1,0.5)(<30,Ph,4:/Cl,3:/F)
+
+ ** default: sw_solid=0
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -910,6 +935,8 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
MCd(1,.6)(0,0.5)(<30,Ph,4:/COOH,3:/NH2)
sw_expand:=1;
MCd(1,.6)(1,0.5)(<30,Ph,4:/COOH,3:/NH2)
+
+ ** default: sw_expand=0
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -948,11 +975,11 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
\begin{verbatim}
beginfont("NO:1")
sw_mol_frame:=1; % <<== Local setting
- MCd(1,.5)(0.0,0.5)(<30,Ph,@(2)N) endfont
+ MCd(1,.5)(0.0,0.5)(<30,Ph) endfont
beginfont("NO:2")
- MCd(1,.5)(0.5,0.5)(<30,Ph,@(2,4)N) endfont
+ MCd(1,.5)(0.5,0.5)(<30,Ph) endfont
beginfont("NO:3")
- MCd(1,.5)(1.0,0.5)(<30,Ph,@(2,4,6)N) endfont
+ MCd(1,.5)(1.0,0.5)(<30,Ph) endfont
\end{verbatim}
\end{minipage}
\MCFstru\MCFstru\MCFstructure%
@@ -963,11 +990,11 @@ beginfont("NO:3")
\begin{verbatim}
sw_mol_frame:=1; % <<== Global setting
beginfont("NO:1")
- MCd(1,.5)(0.0,0.5)(<30,Ph,@(2)N) endfont
+ MCd(1,.5)(0.0,0.5)(<30,Ph) endfont
beginfont("NO:2")
- MCd(1,.5)(0.5,0.5)(<30,Ph,@(2,4)N) endfont
+ MCd(1,.5)(0.5,0.5)(<30,Ph) endfont
beginfont("NO:3")
- MCd(1,.5)(1.0,0.5)(<30,Ph,@(2,4,6)N) endfont
+ MCd(1,.5)(1.0,0.5)(<30,Ph) endfont
\end{verbatim}
\end{minipage}
\MCFstru\MCFstru\MCFstructure%
@@ -1001,5 +1028,131 @@ CAS:CAS number *:default output
\end{verbatim}
\end{minipage}
\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\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{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\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{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\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{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Example(4) Colchicine}
+\begin{verbatim}
+ <30,Ph,@(1,2,6)/OMe,|,-4=?7,
+ |,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OMe,
+ #9\,NH,!,//O,!
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\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{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\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,
+ 5=dl,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{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Example(7) Capsaicin}
+\begin{verbatim}
+ <30,Ph,
+ 1:/OH,6:/OMe,4\,!,NH,!,//O,
+ |,!8,-3=dr,-1:/Me
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Example(8) Quinine}
+\begin{verbatim}
+ <30,Ph,3=Ph,7:N,6:/OMe,
+ 10\,*/OH,/H~zf^-60,!,
+ |,?6,2:N,1:*/H^60,
+ 4*\,!~dr,
+ 2*,165~zf,60,&5~zb
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Example(9) Atoropin}
+\begin{verbatim}
+ <-30,O,!,//O,!,!,Ph,
+ #1\~zb^-120,
+ |,?7`1.1,6*\^190`1.25,N,/Me,&3~wb,
+ #3\~wv,!,OH
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{5mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{90mm}
+\MCFtitle{Example(10) Paclitaxel}
+\begin{verbatim}
+ ?6,5=d,3*,{,``1,36,45,45,45,45,},&#5,
+ -4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
+ @(4^35,4^-35,6)/Me,@(3^-60,15)*/OH,
+ 8:/*H^-60,9:*/Me^60,10://O,
+ 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
+\end{verbatim}
+\end{minipage}
+\MCFstructure
%-----------------------------------------------------------------------------
\end{document}