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Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 103 |
1 files changed, 62 insertions, 41 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index a40f0331f2..415adf1bf0 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2021.06.28 +% Molecular Coding Format manual by Akira Yamaji 2021.07.18 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[pdftex]{graphicx} @@ -228,29 +228,20 @@ tm : triple \index{wb}% \index{zf}% \index{zb}% +\index{vf}% +\index{vb}% \begin{verbatim} -(Wedge) +(Wedge,Vector) wf: wedge forward wb: wedge backward zf: hashed(zebra stripe) wedge foward zb: hashed(zebra stripe) wedge backward - -<-30,!~wf,!,!~wb,!,!~zf,!,!~zb -\end{verbatim} -\MCFgraph -\vspace{-3mm}% -%----------------------------------------------------------------------------- -%%\subsubsection{Vector} -\index{vf}% -\index{vb}% -\begin{verbatim} - -(Vector) vf:vector forward vb:vector backward -<-30,!~vf,!,!~vb +<-30, + !~wf,!,!~wb,!,!~zf,!,!~zb,!,!~vf,!~vb \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -264,25 +255,14 @@ vb:vector backward (Dotted,wave) Bn=bond type : change bond type at Bn -dt : dotted -wv : wave -bd : broad -bz : broad dotted +dt : dotted / wv : wave +bd : broad / bz : broad dotted <-30,!7,1=dt,3=wv,5=bd,7=bz \end{verbatim} \MCFgraph \vspace{-3mm}% %----------------------------------------------------------------------------- -\subsubsection{Change multiple bond type} -\index{vf}% -\begin{verbatim} -{2,4,6}=dr : 2=dr,4=dr,6=dr - -<30,!7,{2,4,6}=dr -\end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- \subsubsection{Over line} \index{si\_}% \index{wf\_}% @@ -310,6 +290,30 @@ dm_ : duble over line \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\subsubsection{Steric ring} +\index{wf\_r}% +\index{wb\_r}% +\index{bd\_r}% +\begin{verbatim} +wf_r : wedge foward (half width) +bd_r : broad (half width, rounded) +wb_r : wedge backward (half width) + +#1.25,-30~wf_r,30~bd_r`1,30~wb_r, + 120,O,30,&1,##,6^$90:/!OH`-.5, + {1^$-90,2^$90,3^$-90,4^$90}:/OH`-.5, +\end{verbatim} +\MCFgraph +%----------------------------------------------------------------------------- +\subsubsection{Change multiple bond type} +\index{vf}% +\begin{verbatim} +{2,4,6}=dr : 2=dr,4=dr,6=dr + +<30,!7,{2,4,6}=dr +\end{verbatim} +\MCFgraph +%----------------------------------------------------------------------------- \subsection{Change bond length} \subsubsection{Chain length} \index{`}% @@ -401,9 +405,13 @@ p_ : positive / n_ : negative \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\newpage +%----------------------------------------------------------------------------- \subsection{Fuse ring} -\subsubsection{Attached 1 bond} +%%%\subsubsection{Attached 1 bond} \begin{verbatim} +(Attached 1 bond) + ?6,3=?6 : fuse ?6 at B3 ** Bn(n:-999<=n<=4095): bond number @@ -434,8 +442,10 @@ attached bond length \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- -\subsubsection{Attached 2 bond} +%%%\subsubsection{Attached 2 bond} \begin{verbatim} +(Attached 2 bond) + (4,11)=?6[4] : fuse 4/6 ring to B11..B4 (4,11)=?5[3] : fuse 3/5 ring to B11..B4 (4,11)=?4[2] : fuse 2/4 ring to B11..B4 @@ -450,8 +460,10 @@ attached bond length \begin{verbatim} \end{verbatim} %----------------------------------------------------------------------------- -\subsubsection{Attached 3 bond} +%%%\subsubsection{Attached 3 bond} \begin{verbatim} +(Attached 3 bond) + (16,4)=?6[3] : fuse 3/6 ring to B16..B4 (16,4)=?5[2] : fuse 2/5 ring to B16..B4 ** ?m[n] (5<=m<=6,n=m-3) @@ -464,8 +476,10 @@ attached bond length \begin{verbatim} \end{verbatim} %----------------------------------------------------------------------------- -\subsubsection{Attached 4 bond} +%%%%\subsubsection{Attached 4 bond} \begin{verbatim} +(Attached 4 bond) + (21,4)=?6[2] : fuse 2/6 ring to B21..B4 MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) @@ -474,7 +488,7 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- -\subsubsection{Spiro ring} +\subsection{Spiro ring} \begin{verbatim} @4,?5 : add ?5 at A4 @@ -487,13 +501,17 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) \index{/}% \index{Ph}% \begin{verbatim} -/ : single -<-30,!,/_,!,/!,!3,/!2,!,/?!, - !3,/??!,!,/Ph^-30,! +/ : group start single bond + +/_ : methyl +/! : ethyl +/!2 : propyl +/?! : isopropyl +/??! : tert-butyl +/Ph : phenyl -** /_ : methyl /! : ethyl - /!2 : propyl /?! : isopropyl - /??! : tert-butyl /Ph : phenyl +<30,!,/_,!2,/!,!2,/!2,!4,/?!, + !4,/??!,!2,/Ph^-60,! \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -532,7 +550,7 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) \subsubsection{Add group} \begin{verbatim} <30,!17,2:/_,4:/!,6:/!2, -10:/?!,14:/??!,16:/Ph^-60 + 10:/?!,14:/??!,16:/Ph^-60 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -552,6 +570,8 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\newpage +%----------------------------------------------------------------------------- \subsection{Chain environment} \subsubsection{Horizontal,vertical} \index{hz}% @@ -600,6 +620,7 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2]) \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\newpage \subsection{Miscellaneous} %----------------------------------------------------------------------------- \subsubsection{Abbreviated parts} @@ -657,7 +678,7 @@ MC(<30,?6,{4,6}:/iBuOH) \index{--}% \begin{verbatim} 6--10 : 6,7,8,9,10 -<30,!14,{2,6--10,14}:/_~bd`0.5 +<30,!14,{2,6--10,14}:/_~bd_r`0.5 \end{verbatim} \MCFgraph \newpage |