diff options
Diffstat (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex')
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 137 |
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 %------------------------------------------------------------------------ |