diff options
author | Karl Berry <karl@freefriends.org> | 2016-02-12 00:20:07 +0000 |
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committer | Karl Berry <karl@freefriends.org> | 2016-02-12 00:20:07 +0000 |
commit | 947e533d6de8e459df04fdcf60d65bbc735b3b12 (patch) | |
tree | 6ac0e9eac2fd2f8ddfb391d454413258b9a6b986 /Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | |
parent | 499f66f0a1368ffd94de79083962eb5a0f4ca8f2 (diff) |
mcf2graph (11feb16)
git-svn-id: svn://tug.org/texlive/trunk@39672 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex')
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 395 |
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,},, + -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} |