diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 254 |
1 files changed, 130 insertions, 124 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index 5debd57a43..d5a5359cba 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2023.05.28 +% Molecular Coding Format manual by Akira Yamaji 2024.01.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% ** mcf2graph.mf must be version 5.02 +% ** mcf2graph.mf must be version 5.10 % ** use main_lib.mcf % ** typeset by LuaLaTeX(luamplib) %---------------------------------------------------------------------------- @@ -37,7 +37,7 @@ \author{Akira Yamaji} \date{\today} \maketitle -\begin{center} mcf2graph version 5.02 \end{center} +\begin{center} mcf2graph version 5.03 \end{center} \begin{center} Located at http://www.ctan.org/pkg/mcf2graph \end{center} \begin{center} Suggestion or request mail to: mcf2graph@gmail.com \end{center} %----------------------------------------------------------------------------- @@ -53,7 +53,7 @@ fmargin:=(2mm,1mm); fsize:=(40mm,24mm); blength:=5mm; sw_frame:=0; -% Glycine", +% Glycine beginfigm \(<30,NH2,!2,COOH) endfigm % L-Alanine beginfigm \(<30,NH2,!~wb,/_,!,COOH) endfigm @@ -166,9 +166,9 @@ beginfigm ratio_chain_ring:=1; %---------------------------------------------------------------------- \(<15,-30,45,-45,60,$300,$0, - {1^$15,2^$345,3^$30,4^$345}:/_~dt,{5,6}=vf, + {1^$15,2^$345,3^$30,4^$345}:/_~dt,{5,6}=vf ) - add( + ++( defaultscale:=0.5; labeloffset:=2bp; drawarrow B7/*.7{B7right}..{B1right}B1/*.7; label.ulft("-30",B7/*.7); @@ -199,7 +199,7 @@ beginfigm \(<-30,!6, {1^-120,2^60,3^-60,4^60,5^-60,6^60}:/_~dt ) - add( + ++( defaultscale:=0.5; labeloffset:=2bp; drawarrow B7/*.7{B7right}..{B1right}B1/*.7; label.ulft("-60",B7/*.7); @@ -354,7 +354,7 @@ beginfigm labeloffset:=2bp; \(#1,0,0,<90,0,<-90,0,<$315,0,<$90,0,<$0,0,{1:7}=vf, {3,4^180}:/_~dt) - add( + ++( drawarrow B8/*.7{B8left}..{B3left}B3/*.7; label.urt("90",B8/*.7); drawarrow B9/*.7{B9right}..{B4right}B4/*.7; label.urt("-90",B9/*.7); ) @@ -392,7 +392,7 @@ beginfigm sw_trimming:=0; ratio_chain_ring:=1; \(<-30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm) - add(defaultscale:=0.6; labeloffset:=0; + ++(defaultscale:=0.6; labeloffset:=0; label.rt("(dm)",A1+(0,-0.7l)); label.rt("(dl)",A3+(0,-0.7l)); label.rt("(dr)",A5+(0,-0.7l)); @@ -431,7 +431,7 @@ beginfigm sw_trimming:=0; ratio_chain_ring:=1; \(<-30,!~wf,!,!~wb,!,!~zf,!,!~zb,!,!~vf,!,!~vb) - add(defaultscale:=0.6; labeloffset:=0; + ++(defaultscale:=0.6; labeloffset:=0; label.rt("(wf)",A1+(0,-0.7l)); label.rt("(wb)",A3+(0,-0.7l)); label.rt("(zf)",A5+(0,-0.7l)); @@ -464,7 +464,7 @@ beginfigm sw_trimming:=1; ratio_chain_ring:=1; \(<-30,!7,1=dt,3=wv,5=bd,7=bz) - add(defaultscale:=0.6; labeloffset:=0; + ++(defaultscale:=0.6; labeloffset:=0; label.rt("(dt)",A1+(0,-0.6l)); label.rt("(wv)",A3+(0,-0.6l)); label.rt("(bd)",A5+(0,-0.6l)); @@ -531,12 +531,12 @@ beginfigm @(0.05,0.5)\(#1.25,-30~wf_r,30~bd_r`1,30~wb_r,120,O,30,&1,##, #.5,{1^$-90,2^$90,3^$-90,4^$90}:/OH,6^$90:/!OH) defaultscale:=0.6; - @(0.5,0.7)\(0~wf_r) add(label.lft("wf_r:",A1);) - @(0.5,0.2)\(0~wf) add(label.lft("wf:",A1);) - @(0.75,0.7)\(0~bd_r) add(label.lft("bd_r:",A1);) - @(0.75,0.2)\(0~bd) add(label.lft("bd:",A1);) - @(1,0.7)\(0~wb_r) add(label.lft("wb_r:",A1);) - @(1,0.2)\(0~wb) add(label.lft("wb:",A1);) + @(0.5,0.7)\(0~wf_r) ++(label.lft("wf_r:",A1);) + @(0.5,0.2)\(0~wf) ++(label.lft("wf:",A1);) + @(0.75,0.7)\(0~bd_r) ++(label.lft("bd_r:",A1);) + @(0.75,0.2)\(0~bd) ++(label.lft("bd:",A1);) + @(1,0.7)\(0~wb_r) ++(label.lft("wb_r:",A1);) + @(1,0.2)\(0~wb) ++(label.lft("wb:",A1);) endfigm \end{mplibcode} %----------------------------------------------------------------------------- @@ -817,13 +817,13 @@ beginfigm sw_numbering:=Bond; ##(1,.9) @( 0,.5)\(<30,?6,{3,11--4}=?6,{11,4}=dt,{12:15}=bd_r) - add(defaultscale:=0.4; label("(1)",p0);) + ++(defaultscale:=0.4; label("(1)",p0);) ##(1,.9) @(.5,.5)\(<30,?6,3=?6,{11--4}=?5,{11,4}=dt,{12:14}=bd_r) - add(defaultscale:=0.4; label("(2)",p0);) + ++(defaultscale:=0.4; label("(2)",p0);) ##(1,.9) @( 1,.5)\(<30,?6,3=?6,{11--4}=?4,{11,4}=dt,{12,13}=bd_r) - add(defaultscale:=0.4; label("(3)",p0);) + ++(defaultscale:=0.4; label("(3)",p0);) endfigm \end{mplibcode} %%%%%%%\vspace{-3mm}% @@ -845,9 +845,9 @@ beginfigm #(60mm,20mm) #@(2mm,2mm) sw_numbering:=Bond; @(0,1)\(?6,{3,10}=?6,16---4=?6,{16,4}=dt,{17:19}=bd_r) - add(defaultscale:=0.4; label("(1)",p0);) + ++(defaultscale:=0.4; label("(1)",p0);) @(1,0)\(?6,{3,10}=?6,16---4=?5,{16,4}=dt,{17,18}=bd_r) - add(defaultscale:=0.4; label("(2)",p0);) + ++(defaultscale:=0.4; label("(2)",p0);) endfigm \end{mplibcode} %%%%%%%%\vspace{-3mm}% @@ -932,7 +932,7 @@ endfigm beginfigm #(70mm,14mm); \(<30,!`1,//O,!2`1,*/H,!2`1,/*H,!2`1,*/*H,!2`1,**?3,!`1) - add(defaultscale:=0.75; + ++(defaultscale:=0.75; label("//",A2-(0,0.45l)); label("*/",A4-(0,0.45l)); label("/*",A6-(0,0.45l)); @@ -1038,7 +1038,7 @@ beginfigm \(?4,{3^-90,3^-30,3^90}:/!3>hz, {1^-60,1,1^60}:/!3>vt ) - add(defaultscale:=0.5; labeloffset:=2bp; + ++(defaultscale:=0.5; labeloffset:=2bp; label.rt(">hz",A8); label.top(">hz",A12); label.top(">hz",A16); @@ -1114,17 +1114,17 @@ endfigm \index{SO}% \index{SOO}% \begin{verbatim} -NH : N,/H~nl N! : N,/_ N!2 : N,/! -SO : S,//O SOO : S,//O^35,//^-35 +NH : N,/H~nl N? : N,/_ N?2 : N,/! +S?O : S,//O S?O?O : S,//O^35,//^-35 -<-30,!2,NH,!2,N!,!2,N!2,SO,!2,SOO,! +<-30,!2,NH,!2,N?,!2,N?2,S?O,!2,S?O?O,! \end{verbatim} %----------------------------------------- \begin{mplibcode} beginfigm - #(60mm,12mm); - sw_trimming:=1; - \(<-30,!2,NH,!2,N!,!2,N!2,!2,SO,!2,SOO,!) +#(60mm,12mm); +sw_trimming:=1; +\(<-30,!2,NH,!2,N?,!2,N?2,!2,S?O,!2,S?O?O,!) endfigm \end{mplibcode} %----------------------------------------------------------------------------- @@ -1133,48 +1133,51 @@ endfigm \index{??"!}% \index{N?"!}% \begin{verbatim} -?! : /_,! ?? : /_^35,/_-35 -/?! : isopropyl /??! : tert-butyl -/N?! : dimethylamino +?? : /_^35,/_-35 /?! : isopropyl +/??! : tert-butyl /N?! : dimethylamino -<30,!9`1,?!,!,??,!,2:??,4:/??,6:/??!,8:/N?! +<30,!11`1,2:??,4:/!,6:/?!,8:/??!,10:/N?! \end{verbatim} %----------------------------------------- \begin{mplibcode} beginfigm - #(60mm,12mm); - sw_trimming:=1; - \(<30,!9`1,?!,!,??,!,2:??,4:/?!,6:/??!,8:/N?!) +#(60mm,10mm); +sw_trimming:=1; +\(<30,!11`1,2:??,4:/!,6:/?!,8:/??!,10:/N?!) endfigm \end{mplibcode} %----------------------------------------------------------------------------- -\subsubsection{Parts definition} +\subsubsection{User definition} \begin{verbatim} '(..) : user defined parts -iBuOH:='(!,/_,!,OH); +iBuOH:='(!?!,OH); \(<30,?6,{4,6}:/iBuOH) \end{verbatim} %----------------------------------------- \begin{mplibcode} beginfigm - #(60mm,13mm); + #(60mm,10mm); sw_trimming:=1; - iBuOH:='(!,/_,!,OH); + iBuOH:='(!?!,OH); \(<30,?6,{4,6}:/iBuOH) endfigm \end{mplibcode} %----------------------------------------------------------------------------- -\subsubsection{Parts inline definition} +\subsubsection{Inline definition} +\index{+}% \begin{verbatim} -<30,!8,{2,6}:/'(!,/_,!,OH) +a+b : '(a,b) + + <30,!8,{2,6}:/!?!+OH + <30,!8,{2,6}:/'(!?!,OH) \end{verbatim} %----------------------------------------- \begin{mplibcode} beginfigm - #(60mm,13mm) #@(2mm,1mm) + #(60mm,12mm) #@(2mm,1mm) sw_trimming:=1; - \(<30,!8,{2,6}:/'(!,/_,!,OH)) + \(<30,!8,{2,6}:/!?!+OH) endfigm \end{mplibcode} %----------------------------------------------------------------------------- @@ -1190,10 +1193,10 @@ endfigm %----------------------------------------- \begin{mplibcode} beginfigm - #(70mm,16mm) #@(2mm,1mm) + #(70mm,13mm) #@(2mm,1mm) sw_trimming:=1; \(<30,?6,@3,\,!3,//O,!,O,n_^60,@$(6,1),H,p_^15) - add(drawdot A1 withpen pencircle scaled 2bp; + ++(drawdot A1 withpen pencircle scaled 2bp; pickup pencircle scaled 0.1bp; for i=0 upto 6: draw (A1+(l*i,l-3bp))--(l*i,l+3bp); @@ -1213,7 +1216,7 @@ endfigm %----------------------------------------- \begin{mplibcode} beginfigm - #(75mm,14mm) |<(8mm) + #(75mm,13mm) |<(8mm) sw_numbering:=Atom; numbering_end:=15; \(<30,!14,{2,6:10,14}:/_~bd_r`0.5) endfigm @@ -1284,10 +1287,10 @@ beginfigm #(50mm,15mm) |=(6mm) mangle:=0; @(0.2,0.5)\(Ph) - add(drawarrow((A1 shifted (aw,0)) rotated A1ang..A1);) + ++(drawarrow((A1 shifted (aw,0)) rotated A1ang..A1);) mangle:=30; @(0.8,0.5)\(Ph) - add(drawarrow((A1 shifted (aw,0)) rotated A1ang..A1);) + ++(drawarrow((A1 shifted (aw,0)) rotated A1ang..A1);) endfigm \end{mplibcode} %------------------------------------------------------------------------------ @@ -1309,7 +1312,7 @@ beginfigm sw_frame:=Bothside; #(40mm,15mm); \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1330,7 +1333,7 @@ beginfigm sw_frame:=Bothside; #(40mm,15mm) |=(0.1) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1351,7 +1354,7 @@ beginfigm sw_frame:=Bothside; #(40mm,15mm) |=(8mm) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1374,7 +1377,7 @@ beginfigm sw_frame:=Bothside+Mol; #(40mm,15mm) ##(1,1) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1394,7 +1397,7 @@ beginfigm sw_frame:=Bothside+Mol; #(40mm,15mm) ##(0.25,1) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1413,7 +1416,7 @@ beginfigm sw_frame:=Bothside+Mol; #(40mm,15mm) ##(11mm,11mm) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1461,7 +1464,7 @@ beginfigm sw_frame:=sw_frame+Mol; #(40mm,15mm) ##(1,0.8) @(10mm,4mm) \(<30,Ph) - ext(drawdot p1 withpen pencircle scaled 3pt; + **(drawdot p1 withpen pencircle scaled 3pt; pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor @@ -1490,7 +1493,7 @@ beginfigm sw_frame:=Outside; #(40mm,12mm); \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1516,7 +1519,7 @@ beginfigm sw_frame:=Bothside+Mol; #(40mm,12mm) #@(10mm,2mm) \(<30,Ph) - ext(pickup pencircle scaled 0.2pt; + **(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -1539,7 +1542,7 @@ beginfigm offset_thickness:=0.0pt; @(0.1,0.5)\(<30,Ph) offset_thickness:=0.2pt; @(0.55,0.5)\(<30,Ph) offset_thickness:=0.5pt; @(1,0.5)\(<30,Ph) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.0pt",(0,1bp)); label.urt("0.2pt",(0.36w,1bp)); label.urt("0.5pt",(0.7w,1bp)); @@ -1559,7 +1562,7 @@ beginfigm offset_bond_gap:=0.0pt; @(0.1, 0.5)\(<30,Ph) offset_bond_gap:=0.3pt; @(0.55,0.5)\(<30,Ph) %<<== default offset_bond_gap:=1.0pt; @(1, 0.5)\(<30,Ph) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.0pt",(0,1bp)); label.urt("0.3pt",(0.36w,1bp)); label.urt("1.0pt",(0.7w,1bp)); @@ -1579,7 +1582,7 @@ beginfigm offset_atom:=0.0pt; @(0.1, .5)\(<30,?6,3:O) offset_atom:=0.8pt; @(.55, .5)\(<30,?6,3:O) %<<== default offset_atom:=2.0pt; @(1, .5)\(<30,?6,3:O) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.0pt",(0,1bp)); label.urt("0.8pt",(0.36w,1bp)); label.urt("2.0pt",(0.7w,1bp)); @@ -1599,7 +1602,7 @@ beginfigm offset_wedge:=0.0pt; @(0.1,0.5)\(<30,?6,5:*/_) offset_wedge:=0.4pt; @(0.55,0.5)\(<30,?6,5:*/_) %<<== default offset_wedge:=1.0pt; @(1, 0.5)\(<30,?6,5:*/_) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.0pt",(0,1bp)); label.urt("0.4pt",(0.36w,1bp)); label.urt("1.0pt",(0.7w,1bp)); @@ -1622,7 +1625,7 @@ beginfigm |<(5mm) @(0, .5)\(<45,?4) |<(8mm) @(.4,.5)\(<45,?4) |<(10mm) @(1, .5)\(<45,?4) %<<== default - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label("5mm", (0.075w,0.5h)); label("8mm", (0.42w,0.5h)); label("10mm",(0.88w,0.5h)); @@ -1644,7 +1647,7 @@ beginfigm ratio_thickness_bond:=0.005; @(0.1,0.5)\(<30,Ph) ratio_thickness_bond:=0.015; @(.55,0.5)\(<30,Ph) %<<== default ratio_thickness_bond:=0.03; @(1, 0.5)\(<30,Ph) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.005",(0,1bp)); label.urt("0.015",(0.36w,1bp)); label.urt("0.030",(0.7w,1bp)); @@ -1664,7 +1667,7 @@ beginfigm ratio_char_bond:=1.0; @(0, 0.5)\(<30,?6,6:O,3:NH) ratio_char_bond:=1.5; @(.5,0.5)\(<30,?6,6:O,3:NH) %<<== default ratio_char_bond:=2.0; @( 1,0.5)\(<30,?6,6:O,3:NH) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("1.0",(0,1bp)); label.urt("1.5",(0.36w,1bp)); label.urt("2.0",(0.7w,1bp)); @@ -1684,7 +1687,7 @@ beginfigm ratio_bondgap_bond:=0.10; @(0.1,0.5)\(<30,Ph) ratio_bondgap_bond:=0.15; @(.55,0.5)\(<30,Ph) %<<== default ratio_bondgap_bond:=0.20; @(1 ,0.5)\(<30,Ph) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.10",(0,1bp)); label.urt("0.15",(0.36w,1bp)); label.urt("0.20",(0.7w,1bp)); @@ -1704,7 +1707,7 @@ beginfigm ratio_atom_bond:=0.25; @(0.1,0.5)\(<30,?6,3:O) ratio_atom_bond:=0.33; @(.55,0.5)\(<30,?6,3:O) %<<== default ratio_atom_bond:=0.45; @(1, 0.5)\(<30,?6,3:O) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.25",(0,1bp)); label.urt("0.33",(0.36w,1bp)); label.urt("0.45",(0.7w,1bp)); @@ -1724,7 +1727,7 @@ beginfigm ratio_wedge_bond:=0.1; @(0.05,.5)\(?6,4:*/_) ratio_wedge_bond:=0.12; @(.55, .5)\(?6,4:*/_) %<<== default ratio_wedge_bond:=0.2; @(1 , .5)\(?6,4:*/_) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.10",(0,1bp)); label.urt("0.12",(0.36w,1bp)); label.urt("0.20",(0.7w,1bp)); @@ -1747,7 +1750,7 @@ beginfigm ratio_atomgap_atom:=0.00; @(0, .5)\(scantokens(mc)) ratio_atomgap_atom:=0.050; @(.5,.5)\(scantokens(mc)) %<<== default ratio_atomgap_atom:=0.12; @(1, .5)\(scantokens(mc)) - ext(defaultscale:=0.75; labeloffset:=1bp; + **(defaultscale:=0.75; labeloffset:=1bp; label.urt("0.00",(0.05w,1bp)); label.urt("0.05",(0.45w,1bp)); label.urt("0.12",(0.85w,1bp)); @@ -1767,7 +1770,7 @@ beginfigm ratio_chain_ring:= 0.4; @(0.05,.5)\(<30,?6,4:/!) ratio_chain_ring:= 0.66; @(.45, .5)\(<30,?6,4:/!) %<<== default ratio_chain_ring:= 1; @(1, .5)\(<30,?6,4:/!) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.40",(0,1bp)); label.urt("0.66",(0.3w,1bp)); label.urt("1.0" ,(0.62w,1bp)); @@ -1788,7 +1791,7 @@ beginfigm ratio_hashgap_bond:=0.06; @(0.08,.5)\(scantokens(mc)) ratio_hashgap_bond:=0.12; @( .55,.5)\(scantokens(mc)) %<<== default ratio_hashgap_bond:=0.20; @(1, .5)\(scantokens(mc)) - ext(defaultscale:=0.6; labeloffset:=1bp; + **(defaultscale:=0.6; labeloffset:=1bp; label.urt("0.06",(0,1bp)); label.urt("0.12",(0.4w,1bp)); label.urt("0.20",(0.77w,1bp)); @@ -2135,7 +2138,7 @@ beginfigm \(<30,Ph,2:N) endfigm (check mcf and compile) beginfigm - ''("<30,Ph,}2:N") % ** extra '}' + ''("<30,Ph,2:") % ** '2:' missing arg if \*(mc)=0: \(scantokens(mc)) fi endfigm ** \*(mc) : error count @@ -2147,13 +2150,13 @@ beginfigm ''("<30,Ph,2:N") sw_trimming:=0; #(12mm,12mm); - \\ + if \*(mc)=0: \(scantokens(mc)) fi endfigm beginfigm - ''("<30,Ph,2):N") + ''("<30,Ph,2:") sw_trimming:=0; #(12mm,12mm); - \\ + if \*(mc)=0: \(scantokens(mc)) fi endfigm \end{mplibcode} %----------------------------------------------------------------------------- @@ -2201,6 +2204,7 @@ putm: put figure \newpage \subsection{add()} \index{add()}% +\index{++()}% \index{plus}% \index{minus}% \index{lonepair}% @@ -2239,6 +2243,7 @@ putm: put figure \begin{verbatim} (Add label to molecule) +++(): add() w: molecular width h: molecular height aw: atom font size @@ -2274,7 +2279,7 @@ lonepair r: ':' rotated r lonepairdiam = 0.3aw (default) lonepairspace = 0.7aw (default) -** : scaled +# : scaled << : rotated a /* b : point b of a @@ -2282,7 +2287,7 @@ beginfigm #(70mm,40mm) ##(.91,.9) |<(10mm) sw_frame:=sw_frame+Atom+Mol; @(.5,.85)\(<30,?6,{2,5}:O) - add( + ++( defaultscale:=.8; labeloffset:=.3aw; dotlabel.lft("p0",p0); @@ -2313,7 +2318,7 @@ beginfigm #(70mm,40mm) ##(.91,.9) |<(10mm) sw_frame:=sw_frame+Atom+Mol; @(.5,.85)\(<30,?6,{2,5}:O) - add( + ++( defaultscale:=.8; labeloffset:=.3aw; dotlabel.lft("p0",p0); @@ -2345,26 +2350,26 @@ beginfigm %--------------------------------------- @(0,0)\(<30,Ph,3=dl,4:/NH2) %--------------------------------------- - add( + ++( labeloffset:=.7aw; label.top(lone_pair 90,A7); drawarrow - (A7+up**1.2aw){A7left} + (A7+up#1.2aw){A7left} ..{B7right}B7/*0.3; drawarrow - B3m..A3+B2up**1.5aw..{A3down}A3; + B3m..A3+B2up#1.5aw..{A3down}A3; ) %--------------------------------------- @(1,0)\(<30,?6,{1,5}=dl,4://NH2) %--------------------------------------- - add( + ++( labeloffset:=.7aw; label.top(plus,A7); label.urt(minus,A3); - label(lonepair A3ang,A3+A3up**.7aw); + label(lonepair A3ang,A3+A3up#.7aw); ) %--------------------------------------- - ext(drawdblarrow (.4w,.4h)..(.55w,.4h);) + **(drawdblarrow (.4w,.4h)..(.55w,.4h);) %--------------------------------------- endfigm \end{verbatim} @@ -2375,26 +2380,27 @@ beginfigm %------------------------------------------- @(0,0)\(<30,Ph,3=dl,4:/NH2) %------------------------------------------- - add(labeloffset:=.7aw; + ++(labeloffset:=.7aw; label.top(lonepair 90,A7); - drawarrow (A7+up**1.2aw){A7left}..{B7right}B7/*0.3; - drawarrow B3m..A3+B2up**1.5aw..{A3down}A3; + drawarrow (A7+up#1.2aw){A7left}..{B7right}B7/*0.3; + drawarrow B3m..A3+B2up#1.5aw..{A3down}A3; ) %------------------------------------------- @(1,0)\(<30,?6,{1,5}=dl,4://NH2) %------------------------------------------- - add(labeloffset:=.7aw; + ++(labeloffset:=.7aw; label.top(plus,A7); label.urt(minus,A3); - label(lonepair A3ang,A3+A3up**.7aw); + label(lonepair A3ang,A3+A3up#.7aw); ) - ext(drawdblarrow (0.4w,0.4h)..(0.55w,0.4h);) + **(drawdblarrow (0.4w,0.4h)..(0.55w,0.4h);) endfigm \end{mplibcode} %----------------------------------------------------------------------------- \newpage \subsection{ext()} \index{ext()}% +\index{**()}% \index{w0}% \index{h0}% \index{aw}% @@ -2405,6 +2411,7 @@ endfigm \begin{verbatim} (Extra label to figure) +**(): ext() w: figure width h: figure height w0: figure width-2xpart(fmargin) @@ -2428,20 +2435,20 @@ beginfigm <-210,60`1,60`1,60`1,{1,3}=dl, 1:/R1,4:/R2^-60 ) - add( + ++( defaultscale:=0.6; label.bot("Diene",p0+(0.5w,0)); ) @(0.4,0.5)\( <-30,-60`1,1=dl,1:/R3,2:/R4^60) - add(defaultscale:=0.6; + ++(defaultscale:=0.6; label.bot("Dienophile",p0+(.5w,0)); ) @(0.9,0.5)\( <30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1 ) %--------------------------------------- - ext( + **( drawarrow (.52w,.5h)..(.6w,.5h); defaultscale:=0.7; label("+",(0.25w,0.5h)); @@ -2461,20 +2468,20 @@ beginfigm <-210,60`1,60`1,60`1,{1,3}=dl, 1:/R1,4:/R2^-60 ) - add( + ++( defaultscale:=0.6; label.bot("Diene",p0+(0.5w,0)); ) @(0.4,0.5)\( <-30,-60`1,1=dl,1:/R3,2:/R4^60) - add(defaultscale:=0.6; + ++(defaultscale:=0.6; label.bot("Dienophile",p0+(.5w,0)); ) @(0.9,0.5)\( <30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1 ) %--------------------------------------- - ext( + **( drawarrow (.52w,.5h)..(.6w,.5h); defaultscale:=0.7; label("+",(0.25w,0.5h)); @@ -2497,7 +2504,7 @@ endfigm beginfigm _"?4"@(0.5,1)\(?4) %------------------------------- - ext(label.top(EN,(0.5w,0));) + **(label.top(EN,(0.5w,0));) %------------------------------- endfigm beginfigm @@ -2516,7 +2523,7 @@ endfigm beginfigm _"?4"#(12mm,15mm)@(0.5,1)\(?4) %------------------------------- - ext(label.top(EN,(0.5w,0));) + **(label.top(EN,(0.5w,0));) %------------------------------- endfigm beginfigm @@ -2608,7 +2615,7 @@ beginfigm ''( "<30,Ph,{1,2,6}:/O!,{-4,-5}=?7, ", " {-1,-4,-6}=dl,-2://O,-3:/O!, ", - " @9,\,NH,!,//O,! ") + " 9:/NH!+?O! ") #(40mm,20mm) \\ endfigm \end{verbatim} @@ -2619,7 +2626,7 @@ beginfigm ''( "<30,Ph,{1,2,6}:/O!,{-4,-5}=?7, ", " {-1,-4,-6}=dl,-2://O,-3:/O!, ", - " @9,\,NH,!,//O,! ") + " 9:/NH!+?O! ") #(40mm,20mm) \\ endfigm \end{mplibcode} @@ -2677,7 +2684,7 @@ beginfigm " @$5,\*^30`1.7,O,!~zb,|,?6`.7,6:O,#.5,5:/*_,2:*/OH,3:/*N?! ") %----------------------------------------------------------------------- \\ - ext(defaultscale:=0.8; + **(defaultscale:=0.8; label.lrt("EN: "&EN,(0,h)); label.lrt("fm: "&fm,(0,h-5mm)); label.lrt("mw: "&mw,(0,h-9mm)); @@ -2701,7 +2708,7 @@ beginfigm " @$5,\*^30`1.7,O,!~zb,|,?6`.7,6:O,#.5,5:/*_,2:*/OH,3:/*N?! ") %----------------------------------------------------------------------- \\ - ext(defaultscale:=0.8; + **(defaultscale:=0.8; label.lrt("EN: "&EN,(0,h)); label.lrt("fm: "&fm,(0,h-5mm)); label.lrt("mw: "&mw,(0,h-9mm)); @@ -2719,7 +2726,7 @@ beginfigm "?6,5=dl,@3,#1,36,45,45,45,45,##,&5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O, ", " 4:??,6:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O, ", " @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>rl,12'^-15>lr}:*/O!+?O! ") %------------------------------------------------------------------ #(140mm,30mm) if \*(mc)=0: @@ -2740,7 +2747,7 @@ beginfigm "?6,5=dl,@3,#1,36,45,45,45,45,##,&5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O, ", " 4:??,6:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O, ", " @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>rl,12'^-15>lr}:*/O!+?O! ") %------------------------------------------------------------------- #(160mm,40mm) if \*(mc)=0: @(0, 0.5)\(scantokens(mc)) @@ -3230,25 +3237,24 @@ file name = 'temp-mc.aux' \paragraph{(Output)} \begin{verbatim} =========================================================================== - No[3],Name<Cytosine>,Category<biological>,File<main_lib.mcf> + No[5],Name<Cytosine>,Category<biological>,File<main_lib.mcf> --------------------------------------------------------------------------- -<30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2 +<30,?6,{4,6}=db,4:N,3://O,2:NH,5:/NH2 --------------------------------------------------------------------------- - Row[1],Length[37],Commands[7],&Code[59],Warning[0] + Row[1],Length[37],Block[7],Code pair[59],Warning[0] --------------------------------------------------------------------------- - =[1]({}=[1]), :[4]({}:[0]), '()[0] - @[0],&[0],<[1],~[0],^[0],`[0],>[0],|[0],||[0],#[0],##[0] + =[1] :[4] ?[1] <[1] --------------------------------------------------------------------------- - Width[30.92432],Height[42.36536], Shift x[0],Shift y[-12.99213] - Bond length[11.33856],Atom size[4.8819] + Width[30.92419],Height[42.36527], Shift x[-1.77635],Shift y[-12.9921] + Bond length[11.33855],Atom size[4.881881] --------------------------------------------------------------------------- Atom[9],Bond[9],Ring[1],Hide H[2] < NO. ><atom(s) >( x axis , y axis )<bond><hideH><chg> A1 C ( 0 , 0 ) 3 1 - A2 N ( 1 , 0 ) 3 + A2 N ( 1 , -1 ) 3 A3 C ( 2 , 0 ) 4 A4 N ( 2 , 1 ) 3 - A5 C ( 1 , 2 ) 4 + A5 C ( 1 , 1 ) 4 A6 C ( 0 , 1 ) 3 1 A7 O ( 3 , 0 ) 2 A8 H ( 1 , -1 ) 1 @@ -3261,19 +3267,19 @@ file name = 'temp-mc.aux' B4 4 -> 5 ( 2) 150 ( 150) 1 ( 11) B5 5 -> 6 ( 1) 210 ( -150) 1 ( 11) B6 6 -> 1 ( 2) 270 ( -90) 1 ( 11) - B7 3 -> 7 ( 2) 330 ( -30) 0.66 ( 7) - B8 2 -> 8 ( 1) 270 ( -90) 0.36 ( 4) - B9 5 -> 9 ( 1) 90 ( 90) 0.66 ( 7) + B7 3 -> 7 ( 2) 330 ( -30)0.660000 ( 7) + B8 2 -> 8 ( 1) 270 ( -90)0.359999 ( 4) + B9 5 -> 9 ( 1) 90 ( 90)0.660000 ( 7) --------------------------------------------------------------------------- <atom>( atom wt )[ mi wt ] < cnt > < sum wt >[ sum mi wt ] - C ( 12.0107)[ 12] * 4 48.04279[ 48] - H ( 1.00793)[ 1.00783] * 5 5.03967[ 5.03914] - N ( 14.0067)[ 14.00307] * 3 42.0201[ 42.0092] - O ( 15.9994)[ 15.99492] * 1 15.9994[ 15.99492] - Molecular Weight [Mono Isotopic] = 111.1019[ 111.04326] + C ( 12.0107)[ 12] * 4 48.0428[ 48] + H (1.0079400)[1.0078250] * 5 5.03969[5.0391251611] + N ( 14.0067)[14.003074] * 3 42.0200[42.009222013] + O ( 15.9994)[15.994914] * 1 15.9994[15.994914619] + Molecular Weight [Mono Isotopic] = 111.1019[ 111.043261] --------------------------------------------------------------------------- - Weight Calc: 111.1019 / Input: 111.10 / weight gap= 0.00195 - Fomula Calc: C4H5N3O + Weight Calc: 111.1019 - Input: 111.10 = 0.0019999 + Fomula Calc: C4H5N3O =========================================================================== \end{verbatim} \newpage |