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-rw-r--r--graphics/mcf2graph/mcf_manual.tex254
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