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-rw-r--r--graphics/mcf2graph/CHANGELOG7
-rw-r--r--graphics/mcf2graph/README38
-rw-r--r--graphics/mcf2graph/mcf2graph.mf31
-rw-r--r--graphics/mcf2graph/mcf_exa_soc.mf4
-rw-r--r--graphics/mcf2graph/mcf_example.pdfbin289548 -> 289530 bytes
-rw-r--r--graphics/mcf2graph/mcf_man_soc-064.mps186
-rw-r--r--graphics/mcf2graph/mcf_man_soc.mf287
-rw-r--r--graphics/mcf2graph/mcf_manual.pdfbin565886 -> 569071 bytes
-rw-r--r--graphics/mcf2graph/mcf_manual.tex363
-rw-r--r--graphics/mcf2graph/mcf_mplib_exa.pdfbin139843 -> 153581 bytes
-rw-r--r--graphics/mcf2graph/mcf_mplib_exa.tex536
11 files changed, 659 insertions, 793 deletions
diff --git a/graphics/mcf2graph/CHANGELOG b/graphics/mcf2graph/CHANGELOG
index bd4cf1eda8..0bc2c7e8dd 100644
--- a/graphics/mcf2graph/CHANGELOG
+++ b/graphics/mcf2graph/CHANGELOG
@@ -1,6 +1,11 @@
*******************************************************************************
- Changelog of mcf2graph software package by Akira Yamaji 2020-07-09
+ Changelog of mcf2graph software package by Akira Yamaji 2020-07-26
*******************************************************************************
+[ver. 4.50 / 2020-07-26]
+ -fix bug in function add()
+ -delete file mcf_man_soc-064.mps
+ -update MCF manual,example
+
[ver. 4.49 / 2020-07-09]
-improve command !,!n
-delete command !0
diff --git a/graphics/mcf2graph/README b/graphics/mcf2graph/README
index bd6f08d832..1ade6632aa 100644
--- a/graphics/mcf2graph/README
+++ b/graphics/mcf2graph/README
@@ -1,17 +1,18 @@
********************************************************************************
mcf2graph : Convert Molecular Coding Format to graphics with METAFONT/METAPOST
Author : Akira Yamaji
- version : 4.49 2020-07-09
+ version : 4.50 2020-07-26
E-mail : mcf2graph@gmail.com
Located at : http://www.ctan.org/pkg/mcf2graph
********************************************************************************
1. Introduction
- Molecular Coding Format(MCF) is new linear notation represent chemical
- structure diagrams. This 'Coding' is named from coding(programing) technique
- adressing,grouping,macro,etc. There are no Meta language commands in MCF.
- mcf2graph.mf(METAFONT/METAPOST macro) convert MCF file to graphics file
- (pk font/PNG/SVG/EPS) or MDL MOL file.
+ Molecular Coding Format(MCF) is new linear notation represent
+ chemical structure diagrams.
+ This Coding is named from programing technique
+ such as operator, array, scope, macro, adressing, etc.
+ mcf2graph convert from MCF to pk font, PNG, SVG, EPS, MOL file.
+ It is also able to calculate molecular weight, exact mass, molecular formula.
2. The distribution of software
( 1) README This file
@@ -19,15 +20,14 @@
( 3) mcf2graph.mf Macro of Metafont / Metapost
( 4) mcf_manual.tex MCF syntax manual(LaTeX file)
( 5) mcf_man_soc.mf Molecular difinition file for mcf_manual.tex
- ( 6) mcf_man_soc-064.mps No.64 eps(with color) file of (4)
- ( 7) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX))
- ( 8) mcf_example.tex LaTeX example,
+ ( 6) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX))
+ ( 7) mcf_example.tex LaTeX example,
Make file 'mcf_exa_soc-info.aux' before typeset
>mpost -s ahlength=1 mcf_exa_soc.mf
- ( 9) mcf_exa_soc.mf Molecular difinition file for mcf_example.tex
- (10) mcf_example.pdf PDF of (8) (used pdftex(LaTeX))
- (11) mcf_mplib_exa.tex luamplib(LuaLaTeX) example
- (12) mcf_example.pdf PDF of (11) typeset with LuaTeX(LuaLaTeX)
+ ( 8) mcf_exa_soc.mf Molecular difinition file for mcf_example.tex
+ ( 9) mcf_example.pdf PDF of (8) (used pdftex(LaTeX))
+ (10) mcf_mplib_exa.tex luamplib(LuaLaTeX) example
+ (11) mcf_example.pdf PDF of (11) typeset with LuaTeX(LuaLaTeX)
3. How to use mcf2graph with Metapost
Minimum requirement to run mcf2graph : mpost.exe,mpost.dll,mpost.mp,plain.mp
@@ -38,12 +38,12 @@
( 5) >mpost -s ahangle=2 FILENAME => output svg file
( 6) >mpost -s ahangle=3 FILENAME => output eps file (.eps)
( 7) >mpost -s ahlength=1 FILENAME => output aux file (tag1:var1;tag2:var2;)
- ( 7) >mpost -s ahlength=2 FILENAME => output aux file (tag1;tag2; var1;var2;)
- ( 8) >mpost -s ahlength=3 FILENAME => output report file
- ( 9) >mpost -s ahlength=5 FILENAME => output mol file(V2000)
- (10) >mpost -s ahlength=6 FILENAME => output mol file(V3000)
- (11) >mpost -s labeloffset=1 FILENAME => use plain.mp 'label','drawarrow'
- (12) >mpost -s labeloffset=2 FILENAME => atomfont="uhvr8r"
+ ( 8) >mpost -s ahlength=2 FILENAME => output aux file (tag1;tag2; var1;var2;)
+ ( 9) >mpost -s ahlength=3 FILENAME => output report file
+ (10) >mpost -s ahlength=5 FILENAME => output mol file(V2000)
+ (11) >mpost -s ahlength=6 FILENAME => output mol file(V3000)
+ (12) >mpost -s labeloffset=1 FILENAME => use plain.mp 'label','drawarrow'
+ (13) >mpost -s labeloffset=2 FILENAME => atomfont="uhvr8r"
4. License
Permission is hereby granted, free of charge, to any person obtaining a copy
diff --git a/graphics/mcf2graph/mcf2graph.mf b/graphics/mcf2graph/mcf2graph.mf
index f0dedd1648..5a4802cb48 100644
--- a/graphics/mcf2graph/mcf2graph.mf
+++ b/graphics/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 4.49 Copyright (c) 2013-2020 Akira Yamaji
+% mcf2graph ver 4.50 Copyright (c) 2013-2020 Akira Yamaji
%
% Permission is hereby granted, free of charge, to any person obtaining a copy of this software
% and associated documentation files (the "Software"), to deal in the Software without restriction,
@@ -46,7 +46,7 @@ string save_str[],tbl_atom_str[],strD[],var[],tag[],mpc_name[],out_file_name,ou
out_file_rep,out_file_mpc,aux_delimiter,atomfont,save_atomfont,save_defaultfont;
pair save_pair[],msize,mposition,fsize,fmargin,save_mposition,posBs,posBe;
picture mol_stru[],save_picture,temp_picture;
-path arrow_path,arrow_head;
+path arrow_path,dottedline_path,line_path,arrow_head;
%-------------------------------------------------------------------------------------------------
char_num:=str_cnt:=proc_end:=mangle:=sw_label_emu:=sw_calc:=sw_ext_all:=0;
sw_numberA:=sw_numberB:=sw_aux_out:=sw_expand:=sw_fframe:=sw_mframe:=sw_aframe:=sw_trimming:=0;
@@ -60,8 +60,6 @@ if (known green)and(known ahlength):
color color_list[];
prologues:=3;
%-----------------------------------------------------------------------------------------
-%% fontmapfile "pdftex.map";
- %-----------------------------------------------------------------------------------------
atomfont:=defaultfont:="";
out_file_aux:=jobname&"-info.aux";
out_file_mpc:=jobname&"-mpc.txt";
@@ -114,6 +112,7 @@ else: f_MP:=0;
def urcorner = urcorner_emu enddef;
def ulcorner = ulcorner_emu enddef;
string defaultfont;
+ defaultscale:=1.2;
dotlabeldiam:=3bp;
def Cp(expr s) = enddef;
def color = transform enddef;
@@ -125,7 +124,7 @@ fi
clearit;
%--------------------------------------------------------------------------------------------------
message "---------------------------------------------";
-message "This is mcf2graph ver 4.49 2020.07";
+message "This is mcf2graph ver 4.50 2020.07";
if f_MP=1:
if bboxmargin=0: message "output no image file";
elseif bboxmargin=1: message "output first font only";
@@ -167,6 +166,7 @@ offset_thickness:=0.2bp; offset_bond_gap:=0.3bp; offset_zebra_gap:=0.1bp
offset_atom:=0.8pt; offset_wedge:=0.4bp; max_labelsize:=20mm;
thickness_fframe:=0.2bp; thickness_mframe:=0.2bp; thickness_aframe:=0.1bp;
max_blength:=10mm; blength:=0; mangle:=0;
+dottedline_gap:=1.5bp;
%--------------------------------------------------------------------------------------------------
fsize:=(30mm,20mm); fmargin:=(0.4mm,0.4mm); msize:=(1,1); mposition:=(0.5,0.5);
%==================================================================================================
@@ -198,7 +198,7 @@ def parameter_list=
lonepairdiam,lonepairspace,blength,offset_atom,offset_wedge,max_blength,offset_zebra_gap,
offset_bond_gap,thickness_fframe,thickness_mframe,thickness_aframe,offset_thickness,
numberA_start,numberA_end,numberB_start,numberB_end,defaultsize,defaultscale,labeloffset,mangle,
- fsize,fmargin,msize,mposition,defaultfont,atomfont,
+ fsize,fmargin,msize,mposition,defaultfont,atomfont,dottedline_gap,
Me,Et,Pr,Bu,iPr,tBu,CF3,CCl3,CBr3,CH3,NH,NH2,NO2,OH,CHO,COOH,CN,SH,OMe,OEt,SMe,SEt,
!CH3,!NH2,!NO2,!OH,!CHO,!COOH,!CN,!SH,!2CH3,!2NH2,!2NO2,!2OH,!2CHO,!2COOH,!2CN,!2SH
enddef;
@@ -533,8 +533,7 @@ def add_to_molecule(text TXT)=
begingroup
save w,h,n,l,p,am,aw,A,B,plus,minus,lonepair,**,<<,/*;
numeric A[]dir,B[]up,A[]ang,B[]ang;
- pair p[],A[],B[]s,B[]e,B[]m,A[]up,A[]left,A[]right,A[]down,
- B[]up,B[]left,B[]right,B[]down;
+ pair p[],A[],B[]s,B[]e,B[]m,A[]up,A[]left,A[]right,A[]down,B[]up,B[]left,B[]right,B[]down;
path B[];
ext_setup;
def plus = circled_plus_add enddef;
@@ -543,7 +542,7 @@ def add_to_molecule(text TXT)=
let ** = scaled;
let << = rotated;
primarydef a /* b = point b of a enddef;
- w:=mol_wd; h:=mol_ht; l:=blength; aw:=atom_wd;
+ w:=mol_wd; h:=mol_ht; l:=blen; aw:=atom_wd;
p0:=(minX,minY);
An:=cntA; Bn:=cntB;
lonepairdiam:=0.3aw;
@@ -692,7 +691,7 @@ vardef dotlabel_emu@#(expr OBJ,POS)=
label_emu@#(OBJ,POS); draw POS withpen pencircle scaled dotlabeldiam;
enddef;
%==================================================================================================
-def drawarrow_emu expr PAT = arrow_path:=PAT; draw_arrow enddef;
+def drawarrow_emu expr PATH = arrow_path:=PATH; draw_arrow enddef;
%-------------------------------------------------------------------------------------------------
def draw_arrow text t = %% modified 'drawarrow' of plain.mp
filldraw arrow_head rotated ahead_angle(reverse arrow_path)
@@ -700,7 +699,7 @@ def draw_arrow text t = %% modified 'drawarrow' of plain.mp
draw arrow_path t
enddef;
%-------------------------------------------------------------------------------------------------
-def drawdblarrow_emu expr PAT = arrow_path:=PAT; draw_dblarrow enddef;
+def drawdblarrow_emu expr PATH = arrow_path:=PATH; draw_dblarrow enddef;
%-------------------------------------------------------------------------------------------------
def draw_dblarrow text t =
filldraw arrow_head rotated ahead_angle(arrow_path) shifted point 0 of arrow_path t;
@@ -708,13 +707,21 @@ def draw_dblarrow text t =
shifted point infinity of arrow_path t;
draw arrow_path t
enddef;
-%-------------------------------------------------------------------------------------------------
+%==================================================================================================
arrow_head:=(0,0)--(ahlength,-(sind 0.5ahangle)*ahlength)--
(ahlength, (sind 0.5ahangle)*ahlength)--cycle;
%-------------------------------------------------------------------------------------------------
def ahead_angle(expr p)=
angle direction .5ahlength/length(point 1 of p - point 0 of p) of p
enddef;
+%-------------------------------------------------------------------------------------------------
+def drawdottedline expr PATH = dottedline_path:=PATH; draw_dottedline enddef;
+def draw_dottedline text t =
+ line_path:=dottedline_path;
+ for i=0 step dottedline_gap/length(point 1 of line_path - point 0 of line_path) until 1:
+ drawdot (point i of line_path) t;
+ endfor
+enddef;
%=================================================================================================
def MCat(expr FW,FH)(text TXT)=
save_mposition:=mposition;
diff --git a/graphics/mcf2graph/mcf_exa_soc.mf b/graphics/mcf2graph/mcf_exa_soc.mf
index f8e99dbbb4..9c4a023839 100644
--- a/graphics/mcf2graph/mcf_exa_soc.mf
+++ b/graphics/mcf2graph/mcf_exa_soc.mf
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.07.09
+% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.07.26
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %%% it must be version 4.49 or later
+input mcf2graph.mf; %%% it must be version 4.50 or later
%-------------------------------------------------------------------------
fsize:=(33mm,24mm);
max_blength:=4.5mm;
diff --git a/graphics/mcf2graph/mcf_example.pdf b/graphics/mcf2graph/mcf_example.pdf
index dc9a638cc8..3dc4e44d11 100644
--- a/graphics/mcf2graph/mcf_example.pdf
+++ b/graphics/mcf2graph/mcf_example.pdf
Binary files differ
diff --git a/graphics/mcf2graph/mcf_man_soc-064.mps b/graphics/mcf2graph/mcf_man_soc-064.mps
deleted file mode 100644
index 0820fc253f..0000000000
--- a/graphics/mcf2graph/mcf_man_soc-064.mps
+++ /dev/null
@@ -1,186 +0,0 @@
-%!PS-Adobe-3.0 EPSF-3.0
-%%BoundingBox: -1 -1 213 57
-%%HiResBoundingBox: -0.1 -0.1 212.69804 56.79282
-%%Creator: MetaPost 2.00
-%%CreationDate: 2020.01.25:0956
-%%Pages: 1
-%%DocumentResources: procset mpost-minimal
-%%+ font uhvr8r cmr8
-%%DocumentSuppliedResources: procset mpost-minimal
-%%DocumentNeededResources: font uhvr8r cmr8
-%%IncludeResource: font uhvr8r
-%%IncludeResource: font cmr8
-%%EndComments
-%%BeginProlog
-%%BeginResource: procset mpost-minimal
-/bd{bind def}bind def/fshow {exch findfont exch scalefont setfont show}bd
-/fcp{findfont dup length dict begin{1 index/FID ne{def}{pop pop}ifelse}forall}bd
-/fmc{FontMatrix dup length array copy dup dup}bd/fmd{/FontMatrix exch def}bd
-/Amul{4 -1 roll exch mul 1000 div}bd/ExtendFont{fmc 0 get Amul 0 exch put fmd}bd
-/ScaleFont{dup fmc 0 get Amul 0 exch put dup dup 3 get Amul 3 exch put fmd}bd
-/SlantFont{fmc 2 get dup 0 eq{pop 1}if Amul FontMatrix 0 get mul 2 exch put fmd}bd
-%%EndResource
-%%EndProlog
-%%BeginSetup
- /uhvr8r /uhvr8r def
- /cmr8 /cmr8 def
-%%EndSetup
-%%Page: 1 1
- 1 0 0 setrgbcolor
-newpath 54.14986 5.99792 moveto
-54.9016 5.99792 lineto
-54.9016 13.38094 lineto
-54.14986 13.38094 lineto
- closepath fill
-newpath 60.78113 5.99792 moveto
-61.53287 5.99792 lineto
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- closepath fill
-newpath 55.20229 13.38094 moveto
-54.14986 13.38094 lineto
-60.48044 5.99792 lineto
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- closepath fill
- 0 0 1 setrgbcolor
-newpath 54.14986 46.15283 moveto
-54.9016 46.15283 lineto
-54.9016 53.53584 lineto
-54.14986 53.53584 lineto
- closepath fill
-newpath 60.78113 46.15283 moveto
-61.53287 46.15283 lineto
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- closepath fill
-newpath 55.20229 53.53584 moveto
-54.14986 53.53584 lineto
-60.48044 46.15283 lineto
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- closepath fill
- 0 0 0 setrgbcolor
-newpath 86.89844 7.16803 moveto
-87.65018 7.16803 lineto
-87.65018 14.55104 lineto
-86.89844 14.55104 lineto
- closepath fill
-newpath 93.52971 7.16803 moveto
-94.28145 7.16803 lineto
-94.28145 14.55104 lineto
-93.52971 14.55104 lineto
- closepath fill
-newpath 87.95087 14.55104 moveto
-86.89844 14.55104 lineto
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- closepath fill
-newpath 94.92334 7.16803 moveto
-95.67508 7.16803 lineto
-95.67508 14.55104 lineto
-94.92334 14.55104 lineto
- closepath fill
- 0 0.75172 dtransform truncate idtransform setlinewidth pop [] 0 setdash
- 1 setlinecap 1 setlinejoin 10 setmiterlimit
-newpath 95.29921 10.85954 moveto
-101.93048 10.85954 lineto stroke
-newpath 101.55461 7.16803 moveto
-102.30635 7.16803 lineto
-102.30635 14.55104 lineto
-101.55461 14.55104 lineto
- closepath fill
- 0 setlinecap
-newpath 103.32411 3.64421 moveto
-103.60684 4.45103 104.14868 5.14159 104.8651 5.60812 curveto
-105.96042 6.32141 107.49776 6.64987 107.74046 7.95448 curveto
-107.96924 9.18422 106.85799 10.2441 105.53229 10.16272 curveto
-104.34424 10.0898 103.397 9.14253 103.32411 7.95448 curveto stroke
-newpath 108.11633 3.15558 moveto
-108.11633 3.90732 lineto
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-102.94824 3.15558 lineto
- closepath fill
- 0 0.50114 dtransform truncate idtransform setlinewidth pop 1 setlinecap
-newpath 40.45374 19.72816 moveto
-53.34746 12.28403 lineto stroke
-newpath 44.04344 21.47943 moveto
-55.0032 15.15187 lineto stroke
-newpath 62.33528 12.28403 moveto
-75.229 19.72816 lineto stroke
- 0 1 0 setrgbcolor 0.50114
- 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 75.229 19.72816 moveto
-75.229 39.80562 lineto stroke
-newpath 71.91751 21.73604 moveto
-71.91751 37.79782 lineto stroke
- 0 0 0 setrgbcolor 0 0.50114 dtransform truncate idtransform setlinewidth pop
-newpath 75.229 39.80562 moveto
-62.33528 47.24976 lineto stroke
-newpath 53.34746 47.24976 moveto
-40.45374 39.80562 lineto stroke
-newpath 55.0032 44.38191 moveto
-44.04344 38.05435 lineto stroke
- 0.50114 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 40.45374 39.80562 moveto
-40.45374 19.72816 lineto stroke
- 0 0.50114 dtransform truncate idtransform setlinewidth pop
-newpath 75.229 19.72816 moveto
-86.09601 13.45413 lineto stroke
-9.22984 46.03944 moveto
-(\(draw\)) uhvr8r 9.96265 fshow
-150.05211 5.99792 moveto
-(N) cmr8 10.80444 fshow
-150.05211 46.15283 moveto
-(N) cmr8 10.80444 fshow
-182.80069 7.16803 moveto
-(N) cmr8 10.80444 fshow
-192.14693 7.16803 moveto
-(H) cmr8 10.80444 fshow
-201.3689 3.13731 moveto
-(2) cmr8 10.80444 fshow
-newpath 136.30315 19.72816 moveto
-149.19687 12.28403 lineto stroke
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-150.85262 15.15187 lineto stroke
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-171.07841 19.72816 lineto stroke
- 0.50114 0 dtransform exch truncate exch idtransform pop setlinewidth
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- 0 0.50114 dtransform truncate idtransform setlinewidth pop
-newpath 171.07841 39.80562 moveto
-159.506 46.48694 lineto stroke
-newpath 149.19687 47.24976 moveto
-136.30315 39.80562 lineto stroke
-newpath 150.85262 44.38191 moveto
-139.89285 38.05435 lineto stroke
- 0.50114 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 136.30315 39.80562 moveto
-136.30315 19.72816 lineto stroke
- 0 0.50114 dtransform truncate idtransform setlinewidth pop
-newpath 171.07841 19.72816 moveto
-181.94542 13.45413 lineto stroke
-104.53125 46.03944 moveto
-(\(cmr8\)) uhvr8r 9.96265 fshow
-newpath -0.1 0.1 moveto
--0.1 -0.1 lineto
-0.1 -0.1 lineto
-212.69804 -0.1 lineto
-212.69804 0.1 lineto
-212.69804 56.79282 lineto
-212.49803 56.79282 lineto
--0.1 56.79282 lineto
--0.1 56.5928 lineto
--0.1 -0.1 lineto
-0.1 -0.1 lineto
-0.1 0.1 lineto
-0.1 56.79282 lineto
-0.1 56.5928 lineto
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-212.49803 -0.1 lineto
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- closepath fill
-showpage
-%%EOF
diff --git a/graphics/mcf2graph/mcf_man_soc.mf b/graphics/mcf2graph/mcf_man_soc.mf
index b13b6cc12b..dfc1cdc1a7 100644
--- a/graphics/mcf2graph/mcf_man_soc.mf
+++ b/graphics/mcf2graph/mcf_man_soc.mf
@@ -1,97 +1,129 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.07.09
+% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.07.26
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %% it must be version 4.49 or later
+input mcf2graph.mf; %% it must be version 4.50 or later
%------------------------------------------------------------------------
sw_mframe:=0;
sw_expand:=0;
%%%%sw_aux_out:=0;
%%%%sw_rep_out:=1;
+%ext(defaultscale:=.5; label.bot(decimal(char_num)&":"&inf_EN,(.5w,0));)
%***********************************************************************
-fsize:=(35mm,25mm);
+fsize:=(40mm,25mm);
blength:=6mm;
-%-------------------------------------------------------------------------
-%ext(defaultscale:=.5; label.bot(decimal(char_num)&":"&inf_EN,(.5w,0));)
%***********************************************************************
beginfont("EN:Glycine")
MC(<30,NH2,!2,COOH)
endfont
%***********************************************************************
-beginfont("EN:Alanine")
- MC(<30,NH2,!,/_,!,COOH)
+beginfont("EN:L-Alanine")
+ MC(<30,NH2,!~wb,/_,!,COOH)
+endfont
+%***********************************************************************
+beginfont("EN:L-Valine")
+ MC(<30,NH2,!~wb,/iPr,!,COOH)
+endfont
+%***********************************************************************
+beginfont("EN:L-Leucine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,/_,!)
+endfont
+%***********************************************************************
+beginfont("EN:L-Isoleucine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,/*_,!2)
endfont
%***********************************************************************
-beginfont("EN:Valine")
- MC(<30,NH2,!,/iPr,!,COOH)
+beginfont("EN:L-Serine")
+ MC(<30,NH2,!~wb,!,COOH,2:/!OH)
endfont
%***********************************************************************
-beginfont("EN:Leucine")
- MC(<30,NH2,!2,COOH,2:\,!,/_,!)
+beginfont("EN:L-Threonine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,/_,!~wf,OH)
endfont
%***********************************************************************
-beginfont("EN:Isoleucine")
- MC(<30,NH2,!2,COOH,2:\,/_,!2)
+beginfont("EN:L-Cysteine")
+ MC(<30,NH2,!~wb,!,COOH,2:/!SH)
endfont
%***********************************************************************
-beginfont("EN:Serine")
- MC(<30,NH2,!2,COOH,2:/!OH)
+beginfont("EN:L-Methionine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!2,SMe)
endfont
%***********************************************************************
-beginfont("EN:Threonine")
- MC(<30,NH2,!2,COOH,2:\,/_,!,OH)
+beginfont("EN:L-Phenylalanine")
+ MC(<30,NH2,!~wb,!,COOH,2:/!Ph)
endfont
%***********************************************************************
-beginfont("EN:Cysteine")
- MC(<30,NH2,!2,COOH,2:/!SH)
+beginfont("EN:L-Tyrosine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,Ph,-3:/OH)
endfont
%***********************************************************************
-beginfont("EN:Methionine")
- MC(<30,NH2,!2,COOH,2:\,!2,SMe)
+beginfont("EN:L-Triptophan")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,<24,|,?5,-4=Ph,2=dr,5=dl,4:NH)
endfont
%***********************************************************************
-beginfont("EN:Phenylalanine")
- MC(<30,NH2,!2,COOH,2:/!Ph)
+beginfont("EN:L-Prorine")
+ MC(<18,?5,3:NH,4:*/COOH)
endfont
%***********************************************************************
-beginfont("EN:Tyrosine")
- MC(<30,NH2,!2,COOH,2:\,!,Ph,-3:/OH)
+beginfont("EN:L-Glutamine")
+ MC(<30,NH2,!~wb,!,COOH,2:\`1,!`1,!,//O,!,NH2)
endfont
%***********************************************************************
-beginfont("EN:Triptophan")
- MC(<30,NH2,!2,COOH,2:\,!,<24,|,?5,-4=Ph,2=dr,5=dl,4:NH)
+beginfont("EN:L-Asparagine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,//O,!,NH2)
endfont
%***********************************************************************
-beginfont("EN:Prorine")
- MC(<18,?5,3:NH,4:/COOH)
+beginfont("EN:L-Aspartic acid")
+ MC(<30,NH2,!~wb,/!COOH,!,COOH)
endfont
%***********************************************************************
-beginfont("EN:Glutamine")
- MC(<30,NH2,!2,COOH,2:\`1,-45,-45,//O,!,NH2)
+beginfont("EN:L-Glutamic acid")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!2,COOH)
endfont
%***********************************************************************
-beginfont("EN:Asparagine")
- MC(<30,NH2,!2,COOH,2:\,!,//O,!,NH2)
+beginfont("EN:L-Lysine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!4,NH2)
endfont
%***********************************************************************
-beginfont("EN:Aspartic acid")
- MC(<30,NH2,!,/!COOH,!,COOH)
+beginfont("EN:L-Arginine")
+ MC(<30,NH2,!~wb,!,COOH,2:\`1,!`1,!2,NH,!,//NH,!,NH2)
endfont
%***********************************************************************
-beginfont("EN:Glutamic acid")
- MC(<30,NH2,!2,COOH,2:\,!2,COOH)
+beginfont("EN:L-Hystidine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,|,?5,{1,3}=dl,3:N,5:NH)
endfont
%***********************************************************************
-beginfont("EN:Lysine")
- MC(<30,NH2,!2,COOH,2:\,!4,NH2)
+beginfont("EN:L-DOPA")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,Ph,{-3,-4}:/OH)
endfont
%***********************************************************************
-beginfont("EN:Arginine")
- MC(<30,NH2,!2,COOH,2:\,-45,-45,60,NH,!,//NH,!,NH2)
+beginfont("EN:Ornithine")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH2)
endfont
%***********************************************************************
-beginfont("EN:Hystidine")
- MC(<30,NH2,!2,COOH,2:\,!,|,?5,{1,3}=dl,3:N,5:NH)
+beginfont("EN:Citrulline")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH,!,//O,!,NH2)
endfont
+%***********************************************************************
+beginfont("EN:GABA")
+ MC(<30,NH2,!4,COOH)
+endfont
+%***********************************************************************
+beginfont("EN:amino Levulinic acid")
+ MC(<30,NH2,!2,//O,!3,COOH)
+endfont
+%***********************************************************************
+beginfont("EN:4-amino benzoic acid")
+ MC(<30,Ph,1:/NH2,4:/COOH)
+endfont
+%***********************************************************************
+beginfont("EN:L-Carboxyl glutamic acid")
+ MC(<30,NH2,!~wb,!,COOH,2:\,!,/COOH,!,COOH)
+endfont
+%***********************************************************************
+beginfont("EN:L-Hydroxy Prorine")
+ MC(<18,?5,1:/OH,3:NH,4:*/COOH)
+endfont
+%***********************************************************************
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fsize:=(60mm,35mm);
blength:=0mm;
@@ -102,7 +134,7 @@ sw_fframe:=1;
fmargin:=(2mm,1mm);
%***********************************************************************
beginfont("EN:Chain 1")
- fsize:=(60mm,20mm);
+ fsize:=(60mm,18mm);
sw_numberB:=1;
numberB_end:=6;
ratio_chain_ring:=1;
@@ -123,7 +155,7 @@ beginfont("EN:Chain 1")
endfont
%***********************************************************************
beginfont("EN:Chain 2")
- fsize:=(60mm,20mm);
+ fsize:=(60mm,18mm);
sw_numberB:=1;
numberB_end:=6;
ratio_chain_ring:=1;
@@ -144,7 +176,7 @@ beginfont("EN:Chain 2")
endfont
%***********************************************************************
beginfont("EN:Jump and Branch")
- fsize:=(60mm,20mm);
+ fsize:=(60mm,18mm);
fmargin:=(2mm,2mm);
sw_trimming:=1;
sw_numberA:=1;
@@ -154,7 +186,7 @@ beginfont("EN:Jump and Branch")
endfont
%***********************************************************************
beginfont("EN:Jump and Branch")
- fsize:=(60mm,20mm);
+ fsize:=(60mm,18mm);
fmargin:=(2mm,2mm);
sw_numberA:=1;
sw_trimming:=1;
@@ -164,7 +196,7 @@ beginfont("EN:Jump and Branch")
endfont
%***********************************************************************
beginfont("EN:branch1")
- fsize:=(60mm,20mm);
+ fsize:=(60mm,18mm);
fmargin:=(2mm,2mm);
sw_numberA:=1;
sw_trimming:=1;
@@ -454,12 +486,12 @@ beginfont("EN:group 5")
endfont
%***********************************************************************
beginfont("EN:chain strech direction mode 1")
- fsize:=(60mm,27mm);
+ fsize:=(60mm,45mm);
sw_trimming:=1;
ratio_chain_ring:=1;
MC(
?4,{3^-90,3^-30,3^90}:/'(!3,"{hz}")>hz,
- {1^-60,1`1.5,1^60}:/'(!2,"{vt}")>vt
+ {1^-60,1,1^60}:/'(!3,"{vt}")>vt
)
endfont
%***********************************************************************
@@ -474,12 +506,17 @@ beginfont("EN:chain strech direction mode 2")
endfont
%***********************************************************************
beginfont("EN:chain strech direction mode 3")
+ fsize:=(40mm,25mm);
+ sw_trimming:=1;
+ ratio_chain_ring:=1;
+ MC(<30,!6,6>45:/!3)
+endfont
+%***********************************************************************
+beginfont("EN:chain strech direction mode 4")
fsize:=(60mm,25mm);
sw_trimming:=1;
ratio_chain_ring:=1;
- MC(<30,!6,{6>45}:/'(!3,"{45}"),
- {3>'(90,-90,90)}:/'(!3,"{'(90,-90,90)}")
- )
+ MC(<30,!6,6>'(90,-90,90,-90,90):/!5)
endfont
%***********************************************************************
beginfont("EN:change atom and group")
@@ -488,24 +525,11 @@ beginfont("EN:change atom and group")
MC(<-30,!2,NH,!2,SO,!2,SOO,!)
endfont
%***********************************************************************
-beginfont("EN:Change color,font")
- fsize:=(75mm,20mm);
- sw_label:=1;
- defaultfont:="cmtt10";
- defaultsize:=10bp;
- fmargin:=(3mm,1mm);
- MCat(0.25,0)(<30,Ph,{2,5}:N,3:/NH2,2:red,5:blue,3=green)
- add(label.lft("(draw)",p0+(0,.9h));)
- atomfont:="cmr8";
- MCat(1,0)(<30,Ph,{2,5}:N,3:/NH2)
- add(label.lft("(cmr8)",p0+(0,.9h));)
-endfont
-%***********************************************************************
beginfont("EN:Make brock")
- fsize:=(60mm,8mm);
- sw_trimming:=1;
+ fsize:=(60mm,15mm);
+% sw_trimming:=1;
sw_numberB:=1;
- MC(<-30,!2,|=1.2,!2,=|,!2)
+ MC(<-30,!2,|=1.2,!4,=|,!2)
endfont
%***********************************************************************
beginfont("EN:User definition")
@@ -519,7 +543,7 @@ beginfont("EN:Inline definition")
fsize:=(60mm,20mm);
fmargin:=(2mm,1mm);
sw_trimming:=1;
- MC(<30,!3,/'(!,/_,!,OH),!3)
+ MC(<30,!8,{2,6}:/'(!,/_,!,OH))
endfont
%***********************************************************************
beginfont("EN:mangle")
@@ -771,7 +795,7 @@ beginfont("EN:ratio_wedge_bond")
endfont
%***********************************************************************
beginfont("EN:ratio_atomgap_atom")
- fsize:=(60mm,8mm);
+ fsize:=(60mm,15mm);
sw_aframe:=1;
ratio_atomgap_atom:=0.00;
MCat(0, .5)(<30,!2,2:O)
@@ -948,7 +972,36 @@ beginfont("EN:MCat()")
endfor
endfont
%***********************************************************************
-beginfont("EN:add()")
+beginfont("EN:add() 1")
+ fsize:=(70mm,43mm);
+ sw_aframe:=sw_mframe:=1;
+ max_blength:=12mm;
+ msize:=(.91,.9);
+ MCat(.5,.85)(<30,?6,{2,5}:O)
+ add(
+ defaultscale:=.8;
+ labeloffset:=.3aw;
+ dotlabel.lft("p0",p0);
+ dotlabel.rt( "p0+(w,h)",p0+(w,h));
+ dotlabel.ulft("A1",A1);
+ drawarrow A1..A1+(l,0)<<A1ang;
+ dotlabel.lrt( "B3s",B3s);
+ dotlabel.rt("B3m",B3m);
+ drawarrow B3m..B3m+(l,0)<<(B3ang+90);
+ dotlabel.ulft("A6",A6);
+ drawarrow A1{A1down}..A6;
+ dotlabel.urt( "B3e",B3e);
+ label.rt("An="&decimal(An)&" / "&
+ "Bn="&decimal(Bn),p0+(-w,-1.5em));
+ label.rt("aw="&decimal(aw),p0+(w,-1.5em));
+ label.rt("em="&decimal(em),p0+(0,-1.5em));
+ label.rt("w="&decimal(w),p0+(-w,-3em));
+ label.rt("h="&decimal(h),p0+(0,-3em));
+ label.rt("l="&decimal(l),p0+(w,-3em));
+ )
+endfont
+%***********************************************************************
+beginfont("EN:add() 2")
fsize:=(70mm,20mm);
msize:=(1,0.85); MCat(0,0)(<30,Ph,3=dl,4:/NH2)
add(labeloffset:=.7aw;
@@ -1039,78 +1092,60 @@ defaultsize:=save_defaultsize;
%***************************************************************************
beginfont("EN:Luciferin","MW:280.33")
fsize:=(60mm,20mm);
- MC(<30,Ph,3=?5,8:\,?5,{9,16}=dl,
- {9,14}:N,{7,11}:S,1:/OH,-2:*/COOH)
-endfont
-%***************************************************************************
-beginfont("EN:Limonin")
- fsize:=(60mm,30mm);
- MC(<30,?6,{-3,-4}=?6,-5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
- {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)
+ MC(
+ <30,Ph,3=?5,8:\,?5,{9,16}=dl,
+ {9,14}:N,{7,11}:S,1:/OH,-2:*/COOH
+ )
endfont
%***************************************************************************
-beginfont("EN:Sesamine")
+beginfont("EN:Colchicine","MW:385.41")
fsize:=(60mm,25mm);
- MC(<54,?5,1=?5,{4,7}:O,{1^-54,2^54}:*/H,
- $5:*\^-12,Ph,-3=?5,{-1,-3}:O,8:*\^-12,Ph,-3=?5,{-1,-3}:O)
+ MC(
+ <30,Ph,{1,2,6}:/O!,|,-4=?7,
+ |,-5=?7,{-1,-4,-6}=dl,-2://O,-3:/O!,
+ $9:\,NH,!,//O,!
+ )
endfont
%***************************************************************************
-beginfont("EN:Colchicine","CAS:477-27-0","FM:C21H23NO6","MW:385.41")
- fsize:=(60mm,25mm);
- MC(<30,Ph,{1,2,6}:/O!,|,-4=?7,
- |,-5=?7,{-1,-4,-6}=dl,-2://O,-3:/O!,
- $9:\,NH,!,//O,!)
+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,||,
+ {4^35,4^-35,6}:/_,{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:*\,O,-60,//O,60,
+ 12:\*^-15,O,60,//O,-60
+ )
endfont
%***************************************************************************
-beginfont("EN:Lycorine","CAS:476-28-8","FM:C16H17NO4","MW:287.31")
+beginfont("EN:Lycorine","MW:287.31")
fsize:=(60mm,25mm);
MC(<30,
- Ph,-4=?6,-2=?6,6=?5,(9,12)=?5[3],13=dl,8:N,{15,17}:O,
+ 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
)
endfont
%***********************************************************************
-beginfont("EN:Gibberellin A3","CAS:77-06-5","FM:C19H22O6","MW:346.37");
+beginfont("EN:Gibberellin A3","MW:346.37");
fsize:=(60mm,20mm);
- MC(<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:#,
- 2:/COOH,7://_,13:*/OH,8:/*OH,14:*/_,{1,4}:*/H^60)
+ MC(
+ <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:#,
+ 2:/COOH,7://_,13:*/OH,8:/*OH,
+ 14:*/_,{1,4}:*/H^60
+ )
endfont
%***************************************************************************
-beginfont("EN:Quinine","CAS:130-95-0","FM:C20H24N2O2","MW:324.42")
+beginfont("EN:Quinine","MW:324.42")
fsize:=(60mm,25mm);
- MC(<30,Ph,3=Ph,7:N,6:/O!,
- 10:\,*/OH,/H~zf^-60,!,|,?6,2:N,1:*/H^60,4:*\,!!,2:@,165~zf,60,5~zb:#)
-endfont
-%***************************************************************************
-beginfont("EN:Atoropin","CAS:51-55-8","FM:C17H23NO3","MW:289.37")
- fsize:=(60mm,22mm);
- MC(<30,O,!,//O,!,!,Ph,
- $1:@,-60~zb,|,?7,6:*\^190`1.12,N,/_,3~wb:#,$3:*\*,!,OH)
-endfont
-%***************************************************************************
-beginfont("EN:Rotenone");
- fsize:=(60mm,30mm);
- MC(<-60,?5,{-3,-2,-3,-4}=?6,{7,9,-2,-4}=dl,{3,17}=dr,
- {2,13,16}=O,10://O,{11^-60,12^60}:*/H,{-2,-3}:/O!,1:*\,/_,!!)
-endfont;
-%***************************************************************************
-beginfont("EN:Pyrethrin I");
- MC(<30,?3,{3^35~wf,3^-35~zf}:/_,1:*\,!!,iPr,
- 2:\*,//O,!,O,-36~zb,|,?5,-2=dl,-1:/_,-3://O,-2:\,!4,{-1,-3}=dl)
-endfont;
-%***************************************************************************
-beginfont("EN:Paclitaxel","CAS:33069-62-4","FM:C47H51NO14","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,||,
- {4^35,4^-35,6}:/_,{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:*\,O,-60,//O,60,
- 12:\*^-15,O,60,//O,-60
+ <30,Ph,3=Ph,7:N,6:/O!,
+ 10:\,*/OH,/H~zf^-60,!,
+ |,?6,2:N,1:*/H^60,4:*\,!!,
+ 2:@,165~zf,60,5~zb:#
)
endfont
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/graphics/mcf2graph/mcf_manual.pdf b/graphics/mcf2graph/mcf_manual.pdf
index 79c8aec1e1..04e3d8108e 100644
--- a/graphics/mcf2graph/mcf_manual.pdf
+++ b/graphics/mcf2graph/mcf_manual.pdf
Binary files differ
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex
index aaf2017799..4c15bbafc1 100644
--- a/graphics/mcf2graph/mcf_manual.tex
+++ b/graphics/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2020.07.07
+% Molecular Coding Format manual by Akira Yamaji 2020.07.26
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\documentclass[a4paper,twoside]{article}
@@ -30,7 +30,7 @@
\htman=45mm%
\wdman=94mm%
\htmans=42mm%
-\fontnum=21%
+\fontnum=29%
\tempnum=1%
%----------------------------------------------------------------------------
\edef\MCFjobname{mcf_man_soc}%
@@ -104,16 +104,16 @@
\begin{center} Suggestion or request mail to: mcf2graph@gmail.com \end{center}
%-----------------------------------------------------------------------------
\thispagestyle{empty}
-\vspace{3mm}%
-\begin{center}
+\vspace{5mm}%
{\@strufont%
-\char1 \raisebox{10mm}{\char2 }\char3 \raisebox{10mm}{\char4}\\
-\char5 \raisebox{10mm}{\char6 }\char7 \raisebox{10mm}{\char8}\\
-\char9 \raisebox{10mm}{\char10}\char11\raisebox{10mm}{\char12}\\
-\char13\raisebox{10mm}{\char14}\char15\raisebox{10mm}{\char16}\\
-\char17\raisebox{10mm}{\char18}\char19\raisebox{10mm}{\char20}\\
+\char1 \char2 \char3 \char4\\
+\char5 \char6 \char7 \char8\\
+\char9 \char10\char11\char12\\
+\char13\char14\char15\char16\\
+\char17\char18\char19\char20\\
+\char21\char22\char23\char24\\
+\char25\char26\char27\char28
}%
-\end{center}
%-----------------------------------------------------------------------------
\twocolumn
\thispagestyle{empty}
@@ -125,11 +125,11 @@
\section{Introduction}
Molecular Coding Format(MCF) is new linear notation
represent chemical structure diagrams.
-This 'Coding' is named from coding(programing) technique
-like adressing,grouping,macro,etc.
-There are no Meta language commands in MCF.
-mcf2graph convert MCF file to graphics file
-pk font,PNG,SVG,EPS or MDL MOL file.
+This Coding is named from programing technique
+such as operator, array, scope, macro, adressing, etc.
+mcf2graph convert from MCF to pk font, PNG, SVG, EPS, MOL file.
+It is also able to calculate molecular weight,
+exact mass, molecular formula.
%-----------------------------------------------------------------------------
\section{MCF syntax}
\subsection{Make bond}
@@ -142,6 +142,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\subsubsection{Chain use !,!n}
\begin{verbatim}
! : take value 60 or -60 depend on
current angle and enviroment
@@ -152,7 +153,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Jump and branch bond}
+\subsubsection{Jump to atom}
\begin{verbatim}
n:@ : Jump to An
** An: atom number(-999<=n<=4095)
@@ -161,6 +162,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%------------------------------------
+\subsubsection{Branch bond}
\begin{verbatim}
3:\ : 3:@,0
@@ -168,7 +170,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Branch bond}
+\subsubsection{Branch modified bond}
\begin{verbatim}
2:\ : 2:@,0
4:*\ : 4:@,0~wf
@@ -346,6 +348,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\subsubsection{Reset brock address}
\begin{verbatim}
|| : reset brock adress
@@ -381,9 +384,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Fuse ring}
+\subsubsection{Attached 1 bond}
\begin{verbatim}
- (Attached 1 bond)
-
?6,3=?6 : fuse ?6 at B3
** Bn(n:-999<=n<=4095): bond number
@@ -414,9 +416,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\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
@@ -432,9 +433,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
1 2 3
\end{verbatim}
%-----------------------------------------------------------------------------
+\subsubsection{Attached 2 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)
@@ -448,10 +448,8 @@ pk font,PNG,SVG,EPS or MDL MOL file.
1 2
\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])
@@ -460,7 +458,7 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Spiro ring}
+\subsubsection{Spiro ring}
\begin{verbatim}
4:@,?5 : add ?5 at A4
@@ -541,8 +539,9 @@ pk font,PNG,SVG,EPS or MDL MOL file.
>hz : horizontal enviroment (default)
>vt : vertical enviroment
- ?4,{3^-90,3^-30,3^90}:/'(!3,"{hz}")>hz,
- {1^-60,1`2,1^60}:/'(!2,"{vt}")>vt
+ ?4,
+ {3^-90,3^-30,3^90}:/'(!3,"{hz}")>hz,
+ {1^-60,1,1^60}:/'(!3,"{vt}")>vt
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -557,13 +556,20 @@ pk font,PNG,SVG,EPS or MDL MOL file.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Fixed angle,multi angle}
+\subsubsection{Fixed rotate angle}
+\begin{verbatim}
+ >45 : rotate 45
+
+ <30,!6,6>45:/!3
+\end{verbatim}
+\MCFgraph
+%-----------------------------------------------------------------------------
+\subsubsection{Multi rotate angle}
\begin{verbatim}
- >45 : fixed angle enviroment
- >'(-90,90,-90) : multi angle enviroment
+ >'(90,-90,...) :rotate 90,-90,...
- <30,!6,2>45:/'(!3,"{45}"),
- {6>'(-90,90,-90)}:/'(!3,"{(-90,90,-90)}")
+ <30,!6,
+ 6>'(90,-90,90,-90,90):/!5
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -576,48 +582,39 @@ pk font,PNG,SVG,EPS or MDL MOL file.
simultaneously
<-30,!2,NH,!,SO,!,SOO,!
+ <-30,!4,3:NH,5:SO,7:SOO
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Change color, atom font}
-\begin{verbatim}
- 1=green : change color of B1 green
- 3:red : change color of A3 red
- atomfont:="cmr8" : use cmr8 for atom font
-
- defaultfont:="cmtt8";
- defaultsize:=8bp;
- MCat(0.25,0)(<30,Ph,{2,5}:N,3:/NH2,
- 2:red,5:blue,3=green)
- add(label.lft("(draw)",p0+(0,0.9h));)
- atomfont:="cmr8"; % default:"draw"
- MCat(1,0)(<30,Ph,{2,5}:N,3:/NH2)
- add(label.lft("(cmr8)",p0+(0,0.9h));)
-\end{verbatim}
-{\MCFformat=0 \MCFgraph}
-%-----------------------------------------------------------------------------
\subsubsection{Make block}
\begin{verbatim}
- |< : start brock
- >| : end brock
- |=n, bond length=n ,=|
+ |< : start brock
+ >| : end brock
+
+ |= : start brock / bond length=n
+ =| : end brock
- <-30,!2,|<,``1.2,!2,>|,!2
- <-30,!2,|=1.2,!2,=|,!2
+ <-30,!2,|<,``1.2,!4,>|,!2
+ <-30,!2,|=1.2,!4,=|,!2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{User definition}
+\subsubsection{Parts definition}
\begin{verbatim}
- user defined parts
- iBuOH:='(!,/_,!,OH)
- <30,?6,{4,6}:/iBuOH
+ '(..) : user defined parts
+
+ iBuOH:='(!,/_,!,OH);
+ MC(<30,?6,{4,6}:/iBuOH)
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\subsubsection{Parts inline definition}
\begin{verbatim}
- Insert user defined parts
- <30,!3,/'(!,/_,!,OH),!3
+ <30,!, /'(!,/_,!,OH),
+ !4,/'(!,/_,!,OH),!3
+
+ <30,!8,
+ {2,6}:/'(!,/_,!,OH)
\end{verbatim}
\MCFgraph
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -951,7 +948,8 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\MCFgraph
\newpage
%-----------------------------------------------------------------------------
-\subsection{Local parameter setting}
+\subsection{Parameter setting}
+\subsubsection{Local parameter setting}
\begin{verbatim}
beginfont()
MC(Ph)
@@ -968,7 +966,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\end{verbatim}
\MCFgraph\MCFgraph\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Global parameter setting}
+\subsubsection{Global parameter setting}
\begin{verbatim}
beginfont()
MC(Ph)
@@ -1026,7 +1024,9 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
mangle:=0;
for i=1 step -0.25 until 0:
for j=0 step 0.25 until 1:
+ %----------------
MCat(j,i)(Ph,4:N)
+ %----------------
add(
drawarrow((A1+A1up**aw)..A1);
label(decimal(mangle),
@@ -1051,6 +1051,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
em: label font size
p0: origin of molecular structure
l: bond length
+
An: atom number
A[m]: atom position
A[m]ang: branch angle of A[m]
@@ -1058,6 +1059,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
A[m]left: dir A[m]ang+90
A[m]right: dir A[m]ang-90
A[m]down: dir A[m]ang+180
+
Bn: bond number
B[m]: bond(path)
B[m]s: bond start position
@@ -1068,45 +1070,84 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
B[m]left: dir B[m]ang+90
B[m]right: dir B[m]ang-90
B[m]down: dir B[m]ang+180
+
plus : '+' circled
minus : '-' circled
circlediam = 0.6aw (default)
circlepen = 0.2bp (default)
+
lonepair r: ':' rotated r
lonepairdiam = 0.3aw (default)
lonepairspace = 0.7aw (default)
+
** : scaled
<< : rotated
a /* b : point b of a
-%----------------------------------------
-beginfont()
+
+beginfont("EN:add() 1")
+ fsize:=(75mm,45mm);
+ sw_aframe:=sw_mframe:=1;
+ max_blength:=12mm;
+ msize:=(.91,.85);
+ MCat(.5,.8)(<30,?6,{2,5}:O)
+ %-------------------------------------
+ add(
+ defaultscale:=.8;
+ labeloffset:=.3aw;
+ dotlabel.lft("p0",p0);
+ dotlabel.rt( "p0+(w,h)",p0+(w,h));
+ dotlabel.ulft("A1",A1);
+ drawarrow A1..A1+(l,0)<<A1ang;
+ dotlabel.lrt( "B3s",B3s);
+ dotlabel.rt("B3m",B3m);
+ drawarrow B3m..B3m+(l,0)<<(B3ang+90);
+ dotlabel.ulft("A6",A6);
+ drawarrow A1{A1down}..A6;
+ dotlabel.urt( "B3e",B3e);
+ label.rt("An="&decimal(An)&" / "&
+ "Bn="&decimal(Bn),p0+(-w,-1.5em));
+ label.rt("aw="&decimal(aw),p0+(w,-1.5em));
+ label.rt("em="&decimal(em),p0+(0,-1.5em));
+ label.rt("w="&decimal(w),p0+(-w,-3em));
+ label.rt("h="&decimal(h),p0+(0,-3em));
+ label.rt("l="&decimal(l),p0+(w,-3em));
+ )
+endfont
+\end{verbatim}
+\MCFgraph
+\begin{verbatim}
+beginfont("EN:add() 2")
fsize:=(60mm,20mm);
msize:=(1,0.85);
%---------------------------------------
MCat(0,0)(<30,Ph,3=dl,4:/NH2)
+ %---------------------------------------
add(
labeloffset:=.7aw;
label.top(lone_pair 90,A7);
- drawarrow (A7+up**1.2aw){A7left}
+ drawarrow
+ (A7+up**1.2aw){A7left}
..{B7right}B7/*0.3;
- drawarrow B3m..A3+B2up**1.5aw
- ..{A3down}A3;
+ drawarrow
+ B3m..A3+B2up**1.5aw..{A3down}A3;
)
%---------------------------------------
MCat(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);
)
+ %---------------------------------------
ext(drawdblarrow (.4w,.4h)..(.55w,.4h);)
%---------------------------------------
endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-%%%\newpage
+\newpage
\subsection{Function ext()}
\begin{verbatim}
(Extra graphic to font)
@@ -1118,10 +1159,12 @@ endfont
aw: atom font size
em: label font size
p0: fmargin
+
n: molecular number
p[m]: molecular origin position
w[m]: molecular width
h[m]: molecular height
+
ratio_thickness_char:
pen thickness / char width
%----------------------------------------
@@ -1129,17 +1172,22 @@ beginfont()
fsize:=(70mm,30mm;);
blength:=0.065;
%---------------------------------------
- MCat(0.1,0.5)
- (<-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));)
- MCat(0.4,0.5)
- (<-30,-60`1,1=dl,1:/R3,2:/R4^60)
+ MCat(0.1,0.5)(
+ <-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));
+ )
+ MCat(0.4,0.5)(
+ <-30,-60`1,1=dl,1:/R3,2:/R4^60)
add(defaultscale:=0.6;
- label.bot("Dienophile",p0+(.5w,0));)
- MCat(0.9,0.5)
- (<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1)
+ label.bot("Dienophile",p0+(.5w,0));
+ )
+ MCat(0.9,0.5)(
+ <30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1
+ )
%---------------------------------------
ext(
drawarrow (.52w,.5h)..(.6w,.5h);
@@ -1154,7 +1202,7 @@ endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Local ext() setting}
+\subsubsection{Local ext() setting}
\begin{verbatim}
beginfont("EN:?3")
fsize:=(12mm,15mm);
@@ -1177,7 +1225,7 @@ beginfont("EN:?5")
endfont
\end{verbatim}
\MCFgraph\MCFgraph\MCFgraph\MCFgraph
-\subsection{Global ext() setting}
+\subsubsection{Global ext() setting}
\begin{verbatim}
ext_clear: reset global ext()
@@ -1206,114 +1254,93 @@ endfont
\end{verbatim}
\MCFgraph\MCFgraph\MCFgraph\MCFgraph
%-----------------------------------------------------------------------------
+\newpage
%-----------------------------------------------------------------------------
\section{MCF example}
%-----------------------------------------------------------------------------
\subsection{Luciferin}
\begin{verbatim}
- <30,Ph,3=?5,8:\,?5,{9,16}=dl,
- {9,14}:N,{7,11}:S,
- 1:/OH,-2:*/COOH
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Limonin}
-\begin{verbatim}
- <30,?6,{-3,-4}=?6,-5=?3,
- -2=wf,-1=wb,6=?5,-4=?6,-5=wf,
- {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
+beginfont("EN:Luciferin","MW:280.33")
+ fsize:=(60mm,20mm);
+ MC(
+ <30,Ph,3=?5,8:\,?5,{9,16}=dl,
+ {9,14}:N,{7,11}:S,1:/OH,-2:*/COOH
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Sesamine}
+\subsection{Colchicine}
\begin{verbatim}
- <54,?5,1=?5,
- {4,7}:O,{1^-54,2^54}:*/H,
- 5:*\^-12,Ph,-3=?5,{-1,-3}:O,
- 8:*\^-12,Ph,-3=?5,{-1,-3}:O
+beginfont("EN:Colchicine","MW:385.41")
+ fsize:=(60mm,25mm);
+ MC(
+ <30,Ph,{1,2,6}:/O!,|,-4=?7,
+ |,-5=?7,{-1,-4,-6}=dl,
+ -2://O,-3:/O!,
+ $9:\,NH,!,//O,!
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsection{Colchicine}
+\subsection{Paclitaxel}
\begin{verbatim}
- <30,Ph,{1,2,6}:/O!,
- -4=?7,-5=?7,
- {-1,-4,-6}=dl,-2://O,-3:/O!,
- 9:\,NH,!,//O,!
+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,||,
+ {4^35,4^-35,6}:/_,{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:*\,O,-60,//O,60,
+ 12:\*^-15,O,60,//O,-60
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{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:/*OMe
+beginfont("EN:Lycorine","MW:287.31")
+ fsize:=(60mm,25mm);
+ MC(<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
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Gibberellin}
\begin{verbatim}
- <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:#,
- 2:/COOH,7://_,13:*/OH,8:/*OH,
- 14:*/_,{1,4}:*/H^60
+beginfont("EN:Gibberellin","MW:346.37");
+ fsize:=(60mm,20mm);
+ MC(
+ <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:#,
+ 2:/COOH,7://_,13:*/OH,8:/*OH,
+ 14:*/_,{1,4}:*/H^60
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Quinine}
\begin{verbatim}
- <30,Ph,3=Ph,7:N,6:/O!,
- 10:\,*/OH,/H~zf^-60,!,
- |,?6,2:N,1:*/H^60,
- 4:*\,!!,
- 2:@,165~zf,60,5~zb:#
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Atoropin}
-\begin{verbatim}
- <-30,O,!,//O,!,!,Ph,
- $1:@,-60~zb,
- |,?7,6:*\^190`1.02,N,/_,3~wb:#,
- $3:*\*,!,OH
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Rotenone}
-\begin{verbatim}
- <-60,?5,{-3,-2,-3,-4}=?6,
- {7,9,-2,-4}=dl,{3,17}=dr,
- {2,13,16}:O,10://O,{11^-60,12^60}:*/H,
- {-2,-3}:/O!,1:*\,/_,!!
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Pyrethrin I}
-\begin{verbatim}
- <30,?3,{3^35~wf,3^-35~zf}:/_,
- 1:*\,!!,iPr,2:\*,//O,!,O,-36~zb,|,
- ?5,-2=d,-1:/_,-3://O,-2\,!4,{-1,-3}=dl
-\end{verbatim}
-\MCFgraph
-%-----------------------------------------------------------------------------
-\subsection{Paclitaxel}
-\begin{verbatim}
- ?6,5=d,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,
- 60~wf,NH,-60,//O,60,Ph,
- 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60,
- 12:\*^-15,O,60,//O,-60
+beginfont("EN:Quinine","MW:324.42")
+ fsize:=(60mm,25mm);
+ MC(
+ <30,Ph,3=Ph,7:N,6:/O!,
+ 10:\,*/OH,/H~zf^-60,!,
+ |,?6,2:N,1:*/H^60,4:*\,!!,
+ 2:@,165~zf,60,5~zb:#
+ )
+endfont
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -1503,8 +1530,8 @@ cFM : molecular formula calculated
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
- >mpost -s ahlength=5 -s FILENAME % MOL(V2000)
- >mpost -s ahlength=6 -s FILENAME % MOL(V3000)
+ >mpost -s ahlength=5 FILENAME % MOL(V2000)
+ >mpost -s ahlength=6 FILENAME % MOL(V3000)
\end{verbatim}
\paragraph{(Output)}
\begin{verbatim}
@@ -1640,14 +1667,14 @@ endfont;
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\INFO{F:mcf_man_soc,C:134,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:135,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:138,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:139,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}%
%############################################################################
%------------------------------------------------------------------------
-\INFO{F:mcf_man_soc,C:134,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:135,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:138,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:139,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
%------------------------------------------------------------------------
\end{document}
diff --git a/graphics/mcf2graph/mcf_mplib_exa.pdf b/graphics/mcf2graph/mcf_mplib_exa.pdf
index 0e12c41a35..00a5684ce2 100644
--- a/graphics/mcf2graph/mcf_mplib_exa.pdf
+++ b/graphics/mcf2graph/mcf_mplib_exa.pdf
Binary files differ
diff --git a/graphics/mcf2graph/mcf_mplib_exa.tex b/graphics/mcf2graph/mcf_mplib_exa.tex
index b20161f9bc..8de170b935 100644
--- a/graphics/mcf2graph/mcf_mplib_exa.tex
+++ b/graphics/mcf2graph/mcf_mplib_exa.tex
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.07.09
+% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.07.26
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% mcf2graph.mf it must be version 4.49 or later
+%%% mcf2graph.mf it must be version 4.50 or later
\documentclass{article}
%------------------------------------------------------------------------------
\usepackage{luamplib}%
@@ -33,119 +33,128 @@
Author : Akira Yamaji \quad Date : \today\\
Located at : http://www.ctan.org/pkg/mcf2graph\vspace{2mm}\\
\end{center}
+%----------------------------------------------------------------------------
+\section{Change color}
\noindent%
-%------------------------------------------------------------------------------------
-{{\tt FM(C) :} molecular formula calculated by mcf2graph\\
-{{\tt MW(C) :} molecular weight calculated by mcf2graph\\
-{{\tt MW(D) :} molecular weight from literature data\vspace{5mm}\\
-%------------------------------------------------------------------------------------
+\begin{minipage}[b]{60mm}
+\begin{verbatim}
+(use with metapost only)
+MC(
+ <30,Ph,{2,5}:N,3:/NH2,4:/COOH,
+ %---------------------
+ 2:red, % red A2
+ 5:blue, % blue A5
+ 3=green % green B3
+ %---------------------
+ )
+\end{verbatim}
+%----------------------------------------------------------------------------
+\end{minipage}
\begin{mplibcode}
- fsize:=(80mm,40mm);
- beginfont("NO:1","EN:Chlorophyll a","MW:893.49")
- msize:=(.9,.9);
- MCat(0,0.5)(<54,
- |=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N,
- -2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,|,?5,5=d,5:N,-2:\~dl,$5:#,
- -1:@,24,/*COO!^15,72,//O,$1:#,=|,||,
- {2,9,15,20~zf}:/_,8:/!,14:\,!!,
- 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#,
- 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_
- )
- ext(
- label.lrt("("&inf_EN&")",(0,h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,h-13mm));
+ fsize:=(70mm,25mm);
+ beginfont("EN:Change color")
+ max_blength:=8mm;
+ sw_label:=1;
+ defaultfont:="cmtt10";
+ defaultsize:=10bp;
+ MC(
+ <30,Ph,{2,5}:N,3:/NH2,4:/COOH,
+ 2:red,5:blue,3=green
)
endfont
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%----------------------------------------------------------------------------
+\section{Change font}
+\noindent%
+\begin{minipage}[b]{60mm}
\begin{verbatim}
-|=1,?5,{2,5}=dl,4:N,3:\,54~dl,
-|,?5,{2,4}=dl,5:N,
--2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,
-|,?5,5=d,5:N,-2:\~dl,$5:#,
--1:@,24,/*COO!^15,72,//O,$1:#,=|,||,
- {2,9,15,20~zf}:/_,8:/!,14:\,!!,
- 4:\`1.45,Mg,17:#,-1:@,11~vb:#,
- -1:@,23~vb:#,
- 21:@,-6~wf,!2,//O,!,O,!2,!!,
-|,!13,{1,5,9,13}:/_
+(use with metapost only)
+%----------------
+atomfont:="cmr8";
+%----------------
+MC(
+ <30,Ph,{2,5}:N,3:/NH2,4:/COOH
+)
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
%----------------------------------------------------------------------------
+\end{minipage}
\begin{mplibcode}
-fsize:=(80mm,20mm);
-beginfont("EN:beta-Carotene","MW:536.888")
- msize:=(.65,1);
- MCat(.9,.5)(
- <30,?6,3=dl,{3,5^35,5^-35}:/_,
- 4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr,{3,7,12,16}:/_,
- |,?6,6=dl,{6,2^35,2^-35}:/_
- )
- ext(
- label.lrt("("&inf_EN&")",(0,h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,h-13mm));
- )
-endfont
+ fsize:=(70mm,25mm);
+ beginfont("EN:Change font")
+ max_blength:=8mm;
+ sw_label:=1;
+ defaultfont:="cmtt10";
+ defaultsize:=10bp;
+ atomfont:="cmr8";
+ MC(<30,Ph,{2,5}:N,3:/NH2,4:/COOH)
+ endfont
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%------------------------------------------------------------------------------------
+\section{MCF example}
+\noindent%
+%------------------------------------------------------------------------------------
+{{\tt FM(C) :} molecular formula calculated by mcf2graph\\
+{{\tt MW(C) :} molecular weight calculated by mcf2graph\\
+{{\tt MW(D) :} molecular weight from literature data
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Chlorophyll a}
+\noindent%
\begin{verbatim}
-<30,?6,3=dl,{3,5^35,5^-35}:/_,
-4:\,|,!18,
-{1,3,5,7,9,11,13,15,17}=dr,
-{3,7,12,16}:/_,
-|,?6,6=dl,{6,2^35,2^-35}:/_
+beginfont("NO:1","EN:Chlorophyll a","MW:893.49")
+ fsize:=(100mm,50mm);
+ MC(
+ <54,|=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N,
+ -2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,|,?5,5=d,5:N,-2:\~dl,$5:#,
+ -1:@,24,/*COO!^15,72,//O,$1:#,=|,||,
+ {2,9,15,20~zf}:/_,8:/!,14:/!!,
+ 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#,
+ 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_
+ )
+endfont
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
-%----------------------------------------------------------------------------
+%------------------------------------------------------------------------------------
\begin{mplibcode}
- fsize:=(80mm,30mm);
- beginfont("NO:2","EN:Limonin","MW:470.51")
- MCat(0.7,0.5)(<30,
- ?6,{-3,-4}=?6,-5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
- {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
- )
- ext(
- label.lrt("("&inf_EN&")",(0,h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,h-13mm));
- )
- endfont
+beginfont("NO:1","EN:Chlorophyll a","MW:893.49")
+ fsize:=(100mm,50mm);
+ MC(
+ <54,|=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N,
+ -2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,|,?5,5=d,5:N,-2:\~dl,$5:#,
+ -1:@,24,/*COO!^15,72,//O,$1:#,=|,||,
+ {2,9,15,20~zf}:/_,8:/!,14:/!!,
+ 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#,
+ 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_
+ )
+ ext(
+ defaultscale:=0.8;
+ label.lrt("FM(C): "&cal_FM,(0,h-5mm));
+ label.lrt("MW(C): "&cal_MW,(0,h-9mm));
+ label.lrt("MW(D): "&inf_MW,(0,h-13mm));
+ )
+endfont
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Gibberellin A3}
+\noindent%
\begin{verbatim}
-<30,?6,{-3,-4}=?6,-5=?3,
--2=wf,-1=wb,6=?5,-4=?6,-5=wf,
-{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
-
+beginfont("NO:4","EN:Gibberellin A3","MW:346.37");
+ fsize:=(120mm,20mm);
+ 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:#,
+ 2:/COOH,7://_,13:*/OH,8:/*OH,14:*/_,{1,4}:*/H^60
+ )
+endfont;
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\%
%----------------------------------------------------------------------------
\begin{mplibcode}
-fsize:=(80mm,20mm);
beginfont("NO:4","EN:Gibberellin A3","MW:346.37");
- MCat(0.8,0.5)(
+ fsize:=(120mm,20mm);
+ 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:#,
2:/COOH,7://_,13:*/OH,8:/*OH,14:*/_,{1,4}:*/H^60)
ext(
- label.lrt("("&inf_EN&")",(0,h));
defaultscale:=0.8;
label.lrt("FM(C): "&cal_FM,(0,h-5mm));
label.lrt("MW(C): "&cal_MW,(0,h-9mm));
@@ -153,50 +162,27 @@ beginfont("NO:4","EN:Gibberellin A3","MW:346.37");
)
endfont;
\end{mplibcode}
-\begin{minipage}[b]{85mm}
-\begin{verbatim}
-<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:#,
-2:/COOH,7://_,13:*/OH,8:/*OH,
-14:*/_,{1,4}:*/H^60)
-\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Erythromycin}
+\noindent%
%----------------------------------------------------------------------------
-\begin{mplibcode}
-fsize:=(80mm,25mm);
-beginfont("EN:Morphine","MW:285.343")
- MCat(0.7,0.5)(
- <30,Ph,2=?6,-4=?6,(1,12)=?5[2],-1:O,-1=zb,
- 7:@,60~wf`0.75,70~si_`1.3,45,N,/_,9~wb:#,
- 15=d,6:/OH,8^180:*/H,12:/*OH
- )
- ext(
- label.lrt("("&inf_EN&")",(0,h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,h-13mm));
- )
-endfont
-\end{mplibcode}
-\begin{minipage}[b]{85mm}
\begin{verbatim}
-<30,Ph,2=?6,-4=?6,(1,12)=?5[2],
--1:O,-1=zb,
-7:@,60~wf`0.75,70~si_`1.3,
-45,N,/_,9~wb:#,
-15=dl,
-6:/OH,8^180:*/H,12:/*OH
+beginfont("NO:5","EN:Erythromycin","MW:733.93");
+ fsize:=(120mm,35mm);
+ MC(
+ <30,|=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,=|,1:#,
+ 14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_,
+ {6^35,11,12^-35}:*/OH,
+ $3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!,
+ $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe
+ )
+endfont;
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
%----------------------------------------------------------------------------
\begin{mplibcode}
-fsize:=(80mm,35mm);
beginfont("NO:5","EN:Erythromycin","MW:733.93");
- MCat(0.8,0.5)(
+ fsize:=(120mm,35mm);
+ MC(
<30,|=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,=|,1:#,
14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_,
{6^35,11,12^-35}:*/OH,
@@ -204,40 +190,38 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93");
$5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe
)
ext(
- label.lrt("("&inf_EN&")",(0,h));
defaultscale:=0.8;
label.lrt("FM(C): "&cal_FM,(0,h-5mm));
label.lrt("MW(C): "&cal_MW,(0,h-9mm));
label.lrt("MW(D): "&inf_MW,(0,h-13mm));
)
- endfont;
+endfont;
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Paclitaxel}
+\noindent%
\begin{verbatim}
-<30,|=1,<-120,60,60,60,-60,60,
-60,-60,60,60,60,-60,60,60,=|,1:#,
-14:O,13:/*Et,{1,9}://O,{2,10}:*/_,
-{4,6^-35,8,12^35}:/*_,
-{6^35,11,12^-35}:*/OH,
-$3:\*,O,30,|,?6`.7,2:O,
-{3,5^35}:/_,4:/OH,5^-35:/O!,
-$5:\*^30`1.7,O,!,|,?6`.7,6:O,
-5:/_,2:/OH,3:/NMeMe
+beginfont("EN:Paclitaxel","MW:853.918")
+ fsize:=(120mm,35mm);
+ MC(
+ ?6,5=d,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,60~wf,NH,-60,//O,60,Ph,
+ $7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60
+ )
+endfont
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
%----------------------------------------------------------------------------
\begin{mplibcode}
-fsize:=(80mm,35mm);
beginfont("EN:Paclitaxel","MW:853.918")
- MCat(0.8,0.5)(
+ fsize:=(120mm,35mm);
+ MC(
?6,5=d,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,60~wf,NH,-60,//O,60,Ph,
$7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60
)
ext(
- label.lrt("("&inf_EN&")",(0,h));
defaultscale:=0.8;
label.lrt("FM(C): "&cal_FM,(0,h-5mm));
label.lrt("MW(C): "&cal_MW,(0,h-9mm));
@@ -245,132 +229,120 @@ beginfont("EN:Paclitaxel","MW:853.918")
)
endfont
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newpage
+%----------------------------------------------------------------------------
+\subsection{Vancomycin}
+\noindent%
+%----------------------------------------------------------------------------
\begin{verbatim}
-?6,5=d,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,
-60~wf,NH,-60,//O,60,Ph,
-$7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,
-$12:\*^-15,O,60,//O,-60)
+beginfont("NO:6","EN:Vancomycin","MW:1449.25");
+fsize:=(150mm,50mm);
+MC(<-30,|=1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60,
+ Ph,-4:/Cl,-3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl,-3:\,/*OH,*/H^-60,$1:#,
+ $7:@,$26:#,$1:@,60,//O,60,NH,60,/*H,*/COOH^180,-60,
+ Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|,
+ {3^40,6,9,12}://O,{2,5,8,11}:NH,{1,4^180}:*/H,{7^-60,10^60,14^60}:/*H,||,
+ 10:*\^-60,60,//O,!,NH2,13:*\,NH,!,//O,!,/!iPr^-35>60,*/H^60,!~zf,NH,!,
+ 23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH,
+ -1:\,O,!,|,?6`.7,6:O,{3^35,5}:/_,3^-35:/NH2,4:/OH)
+endfont;
\end{verbatim}
-\end{minipage}
-\vspace{7mm}\\
%----------------------------------------------------------------------------
-\noindent
\begin{mplibcode}
-fsize:=(80mm,70mm);
beginfont("NO:6","EN:Vancomycin","MW:1449.25");
- MCat(0.9,0)(
- <-30,
- |=1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60,
- Ph,-4:/Cl,-3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl,-3:\,/*OH,*/H^-60,$1:#,
- $7:@,$26:#,$1:@,60,//O,60,NH,60,/*H,*/COOH^180,-60,
- Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|,
- {3^40,6,9,12}://O,{2,5,8,11}:NH,
- {1,4^180}:*/H,{7^-60,10^60,14^60}:/*H,
- $10:*\^-60,60,//O,!,NH2,
- $13:*\,NH,!,//O,!,/!iPr^-35>60,*/H^60,!~zf,NH,!,
- $23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH,
- -1:\,O,!,|,?6`.7,6:O,{3^35,5}:/_,3^-35:/NH2,4:/OH
- )
- ext(
- label.lrt("("&inf_EN&")",(0,h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,h-13mm));
- )
+fsize:=(150mm,45mm);
+MC(<-30,|=1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60,
+ Ph,-4:/Cl,-3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl,-3:\,/*OH,*/H^-60,$1:#,
+ $7:@,$26:#,$1:@,60,//O,60,NH,60,/*H,*/COOH^180,-60,
+ Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|,
+ {3^40,6,9,12}://O,{2,5,8,11}:NH,{1,4^180}:*/H,{7^-60,10^60,14^60}:/*H,||,
+ 10:*\^-60,60,//O,!,NH2,13:*\,NH,!,//O,!,/!iPr^-35>60,*/H^60,!~zf,NH,!,
+ 23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH,
+ -1:\,O,!,|,?6`.7,6:O,{3^35,5}:/_,3^-35:/NH2,4:/OH)
+ ext(
+ defaultscale:=0.8;
+ label.lrt("FM(C): "&cal_FM,(0,h-4mm));
+ label.lrt("MW(C): "&cal_MW,(0,h-8mm));
+ label.lrt("MW(D): "&inf_MW,(0,h-12mm));
+ )
endfont;
\end{mplibcode}
-\begin{minipage}[b]{85mm}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Maitotoxin}
+\noindent%
+%--------------------------------------------------------------------------------
\begin{verbatim}
-<-30,|=1,!12,{1,3,12}=zf,7=wf,
-/H^-60,60,*/OH,60,Ph,-4:/Cl,
--3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl,
--3:\,/*OH,*/H^-60,$1:#,
-$7:@,$26:#,$1:@,120,//O,60,NH,60,
- /*H,*/COOH^180,-60,
-Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|,
-{3^40,6,9,12}://O,{2,5,8,11}:NH,
-{1,4^180}:*/H,
-{7^-60,10^60,14^60}:/*H,
-$10:*\^-60,60,//O,!,NH2,$13:*\,NH,!,//O,!,
- /!iPr^-35>60,*/H^60 ,!~zf,NH,!,
-$23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH,
--1:\,O,!,|,?6`.7,6:O,
-{3^35,5}:/_,3^-35:/NH2,4:/OH
+beginfont("NO:7","EN:Maitotoxin","MW:3425.86")
+fsize:=(170mm,70mm);
+MC(<55.8,?6,-4=?7 ,{-4,-3,-3,-3}=?6,-3:\,!3,?6,{-4,-3,-3,-3}=?6,-3:\,?6,-3=?6,
+ -3:\,!3,60,<-30,?6,-3=?6,-3:@,30,<30,?6,{-3,-3}=?6,-3=?7,{-4,-3,-3}=?6,
+ -2:\,?6,-3=?6,-3=?7,{-3,-3}=?6,-3=?8,-3=dl,{-5,-3,-3,-3}=?6,
+ {5,7,15,16,23,24,32,40,41,48,49,58,59,72,73,82,83,90,91,99,
+ 100,107,113,114,122,123,130,131,140,141,148,149}:O,
+ {1^60,2,26,28,29,51,54,61,63,68,75^60,78,109}:*/OH,
+ {11,20,35,45,52,55,65,69,86}:/*OH,{47,57,71}:/*H^60,
+ {3,8,13,17,21,33,38,42,56,70,84,92,101,106,111,128,138,142,146,150}:/*H^-60,
+ {4,14,22,34,39,43,81,89,98,102,116,121,125,129,133}:*/H^60,
+ {6,46,50,53,60,67,74}:*/H^-60,
+ {9,18,85,93,112,139,143,147}:*/_`1^60,
+ {80,88,97,115,120,124}:/*_`1^-60,108:*/_`1^-60,
+ 6:\,|,!11,60~dr,-60,60,OH,2:/*OH,{7,10}:*/OH,{1,3}:*/_,{8~zf,11~dm,12}:/_,
+ 6:\,O,30,SOO,30,"O{Na}",
+ 36:@,-45~zf,O,30,SOO,30,"O{Na}",
+ 150:\,|,!7,{1,2}:/*OH,4:*/_,5:/*_,7=dl)
+endfont
\end{verbatim}
-\end{minipage}
-\vspace{10mm}\\%
-%----------------------------------------------------------------------------
+%--------------------------------------------------------------------------------
\begin{mplibcode}
- fsize:=(170mm,70mm);
- beginfont("NO:7","EN:Maitotoxin","MW:3425.86")
- MC(
- <55.8,?6,-4=?7 ,{-4,-3,-3,-3}=?6,-3:\,!3,?6,{-4,-3,-3,-3}=?6,-3:\,?6,-3=?6,
- -3:\,!3,60,<-30,?6,-3=?6,-3:@,30,<30,?6,{-3,-3}=?6,-3=?7,{-4,-3,-3}=?6,
- -2:\,?6,-3=?6,-3=?7,{-3,-3}=?6,-3=?8,-3=dl,{-5,-3,-3,-3}=?6,
- {5,7,15,16,23,24,32,40,41,48,49,58,59,72,73,82,83,90,91,99,
- 100,107,113,114,122,123,130,131,140,141,148,149}:O,
- {1^60,2,26,28,29,51,54,61,63,68,75^60,78,109}:*/OH,
- {11,20,35,45,52,55,65,69,86}:/*OH,{47,57,71}:/*H^60,
- {3,8,13,17,21,33,38,42,56,70,84,92,101,106,111,128,138,142,146,150}:/*H^-60,
- {4,14,22,34,39,43,81,89,98,102,116,121,125,129,133}:*/H^60,
- {6,46,50,53,60,67,74}:*/H^-60,
- {9,18,85,93,112,139,143,147}:*/_`1^60,
- {80,88,97,115,120,124}:/*_`1^-60,108:*/_`1^-60,
- $6:\,|,!11,60~dr,-60,60,OH,2:/*OH,{7,10}:*/OH,{1,3}:*/_,{8~zf,11~dm,12}:/_,
- 6:\,O,30,SOO,30,"O{Na}",
- $36:@,-45~zf,O,30,SOO,30,"O{Na}",
- $150:\,|,!7,{1,2}:/*OH,4:*/_,5:/*_,7=dl
- )
- ext(
- label.lrt("("&inf_EN&")",(0,.8h));
- defaultscale:=0.8;
- label.lrt("FM(C): "&cal_FM,(0,.8h-5mm));
- label.lrt("MW(C): "&cal_MW,(0,.8h-9mm));
- label.lrt("MW(D): "&inf_MW,(0,.8h-13mm));
- )
- endfont
-\end{mplibcode}
-\begin{verbatim}
- <55.8,?6,-4=?7,{-4,-3,-3,-3}=?6,
- -3:\,!3,?6,{-4,-3,-3,-3}=?6,-3:\,?6,-3=?6,-3:\,!3,60,<-30,?6,-3=?6,
- -3:@,30,<30,?6,{-3,-3}=?6,-3=?7,{-4,-3,-3}=?6,
+fsize:=(170mm,60mm);
+beginfont("NO:7","EN:Maitotoxin","MW:3425.86")
+MC(<55.8,?6,-4=?7 ,{-4,-3,-3,-3}=?6,-3:\,!3,?6,{-4,-3,-3,-3}=?6,-3:\,?6,-3=?6,
+ -3:\,!3,60,<-30,?6,-3=?6,-3:@,30,<30,?6,{-3,-3}=?6,-3=?7,{-4,-3,-3}=?6,
-2:\,?6,-3=?6,-3=?7,{-3,-3}=?6,-3=?8,-3=dl,{-5,-3,-3,-3}=?6,
{5,7,15,16,23,24,32,40,41,48,49,58,59,72,73,82,83,90,91,99,
- 100,107,113,114,122,123,130,131,140,141,148,149}:O,
+ 100,107,113,114,122,123,130,131,140,141,148,149}:O,
{1^60,2,26,28,29,51,54,61,63,68,75^60,78,109}:*/OH,
{11,20,35,45,52,55,65,69,86}:/*OH,{47,57,71}:/*H^60,
{3,8,13,17,21,33,38,42,56,70,84,92,101,106,111,128,138,142,146,150}:/*H^-60,
{4,14,22,34,39,43,81,89,98,102,116,121,125,129,133}:*/H^60,
- {6,46,50,53,60,67,74}:*/H^-60,{9,18,85,93,112,139,143,147}:*/_`1^60,
+ {6,46,50,53,60,67,74}:*/H^-60,
+ {9,18,85,93,112,139,143,147}:*/_`1^60,
{80,88,97,115,120,124}:/*_`1^-60,108:*/_`1^-60,
$6:\,|,!11,60~dr,-60,60,OH,2:/*OH,{7,10}:*/OH,{1,3}:*/_,{8~zf,11~dm,12}:/_,
- 6:\,O,30,SOO,30,"O{Na}",
- $36:@,-45~zf,O,30,SOO,30,"O{Na}",$150:\,|,!7,{1,2}:/*OH,4:*/_,5:/*_,7=dl
-\end{verbatim}
-\vspace{8mm}%
-%----------------------------------------------------------------------------
+ 6:\,O,30,SOO,30,"O{Na}",
+ $36:@,-45~zf,O,30,SOO,30,"O{Na}",
+ $150:\,|,!7,{1,2}:/*OH,4:*/_,5:/*_,7=dl
+ )
+ ext(
+ defaultscale:=0.8;
+ label.lrt("FM(C): "&cal_FM,(0,.8h-5mm));
+ label.lrt("MW(C): "&cal_MW,(0,.8h-9mm));
+ label.lrt("MW(D): "&inf_MW,(0,.8h-13mm));
+ )
+endfont
+\end{mplibcode}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newpage
+\subsection{TCA cycle}
+\noindent%
\begin{mplibcode}
beginfont("EN:TCA cycle")
fsize:=(160mm,75mm);
max_blength:=5mm;
%------------------------------------------------------------------------
-MCat(0.33, 1)(<30,O[-1],!,//O,!,//O,!2,//O,!,O[-1])
-MCat(0.66, 1)(<30,O[-1],!,//O,!4,//O,!,O[-1],-4`1:\,//O,!,O[-1],4:/OH^-165)
-MCat(1, 1)(<30,O[-1],!,//O,!2,!~dr,!,//O,!,O[-1],-4`1:\,//O,!,O[-1])
-MCat(1, 0.55)(<30,O[-1],!,//O,!4,//O,!,O[-1],-4:\`1,//O,!,O[-1])
-MCat(1, 0.05)(<30,O[-1],!,//O,!3,//O,!,//O,!,O[-1],-4:\`1,//O,!,O[-1])
-MCat(0.66,0.05)(<30,O[-1],!,//O,!3,//O,!,//O,!,O[-1])
-MCat(0.33,0.05)(<30,O[-1],!,//O,!3,//O,!,"{S-CoA}")
-MCat(0, 0.05)(<30,O[-1],!,//O,!3,//O,!,O[-1])
-MCat(0, 0.55)(<30,O[-1],!,//O,!,!~dr,!,//O,!,O[-1])
-MCat(0, 1)(<30,O[-1],!,//O,!3,//O,!,O[-1],3:/OH)
+COOm:='(//O,!,O[-1]);
+OmCO:='(O[-1],!,//O);
+MCat(0.33, 1)(<30,OmCO,!,//O,!2,COOm)
+MCat(0.66, 1)(<30,OmCO,!4,COOm,-4`1:\,COOm,4:/OH^-165)
+MCat(1, 1)(<30,OmCO,!2,!~dr,!,COOm,-4`1:\,COOm)
+MCat(1, 0.55)(<30,OmCO,!4,COOm,-4:\`1,COOm)
+MCat(1, 0.05)(<30,OmCO,!3,//O,!,COOm,-4:\`1,COOm)
+MCat(0.66,0.05)(<30,OmCO,!3,//O,!,COOm)
+MCat(0.33,0.05)(<30,OmCO,!3,//O,!,"{S-CoA}")
+MCat(0, 0.05)(<30,OmCO,!3,COOm)
+MCat(0, 0.55)(<30,OmCO,!,!~dr,!,COOm)
+MCat(0, 1)(<30,OmCO,!3,COOm,3:/OH)
%-------------------------------------------------------------------------
ext(
defaultfont:="uhvr8r";
@@ -381,7 +353,7 @@ def sel_dir(expr rot)=
if (nA<30)or(nA>330): def tx=top enddef; elseif (nA>=30)and(nA<=150): def tx=lft enddef;
elseif (nA>150)and(nA<210): def tx=bot enddef; elseif (nA>=210)and(nA<=330): def tx=rt enddef; fi
enddef;
-def r_arrow(expr a)(expr r)(expr p)(expr sa,la)(expr sb,lb)(expr sc,lc)(expr sd,ld)=
+def reaction_arrow(expr a)(expr r)(expr p)(expr sa,la)(expr sb,lb)(expr sc,lc)(expr sd,ld)=
drawarrow ((0,0)..(a,0)) rotated r shifted p;
if sa<>"": draw ((0.5a,0){dir 180}..{dir 90}(0,.5a*la)) rotated r shifted p;
sel_dir(r); label.tx(sa,p+((0,0.5a*la) rotated r)); fi
@@ -392,6 +364,9 @@ def r_arrow(expr a)(expr r)(expr p)(expr sa,la)(expr sb,lb)(expr sc,lc)(expr sd,
if sd<>"": draw ((0.5a,0){dir 0}..{dir -90}(a,-.5a*ld)) rotated r shifted p;
sel_dir(r+180); label.tx(sd,p+((a,-0.5a*ld) rotated r)); fi
enddef;
+def r_arrow(expr a)(expr r)(expr p)(expr sc,lc)(expr sd,ld)=
+ reaction_arrow(a)(r)(p)("",0)("",0)(sc,lc)(sd,ld)
+enddef;
%------------------------------------------------------------------------
save dx; pair dx; dx:=(12mm,0);
label.bot("Oxaloacetate",p1+dx); label.bot("Citrate",p2+dx);
@@ -401,35 +376,38 @@ label.bot("Succinyl-CoA",p7+dx); label.bot("Succinate",p8+dx);
label.bot("Fumarate",p9+dx); label.bot("L-Malate",p10+dx);
sw_label_emu:=1;
ext_setup;
-r_arrow(10mm)( 0)(p1+(1.1w1,.3h1))("",0)("",0)("Acetyl-CoA",1.5)(" CoA-SH",1);
-r_arrow(10mm)( 0)(p2+(1.1w2,.4h2))("",0)("",0)("",0)("H_2_O",1);
-r_arrow( 8mm)(270)(p3+(.5w3,-.4h3))("",0)("",0)("H_2_O",1)("",0);
-r_arrow( 8mm)(270)(p4+(.5w4,-.4h4))("",0)("",0)("NAD^+",1)("NADH2^+",1);
-r_arrow(10mm)(180)(p5+(-.1w5,.4h5))("",0)("",0)("",0)("CO_2_",1);
-r_arrow(10mm)(180)(p6+(-.1w6,.5h6))("",0)("",0)("NAD^+^,CoA-SH",1.7)("NADH2^+^,CO_2",1);
-r_arrow(10mm)(180)(p7+(-.1w7,.5h7))("",0)("",0)("GDP,Pi",1.7)("GTP,CoA-SH",1);
-r_arrow( 8mm)( 90)(p8+(.4w8,1.2h8))("",0)("",0)("FAD",1)("FADH2",1);
-r_arrow( 8mm)( 90)(p9+(.4w9,1.2h9))("",0)("",0)("H_2_O",1)("",0);
-r_arrow(10mm)( 0)(p10+(1.1w10,.3h10))("",0)("",0)("NAD^+",1)("NADH2^+",1.5);
+r_arrow(10mm)( 0)(p1+ ( 1.1w1, 0.3h1))("Acetyl-CoA",1.5)(" CoA-SH",1);
+r_arrow(10mm)( 0)(p2+ ( 1.1w2, 0.4h2))("",0)("H_2_O",1);
+r_arrow( 8mm)(270)(p3+ ( 0.5w3,-0.4h3))("H_2_O",1)("",0);
+r_arrow( 8mm)(270)(p4+ ( 0.5w4,-0.4h4))("NAD^+",1)("NADH2^+",1);
+r_arrow(10mm)(180)(p5+ (-0.1w5, 0.4h5))("",0)("CO_2_",1);
+r_arrow(10mm)(180)(p6+ (-0.1w6, 0.5h6))("NAD^+^,CoA-SH",1.7)("NADH2^+^,CO_2",1);
+r_arrow(10mm)(180)(p7+ (-0.1w7, 0.5h7))("GDP,Pi",1.7)("GTP,CoA-SH",1);
+r_arrow( 8mm)( 90)(p8+ ( 0.4w8, 1.2h8))("FAD",1)("FADH2",1);
+r_arrow( 8mm)( 90)(p9+ ( 0.4w9, 1.2h9))("H_2_O",1)("",0);
+r_arrow(10mm)( 0)(p10+( 1.1w10,0.3h10))("NAD^+",1)("NADH2^+",1.5);
defaultscale:=1.5;
label("TCA-cycle",(0.5w,0.5h));
)
endfont
\end{mplibcode}
+%------------------------------------------------------------------------
\begin{verbatim}
beginfont("EN:TCA cycle")
fsize:=(160mm,75mm);
max_blength:=5mm;
-MCat(0.33, 1)(<30,O[-1],!,//O,!,//O,!2,//O,!,O[-1])
-MCat(0.66, 1)(<30,O[-1],!,//O,!4,//O,!,O[-1],-4`1:\,//O,!,O[-1],4:/OH^-165)
-MCat(1, 1)(<30,O[-1],!,//O,!2,!~dr,!,//O,!,O[-1],-4`1:\,//O,!,O[-1])
-MCat(1, 0.55)(<30,O[-1],!,//O,!4,//O,!,O[-1],-4:\`1,//O,!,O[-1])
-MCat(1, 0.05)(<30,O[-1],!,//O,!3,//O,!,//O,!,O[-1],-4:\`1,//O,!,O[-1])
-MCat(0.66,0.05)(<30,O[-1],!,//O,!3,//O,!,//O,!,O[-1])
-MCat(0.33,0.05)(<30,O[-1],!,//O,!3,//O,!,"{S-CoA}")
-MCat(0, 0.05)(<30,O[-1],!,//O,!3,//O,!,O[-1])
-MCat(0, 0.55)(<30,O[-1],!,//O,!,!~dr,!,//O,!,O[-1])
-MCat(0, 1)(<30,O[-1],!,//O,!3,//O,!,O[-1],3:/OH)
+COOm:='(//O,!,O[-1]);
+OmCO:='(O[-1],!,//O);
+MCat(0.33, 1)(<30,OmCO,!,//O,!2,COOm)
+MCat(0.66, 1)(<30,OmCO,!4,COOm,-4`1:\,COOm,4:/OH^-165)
+MCat(1, 1)(<30,OmCO,!2,!~dr,!,COOm,-4`1:\,COOm)
+MCat(1, 0.55)(<30,OmCO,!4,COOm,-4:\`1,COOm)
+MCat(1, 0.05)(<30,OmCO,!3,//O,!,COOm,-4:\`1,COOm)
+MCat(0.66,0.05)(<30,OmCO,!3,//O,!,COOm)
+MCat(0.33,0.05)(<30,OmCO,!3,//O,!,"{S-CoA}")
+MCat(0, 0.05)(<30,OmCO,!3,COOm)
+MCat(0, 0.55)(<30,OmCO,!,!~dr,!,COOm)
+MCat(0, 1)(<30,OmCO,!3,COOm,3:/OH)
ext(
defaultfont:="uhvr8r";
defaultscale:=0.75;
@@ -442,16 +420,16 @@ label.bot("Succinyl-CoA",p7+dx); label.bot("Succinate",p8+dx);
label.bot("Fumarate",p9+dx); label.bot("L-Malate",p10+dx);
sw_label_emu:=1;
ext_setup;
-r_arrow(10mm)( 0)(p1+(1.1w1,.3h1))("",0)("",0)("Acetyl-CoA",1.5)(" CoA-SH",1);
-r_arrow(10mm)( 0)(p2+(1.1w2,.4h2))("",0)("",0)("",0)("H_2_O",1);
-r_arrow( 8mm)(270)(p3+(.5w3,-.4h3))("",0)("",0)("H_2_O",1)("",0);
-r_arrow( 8mm)(270)(p4+(.5w4,-.4h4))("",0)("",0)("NAD^+",1)("NADH2^+",1);
-r_arrow(10mm)(180)(p5+(-.1w5,.4h5))("",0)("",0)("",0)("CO_2_",1);
-r_arrow(10mm)(180)(p6+(-.1w6,.5h6))("",0)("",0)("NAD^+^,CoA-SH",1.7)("NADH2^+^,CO_2",1);
-r_arrow(10mm)(180)(p7+(-.1w7,.5h7))("",0)("",0)("GDP,Pi",1.7)("GTP,CoA-SH",1);
-r_arrow( 8mm)( 90)(p8+(.4w8,1.2h8))("",0)("",0)("FAD",1)("FADH2",1);
-r_arrow( 8mm)( 90)(p9+(.4w9,1.2h9))("",0)("",0)("H_2_O",1)("",0);
-r_arrow(10mm)( 0)(p10+(1.1w10,.3h10))("",0)("",0)("NAD^+",1)("NADH2^+",1.5);
+r_arrow(10mm)( 0)(p1+ ( 1.1w1, 0.3h1))("Acetyl-CoA",1.5)(" CoA-SH",1);
+r_arrow(10mm)( 0)(p2+ ( 1.1w2, 0.4h2))("",0)("H_2_O",1);
+r_arrow( 8mm)(270)(p3+ ( 0.5w3,-0.4h3))("H_2_O",1)("",0);
+r_arrow( 8mm)(270)(p4+ ( 0.5w4,-0.4h4))("NAD^+",1)("NADH2^+",1);
+r_arrow(10mm)(180)(p5+ (-0.1w5, 0.4h5))("",0)("CO_2_",1);
+r_arrow(10mm)(180)(p6+ (-0.1w6, 0.5h6))("NAD^+^,CoA-SH",1.7)("NADH2^+^,CO_2",1);
+r_arrow(10mm)(180)(p7+ (-0.1w7, 0.5h7))("GDP,Pi",1.7)("GTP,CoA-SH",1);
+r_arrow( 8mm)( 90)(p8+ ( 0.4w8, 1.2h8))("FAD",1)("FADH2",1);
+r_arrow( 8mm)( 90)(p9+ ( 0.4w9, 1.2h9))("H_2_O",1)("",0);
+r_arrow(10mm)( 0)(p10+( 1.1w10,0.3h10))("NAD^+",1)("NADH2^+",1.5);
defaultscale:=1.5;
label("TCA-cycle",(0.5w,0.5h));
)