diff options
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG | 7 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/README | 38 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf | 4 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf | bin | 289548 -> 289530 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps | 186 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf | 287 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf | bin | 565886 -> 569071 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 363 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf | bin | 139843 -> 153581 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex | 536 | ||||
| -rw-r--r-- | Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf | 31 |
11 files changed, 659 insertions, 793 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG index bd4cf1eda84..0bc2c7e8dd6 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG +++ b/Master/texmf-dist/doc/metapost/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/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README index bd6f08d8320..1ade6632aab 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/README +++ b/Master/texmf-dist/doc/metapost/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/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf index f8e99dbbb45..9c4a0238398 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf +++ b/Master/texmf-dist/doc/metapost/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/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf Binary files differindex dc9a638cc87..3dc4e44d112 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps deleted file mode 100644 index 0820fc253f6..00000000000 --- a/Master/texmf-dist/doc/metapost/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 -61.53287 13.38094 lineto -60.78113 13.38094 lineto - closepath fill -newpath 55.20229 13.38094 moveto -54.14986 13.38094 lineto -60.48044 5.99792 lineto -61.53287 5.99792 lineto - closepath fill 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-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 -212.69804 56.5928 lineto -212.49803 56.5928 lineto -212.49803 -0.1 lineto -212.49803 0.1 lineto - closepath fill -showpage -%%EOF diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf index b13b6cc12ba..dfc1cdc1a77 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf +++ b/Master/texmf-dist/doc/metapost/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/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf Binary files differindex 79c8aec1e14..04e3d8108ee 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index aaf20177991..4c15bbafc19 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 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/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf Binary files differindex 0e12c41a352..00a5684ce29 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex index b20161f9bc6..8de170b935d 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex +++ b/Master/texmf-dist/doc/metapost/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)); ) diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf index f0dedd16483..5a4802cb487 100644 --- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf +++ b/Master/texmf-dist/metapost/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; |