From 5fcfa99e5deaf9c601ba9e338f07fbefdd5d4487 Mon Sep 17 00:00:00 2001 From: Norbert Preining Date: Mon, 7 Nov 2022 03:04:25 +0000 Subject: CTAN sync 202211070304 --- graphics/mcf2graph/CHANGELOG | 12 +++++++- graphics/mcf2graph/README | 2 +- graphics/mcf2graph/mcf2graph.mp | 56 ++++++++++++++--------------------- graphics/mcf2graph/mcf_exa_code.pdf | Bin 78850 -> 78850 bytes graphics/mcf2graph/mcf_exa_code.tex | 4 +-- graphics/mcf2graph/mcf_exa_soc.mp | 10 +++---- graphics/mcf2graph/mcf_example.pdf | Bin 449243 -> 449558 bytes graphics/mcf2graph/mcf_example.tex | 4 +-- graphics/mcf2graph/mcf_library.mcf | 29 +++++++++--------- graphics/mcf2graph/mcf_man_soc.mp | 18 +++++------ graphics/mcf2graph/mcf_manual.pdf | Bin 289188 -> 289236 bytes graphics/mcf2graph/mcf_manual.tex | 40 +++++++++++-------------- graphics/mcf2graph/mcf_mplib_exa.pdf | Bin 195490 -> 195837 bytes graphics/mcf2graph/mcf_mplib_exa.tex | 4 +-- 14 files changed, 87 insertions(+), 92 deletions(-) (limited to 'graphics/mcf2graph') diff --git a/graphics/mcf2graph/CHANGELOG b/graphics/mcf2graph/CHANGELOG index a5160a5a14..d8a9090da3 100644 --- a/graphics/mcf2graph/CHANGELOG +++ b/graphics/mcf2graph/CHANGELOG @@ -1,6 +1,16 @@ ******************************************************************************* - Changelog of mcf2graph software package by Akira Yamaji 2022-10-10 + Changelog of mcf2graph software package by Akira Yamaji 2022-11-06 ******************************************************************************* +[ver. 4.89 / 2022-11-06] + -change syntax of fused ring + (a,b)=?n => {a--b}=?n + {(a,b), ..}=?n => {a--b, ..}=?n + {(a',b), ..}=?n => {a---b, ..}=?n + {(a',b'), ..}=?n => {a----b, ..}=?n + -fix bug in MOL(V3000) file output + -update MCF manual,example + -update mcf_library.mcf + [ver. 4.88 / 2022-10-10] -change format of mcf_library.mcf -update MCF manual,example diff --git a/graphics/mcf2graph/README b/graphics/mcf2graph/README index bbeb4dcb83..76578d6375 100644 --- a/graphics/mcf2graph/README +++ b/graphics/mcf2graph/README @@ -1,7 +1,7 @@ ******************************************************************************** mcf2graph : Convert Molecular Coding Format to graphics with MetaPost Author : Akira Yamaji - version : 4.88 2022-10-10 + version : 4.89 2022-11-06 E-mail : mcf2graph@gmail.com Located at : http://www.ctan.org/pkg/mcf2graph ******************************************************************************** diff --git a/graphics/mcf2graph/mcf2graph.mp b/graphics/mcf2graph/mcf2graph.mp index 729be297d0..1961a2ee89 100644 --- a/graphics/mcf2graph/mcf2graph.mp +++ b/graphics/mcf2graph/mcf2graph.mp @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% mcf2graph ver 4.88 Copyright (c) 2013-2022 Akira Yamaji +% mcf2graph ver 4.89 Copyright (c) 2013-2022 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, @@ -33,7 +33,7 @@ % Set output MOL file (V3000) : mpost -s ahlength=6 FILENAME % Set output report : mpost -s ahlength=7 FILENAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -message "* This is mcf2graph ver 4.88 2022.10.10"; +message "* This is mcf2graph ver 4.89 2022.11.06"; tracingstats:=1; prologues:=3; warningcheck:=0; %------------------------------------------------------------------------------------------------- newinternal string EN_; @@ -338,6 +338,9 @@ vardef read_ud(text t)= parts_num:=parts_num+1; read_mcf(parts_num)(dum,dum,|,t,(_com,_rest)); parts_num enddef; vardef abs_adress primary n = if n LT 0:: (n+360)-4095 else:: n-4095 fi enddef; primarydef a from_until b = (_from,a),(_until,b) enddef; +tertiarydef a bond__bond b = (a,b) enddef; +tertiarydef a bond___bond b = (a+0.5,b) enddef; +tertiarydef a bond____bond b = (a+0.5,b+0.5) enddef; tertiarydef a op_equ b = if (known a)and(known b):: change_bond(a,b) else:: _nop fi enddef; tertiarydef a op_col b = if (known a)and(known b):: change_atom(a,b) else:: _nop fi enddef; tertiarydef a op_hat b = if known b:: (_tmp_rot,b),a else:: _nop,a fi enddef; @@ -393,8 +396,9 @@ def read_mcf(expr n)(text t)= enddef; %------------------------------------------------------------------------------------------------- vardef read_number(text t)= - save :,','`; - let : == from_until; def ' == +0.5 enddef; def '` == +0.5` enddef; parts_int:=parts_int+1; + save --,---,----,:,','`; + let : == from_until; let -- == bond__bond; let --- == bond___bond; let ---- == bond____bond; + def ' == +0.5 enddef; def '` == +0.5` enddef; parts_int:=parts_int+1; nA:=0; for list==t:: if known list:: @@ -470,22 +474,15 @@ vardef change_bond(expr a,b) = if b==?6:: if (frac parts_com[a][i]==0)and(frac parts_par[a][i]==0):: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),6,4) - ef frac parts_com[a][i]==0:: - fuse_ring_bonds((parts_com[a][i],floor parts_par[a][i]),6,3) ef frac parts_par[a][i]==0:: fuse_ring_bonds((floor parts_com[a][i],parts_par[a][i]),6,3) else:: fuse_ring_bonds((floor parts_com[a][i],floor parts_par[a][i]),6,2) fi ef b==?5:: if (frac parts_com[a][i]==0)and(frac parts_par[a][i]==0):: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),5,3) - ef frac parts_com[a][i]==0:: - fuse_ring_bonds((parts_com[a][i],floor parts_par[a][i]),5,2) ef frac parts_par[a][i]==0:: fuse_ring_bonds((floor parts_com[a][i],floor parts_par[a][i]),5,2) fi ef b==?4:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),4,2) - ef b==?6[3]:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),6,3) - ef b==?6[2]:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),6,2) - ef b==?5[2]:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),5,2) ef b==Ph1:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),6,4) CA(_set_line,dl,-1) CA(_set_line,dl,-3) ef b==Ph2:: fuse_ring_bonds((parts_com[a][i],parts_par[a][i]),6,4) @@ -498,15 +495,8 @@ vardef change_bond(expr a,b) = ef (b>=?7[11])and(b<=?7[15]):: fuse_ring_size(a,7,b-?7[11]+11) ef (b>=?8[11])and(b<=?8[15]):: fuse_ring_size(a,8,b-?8[11]+11) else:: fuse_ring(a,b-?3+3) fi fi - ef pair a:: - if b==?6:: fuse_ring_bonds(a,6,4) - ef b==?5:: fuse_ring_bonds(a,5,3) - ef b==?4:: fuse_ring_bonds(a,4,2) - ef b==?6[3]:: fuse_ring_bonds(a,6,3) - ef b==?6[2]:: fuse_ring_bonds(a,6,2) - ef b==?5[2]:: fuse_ring_bonds(a,5,2) - ef b==Ph1:: fuse_ring_bonds(a,6,4) CA(_set_line,dl,-1) CA(_set_line,dl,-3) - ef b==Ph2:: fuse_ring_bonds(a,6,4) CA(_set_line,dl,-2) CA(_set_line,dl,-4) fi fi fi + fi + fi elseif color b:: color_list[incr cntC]:=b; CA(_set_colorB,cntC,a) fi parts_cnt[parts_int]:=nC; parts_int fi enddef; @@ -515,7 +505,7 @@ vardef change_atom(expr a,b)= if known b:: parts_int:=parts_int+1; nC:=0; if numeric b:: if (b GT parts_emb_start)and(b<=parts_atom_end):: CA(_chg_atom,b,a) - ef b==NH:: CA(_chg_atom,N,a) if NH<>xNH:: CP(_tmp_line,nl) fi + ef b==NH:: CA(_chg_atom,N,a) CP(_tmp_line,nl) CP(_com,_group_s) CA(_group_si,H,a) CP(_com,_group_e) ef b==N!:: CA(_chg_atom,N,a) CP(_com,_group_s) CA(_group_si,_,a) CP(_com,_group_e) ef b==N!2:: CA(_chg_atom,N,a) CP(_com,_group_s) CA(_group_si,!,a) CP(_com,_group_e) @@ -1322,7 +1312,7 @@ def proc_mol_out(expr n)= %-V3000--------------------------------------------------------------------------------------- elseif n=2: printf ""; printf " -MCFtoMOL- "&fsl(20)(info_s[1]); printf ""; - printf " 0 0 0 0 0 999 V3000"; + printf " 0 0 0 0 0 0 0 0 0 0 0 V3000"; printf "M V30 BEGIN CTAB"; printf "M V30 COUNTS "&decimal(cntA)&" "&decimal(cntB)&" 0 0 0"; printf "M V30 BEGIN ATOM"; @@ -1416,7 +1406,6 @@ tbl_group_end:=tbl_cnt; parts_atom_end:=parts_num; for i=3 upto 20: ?[i]:='((_com,_len_ss),(_get_len,_ring_len),<((-180 DIV i)-90) for j==2 upto i:: ,(360 DIV i) endfor,(_cyc_sB,1-i),(_com,_len_ee)); endfor Ph:=Ph1:='(?6,-2=dl,-4=dl,-6=dl); Ph2:='(?6,-1=dl,-3=dl,-5=dl); -for i=4,5,6: for j=2 upto i-2: ?[i][j]:='(); endfor endfor for i=5,6,7,8: for j=11 upto 15: ?[i][j]:='(); endfor endfor %------------------------------------------------------------------------------------------------- !:=!1:='((_mk_bond,_arrange_ang)); !!:='(!~db); !!!:='(!~tm); @@ -1455,9 +1444,10 @@ R6:='("R6"); R7:='("{R^7^}"); R8:='("{R^8^}"); R9:='("{R^9^}"); R10:='("R^10^"); hexose_hp:='(#1.4,-30~wf_r,30~bd_r`1,30~wb_r,120,O,30,&1,##); Pyranose_hp:='(#1.4,-35~wf_r,35~bd_r`1,30~wb_r,130`1.66,O,&1,##); %------------------------------------------------------------------------------------------------- -xCH3:='(/H,/H^60,/H^-60); xNH:='(N,/H); xNH2:='(N,/H^60,/H^-60); xNO2:='(N,//O^60,//O^-60); -xOH:='(O,/H); xNO:='(N,//O); xSO2H:='(S,//O^60,/OH^-60); xSO3H:='(S,/OH,//O^60,//O^-60); -xCHO:='(//O^-60,/H^60); xCOOH:='(//O^-60,/xOH^60); xCN:='(/N~tm); xSH:='(S,/H); +xCH3:='(/H,/H^60,/H^-60); xNH:='(N,/H~nl); xNH2:='(N,/H~nl^60,/H~nl^-60); +xNO2:='(N,//O^60,//O^-60); xOH:='(O,/H~nl); xNO:='(N,//O); +xSO2H:='(S,//O^60,/OH^-60); xSO3H:='(S,/OH,//O^60,//O^-60); +xCHO:='(//O^-60,/H^60); xCOOH:='(//O^-60,/xOH^60); xCN:='(/N~tm); xSH:='(S,/H~nl); !xOH:='(!,xOH); !xCHO:='(!,xCHO); !xCOOH:='(!,xCOOH); !xCH3:='(!,xCH3); !xCN:='(!,xCN); !xNH2:='(!,xNH2); !xNO2:='(!,xNO2); !xSH:='(!,xSH); %================================================================================================= @@ -1555,10 +1545,10 @@ def proc_err(expr e,n)= err_adr[incr err_cnt]:=n; err_code[err_cnt]:=e; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def mc_query(text s)= begingroup - save f_mcf,f_line,unit_row,unit_cnt,line_s,row_cnt,semic_cnt,info_cnt,order,min_n,max_n, + save f_mcf,f_line,unit_row,unit_cnt,line_s,row_cnt,semic_cnt,info_cnt,order,min_n,max_n,firstc, sign_at,sign_n,filter_n,filter_tag,filter_var,filter_sign,filter_cnt,filter_p,lib_unit_cnt, at_colon,at_equal,at_less,at_greater,at_n,sort_tbl,key_s,sort_s,sign_s,sV,sS,sT,sort_oder; - string line_s[][],sort_s,sort_tbl[],key_s,filter_tag[],filter_var[],sign_s[],sV,sS,sT; + string line_s[][],sort_s,sort_tbl[],key_s,filter_tag[],filter_var[],sign_s[],sV,sS,sT,firstc; numeric row_cnt[],order[],order_tbl[],filter_sign[],filter_p[]; unit_row:=f_mcf:=mc_row:=info_cnt:=filter_cnt:=lib_unit_cnt:=0; unit_cnt:=1; file_input:=default_library; file_output:=default_temp_file; @@ -1592,10 +1582,10 @@ def mc_query(text s)= endfor %----------------------------------------------------------------------------------------------- forever: - temps:=readfrom file_input; exitif temps=EOF; - if subc(1,temps)<>"%": + temps:=readfrom file_input; exitif temps=EOF; firstc:=subc(1,temps); + if firstc<>"%": line_s[unit_cnt][incr unit_row]:=temps; - if subc(1,temps)=";": + if firstc=";": row_cnt[unit_cnt]:=unit_row; f_mcf:=unit_row:=0; filter_n:=1; for i=1 upto filter_cnt: filter_p[i]:=0; endfor sort_s:=""; @@ -1616,8 +1606,8 @@ def mc_query(text s)= for i=1 upto filter_cnt: if filter_p[i]=0: filter_n:=0; fi endfor info_cnt:=0; lib_unit_cnt:=lib_unit_cnt+1; if filter_n=1: if key_s<>"": sort_tbl[unit_cnt]:=sort_s; fi unit_cnt:=unit_cnt+1; fi - ef (subc(1,temps)=":")or(subc(1,temps)="="): f_mcf:=1; mc_row:=1; - ef subc(1,temps)<>"%": + ef (firstc=":")or(firstc="="): f_mcf:=1; mc_row:=1; + ef firstc<>"%": if f_mcf=1: mc_row:=mc_row+1; else: info_cnt:=split_str(temps,";")(arg_s); fi fi fi endfor diff --git a/graphics/mcf2graph/mcf_exa_code.pdf b/graphics/mcf2graph/mcf_exa_code.pdf index b0efde435d..4e0f118ce4 100644 Binary files a/graphics/mcf2graph/mcf_exa_code.pdf and b/graphics/mcf2graph/mcf_exa_code.pdf differ diff --git a/graphics/mcf2graph/mcf_exa_code.tex b/graphics/mcf2graph/mcf_exa_code.tex index 7500dcfdf3..a27bb71714 100644 --- a/graphics/mcf2graph/mcf_exa_code.tex +++ b/graphics/mcf2graph/mcf_exa_code.tex @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Print out mcf data list by A.Yamaji 2022.10.10 +% Print out mcf data list by A.Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% ** mcf2graph.mf must be version 4.88 +% ** mcf2graph.mf must be version 4.89 % ** use mcf_library.mcf % ** typeset by LuaLaTeX(luamplib) \documentclass{article} diff --git a/graphics/mcf2graph/mcf_exa_soc.mp b/graphics/mcf2graph/mcf_exa_soc.mp index 4757efc670..d3d54052db 100644 --- a/graphics/mcf2graph/mcf_exa_soc.mp +++ b/graphics/mcf2graph/mcf_exa_soc.mp @@ -1,8 +1,8 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format by Akira Yamaji 2022.10.10 +% Molecular Coding Format by Akira Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph; %%% it must be version 4.88 -message "* mcf_exa_soc 2022.10.10"; +input mcf2graph; %%% it must be version 4.89 +message "* mcf_exa_soc 2022.11.06"; message ""; %------------------------------------------------------------------------------ %%%%sw_frame:=Outside; @@ -21,8 +21,8 @@ tag1:="J"; tag2:="C"; tag3:="fm"; tag4:="mw"; tag5:="EN"; tag6:="MW"; %ext(defaultfont:=mpfont; defaultscale:=.3; %label.rt(inf_EN&" / "&cal_MW&" / "&decimal(num_MW-scantokens(inf_MW)),(0,0));) %------------------------------------------------------------------------------ -%%%%mc_query("Cat=biological","MW<200","s:MW"); -%%%%mc_query("Cat=biological","MW<110.0","s:EN"); +%%%%mc_query("Cat=biological","MW<200","a:MW"); +%%%%mc_query("Cat=biological","MW<50.0","a:EN"); %%%%mc_query("Cat=biological","MW>=150","MW<=200","a:EN"); %%%%mc_query("Cat=biological","MW>=100","MW<=250","a:MW"); %****************************************************************************** diff --git a/graphics/mcf2graph/mcf_example.pdf b/graphics/mcf2graph/mcf_example.pdf index fd1caad561..8fbbc5affe 100644 Binary files a/graphics/mcf2graph/mcf_example.pdf and b/graphics/mcf2graph/mcf_example.pdf differ diff --git a/graphics/mcf2graph/mcf_example.tex b/graphics/mcf2graph/mcf_example.tex index 8d5ea965f0..8ae368ba5f 100644 --- a/graphics/mcf2graph/mcf_example.tex +++ b/graphics/mcf2graph/mcf_example.tex @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Example of MCF Typeset with LuaLaTeX(luamplib) by A.Yamaji 2022.10.10 +% Example of MCF Typeset with LuaLaTeX(luamplib) by A.Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% ** mcf2graph.mf must be version 4.88 +% ** mcf2graph.mf must be version 4.89 % ** use mcf_library.mcf % ** typeset by LuaLaTeX(luamplib) \documentclass{article} diff --git a/graphics/mcf2graph/mcf_library.mcf b/graphics/mcf2graph/mcf_library.mcf index 61909067d0..3235ad1292 100644 --- a/graphics/mcf2graph/mcf_library.mcf +++ b/graphics/mcf2graph/mcf_library.mcf @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% molecular library file mcf_library.mcf by Akira Yamaji 2022.10.10 +% molecular library file mcf_library.mcf by Akira Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % tag1:var1;tag2:var2;tag3:var3 ..... % first character of line "%" comment out @@ -620,7 +620,7 @@ Cat:biological;EN:Febrifugine;MW:301.34;EXA:1 %------------------------------------------------------------------------------ Cat:biological;EN:Hypericin;MW:504.44;EXA:1 : -<30,Ph,{-4,-3,(11,4),(16',17),19,(23',24),(22,29)}=?6, +<30,Ph,{-4,-3,11--4,16---17,19,23---24,22--29}=?6, {12,14,16,17,22',24,26,28,33,35}=dl, {7,25}://O,{13,26}:/_, {2,6,11,21,23,28}:/OH ; @@ -706,7 +706,7 @@ Cat:biological;EN:Sesamine;MW:354.35;EXA:1 %------------------------------------------------------------------------------ Cat:biological;EN:Morphine;MW:285.343;EXA:1 : -<30,Ph,{2,-4}=?6,(1,12)=?5[2],-1:O,-1=zb, +<30,Ph,{2,-4}=?6,{1---12}=?5,-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 ; %------------------------------------------------------------------------------ @@ -728,7 +728,7 @@ Cat:biological;EN:Colchicine;MW:399.443;EXA:1 %------------------------------------------------------------------------------ Cat:biological;EN:Lycorine;MW:287.315;EXA:1 : -<30,Ph,{-4,-2}=?6,{6,(9,12)}=?5,13=dl,8:N,{15,17}:O, +<30,Ph,{-4,-2}=?6,{6,9--12}=?5,13=dl,8:N,{15,17}:O, {9'^180,10^60}:*/H,{13,14'}:*/OH ; %------------------------------------------------------------------------------ @@ -881,18 +881,17 @@ Cat:synthetic;EN:Chrysene;MW:228.3;EXA:- %------------------------------------------------------------------------------ Cat:synthetic;EN:Pyrene;MW:202.25;EXA:- : -<30,Ph2,{6,4}=Ph,(16,7)=?6[3],-2=dl +<30,Ph2,{6,4}=Ph,{16---7}=?6,-2=dl ; %------------------------------------------------------------------------------ Cat:synthetic;EN:Coronene;MW:300.35;EXA:1 : -<30,Ph,{1,(11,2),(15,3),(19,4),(23,5),(27',7)}=?6, - {9,12,14,17,20,22,25,28,30}=dl +<30,Ph,{1,11--2,15--3,19--4,23--5,27---7}=?6,{9,12,14,17,20,22,25,28,30}=dl ; %------------------------------------------------------------------------------ Cat:synthetic;EN:Kekulene;MW:600.7;EXA:1 : -<30,?6,{3,-3,-2,-3,-2,-3,-2,-3,-2,-3,(-2',5'),(5',-4')}=?6, +<30,?6,{3,-3,-2,-3,-2,-3,-2,-3,-2,-3,-2----5,5---- -4}=?6, {1,5',7,9,11,13,17,19,21,23,27,29,31,33,37,39,41,43,47,49,51,53,57,60}=dl ; %============================================================================== @@ -1181,7 +1180,7 @@ Cat:antibiotics;EN:Emamectine;MW:886.133;EXA:1 : <24,?6,6=?5,3=dl,9:O,2:*/OH,3:/_,6:/*OH^-60, @5,#1.04,6,//O,-60,O,60~wb,60,-60,60~wf,60,-60,60,60,60,-60,60,##,&7, - {-1,-3,-7}=dl,(-11,-10)=?6,@-2,?6,-6=wf,-1=zb,-5=dl, + {-1,-3,-7}=dl,{-11-- -10}=?6,@-2,?6,-6=wf,-1=zb,-5=dl, {-1,-6}:O,-3:*/_,@-2,\,*/_,!2, 17:/_,19:/*_,@18,\,O,!,?6`.7,-1:O,#.5,-2:*/_,-4:*/O!,##, @-3,\,O,60,?6`.7,-5:O,#.5,-4:*/_,-3:/*NH!,-2:*/O! @@ -1199,7 +1198,7 @@ Cat:antibiotics;EN:Spinosad;MW:731.968;EXA:2 Cat:antibiotics;EN:Natamycin;MW:665.733;EXA:1 : <-90,#1,60,60,-60,60,-60,60,-60,60,-60,60,60,60,O,-60, - 60,60,-60,60,-60,60,-60,60,60,-60,&1,##,(12,13)=?6, + 60,60,-60,60,-60,60,-60,60,60,-60,&1,##,{12--13}=?6, {2,4,6,8,20}=dl,11=zb,23:O,-2:/*OH,-3:*/COOH, 18=?3,-1=wb,-2=wf,-1:O,22://O,24:*/_,{14^60,16}:*/OH, @10,*\^15,O,90,?6`.7,-1:O,#.5,{-3,-5'}:*/OH,-4:/*NH2,-2:/*_ @@ -1881,7 +1880,7 @@ Cat:pesticide;EN:Pyrimethanil;MW:199.257;EXA:- %------------------------------------------------------------------------------ Cat:pesticide;EN:Pyroquilon;MW:173.2;EXA:- : -<30,Ph,3=?6,10:N,9://O,(11,4)=?5 +<30,Ph,3=?6,10:N,9://O,{11_4}=?5 ; %------------------------------------------------------------------------------ Cat:pesticide;EN:Vinclozolin;MW:286.108;EXA:- @@ -2307,10 +2306,12 @@ Cat:pesticide;EN:Indoxacarb;MW:527.837;EXA:- <-6,Ph,3=?5,9=?6,15=dl,10:O,{12,13}:N,1:/Cl,8`1^-54:/COO!, @12,\,//O,!,N,/COO!,!,Ph,@-3,\,O,!,CF3 ; +%------------------------------------------------------------------------------ Cat:pesticide;EN:Oxamyl;MW:219.3;EXA:- : <-30,!,N,?!,//O,!,/S!,!!,N,!,O,!,//O,!,NH,! ; +%------------------------------------------------------------------------------ Cat:pesticide;EN:Oryzalin;MW:346.4;EXA:- : <30,Ph,{1,3}:/NO2,@5,\,SOO,!,NH2,@2,\,/!2,N,!3 @@ -2635,7 +2636,7 @@ Cat:antibacterial;EN:Sulfapyrizine;MW:249.288;EXA:- %------------------------------------------------------------------------------ Cat:antibacterial;EN:Marbofloxacin;MW:362.361;EXA:- : -<30,Ph,{3,(2,7)}=?6,9=dl,6:/F,{7,13}:N,11:O,9:/COOH,10://O,13:/_, +<30,Ph,{3,2--7}=?6,9=dl,6:/F,{7,13}:N,11:O,9:/COOH,10://O,13:/_, @1,\,|,?6,{1,4}:N,4:/_ ; %------------------------------------------------------------------------------ @@ -2651,7 +2652,7 @@ Cat:antibacterial;EN:Trimethoprim;MW:290.323;EXA:- %------------------------------------------------------------------------------ Cat:antibacterial;EN:Ofloxacin;MW:361.373;EXA:- : -<30,Ph,{3,(2,7)}=?6,9=dl,7:N,11:O, +<30,Ph,{3,2--7}=?6,9=dl,7:N,11:O, 6:/F,9:/COOH,10://O,13:/_,@1,\,|,?6,{1,4}:N,4:/_ ; %------------------------------------------------------------------------------ @@ -2770,7 +2771,7 @@ Cat:antibacterial;EN:Flubendazole;MW:313.288;EXA:- %------------------------------------------------------------------------------ Cat:antibacterial;EN:Flumequine;MW:261.225;EXA:- : -<30,Ph,{3,(2,7)}=?6,9=dl,7:N,6:/F,9:/COOH,10://O,13:/_ +<30,Ph,{3,2--7}=?6,9=dl,7:N,6:/F,9:/COOH,10://O,13:/_ ; %------------------------------------------------------------------------------ 34;Cat:antibacterial;EN:Sulfanitran;MW:335.334;EXA:- diff --git a/graphics/mcf2graph/mcf_man_soc.mp b/graphics/mcf2graph/mcf_man_soc.mp index 2443a83c70..a2cc417f86 100644 --- a/graphics/mcf2graph/mcf_man_soc.mp +++ b/graphics/mcf2graph/mcf_man_soc.mp @@ -1,9 +1,9 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% MCF file for mcf_manual.tex by Akira.Yamaji 2022.10.10 +% MCF file for mcf_manual.tex by Akira.Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph; %% it must be version 4.88 +input mcf2graph; %% it must be version 4.89 % ** use library file 'mcf_library.mcf' -message "mcf_man_soc 2022.10.10"; message ""; +message "mcf_man_soc 2022.11.06"; message ""; %------------------------------------------------------------------------ sw_mframe:=0; sw_expand:=0; @@ -447,13 +447,13 @@ beginfigm("EN:fused ring 2") fmargin:=(2mm,2mm); sw_numbering:=Bond; msize:=(1,.9); - MCat( 0,.5)(<30,?6,{3,(11,4)}=?6,{11,4}=dt,{12:15}=bd_r) + MCat( 0,.5)(<30,?6,{3,11--4}=?6,{11,4}=dt,{12:15}=bd_r) add(defaultscale:=0.4; label("(1)",p0);) msize:=(1,.9); - MCat(.5,.5)(<30,?6,3=?6,(11,4)=?5,{11,4}=dt,{12:14}=bd_r) + MCat(.5,.5)(<30,?6,3=?6,{11--4}=?5,{11,4}=dt,{12:14}=bd_r) add(defaultscale:=0.4; label("(2)",p0);) msize:=(1,.9); - MCat( 1,.5)(<30,?6,3=?6,(11,4)=?4,{11,4}=dt,{12,13}=bd_r) + MCat( 1,.5)(<30,?6,3=?6,{11--4}=?4,{11,4}=dt,{12,13}=bd_r) add(defaultscale:=0.4; label("(3)",p0);) endfigm %*********************************************************************** @@ -461,9 +461,9 @@ beginfigm("EN:fused ring 3") fsize:=(60mm,20mm); fmargin:=(2mm,2mm); sw_numbering:=Bond; - MCat(0,1)(?6,{3,10}=?6,(16,4)=?6[3],{16,4}=dt,{17:19}=bd_r) + MCat(0,1)(?6,{3,10}=?6,{16---4}=?6,{16,4}=dt,{17:19}=bd_r) add(defaultscale:=0.4; label("(1)",p0);) - MCat(1,0)(?6,{3,10}=?6,(16,4)=?5[2],{16,4}=dt,{17,18}=bd_r) + MCat(1,0)(?6,{3,10}=?6,{16---4}=?5,{16,4}=dt,{17,18}=bd_r) add(defaultscale:=0.4; label("(2)",p0);) endfigm %*********************************************************************** @@ -471,7 +471,7 @@ beginfigm("EN:fused ring 4") fsize:=(60mm,20mm); fmargin:=(2mm,2mm); sw_numbering:=Bond; - MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2],{21,4}=dt,{22,23}=bd_r) + MC(<-30,?6,{3,10,15}=?6,{21----4}=?6,{21,4}=dt,{22,23}=bd_r) endfigm %*********************************************************************** beginfigm("EN:Spiro ring ") diff --git a/graphics/mcf2graph/mcf_manual.pdf b/graphics/mcf2graph/mcf_manual.pdf index 24bd35cb07..c407c4fd54 100644 Binary files a/graphics/mcf2graph/mcf_manual.pdf and b/graphics/mcf2graph/mcf_manual.pdf differ diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index a756a684e1..6588d356a0 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2022.10.10 +% Molecular Coding Format manual by Akira Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%\usepackage{graphicx} @@ -429,16 +429,17 @@ attached bond length \MCFgraph %----------------------------------------------------------------------------- %%%\subsubsection{Attached 2 bond} +\index{--}% \begin{verbatim} (Attached 2 bond) -(4,11)=?6 : fuse 4/6 ring to B11..B4 -(4,11)=?5 : fuse 3/5 ring to B11..B4 -(4,11)=?4 : fuse 2/4 ring to B11..B4 +{4--11}=?6 : fuse 4/6 ring to B11..B4 +{4--11}=?5 : fuse 3/5 ring to B11..B4 +{4--11}=?4 : fuse 2/4 ring to B11..B4 -1:<30,?6,3=?6,(11,4)=?6 -2:<30,?6,3=?6,(11,4)=?5 -3:<30,?6,3=?6,(11,4)=?4 +1:<30,?6,3=?6,{11--4}=?6 +2:<30,?6,3=?6,{11--4}=?5 +3:<30,?6,3=?6,{11--4}=?4 \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -446,17 +447,16 @@ attached bond length \end{verbatim} %----------------------------------------------------------------------------- %%%\subsubsection{Attached 3 bond} +\index{---}% \begin{verbatim} (Attached 3 bond) -(16,4)=?6[3] or {(16',4)}=?6 - : fuse 3/6 ring to B16..B4 -(16,4)=?5[2] or {(16',4)}=?5 - : fuse 2/5 ring to B16..B4 -** ?m[n] (5<=m<=6,n=m-3) +{16---4}=?6 : fuse 3/6 ring to B16..B4 +{16---4}=?5 : fuse 2/5 ring to B16..B4 + +1:?6,{3,10,16---4}=?6 +2:?6,{3,10}=?6,{16---4}=?5 -1:?6,{3,10,(16',4)}=?6 -2:?6,{3,10}=?6,(16,4)=?5[2] \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -464,15 +464,14 @@ attached bond length \end{verbatim} %----------------------------------------------------------------------------- %%%%\subsubsection{Attached 4 bond} +\index{----}% \begin{verbatim} (Attached 4 bond) -(21,4)=?6[2] or {(21',4')}=?6 - : fuse 2/6 ring to B21..B4 +{21----4}=?6 : fuse 2/6 ring to B21..B4 -<-30,?6,{3,10,15,(21',4')}=?6 +<-30,?6,{3,10,15,21----4}=?6 -** ?m[n] (m=6,n=2) \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -1651,29 +1650,24 @@ Cat:biological;EN:Atoropin;MW:289.375;EXA:1 : <30,O,!,//O,!2,Ph,@$1,\~zb^-60,|,?7`1.1,@6,*\^190`1.25,N!,&3~wb,$3:/!OH~wv ; -%------------------------------------------------------------------------------ Cat:biological;EN:Luteolin;MW:286.24;EXA:- : <30,Ph,3=?6,9=dl,10:O,7://O,@9,\,Ph,{2,6,14,15}:/OH ; -%------------------------------------------------------------------------------ Cat:biological;EN:Lycorine;MW:287.315;EXA:1 : <30,Ph,{-4,-2}=?6,{6,(9,12)}=?5,13=dl,8:N,{15,17}:O, {9'^180,10^60}:*/H,{13,14'}:*/OH ; -%------------------------------------------------------------------------------ Cat:biological;EN:Morphine;MW:285.343;EXA:1 : <30,Ph,{2,-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 ; -%------------------------------------------------------------------------------ Cat:biological;EN:Piperine;MW:285.343;EXA:1 : <30,Ph,-1=?5,{-1,-3}:O,@4,\,!!,!,!!,!,//O,!,?6,-6:N ; -%------------------------------------------------------------------------------ \end{verbatim} %------------------------------------------------------------------------------ \noindent% diff --git a/graphics/mcf2graph/mcf_mplib_exa.pdf b/graphics/mcf2graph/mcf_mplib_exa.pdf index 749c4ce4f6..f3677cd833 100644 Binary files a/graphics/mcf2graph/mcf_mplib_exa.pdf and b/graphics/mcf2graph/mcf_mplib_exa.pdf differ diff --git a/graphics/mcf2graph/mcf_mplib_exa.tex b/graphics/mcf2graph/mcf_mplib_exa.tex index 7106de782c..e7cc265369 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 2022.10.10 +% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2022.11.06 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% ** mcf2graph.mp must be version 4.88 +% ** mcf2graph.mp must be version 4.89 % ** use mcf_library.mcf \documentclass{article} %------------------------------------------------------------------------------ -- cgit v1.2.3