mcf2graph (21aug16)

git-svn-id: svn://tug.org/texlive/trunk@41900 c570f23f-e606-0410-a88d-b1316a301751

10 files changed, 66 insertions, 42 deletions

diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
index 611d4ab2851..0191b91b22c 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 2016-08-06
+ Changelog of mcf2graph software package        by Akira Yamaji 2016-08-21
 *******************************************************************************
+[ver. 3.97  / 2016-08-21]
+  -change bond type name 'ov' to 'si_'
+  -add bond type 'wf_','wb_','bd_'
+  -update MCF syntax manual
+
 [ver. 3.96  / 2016-08-06]
   -large scaled rings can fuse
    5,6,7,8 membered ring scaled 11/10,12/10,13/10,14/10,15/10
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README
index 9a1a8a58a9a..1711f2d0217 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/README
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/README
@@ -1,7 +1,7 @@
 ********************************************************************************
  mcf2graph  : Convert Molecular Coding Format to graphics with METAFONT/METAPOST
  Author     : Akira Yamaji
- version    : 3.96 2016-08-06
+ version    : 3.97 2016-08-21
  E-mail     : mcf2graph@gmail.com
  Located at : http://www.ctan.org/pkg/mcf2graph
 ********************************************************************************
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 e0833ba7e6e..fbe8c08ee82 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  2016.08.06
+% Molecular Coding Format for mcf_example.tex  by Akira Yamaji  2016.08.21
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf;
+input mcf2graph.mf;   %%% it must be version 3.97 or later
 %-------------------------------------------------------------------------
 font_wd#:=33mm#;
 font_ht#:=24mm#;
@@ -238,7 +238,7 @@ endfont
 %**************************************************************************
 beginfont("EN:Tetrodotoxine")
   MCf({,``1,<60,-90,60,-30`1.15,150,60,&#1,#3*,-135,60,-30`1.15,150,&#4,
-     #10\,O,60`1.33,60,&#3~ov,#8*,-15~ov,O,&#12,},#9*,45,-60,OH,1^120://NH,
+     #10\,O,60`1.33,60,&#3~si_,#8*,-15~si_,O,&#12,},#9*,45,-60,OH,1^120://NH,
      @(5~zf^-15,7,9^-75,12,13~zf)/OH,@(2,6^180)NH)
 endfont
 %***************************************************************************
@@ -370,7 +370,7 @@ endfont
 %**************************************************************************
 beginfont("EN:Morphine")
   MCf(<30,Ph,2=?6,-4=?6,(1,12)=?5[2],-1:O,-1=zb,
-    7*,60~wf`0.75,70~ov`1.3,45,N,/Me,&9~wb,
+    7*,60~wf`0.75,70~si_`1.3,45,N,/Me,&9~wb,
     15=dl,6:/OH,8^180:*/H,12:/*OH)
 endfont
 %**************************************************************************
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
index be83fbebaf0..9cdc045a25a 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.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
index 8dcf33c778e..07a530f60c8 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex  by Akira.Yamaji 2016.08.06
+% Molecular Coding Format file for mcf_manual.tex  by Akira.Yamaji 2016.08.21
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf;
+input mcf2graph.mf;   %% it must be version 3.97 or later
 %------------------------------------------------------------------------
 font_wd#:=60mm#;%                       font width
 font_ht#:=40mm#;%                       font height
@@ -55,14 +55,17 @@ beginfont("EN:Connect atom")
 endfont
 %***********************************************************************
 beginfont("EN:ring")
+  max_bond_width:=0.25;
   sw_numberB:=1;
   sw_start_vector:=1;
   MCf(?6)
 endfont
 %***********************************************************************
 beginfont("EN:rotate 1")
+  max_bond_width:=0.25;
+  sw_numberB:=1;
   sw_start_vector:=1;
-  MCf(<30,!4,<30,?6)
+  MCf(``1,0~vf,0~vf,<90,0~vf,<-90,0~vf)
 endfont
 %***********************************************************************
 beginfont("EN:change bond 1")
@@ -72,22 +75,23 @@ endfont
 %***********************************************************************
 beginfont("EN:change bond 2")
   ratio_chain_ring:=1;
-  MCf(<30,!~wf,!~wb,!~zf,!~zb)
+  MCf(<30,!~wf,!~wb,!~zf,!~zb,!~vf)
 endfont
 %***********************************************************************
 beginfont("EN:change bond 3")
   ratio_chain_ring:=1;
-  MCf(<30,!4,1=vf,2=vb,3=dt,4=wv)
+  MCf(<30,!5,1=vb,2=dt,3=wv,4=bd,5=bz)
 endfont
 %***********************************************************************
 beginfont("EN:change bond 4")
   ratio_chain_ring:=1;
-  MCf(<30,!3,!`2,!,@(3~bd`2^-30,5~ov^85`3,3~bz`3^-70)/Me)
+  MCf(<30,!7,$(2,4,6)dr)
 endfont
 %***********************************************************************
-beginfont("EN:change bond 4")
+beginfont("EN:over line")
   ratio_chain_ring:=1;
-  MCf(<30,!7,$(2,4,6)dr)
+  max_bond_width:=0.25;
+  MCf(<-30,!8`.4,!`.2,60`.6,90`3,@(2~si_,4~wf_,6~wb_,8~bd_)/Me`1)
 endfont
 %***********************************************************************
 beginfont("EN:change bond length1")
@@ -597,7 +601,7 @@ endfont
 %***************************************************************************
 beginfont("EN:Atoropin","CAS:51-55-8","FM:C17H23NO3","MW:289.37")
   MCf(<-30,O,!,//O,!,!,Ph,
-     #1\~zb^-120,|,?7`1.1,6*\^190`1.25,N,/Me,&3~wb,#3\~wv,!,OH)
+     #1\~zb^-120,|,?7,6*\^190`1.12,N,/Me,&3~wb,#3\~wv,!,OH)
 endfont
 %***************************************************************************
 beginfont("EN:Validamycin")
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
index 9eb75f91201..e6e758e1d5d 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 fbcf34b1d9e..7a2bf1d9fc7 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 2016.08.06
+%  Molecular Coding Format manual          by  Akira Yamaji 2016.08.21
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \documentclass[a4paper]{article}
 \usepackage{graphicx}
@@ -96,7 +96,7 @@ beginfont("NO:1","EN:Ampicillin")                 > begin font(information)
   MCf(<45,?4,2:N,2=?5,-1:S,                             > begin MCF (1)
      @(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18,            >
      @(6^35,6^-35)/Me,                                  >
-     4\^75,NH,!,//O,!,/*NH,!,Ph)                          > end MCF 
+     4\^75,NH,!,//O,!,/*NH,!,Ph)                        > end MCF 
 endfont                                                 > end font
 %------------------------------------------------------------------------
 beginfont("NO:2","EN:Cholesterol")                > begin font(information)
@@ -267,7 +267,8 @@ n* : Jump to An
 \begin{verbatim}
 <angle : rotate current angle
 
-  <30,!4,<30,?6
+ ``1,
+ 0~vf,0~vf,<90,0~vf,<-90,0~vf
 \end{verbatim}
 \end{minipage}
 \MCFstructure
@@ -289,57 +290,61 @@ tm : triple
 \vspace{\gpman}\\
 %-----------------------------------------------------------------------------
 \begin{minipage}[t][\htman]{90mm}
-\MCFtitle{Change bond type (1)}
+\MCFtitle{Change bond type (2)}
 \begin{verbatim}
 a~type : ~~type,a
 wf : wedge forward
 wb : wedge backward
 zf : wedge dotted
 zb : wedge dotted backward
+vf : vector forward
 
-  <30,!~wf,!~wb,!~zf,!~zb
+  <30,!~wf,!~wb,!~zf,!~zb,!~vf,!~vb
 \end{verbatim}
 \end{minipage}
 \MCFstructure
 \vspace{\gpman}\\
 %-----------------------------------------------------------------------------
 \begin{minipage}[t][\htman]{90mm}
-\MCFtitle{Change bond type (2)}
+\MCFtitle{Change bond type (3)}
 \begin{verbatim}
 Bn=bond type : change bond type at Bn
-vf : vector forward
 vb : vector backward
 dt : dotted
 wv : wave
+bd : broad
+bz : broad dotted 
 
-  <30,!4,1=vf,2=vb,3=dt,4=wv
+  <30,!5,1=vb,2=dt,3=wv,4=bd,5=bz
 \end{verbatim}
 \end{minipage}
 \MCFstructure
 \vspace{\gpman}\\
 %-----------------------------------------------------------------------------
 \begin{minipage}[t][\htman]{90mm}
-\MCFtitle{Change bond type (3)}
+\MCFtitle{Change bond type (4)}
 \begin{verbatim}
-bd : broad single
-bz : broad dotted 
-ov : over line
+$(2,4,6)dr : 2=dr,4=dr,6=dr
+
+<30,!7,$(2,4,6)dr
 
-<30,!3,!`2,!,
-  @(3~bd`2^-30,5~ov`3^85,3~bz`3^-70)/Me
+** <30,!7,2=dr,4=dr,6=dr
 
-** 3~bd^-45`2 : ~~bd,^^-45,'`2,3
 \end{verbatim}
 \end{minipage}
 \MCFstructure
 \vspace{\gpman}\\
 %-----------------------------------------------------------------------------
 \begin{minipage}[t][\htman]{90mm}
-\MCFtitle{Change bond type (4)}
+\MCFtitle{Over line}
 \begin{verbatim}
-$(2,4,6)dr : 2=dr,4=dr,6=dr
+si_ : single over line 
+wf_ : wedge forward over line 
+wb_ : wedge backward over line 
+bd_ : broad over line 
 
-<30,!7,$(2,4,6)dr
+<-30,!8`.4,!`.2,60`.6,90`3,
+@(2~si_,4~wf_,6~wb_,8~bd_)/Me`1
 
 \end{verbatim}
 \end{minipage}
@@ -1411,7 +1416,7 @@ mcf_man_soc;91;1;Ampicillin
 \begin{verbatim}
   <-30,O,!,//O,!,!,Ph,
   #1\~zb^-120,
-  |,?7`1.1,6*\^190`1.25,N,/Me,&3~wb,
+  |,?7,6*\^190`1.02,N,/Me,&3~wb,
   #3\~wv,!,OH
 \end{verbatim}
 \end{minipage}
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf
index 0e60edde594..cb68fe31e7d 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 9d0f1b99042..207ec7cfd83 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex
@@ -1,6 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of  MCF typest with LuaLaTeX(luamplib)       by A.Yamaji   2016.8.06
+% Example of  MCF typest with LuaLaTeX(luamplib)       by A.Yamaji   2016.8.21
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% mcf2graph.mf it must be version 3.97 or later
 \documentclass{article}
 %------------------------------------------------------------------------------
 \usepackage{luamplib}%
diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
index a778a1da880..b674e468a9c 100644
--- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
+++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 3.96     Copyright (c) 2013-2016   Akira Yamaji
+% mcf2graph ver 3.97     Copyright (c) 2013-2016   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,
@@ -90,7 +90,7 @@ def_com(-4000)(_term,_jp_atom,_jp_atom_abs,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_li
  _dl,_N,_O,_S,_H,_tmp_line,_chg_len,_get_len,_ring_len,_tmp_len,_rot_ang,_set_ang,_adj_ang,_chg_env,
  _tmp_env,_set_colorA,_set_colorB,_postA,_postB,_postC,_postD,_postE,_postF,_set_psA,_stack_reset,
  _set_clr,_set_adr,_mk_bond,_set_atom,_arg_ang,_chg_atom,_tmp_rot,_fuse,_push,_pop,_size_a);
-def_com(1)(si,dl,dr,dm,tm,wf,wb,bd,bz,zf,zb,ov,dt,no,ar,vf,vb,wv,nl);
+def_com(1)(si,dl,dr,dm,tm,wf,wb,bd,bz,zf,zb,dt,no,ar,vf,vb,wv,nl,si_,wf_,wb_,bd_);
 %-------------------------------------------------------------------------------------------------
 def parameter_list=
   sw_checklist,sw_numberA,sw_numberB,sw_mol_frame,sw_auxout,sw_solid,sw_expand,sw_MOLout,
@@ -279,7 +279,7 @@ def PB(expr a,b)= cntBS:=cntBS+1; comMC[ab_num][cntBS]:=a; parMC[ab_num][cntBS]:
 def $$(text t)(expr e) =
    begingroup  save cntBS; cntBS:=0; ab_num:=ab_num+1;
   if known e:: if numeric e::
-    if (e>=si)and(e<=nl):: if     e==dl:: for list==t:: PB(_dl,list) endfor
+    if (e>=si)and(e<=bd_):: if e==dl:: for list==t:: PB(_dl,list) endfor
                            else:: for list==t:: PB(_set_adr,list) PB(_set_line,e) endfor fi
     elseif (e>=?3)and(e<=?20):: for list==t:: !?(list)(e-?3+3) endfor
     elseif e==Ph1:: !?(t)(6) PB(_dl,-2) PB(_dl,-4)
@@ -382,8 +382,8 @@ def MCd(expr RW,RH)(expr FW,FH)(text s)=
         else: for i=1 upto 4: proc_skeleton; scaling; resize(RW,RH); size_setup; endfor fi fi
   font_setup;
   if sw_subst_off=1: cntA:=cntA_skeleton; cntB:=cntB_skeleton; fi
-  for i=1 upto cntB: if lineB[i]<>ov: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
-  for i=1 upto cntB: if lineB[i]=ov:  draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
+  for i=1 upto cntB: if lineB[i]<si_ : draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
+  for i=1 upto cntB: if lineB[i]>=si_: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
   for i=1 upto cntA:
     if (sw_numberA>=1)and(i>=numberA_start)and(i<=numberA_end):
        if     sw_numberA=2: nA:=i-numberA_start+1;
@@ -605,9 +605,18 @@ if (nC>0)and(LN<>0):
   elseif LN=zb:wz_put(Le,sfB(Ls,ww,am),sfB(Ls,ww,ap),nB);
   elseif LN=dt:for i=0 step .75zebra_gap/length(Le-Ls) until 1: drawdot i[Ls,Le]; endfor
   elseif LN=wv:draw_wv;
-  elseif LN=ov:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs gap; draw pA Cp(nB);
   elseif LN=vf:draw pA Cp(nB);draw sfB(Le,gap,ANG-150)--Le--sfB(Le,gap,ANG+150) Cp(nB);
-  elseif LN=vb:draw pA Cp(nB);draw sfB(Ls,gap,ANG-30)--Ls--sfB(Ls,gap,ANG+30) Cp(nB); fi
+  elseif LN=vb:draw pA Cp(nB);draw sfB(Ls,gap,ANG-30)--Ls--sfB(Ls,gap,ANG+30) Cp(nB);
+  elseif LN=si_:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs .75gap; draw pA Cp(nB);
+  elseif LN=wf_:erase fill sfB(0.15[Ls,Le],.5ww,ap)--sfB(0.15[Ls,Le],.5ww,am)--
+                           sfB(0.85[Ls,Le],1.25ww,am)--sfB(0.85[Ls,Le],1.25ww,ap)--cycle;
+                fill Ls--sfB(Le,ww,am)--sfB(Le,ww,ap)--cycle;
+  elseif LN=wb_:erase fill sfB(0.15[Ls,Le],1.25ww,ap)--sfB(0.15[Ls,Le],1.25ww,am)--
+                           sfB(0.85[Ls,Le],.5ww,am)--sfB(0.85[Ls,Le],.5ww,ap)--cycle;
+                fill sfB(Ls,ww,am)--Le--sfB(Ls,ww,ap)--cycle;
+  elseif LN=bd_:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs 1.5gap;
+                draw pA withpen penrazor rotated ap scaled gap Cp(nB);
+  fi
   if (sw_numberB>=1)and(n>=numberB_start)and(n<=numberB_end):
       if     sw_numberB=2: nB:=n-numberB_start+1;
       elseif sw_numberB=3: if numberB_end<cntB: nB:=numberB_end-n+1; else: nB:=cntB-n+1; fi