texshade (10jan24)

git-svn-id: svn://tug.org/texlive/trunk@69371 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 44 insertions, 11 deletions

diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index c471186e8dd..77942c25737 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -13,8 +13,8 @@
 %% 
 
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2023/06/04 LaTeX TeXshade (v1.27)]
-\message{Package `texshade', Version 1.27 of 2024/01/06.}
+\ProvidesPackage{texshade}[2024/01/10 LaTeX TeXshade (v1.28)]
+\message{Package `texshade', Version 1.28 of 2024/01/10}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -158,6 +158,7 @@
 \xdef\rulername@top{} \xdef\rulername@bottom{}
 \xdef\rulernamecolor@top{n} \xdef\rulernamecolor@bottom{n}
 \xdef\rulername@family{n} \xdef\rulername@size{n}
+\xdef\exp@rt@pymol{n}
 \expandafter\def\csname fg@textcolor/\endcsname{White}
 \expandafter\def\csname fg@color/\endcsname{White}
 \expandafter\def\csname func@style/\endcsname{\csname textup\endcsname}
@@ -1639,6 +1640,10 @@
 \definecolor{TC8}           {cmyk}{0,0.8,1,0}
 \definecolor{TC9}           {cmyk}{0,0.875,1,0}
 \definecolor{TC99}          {cmyk}{0,0,0,0}
+\definecolor{BrewerC}      {cmyk}{0.35,0.07,0,0}
+\definecolor{BrewerG}      {cmyk}{0.90,0.30,0,0}
+\definecolor{BrewerT}      {cmyk}{0.30,0,0.45,0}
+\definecolor{BrewerA}      {cmyk}{0.80,0,1,0} 
 \definecolor{LightGreenYellow}   {cmyk}{0.08,0,0.35,0}
 \definecolor{LightYellow}        {cmyk}{0,0,0.50,0}
 \definecolor{LightGoldenrod}     {cmyk}{0,0.05,0.42,0}
@@ -2919,8 +2924,15 @@
       \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
       \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
    \else
+   \xdef\second@{DNA}
+   \ifx\temp@\second@
+      \funcgroup{C}{Cc}{Black}{BrewerC}{upper}{up}
+      \funcgroup{G}{Gg}{White}{BrewerG}{upper}{up}
+      \funcgroup{A}{Aa}{Black}{BrewerA}{upper}{up}
+      \funcgroup{T, U}{TtUu}{Black}{BrewerT}{upper}{up}
+   \else
    \message{<Unknown shading mode - clearing `funcgroups'>}
-   \fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi
 }
 \def\shadeallresidues{\all@fshadetrue}
 \def\get@fromstack#1;#2;#3;#4;#5@{%
@@ -6127,9 +6139,7 @@
    \else
    \xdef\first@{functional}
    \ifx\first@\last@
-      \if\seq@type N \message{<No functional shading on DNA sequences>}
-      \else \simmodefalse \funcmodetrue \func@shading{#1}
-            \xdef\seq@type{P} \xdef\prefix@{pep} \fi
+     \simmodefalse \funcmodetrue \func@shading{#1}
    \else
    \xdef\first@{T-Coffee}
    \ifx\first@\last@
@@ -6443,7 +6453,16 @@
       \logocolor{CFH}{BlueRed60}
       \logocolor{MY}{BlueRed80}
       \logocolor{W}{BlueRed100}
-   \fi\fi\fi\fi\fi\fi\fi\fi
+   \else
+   \xdef\second@{DNA}
+   \ifx\first@\second@
+      \clearlogocolors
+      \logocolor{A}{BrewerA}
+      \logocolor{C}{BrewerC}
+      \logocolor{G}{BrewerG}
+      \logocolor{T}{BrewerT}
+      \logocolor{U}{BrewerT}
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi
 }
 \newcommand\findsubfamily[2][n]{%
    \xdef\first@{#1}
@@ -7750,13 +7769,15 @@
    \ifx\temp@\first@ \xdef\tr@nstextstyle{4}\fi
 }
 
-\newcommand\exportconsensus[2][export.txt]{%
+\newcommand\exportconsensus[3][chimera]{%
    \ifx\exp@rt\n@
+      \xdef\first@{#1}\xdef\second@{pymol}
+      \ifx\first@\second@\xdef\exp@rt@pymol{y}\fi
       \xdef\first@{#2 @} \expandafter\check@letter\first@
       \xdef\first@{#2}   \ifletter \get@name@number \fi
       \xdef\exp@rt@num{\first@}
       \xdef\exp@rt{y}
-      \immediate\openout\exp@rtfile = #1
+      \immediate\openout\exp@rtfile = #3
    \fi
 }
 
@@ -10889,7 +10910,12 @@
                 \multiply\outerloopcount by 5
                 \ifnum\outerloopcount<5\relax\outerloopcount=5\fi
                 \xdef\seventh@{n}
-                \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
+                \ifx\exp@rt@pymol\y@
+                   \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
+                \else
+                   \immediate\write\exp@rtfile{\string setattr a color col\the\outerloopcount \space :\sixth@}
+                   \immediate\write\exp@rtfile{\string setattr r ribbonColor col\the\outerloopcount \space :\sixth@}
+                \fi
              \fi
          \fi
 
@@ -10993,10 +11019,17 @@
  \fi}
 
 \def\prep@reexp@rtfile{
+  \def\get@c@nsc@l[##1,##2,##3]{\xdef\first@{##1} \xdef\second@{##2} \xdef\third@{##3}}
    \loopcount=0
    \loop
       \advance\loopcount by 5
-      \immediate\write\exp@rtfile{\string set_color col\the\loopcount, \csname\c@nsc@l\the\loopcount\endcsname}
+      \ifx\exp@rt@pymol\y@
+         \immediate\write\exp@rtfile{\string set_color col\the\loopcount, \csname\c@nsc@l\the\loopcount\endcsname}
+      \else
+         \xdef\first@{\csname\c@nsc@l\the\loopcount\endcsname}
+         \expandafter\get@c@nsc@l\first@
+         \immediate\write\exp@rtfile{\string colordef col\the\loopcount \space\first@ \space\second@ \space\third@}
+      \fi
    \ifnum\loopcount>95\else\repeat
 }