texlive[69371] Master/texmf-dist: texshade (10jan24)
commits+karl at tug.org
commits+karl at tug.org
Wed Jan 10 21:44:24 CET 2024
Revision: 69371
https://tug.org/svn/texlive?view=revision&revision=69371
Author: karl
Date: 2024-01-10 21:44:24 +0100 (Wed, 10 Jan 2024)
Log Message:
-----------
texshade (10jan24)
Modified Paths:
--------------
trunk/Master/texmf-dist/doc/latex/texshade/README
trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
Modified: trunk/Master/texmf-dist/doc/latex/texshade/README
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/README 2024-01-10 20:44:04 UTC (rev 69370)
+++ trunk/Master/texmf-dist/doc/latex/texshade/README 2024-01-10 20:44:24 UTC (rev 69371)
@@ -1,4 +1,4 @@
- TeXshade v1.27
+ TeXshade v1.28
>>
>> A LaTeX package for setting nucleotide and peptide alignments.
>>
Modified: trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
===================================================================
(Binary files differ)
Modified: trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
===================================================================
--- trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2024-01-10 20:44:04 UTC (rev 69370)
+++ trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2024-01-10 20:44:24 UTC (rev 69371)
@@ -426,8 +426,14 @@
% Introduction: a second full ruler with independent [top] and [bottom]
% options, and the possibility to show ruler names.}
%
+% \changes{1.28}{2024-01-10}{%
+% Introduction: functional shading on DNA sequences using the
+% Brewer color scheme.
+% Corrections: the consensus export file format is now set by
+% default to chimera with pymol as an alternative option.}
%
%
+%
% \CharacterTable
% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
@@ -465,7 +471,7 @@
% for further information, updates and on-line documentation
% see my homepage at
% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-% \date{\small v1.27; 2024/01/06\\[2pt]}
+% \date{\small v1.28; 2024/01/10\\[2pt]}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -549,10 +555,21 @@
%
% \subsection{Version History}
%
-% \textbf{v1.7 2024/01/06}
+% \textbf{v1.28 2024/01/10}
% \medskip
%
% \emph{Introduction:}
+% Functional shading on DNA sequences was added.
+%
+% \emph{Correction}: Consensus export files can be in chimera
+% or pymol format.
+%
+% \medskip
+%
+% \textbf{v1.27 2024/01/06}
+% \medskip
+%
+% \emph{Introduction:}
% The possibility to show a second full ruler at the [top] or [bottom]
% was introduced plus the option to show ruler names by
% |\nameruler|. The |rulername| style can be adjusted using the
@@ -1874,11 +1891,12 @@
% relative frequency of a base or amino acid at this
% position [7]. Thus, more information is contained in logos than in
% a standard consensus sequence.
-% The example below shows a DNA sequence alignment with the logo on the
-% top.
+% The example below shows a DNA sequence alignment with functional
+% shading and the logo on the top (the logo also use the `functional'
+% colors, p.\pageref{funcdef}).
%
% It must be remarked that a logo from only five sequences does not
-% produce meaningful results - it rather illustrates the technique.
+% produce too meaningful results---it rather illustrates the technique.
%
% \medskip
%
@@ -1885,6 +1903,7 @@
% \begin{texshade}{AQPDNA.MSF}
% \setends{1}{414..443}
% \showsequencelogo{top}
+% \shadingmode[DNA]{functional}
% \end{texshade}
%
% Code:\medskip
@@ -1894,6 +1913,7 @@
% \begin{texshade}{AQPDNA.MSF}
% \setends{1}{414..443}
% \showsequencelogo{top}
+% \shadingmode[DNA]{functional}
% \end{texshade}
% \end{verbatim}}
%
@@ -1943,7 +1963,7 @@
% The same logo is shown below but with frequency correction turned
% on (|\dofrequencycorrection|), see p.\pageref{Lshowsequencelogo}.
% This takes into account the difference between the amino acid
-% distribution in the alignment and the equal distribution of
+% distribution in the alignment and an equal distribution of
% 5\% for each residue.
% \medskip
%
@@ -2645,8 +2665,8 @@
%
% \item |\shadingmode[|\meta{type}|]{functional}|\label{funcdef}
% There are seven different functional shading modes available for
-% peptide sequences; nucleotide sequences can not be shaded due
-% to functional aspects. Five of \TeXshade's functional modes
+% peptide sequences, and one for DNA sequences.
+% Five of \TeXshade's functional modes
% correspond to the four `alphabets' employed by \textsc{Karlin}
% and \textsc{Ghandour} for peptide alignments [2] or by the
% rasmol software. Additional
@@ -2686,7 +2706,7 @@
% of the residue in \AA$^2$, i.\,e. it is a measure for the size
% of a residue's sidechain. The accessible area value (also in
% \AA$^2$) gives information about the size of the surface area
-% which is accessible by solvent molecules within the folded
+% which is typically accessible by solvent molecules within the folded
% protein. A very small area means that the residue is
% strongly buried and is thus very hydrophobic. Hydrophilic
% residues in turn possess large accessible areas due
@@ -2705,6 +2725,12 @@
%
% \end{itemize}
%
+% Functional shading can also be shown for DNA sequences
+% using:
+% \begin{itemize}
+% \item \meta{type} = |DNA|
+% \end{itemize}
+%
% \label{Lclearfuncgroups}
% If no \meta{type} or an unknown \meta{type} is designated as option
% all functional groups and shading colors are cleared. This is
@@ -2838,8 +2864,8 @@
%
% with
% \meta{scale} |Gray|, |BlueRed|, |RedBlue|, |GreenRed|, |RedGreen|,
-% |ColdHot| (recommended), |HotCold|, or |T-Coffee| \ref{TCoffee}, and \meta{position} |top|
-% or |bottom|.
+% |ColdHot| (recommended), |HotCold|, or |T-Coffee| (see \ref{TCoffee}), and
+% \meta{position} |top| or |bottom|.
%
% The first color defines the foreground, i.e. the letters, the
% second color---if specified---defines the background.
@@ -2848,11 +2874,10 @@
% weight tables below). For an example output see page
% \pageref{shadecons}. You can find more information on color scales
% on page \pageref{Lgraphs}. The calculated consensus colors can be exported
-% as a Pymol [8] \label{Lexportconsensus}
-% script by |\exportconsensus[|\meta{filename}|]{|\meta{seqref}|}|.
-% If no \meta{filename} is specified |export.txt| will be used. The
-% generated file can be opened in Pymol in order to shade a 3D model
-% of the sequence \meta{seqref}.
+% as a Pymol [8] \label{Lexportconsensus} script or Chimera command file (default)
+% by |\exportconsensus[|\meta{pymol/chimera}|]{|\meta{seqref}|}{|\meta{filename}|}|.
+% The generated file can be opened in Pymol or Chimera, resp., in order to
+% shade a 3D model of the sequence \meta{seqref}.
%
% To hide the consensus use
% |\hideconsensus|. The consensus
@@ -3038,7 +3063,7 @@
%
% Optional color sets correspond to the functional shading modes
% |chemical|, |rasmol|, |hydropathy|, |structure|, |standard area|,
-% |accessible area| (see p.\pageref{funcdef}). The |\showsequencelogo|
+% |accessible area|, |DNA| (see p.\pageref{funcdef}). The |\showsequencelogo|
% command can be reversed by |\hidesequencelogo|.
%
% \label{Llogocolor}\label{Lclearlogocolors}
@@ -5770,7 +5795,8 @@
% & & |chemical| \\
% & & |rasmol| \\
% & & |standard area| \\
-% & & |accessible area| \\ \hline
+% & & |accessible area| \\
+% & & |DNA| \\ \hline
% \end{tabular}
% \end{center}
% \medskip
@@ -5801,7 +5827,6 @@
% \quad|\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
%
% \quad|\defshadingcolors{|\meta{name}|}|
-% \newpage
%
% \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.color}|}|
%
@@ -5850,7 +5875,7 @@
% \quad|\showconsensus[|\meta{color/scale}|[,|\meta{color/scale}|]]{|\meta{top/bot.}|}|
% \hfill[\pageref{Lshowconsensus}]
%
-% \quad|\exportconsensus[|\meta{filename}|]{|\meta{seqref}|}|
+% \quad|\exportconsensus[|\meta{pymol/chimera}|]{|\meta{seqref}|}{|\meta{filename}|}|
% \hfill[\pageref{Lexportconsensus}]
%
% \quad|\hideconsensus|
@@ -5883,7 +5908,8 @@
% \hfill[\pageref{Lgappenalty}]
%
% \vspace{1.5\baselineskip}
-%
+% \newpage
+%
% \textbf{Sequence logos}
% \medskip
%
@@ -5917,7 +5943,7 @@
% \quad|\undofrequencycorrection|
% \hfill[\pageref{Lundofrequencycorrection}]
%
-% \vspace{1.5\baselineskip}
+% \bigskip
%
% \textbf{Subfamily logos}
% \medskip
@@ -5951,7 +5977,7 @@
%
%
%
-% \vspace{1.5\baselineskip}
+% \bigskip
%
% \textbf{Structure memes}
% \medskip
@@ -6642,8 +6668,8 @@
% \begin{macrocode}
%<*texshade>
\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}
@@ -6787,6 +6813,7 @@
\xdef\rulername at top{} \xdef\rulername at bottom{}
\xdef\rulernamecolor at top{n} \xdef\rulernamecolor at bottom{n}
\xdef\rulername at family{n} \xdef\rulername at size{n}
+\xdef\exp at rt@pymol{n}
\expandafter\def\csname fg at textcolor/\endcsname{White}
\expandafter\def\csname fg at color/\endcsname{White}
\expandafter\def\csname func at style/\endcsname{\csname textup\endcsname}
@@ -8276,6 +8303,10 @@
\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}
@@ -9559,8 +9590,15 @@
\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 at fshadetrue}
\def\get at fromstack#1;#2;#3;#4;#5@{%
@@ -12772,9 +12810,7 @@
\else
\xdef\first@{functional}
\ifx\first@\last@
- \if\seq at type N \message{<No functional shading on DNA sequences>}
- \else \simmodefalse \funcmodetrue \func at shading{#1}
- \xdef\seq at type{P} \xdef\prefix@{pep} \fi
+ \simmodefalse \funcmodetrue \func at shading{#1}
\else
\xdef\first@{T-Coffee}
\ifx\first@\last@
@@ -13088,7 +13124,16 @@
\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}
@@ -14395,13 +14440,15 @@
\ifx\temp@\first@ \xdef\tr at nstextstyle{4}\fi
}
-\newcommand\exportconsensus[2][export.txt]{%
+\newcommand\exportconsensus[3][chimera]{%
\ifx\exp at rt\n@
+ \xdef\first@{#1}\xdef\second@{pymol}
+ \ifx\first@\second@\xdef\exp at rt@pymol{y}\fi
\xdef\first@{#2 @} \expandafter\check at letter\first@
\xdef\first@{#2} \ifletter \get at name@number \fi
\xdef\exp at rt@num{\first@}
\xdef\exp at rt{y}
- \immediate\openout\exp at rtfile = #1
+ \immediate\openout\exp at rtfile = #3
\fi
}
@@ -17547,7 +17594,12 @@
\multiply\outerloopcount by 5
\ifnum\outerloopcount<5\relax\outerloopcount=5\fi
\xdef\seventh@{n}
- \immediate\write\exp at rtfile{\string color col\the\outerloopcount, resi \sixth@}
+ \ifx\exp at rt@pymol\y@
+ \immediate\write\exp at rtfile{\string color col\the\outerloopcount, resi \sixth@}
+ \else
+ \immediate\write\exp at rtfile{\string setattr a color col\the\outerloopcount \space :\sixth@}
+ \immediate\write\exp at rtfile{\string setattr r ribbonColor col\the\outerloopcount \space :\sixth@}
+ \fi
\fi
\fi
@@ -17651,10 +17703,17 @@
\fi}
\def\prep at reexp@rtfile{
+ \def\get at c@nsc at l[##1,##2,##3]{\xdef\first@{##1} \xdef\second@{##2} \xdef\third@{##3}}
\loopcount=0
\loop
\advance\loopcount by 5
- \immediate\write\exp at rtfile{\string set_color col\the\loopcount, \csname\c at nsc@l\the\loopcount\endcsname}
+ \ifx\exp at rt@pymol\y@
+ \immediate\write\exp at rtfile{\string set_color col\the\loopcount, \csname\c at nsc@l\the\loopcount\endcsname}
+ \else
+ \xdef\first@{\csname\c at nsc@l\the\loopcount\endcsname}
+ \expandafter\get at c@nsc at l\first@
+ \immediate\write\exp at rtfile{\string colordef col\the\loopcount \space\first@ \space\second@ \space\third@}
+ \fi
\ifnum\loopcount>95\else\repeat
}
Modified: trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
===================================================================
--- trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2024-01-10 20:44:04 UTC (rev 69370)
+++ trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2024-01-10 20:44:24 UTC (rev 69371)
@@ -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 at top{} \xdef\rulername at bottom{}
\xdef\rulernamecolor at top{n} \xdef\rulernamecolor at bottom{n}
\xdef\rulername at family{n} \xdef\rulername at size{n}
+\xdef\exp at rt@pymol{n}
\expandafter\def\csname fg at textcolor/\endcsname{White}
\expandafter\def\csname fg at color/\endcsname{White}
\expandafter\def\csname func at 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 at fshadetrue}
\def\get at fromstack#1;#2;#3;#4;#5@{%
@@ -6127,9 +6139,7 @@
\else
\xdef\first@{functional}
\ifx\first@\last@
- \if\seq at type N \message{<No functional shading on DNA sequences>}
- \else \simmodefalse \funcmodetrue \func at shading{#1}
- \xdef\seq at type{P} \xdef\prefix@{pep} \fi
+ \simmodefalse \funcmodetrue \func at 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 at nstextstyle{4}\fi
}
-\newcommand\exportconsensus[2][export.txt]{%
+\newcommand\exportconsensus[3][chimera]{%
\ifx\exp at rt\n@
+ \xdef\first@{#1}\xdef\second@{pymol}
+ \ifx\first@\second@\xdef\exp at rt@pymol{y}\fi
\xdef\first@{#2 @} \expandafter\check at letter\first@
\xdef\first@{#2} \ifletter \get at name@number \fi
\xdef\exp at rt@num{\first@}
\xdef\exp at rt{y}
- \immediate\openout\exp at rtfile = #1
+ \immediate\openout\exp at rtfile = #3
\fi
}
@@ -10889,7 +10910,12 @@
\multiply\outerloopcount by 5
\ifnum\outerloopcount<5\relax\outerloopcount=5\fi
\xdef\seventh@{n}
- \immediate\write\exp at rtfile{\string color col\the\outerloopcount, resi \sixth@}
+ \ifx\exp at rt@pymol\y@
+ \immediate\write\exp at rtfile{\string color col\the\outerloopcount, resi \sixth@}
+ \else
+ \immediate\write\exp at rtfile{\string setattr a color col\the\outerloopcount \space :\sixth@}
+ \immediate\write\exp at rtfile{\string setattr r ribbonColor col\the\outerloopcount \space :\sixth@}
+ \fi
\fi
\fi
@@ -10993,10 +11019,17 @@
\fi}
\def\prep at reexp@rtfile{
+ \def\get at c@nsc at l[##1,##2,##3]{\xdef\first@{##1} \xdef\second@{##2} \xdef\third@{##3}}
\loopcount=0
\loop
\advance\loopcount by 5
- \immediate\write\exp at rtfile{\string set_color col\the\loopcount, \csname\c at nsc@l\the\loopcount\endcsname}
+ \ifx\exp at rt@pymol\y@
+ \immediate\write\exp at rtfile{\string set_color col\the\loopcount, \csname\c at nsc@l\the\loopcount\endcsname}
+ \else
+ \xdef\first@{\csname\c at nsc@l\the\loopcount\endcsname}
+ \expandafter\get at c@nsc at l\first@
+ \immediate\write\exp at rtfile{\string colordef col\the\loopcount \space\first@ \space\second@ \space\third@}
+ \fi
\ifnum\loopcount>95\else\repeat
}
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