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| systems/texlive/tlnet/archive/arara.r58720.tar.xz 2021/04/05 | 103372 | systems/texlive/tlnet/archive/siunitx.source.r58714.tar.xz -2021/04/05 | 103324 | systems/win32/miktex/tm/packages/next/miktex-lua53-bin-x64-2.9.tar.lzma -2021/04/05 | 101763 | systems/win32/miktex/tm/packages/next/miktex-mfware-bin-x64-2.9.tar.lzma 2021/04/05 | 101696 | systems/texlive/tlnet/archive/biblatex-chicago.r58715.tar.xz -2021/04/05 | 100124 | systems/texlive/tlnet/archive/arara.source.r58720.tar.xz 2021/04/04 | 987750 | macros/latex/contrib/reledmac/reledpar.pdf 2021/04/04 | 984 | support/arara/scripts/rules/arara-rule-make.yaml 2021/04/04 | 950 | support/arara/scripts/rules/arara-rule-gnuplot.yaml @@ -555,7 +699,6 @@ 2021/04/04 | 40086 | support/arara/doc/arara-quickstart.tex 2021/04/04 | 39 | support/arara/doc/arararc.yaml 2021/04/04 | 393856 | graphics/pgf/contrib/circuitikz/tex/circuitikz-0.6.sty -2021/04/04 | 388 | systems/texlive/tlnet/archive/texlive-docindex.r58706.tar.xz 2021/04/04 | 3872 | macros/latex/contrib/easybook/doc/chapter2.tex 2021/04/04 | 377674 | graphics/pgf/contrib/figchild.zip 2021/04/04 | 374447 | graphics/mcf2graph/mcf_manual.pdf @@ -614,7 +757,6 @@ 2021/04/04 | 229076 | graphics/pgf/contrib/circuitikz/tex/pgfcircbipoles.tex 2021/04/04 | 221703 | macros/latex/contrib/reledmac/examples/4-reledpar_one_series_per_pstart.pdf 2021/04/04 | 216567 | language/marathi.zip -2021/04/04 | 211616 | systems/texlive/tlnet/archive/texlive-scripts.doc.r58706.tar.xz 2021/04/04 | 2108 | support/arara/doc/chapters/license.tex 2021/04/04 | 210267 | macros/latex/contrib/reledmac/examples/4-reledpar_column_mix_with_not_column-continuous-numbering.pdf 2021/04/04 | 2100 | support/arara/scripts/rules/arara-rule-perltex.yaml @@ -652,7 +794,6 @@ 2021/04/04 | 1877 | graphics/pgf/contrib/circuitikz/tex/ctikzstyle-romano.tex 2021/04/04 | 1837 | support/arara/scripts/rules/arara-rule-detex.yaml 2021/04/04 | 17743 | graphics/pgf/contrib/circuitikz/doc/circuitikz-context.pdf -2021/04/04 | 174164 | systems/texlive/tlnet/archive/texlive-docindex.doc.r58706.tar.xz 2021/04/04 | 172606 | macros/latex/contrib/reledmac/examples/3-reledpar_mwe.pdf 2021/04/04 | 1724 | support/arara/doc/arara.1 2021/04/04 | 1722 | support/arara/scripts/rules/arara-rule-pythontex.yaml @@ -710,7 +851,6 @@ 2021/04/04 | 1111 | support/arara/scripts/rules/arara-rule-xdvipdfmx.yaml 2021/04/04 | 1107 | support/arara/scripts/rules/arara-rule-animate.yaml 2021/04/04 | 1105 | support/arara/scripts/rules/arara-rule-authorindex.yaml -2021/04/04 | 107064 | systems/texlive/tlnet/archive/texlive-scripts.r58706.tar.xz 2021/04/04 | 1062 | support/arara/scripts/rules/arara-rule-etex.yaml 2021/04/04 | 105913 | graphics/pgf/contrib/circuitikz/tex/pgfcircmultipoles.tex 2021/04/04 | 1050 | support/arara/scripts/rules/arara-rule-tex.yaml @@ -744,7 +884,6 @@ 2021/04/03 | 68 | indexing/upmendex/source/tests/foo.idx 2021/04/03 | 68662 | macros/latex/contrib/biblatex-contrib/biblatex-gb7714-2015/README.md 2021/04/03 | 68289 | language/marathi/marathi.dtx -2021/04/03 | 6794 | systems/texlive/tlnet/tlpkg/installer/ctan-mirrors.pl 2021/04/03 | 6734 | indexing/xindy/contrib/xindy-persian/source/variant3-utf8.pl.in 2021/04/03 | 6720 | indexing/xindy/contrib/xindy-persian/source/variant2-utf8.pl.in 2021/04/03 | 6720 | indexing/xindy/contrib/xindy-persian/source/variant1-utf8.pl.in @@ -768,7 +907,6 @@ 2021/04/03 | 479 | macros/latex/contrib/thuthesis/thuthesis-author-year.bbx 2021/04/03 | 47154 | macros/latex/contrib/thuthesis/thuthesis-author-year.bst 2021/04/03 | 46876 | indexing/upmendex/source/Makefile.in -2021/04/03 | 465796 | systems/texlive/tlnet/archive/xcharter.doc.r58704.tar.xz 2021/04/03 | 4656 | macros/latex/contrib/thuthesis/data/chap01.tex 2021/04/03 | 463 | indexing/upmendex/doc/samples/german.idx 2021/04/03 | 462 | macros/latex/contrib/thuthesis/data/resolution.tex @@ -838,7 +976,6 @@ 2021/04/03 | 2144 | indexing/upmendex/doc/samples/alphabet/alpha_zhz.idx 2021/04/03 | 213 | indexing/upmendex/source/tests/pprecA.idx 2021/04/03 | 2105 | indexing/upmendex/source/var.h -2021/04/03 | 2067796 | systems/texlive/tlnet/archive/xcharter.r58704.tar.xz 2021/04/03 | 2047 | language/marathi/glossaries.gls 2021/04/03 | 2043421 | systems/doc/luatex.zip 2021/04/03 | 20365 | systems/texlive/tlnet/tlpkg/TeXLive/TLCrypto.pm @@ -901,6 +1038,7 @@ 2021/04/03 | 1236 | language/marathi/namuna-para.tex 2021/04/03 | 1200 | indexing/upmendex/doc/samples/alphabet/alpha_zhs.idx 2021/04/03 | 1190 | indexing/upmendex/source/kp.c +2021/04/03 | 1155542 | macros/latex/contrib/texshade/texshade.dtx 2021/04/03 | 115105 | macros/latex/contrib/biblatex-contrib/biblatex-gb7714-2015/gb7714-2015ms.bbx 2021/04/03 | 1144457 | macros/latex/contrib/thuthesis/thuthesis.pdf 2021/04/03 | 1095 | indexing/upmendex/doc/samples/option/attri1.idx @@ -1293,6 +1431,7 @@ 2021/04/01 | 2497 | macros/latex/contrib/easybook/README.md 2021/04/01 | 24768 | fonts/xcharter/tfm/XCharter1-Slanted-tosf-sc-t1.tfm 2021/04/01 | 24768 | fonts/xcharter/tfm/XCharter1-Bold-tosf-sc-t1.tfm +2021/04/01 | 2475 | macros/latex/contrib/texshade/texshade.ins 2021/04/01 | 24756 | fonts/xcharter/tfm/XCharter-Slanted-tosf-sc-t1.tfm 2021/04/01 | 24724 | fonts/xcharter/tfm/XCharter-Bold-tosf-sc-t1.tfm 2021/04/01 | 24720 | fonts/xcharter/tfm/XCharter-Slanted-tlf-sc-t1.tfm @@ -1864,25 +2003,3 @@ 2021/03/31 | 108415 | macros/latex/contrib/tudscr/source/tudscr-pagestyle.dtx 2021/03/31 | 1083765 | macros/latex/contrib/tudscr/doc/tudscr_print.pdf 2021/03/31 | 1055711 | macros/latex/contrib/tudscr/doc/tudscrsource.pdf -2021/03/30 | 835 | support/tikztosvg/Makefile -2021/03/30 | 7965726 | graphics/pstricks/base.zip -2021/03/30 | 7723 | support/tikztosvg/example/example.svg -2021/03/30 | 670 | support/tikztosvg/CHANGELOG.md -2021/03/30 | 44180 | macros/latex/contrib/scrlayer-fancyhdr/scrlayer-fancyhdr.dtx -2021/03/30 | 4236 | support/tikztosvg/tikztosvg -2021/03/30 | 421014648 | systems/win32/w32tex/ltxpkgdocs.tar.xz -2021/03/30 | 36434 | graphics/pstricks/base/dvips/pstricks.pro -2021/03/30 | 34057584 | systems/win32/w32tex/ltxpkgs.tar.xz -2021/03/30 | 2591 | macros/latex/contrib/scrlayer-fancyhdr/README.md -2021/03/30 | 254406 | macros/latex/contrib/scrlayer-fancyhdr.zip -2021/03/30 | 2457 | support/tikztosvg/man/tikztosvg.1 -2021/03/30 | 243390 | macros/latex/contrib/scrlayer-fancyhdr/scrlayer-fancyhdr.pdf -2021/03/30 | 23601 | graphics/pstricks/base/Changes -2021/03/30 | 2262 | support/tikztosvg/README.md -2021/03/30 | 190908 | support/tikztosvg.zip -2021/03/30 | 1782 | support/tikztosvg/man/man.adoc -2021/03/30 | 168699 | support/tikztosvg/tikztosvg.pdf -2021/03/30 | 153 | support/tikztosvg/example/example.tikz -2021/03/30 | 1510 | support/tikztosvg/install.sh -2021/03/30 | 139513 | graphics/pstricks/base/generic/pstricks.tex -2021/03/30 | 1081 | macros/latex/contrib/scrlayer-fancyhdr/LICENSE.md diff --git a/graphics/pstricks/contrib/pst-func/Changes b/graphics/pstricks/contrib/pst-func/Changes index 32534e1f7f..1aadfbe9be 100644 --- a/graphics/pstricks/contrib/pst-func/Changes +++ b/graphics/pstricks/contrib/pst-func/Changes @@ -1,5 +1,6 @@ ..... pst-func.tex -0.95 2020-06-06 - another two more polynomial functions +0.96 2021-04-06 - added start/endAngle for \psLame +0.95 2020-06-07 - another two more polynomial functions 0.94 2020-01-01 - small fixes 0.93 2019-05-17 - fix for missing end in a local dictionary (\psBinomialX) 0.92 2018-12-13 - allow algebraic mode for \pscumIntegral diff --git a/graphics/pstricks/contrib/pst-func/doc/pst-func-doc.pdf b/graphics/pstricks/contrib/pst-func/doc/pst-func-doc.pdf index 740e2568d6..12ee728910 100644 Binary files a/graphics/pstricks/contrib/pst-func/doc/pst-func-doc.pdf and b/graphics/pstricks/contrib/pst-func/doc/pst-func-doc.pdf differ diff --git a/graphics/pstricks/contrib/pst-func/dvips/pst-func.pro b/graphics/pstricks/contrib/pst-func/dvips/pst-func.pro index 1eca86df51..09252c19a3 100644 --- a/graphics/pstricks/contrib/pst-func/dvips/pst-func.pro +++ b/graphics/pstricks/contrib/pst-func/dvips/pst-func.pro @@ -366,10 +366,11 @@ tx@FuncDict begin } def %end{vasicek density} % - +end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % subroutines for complex numbers, given as an array [a b] % which is a+bi = Real+i Imag +%% Global defined % /cxadd { % [a1 b1] [a2 b2] = [a1+a2 b1+b2] dup 0 get % [a1 b1] [a2 b2] a2 @@ -504,4 +505,15 @@ tx@FuncDict begin RadtoDeg dup sin exch cos cxmake2 } def % -end +% cxexp z^k with k as a natural number +/cxexp { % z k + 3 dict begin + dup 0 eq { pop pop [1 0] }{ + /k ED + /z ED + /sol [1 0] def + k { sol z cxmul /sol ED } repeat + sol } ifelse + end +} def +% diff --git a/graphics/pstricks/contrib/pst-func/tex/pst-func.tex b/graphics/pstricks/contrib/pst-func/tex/pst-func.tex index c581b1e49f..abd00a74c1 100644 --- a/graphics/pstricks/contrib/pst-func/tex/pst-func.tex +++ b/graphics/pstricks/contrib/pst-func/tex/pst-func.tex @@ -31,8 +31,8 @@ % interface to the `xkeyval' package \pst@addfams{pst-func} % -\def\fileversion{0.95} -\def\filedate{2020/06/06} +\def\fileversion{0.96} +\def\filedate{2021/04/05} \message{`PST-func' v\fileversion, \filedate\space (hv)} % \pstheader{pst-func.pro} @@ -270,9 +270,10 @@ % \define@key[psset]{pst-func}{n}[1]{\def\psk@func@n{#1 }} \psset[pst-func]{n=0} -\def\psLaguerre{\@ifnextchar[{\psLaguerre@i}{\psLaguerre@i[]}}%% hv 20200111 +% +\def\psLaguerre{\@ifnextchar[\psLaguerre@i{\psLaguerre@i[]}}%% hv 20200111 \def\psLaguerre@i[#1](#2,#3){{%%% n - \pst@killglue% + \pst@killglue \psplot[#1]{#2}{#3}{% /L_n 1 def 0 1 \psk@func@n { @@ -287,6 +288,274 @@ }% }\ignorespaces} % +\def\psLaguerreC{\pst@object{psLaguerreC}}%% hv 20200612 +\def\psLaguerreC@i(#1,#2)(#3,#4){{%%% n (xMin,xMax)(yMin,yMax) + \pst@killglue + \begin@SpecialObj + \addto@pscode{% +% 20 dict begin + /yC #3 def + /dx #2 #1 sub \psk@plotpoints div def + /dy #4 #3 sub \psk@plotpoints div def + /L_i { + 5 userdict begin + /X ED + /n_i ED + /L_n 0 def + 0 1 n_i { + /k_i ED + -1 k_i exp k_i factorial div + n_i k_i MoverN mul + X k_i exp mul L_n add + /L_n ED + } for + L_n % return L_n(x) + end + } def + /n \psk@func@n def + [ % start array of x/y values + \psk@plotpoints { /xC #1 def \psk@plotpoints { + /Re 0 def + 0 1 \psk@func@n 2 div floor { + /j ED % loop index + /j2 j dup add def % 2j + n j2 sub xC L_i % calculate L_{n-2j}(x) + j2 exp % L_{n-2j}^{2j}(x) + -1 j exp yC j2 exp mul % (-1^j)*y^(2j) + j2 factorial % (2*j)! + div + mul + Re add /Re ED + } for + /Im 0 def + 0 1 \psk@func@n 1 sub 2 div floor { + /j ED % loop index + /j2 j dup add def % 2j + n j2 sub 1 sub xC L_i % calculate L_{n-2j-1}(x) + j2 1 add exp % L_{n-2j}^{2j+1}(x) + -1 j 1 sub exp yC j2 1 add exp mul % (-1^j)*y^(2j+1) + j2 1 add factorial % (2*j+1)! + div + mul + Im add /Im ED + } for + Re Im 2 copy \tx@ScreenCoor +% Re Im dup mul exch dup mul add sqrt dup 4 gt {pop 4} if 4 div setgray +% xC yC \tx@ScreenCoor 0 360 2 arc gsave fill stroke grestore + xC dx add /xC ED + } repeat + yC dy add /yC ED + } repeat + false \tx@NArray + \psk@dotsize + \@nameuse{psds@\psk@dotstyle} + \tx@setStrokeTransparency + newpath + n { transform floor .5 add exch floor .5 add exch itransform Dot } repeat +%% end + }% + \end@SpecialObj +}\ignorespaces} +% + +\def\psLaguerreCC{\pst@object{psLaguerreCC}}%% hv 20200612 +\def\psLaguerreCC@i(#1,#2)(#3,#4){{%%% n (xMin,xMax)(yMin,yMax) + \pst@killglue + \begin@SpecialObj + \addto@pscode{% +% 20 dict begin +gsave + /yC #3 def + /dx #2 #1 sub \psk@plotpoints div def + /dy #4 #3 sub \psk@plotpoints div def + /n \psk@func@n def + [ % start array of x/y values + \psk@plotpoints { /xC #1 def \psk@plotpoints { +/z [xC yC ] def +/L0 [1 0] def +/L1 [1 z {-1 mul} forall 3 1 roll add exch] def +n 1 le { + n 0 eq {/L1 L0 def} if + n 1 eq {/L1 L1 def} if + }{ +/m 1 def +n 1 sub + { + /L2 1 m 1 add div + [2 m mul 1 add z {-1 mul} forall 3 1 roll add exch] L1 cxmul + L0 m neg cxrmul cxadd + exch cxrmul def + /L0 L1 def + /L1 L2 def +/m m 1 add def +} repeat +} ifelse +L1 aload pop \tx@ScreenCoor + xC dx add /xC ED + } repeat + yC dy add /yC ED + } repeat + false \tx@NArray + \psk@dotsize + \@nameuse{psds@\psk@dotstyle} + \tx@setStrokeTransparency + newpath + n { transform floor .5 add exch floor .5 add exch itransform Dot } repeat +grestore +%% end + }% + \end@SpecialObj +}\ignorespaces} +% + +\def\psLaguerreCCC{\pst@object{psLaguerreCCC}}%% hv 20200612 +\def\psLaguerreCCC@i(#1,#2)(#3,#4){{%%% n (xMin,xMax)(yMin,yMax) + \pst@killglue + \begin@SpecialObj + \addto@pscode{% +% 20 dict begin + /yC #3 def + /dx #2 #1 sub \psk@plotpoints div def + /dy #4 #3 sub \psk@plotpoints div def + [ % start array of x/y values + \psk@plotpoints { + /xC #1 def + \psk@plotpoints { + /Z [xC yC] def + /L [1 0] def + 0 1 \psk@func@n { + /k ED + \psk@func@n k MoverN -1 k exp k factorial div mul + Z k + tx@FuncDict begin cxexp exch + cxrmul L cxadd end /L ED + } for + L aload pop \tx@ScreenCoor + xC dx add /xC ED + } repeat + yC dy add /yC ED + } repeat +% ] aload length 3 1 roll moveto 2 div cvi 1 sub { lineto } repeat 1 0 0 setrgbcolor 0.1 setlinewidth stroke + false \tx@NArray + \psk@dotsize + \@nameuse{psds@\psk@dotstyle} + \tx@setStrokeTransparency + newpath + n { transform floor .5 add exch floor .5 add exch itransform Dot } repeat +%% end + }% + \end@SpecialObj +}\ignorespaces} +% +\def\psLaguerreCCCC{\pst@object{psLaguerreCCCC}}%% hv 20200612 +\def\psLaguerreCCCC@i(#1,#2)(#3,#4){{%%% n (xMin,xMax)(yMin,yMax) + \pst@killglue + \begin@SpecialObj + \addto@pscode{% +% 20 dict begin + /yC #3 def + /dx #2 #1 sub \psk@plotpoints div def + /dy #4 #3 sub \psk@plotpoints div def + % start array of x/y values + \psk@plotpoints { + /xC #1 def + [ + \psk@plotpoints { + /Z [xC yC] def + /L [1 0] def + 0 1 \psk@func@n { + /k ED + \psk@func@n k MoverN -1 k exp k factorial div mul + Z k + tx@FuncDict begin cxexp exch + cxrmul L cxadd end /L ED + } for + L aload pop \tx@ScreenCoor + xC dx add /xC ED + } repeat + ] + aload length 3 1 roll moveto 2 div cvi 1 sub { lineto } repeat 1 0 0 setrgbcolor 0.1 setlinewidth stroke + yC dy add /yC ED + } repeat +% ] aload length 3 1 roll moveto 2 div cvi 1 sub { lineto } repeat 1 0 0 setrgbcolor 0.1 setlinewidth stroke +% false \tx@NArray +% \psk@dotsize +% \@nameuse{psds@\psk@dotstyle} +% \tx@setStrokeTransparency +% newpath +% n { transform floor .5 add exch floor .5 add exch itransform Dot } repeat +%% end + }% + \end@SpecialObj +}\ignorespaces} +% +\def\psContourLaguerre{\pst@object{psContourLaguerre}}%% hv 20200612 +\def\psContourLaguerre@i(#1,#2)(#3,#4){{%%% n (xMin,xMax)(yMin,yMax) + \pst@killglue + \begin@SpecialObj + \addto@pscode{% + /yC #3 def + /dx #2 #1 sub \psk@plotpoints div def + /dy #4 #3 sub \psk@plotpoints div def + /contourdata [ % start array of x/y values + \psk@plotpoints { + /xC #1 def + [ + \psk@plotpoints { + /Z [xC yC] def + /L [1 0] def + 0 1 \psk@func@n { + /k ED + \psk@func@n k MoverN -1 k exp k factorial div mul + Z k + tx@FuncDict begin cxexp exch + cxrmul L cxadd end /L ED + } for +% L aload cxnorm exch pop + xC yC L cxre exch pop + xC dx add /xC ED + } repeat + ] + yC dy add /yC ED + } repeat + ] def + /zMax 0 def /zMin 0 def % lowest and highest value + contourdata aload length /N ED % get the no of arrays + N { % inside contourdata + /data ED % save first inner array + data aload length 3 div round cvi { % get the records + \psk@colorOffset + dup zMin lt % z\ProvidesClass{apa7}[2021/03/04 v2.10 APA formatting (7th edition)] +%\ProvidesClass{apa7}[2021/04/05 v2.11 APA formatting (7th edition)] % % %<*internal> % -\def\apaSevenVersionDate{2021/03/04} -\def\apaSevenVersionNumber{2.10} +\def\apaSevenVersionDate{2021/04/05} +\def\apaSevenVersionNumber{2.11} % % % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -269,6 +269,8 @@ and the derived files apa7.ins, % % \changes{v2.10}{2021/03/04}{Update BibLaTex instructions to remove DeclareLanguageMapping and remove commands that are no longer required. } % +% \changes{v2.11}{2021/04/05}{Updated linebreaks in caption separators to prevent warning. } +% % \begin{abstract} % The \textit{Publication Manual} of the American Psychological % Association is widely used in the social sciences. The most @@ -1844,12 +1846,12 @@ and the derived files apa7.ins, \DeclareCaptionLabelFormat{tablelabel}{\hspace{-\parindent}\raggedright\textbf{#1 #2}} \DeclareCaptionLabelFormat{figurelabel}{\hspace{-\parindent}\raggedright\textbf{#1 #2}} \DeclareCaptionTextFormat{tabletext}{\hspace{-\parindent}\textit{#1}} - \DeclareCaptionLabelSeparator{apalabelsep}{\\ \\} + \DeclareCaptionLabelSeparator{apalabelsep}{\\[\baselineskip]} }{% doc \DeclareCaptionLabelFormat{tablelabel}{\hspace{-\parindent}\raggedright\textbf{#1 #2}} \DeclareCaptionLabelFormat{figurelabel}{\hspace{-\parindent}\raggedright\textbf{#1 #2}} \DeclareCaptionTextFormat{tabletext}{\hspace{-\parindent}\raggedright\textit{#1}} - \DeclareCaptionLabelSeparator{apalabelsep}{\\ \\} + \DeclareCaptionLabelSeparator{apalabelsep}{\\[\baselineskip]} } \captionsetup[table]{position=above,skip=0pt,labelformat=tablelabel,labelsep=apalabelsep,textformat=tabletext} \captionsetup[figure]{position=above,skip=0pt,labelformat=figurelabel,labelsep=apalabelsep,textfont=it} diff --git a/macros/latex/contrib/apa7/apa7.pdf b/macros/latex/contrib/apa7/apa7.pdf index fcfd0c2041..aa32a866a6 100644 Binary files a/macros/latex/contrib/apa7/apa7.pdf and b/macros/latex/contrib/apa7/apa7.pdf differ diff --git a/macros/latex/contrib/apa7/samples/longsample.pdf b/macros/latex/contrib/apa7/samples/longsample.pdf index 35f4b63630..0a0b7b6545 100644 Binary files a/macros/latex/contrib/apa7/samples/longsample.pdf and b/macros/latex/contrib/apa7/samples/longsample.pdf differ diff --git a/macros/latex/contrib/apa7/samples/shortsample.pdf b/macros/latex/contrib/apa7/samples/shortsample.pdf index 135d919beb..83984dbc31 100644 Binary files a/macros/latex/contrib/apa7/samples/shortsample.pdf and b/macros/latex/contrib/apa7/samples/shortsample.pdf differ diff --git a/macros/latex/contrib/easybook/doc/easybook-demo.pdf b/macros/latex/contrib/easybook/doc/easybook-demo.pdf index 5a2fb630ee..f98213bf6b 100644 Binary files a/macros/latex/contrib/easybook/doc/easybook-demo.pdf and b/macros/latex/contrib/easybook/doc/easybook-demo.pdf differ diff --git a/macros/latex/contrib/easybook/doc/easybook-demo.tex b/macros/latex/contrib/easybook/doc/easybook-demo.tex index 63dc917aab..af86342bfa 100644 --- a/macros/latex/contrib/easybook/doc/easybook-demo.tex +++ b/macros/latex/contrib/easybook/doc/easybook-demo.tex @@ -67,6 +67,7 @@ }, tocset = { + line-align = true, part = { format = \addvspace{1pc}\sffamily\large, @@ -99,7 +100,7 @@ \url{https://latexstudio.net} \\ \url{https://gitee.com/texl3/easybook}\thanks{Gitee为项目ç„主è¦å‘布地å€ă€‚} } -\date{2021/04/05\hskip\ccwd\relax v1.24e} +\date{2021/04/06\hskip\ccwd\relax v1.24f} \frontmatter[roman] \maketitle diff --git a/macros/latex/contrib/easybook/doc/easybook.pdf b/macros/latex/contrib/easybook/doc/easybook.pdf index e5042a675f..3fd17d4eb6 100644 Binary files a/macros/latex/contrib/easybook/doc/easybook.pdf and b/macros/latex/contrib/easybook/doc/easybook.pdf differ diff --git a/macros/latex/contrib/easybook/easybook.dtx b/macros/latex/contrib/easybook/easybook.dtx index 80c214a527..caa02d9289 100644 --- a/macros/latex/contrib/easybook/easybook.dtx +++ b/macros/latex/contrib/easybook/easybook.dtx @@ -55,7 +55,7 @@ The latest version of this license is in % % \title{\sffamily easybook书ç±æ–‡æ¡£ç±»} % \author{ç¿æ¯…} -% \date{2021/04/05\hskip\ccwd\relax v1.24e\thanks{\url{https://gitee.com/texl3/easybook}}} +% \date{2021/04/06\hskip\ccwd\relax v1.24f\thanks{\url{https://gitee.com/texl3/easybook}}} % \maketitle % \begin{abstract} % \cls{easybook} æ˜¯åŸºäº \cls{ctexbook} 书ç±æ–‡æ¡£ç±»åˆ›å»ºä»¥æ简为é£æ ¼ç„模æ¿ï¼Œå¯ä»¥çœ‹ä½œå¯¹ \cls{ctexbook} ç„è¿›ä¸€æ­¥åŒ…è£…ă€‚è™½ç„¶\CTeX 文档类æ供了较好ç„中文支æŒï¼Œä½†æƒ³å®ç°ä¸ªæ€§åŒ–åŸèƒ½ä¸€èˆ¬éœ€è¦åœ¨å…¶åŸºç¡€ä¸è½½å…¥æ›´å¤å®åŒ…æ¥å®åˆ¶ă€‚\cls{easybook} 考虑了一些细è‚并载入一些常用å®åŒ…å®ç°ä¸€èˆ¬ç„æ’版需求,它适用äºæ’版中英文书ç±æˆ–笔记,ç”至å¯ç¨å è°ƒæ•´æˆä¸ºå­¦ä½è®ºæ–‡æ¨¡æ¿ă€‚ @@ -64,10 +64,10 @@ The latest version of this license is in % % \begin{documentation} % \section{编译方å¼} -% 模æ¿å«æœ‰ä¸€ä¸ªä½¿ç”¨ç¤ºä¾‹æ–‡ä»¶ \opt{easybook-demo.tex},编译å‰å»ºè®®æ»¡è¶³ä»¥ä¸‹ç„æ¡ä»¶ +% 文档类å«æœ‰ä¸€ä¸ªä½¿ç”¨ç¤ºä¾‹æ–‡ä»¶ \opt{easybook-demo.tex},编译å‰å»ºè®®æ»¡è¶³ä»¥ä¸‹ç„æ¡ä»¶ % \begin{itemize} % \item 使用 \hologo{XeLaTeX}(æ¨è)或 \hologo{LuaLaTeX} 两ç§ç¼–译方å¼ă€‚ -% \item ç”±äºç”¨åˆ°äº†ä¸€äº›å®åŒ…较新ç„åŸèƒ½ï¼Œå»ºè®®å®‰è£…最新ç„\TeX å‘行版并将所有å®åŒ…å‡çº§ä¸ºæœ€æ–°ï¼Œç›®å‰åœ¨ \hologo{MiKTeX} 21.2å’Œ \TeX Live 2021å¯ä»¥æ­£å¸¸ç¼–è¯‘ă€‚ +% \item ç”±äºç”¨åˆ°äº†ä¸€äº›å®åŒ…较新ç„åŸèƒ½ï¼Œå»ºè®®å®‰è£…最新ç„\TeX å‘行版,例如 \TeX Live 2021或 \hologo{MiKTeX} 21.2之åç„ç‰ˆæœ¬ă€‚ % \end{itemize} % % \subsection{编译步骤} @@ -78,7 +78,7 @@ The latest version of this license is in % xelatex -shell-escape easybook-demo % xelatex -shell-escape easybook-demo % \end{frameverb} -% 需注æ„,正确\textbf{编译索引}需è¦å¢å  \opt{-shell-escape} å‘½ä»¤è¡Œé€‰é¡¹ă€‚ +% \ding{72} 需è¦æ³¨æ„正确\textbf{编译索引}è¦å¢å  \opt{-shell-escape} å‘½ä»¤è¡Œé€‰é¡¹ă€‚ % % \subsection{字体设置} % \label{subsec:font settings} @@ -168,7 +168,7 @@ The latest version of this license is in % \end{syntax} % \opt{multoc} ä¸ \opt{style/multoc} 选项具有相åŒç„效æœï¼Œä½†æ˜¯å…·æœ‰ä¼˜å…ˆæ€§ä¸”å¯å•ç‹¬è®¾ç½®ä¸åŒç›®å½•æ˜¯å¦åŒæ æ’ç‰ˆă€‚å·²ç»é¢„置了中英文ç„目录标题,å¯ä»¥ä½¿ç”¨ \opt{title} 选项更改目录标题ç„å称。\opt{book} 选项使目录标题按照 \opt{chapter} 级别输出,\opt{article} 选项使目录标题按照 \opt{article} 级别输出,默认为 \opt{chapter} çº§åˆ«ă€‚ % \changes{v1.23}{2021/03/15}{为几个目录å¢å é”®å€¼åˆ—表ç„选项,å¯è®¾ç½®æ ‡é¢˜è¾“出级别以å是å¦å å…¥ä¸»ç›®å½•ă€‚} -% \changes{v1.24e}{2021/04/04}{目录命令ç„å¯é€‰å‚æ•°å¢å æ ‡é¢˜é”®å€¼ă€‚} +% \changes{v1.24f}{2021/04/04}{目录命令ç„å¯é€‰å‚æ•°å¢å æ ‡é¢˜é”®å€¼ă€‚} % \end{function} % % \section{æ¥å£é€‰é¡¹} @@ -256,7 +256,7 @@ The latest version of this license is in % \ding{229} 以ä¸é€‰é¡¹è·¯å¾„为 \opt{link/...} \\ % \opt{link} 将超链æ¥é€‰é¡¹ï¼ˆåŒ…括以ä¸é€‰é¡¹ï¼‰äº¤ç»™ \pkg{hyperref} 处ç†ï¼Œé™¤äº†ä¸€äº›å…³äº pdf 书签ç„选项å¯èƒ½ä¼å¤±æ•ˆï¼Œå…¶å®ƒç”±é”®å€¼é€‰é¡¹å‘½ä»¤ \tn{hypersetup} 支æŒç„å¤æ•°é€‰é¡¹å¯ç”¨ă€‚ % \changes{v1.10}{2021/01/08}{ä¿®å¤äº† \opt{linktopage} 选项关闭时目录中标题编å·æ— è¶…链æ¥ç„é—®é¢˜ă€‚} -% \changes{v1.24e}{2021/04/05}{å¢å  \pkg{hyperref} 超链æ¥é€‰é¡¹å®Œæ•´ç„支æŒă€‚} +% \changes{v1.24f}{2021/04/05}{å¢å  \pkg{hyperref} 超链æ¥é€‰é¡¹å®Œæ•´ç„支æŒă€‚} % \end{function} % % \begin{optdesc} @@ -452,7 +452,7 @@ The latest version of this license is in % % \subsection{页眉页è„} % \label{subsec:header and footer} -% \begin{function}[EXP,added = 2021-01-13,updated = 2021-03-14]{head-foot,chap-mark,sec-mark,headrule,footrule,footnoterule} +% \begin{function}[EXP,added = 2021-01-13,updated = 2021-04-06]{head-foot,chap-mark,sec-mark,headrule,footrule,footnoterule} % \begin{syntax} % head-foot = <页眉页è„中ç„内容> % chap-mark = <\tn{chaptermark} 标志命令 \tn{markboth} 中ç„内容> @@ -462,14 +462,14 @@ The latest version of this license is in % footnoterule = <è„注横线格å¼> % \end{syntax} % \ding{229} 以ä¸é€‰é¡¹è·¯å¾„为 \opt{hdrset/...} \\ -% \opt{hdrset} 设置ç„命令由 \pkg{fancyhdr} å®åŒ…æ供支æŒï¼Œ\opt{headrule}ă€\opt{footrule} å’Œ \opt{footnoterule} 三个横线选项一般å¯ä»¥ä½¿ç”¨ \tn{hrule} width \meta{长度} height \meta{高度} 命令æ¥ç»˜åˆ¶ï¼Œè„æ³¨æ¨ªçº¿é»˜è®¤ä¸ºç©ºă€‚å½“ç„¶ï¼Œæ‰‹å¨ç»˜åˆ¶æ¨ªçº¿æ—¶çº¿æ¡ç²—细选项 \opt{style/rulewidth} ä¼å¤±æ•ˆă€‚ +% \opt{hdrset} 设置ç„命令由 \pkg{fancyhdr} å®åŒ…æ供支æŒă€‚ç« è‚标志选项 \opt{chap-mark} å’Œ \opt{sec-mark} 中å‚æ•°\#1代表当å‰ç« æˆ–è‚ç„æ ‡é¢˜ă€‚\opt{headrule}ă€\opt{footrule} å’Œ \opt{footnoterule} 三个横线选项一般å¯ä»¥ä½¿ç”¨ \tn{hrule} width \meta{长度} height \meta{高度} 命令æ¥ç»˜åˆ¶ï¼Œè„æ³¨æ¨ªçº¿é»˜è®¤ä¸ºç©ºă€‚å½“ç„¶ï¼Œæ‰‹å¨ç»˜åˆ¶æ¨ªçº¿æ—¶çº¿æ¡ç²—细选项 \opt{style/rulewidth} ä¼å¤±æ•ˆă€‚ % \changes{v1.21}{2021/01/11}{ä¿®å¤å•é¢æ–‡æ¡£æ—¶é¡µçœ‰æ¨ªçº¿æ¶ˆå¤±ç„é—®é¢˜ă€‚} % \changes{v1.21}{2021/01/13}{å¢å é…置页眉页è„ç„é€‰é¡¹ă€‚} % \changes{v1.23}{2021/03/08}{优化页眉页è„设置,å¢å  \opt{chap-mark} å’Œ \opt{sec-mark} é€‰é¡¹ă€‚} % \changes{v1.23}{2021/03/14}{å¯ä»¥æ‰‹å¨ç»˜åˆ¶é¡µçœ‰ă€é¡µè„å’Œè„注ç„æ¨ªçº¿ă€‚} % \end{function} % -% \begin{function}[added = 2021-01-13,updated = 2021-03-14]{,\easyhead,\easyfoot} +% \begin{function}[added = 2021-01-13,updated = 2021-03-14]{\easyhead,\easyfoot} % \begin{syntax} % \tn{easyhead}\oarg{ä½ç½®}\marg{内容} % \tn{easyfoot}\oarg{ä½ç½®}\marg{内容} @@ -484,7 +484,7 @@ The latest version of this license is in % \easyhead[OL]{\rightmark} % \easyhead[EL,OR]{\textbf{\thepage}} % }, -% sec-mark = \CTEXthesection\hspace{0.5\ccwd}, +% sec-mark = \CTEXthesection\hspace{0.5\ccwd}#1, % headrule = \hrule width \textwidth height 1pt % } % \end{ctexexam} @@ -505,33 +505,35 @@ The latest version of this license is in % \changes{v1.21}{2021/01/13}{å¢å é…置目录样å¼ç„é€‰é¡¹ă€‚} % \end{function} % -% \begin{function}[EXP,added = 2021-01-13,updated = 2021-04-05]{lists/lolskip,lists/labelname-fig,lists/labelname-tab,lists/labelname-lst,lists/belowoffset,tocset/belowoffset} +% \begin{function}[EXP,added = 2021-01-13,updated = 2021-04-06]{lists/lolskip,lists/belowoffset,tocset/tocline-fig,tocset/tocline-tab,tocset/tocline-lst,tocset/belowoffset,tocset/line-align} % \begin{syntax} % lolskip = <(0.8pc)> -% labelname-fig = <图片目录标签> -% labelname-tab = <表格目录标签> -% labelname-lst = <代ç ç›®å½•æ ‡ç­¾> % belowoffset = <(0pc)> +% tocline-fig = <图片目录标签> +% tocline-tab = <表格目录标签> +% tocline-lst = <代ç ç›®å½•æ ‡ç­¾> % belowoffset = <(-1pc)> +% line-align = <(true)|false> % \end{syntax} -% \opt{lolskip} 是代ç ç›®å½•ä¸­ç« ä¹‹é—´ç„代ç æ ‡é¢˜ç„è·ç¦»ï¼Œä¸\CTeX ç„表格目录和图片目录中章之间ç„标题è·ç¦»é€‰é¡¹ \opt{lotskip} å’Œ \opt{lofskip} 类似,它们ç„值å‡é»˜è®¤0.8 pc,在 \opt{article} 模å¼ä¸­æ­¤é€‰é¡¹å¤±æ•ˆă€‚目录标签整体使用 \opt{labelname} 设置,也å¯ä½¿ç”¨å°è‚ \ref{subsec:page margins} ç„ \opt{list-labelsep} 选项åªè®¾ç½®ç¼–å·ä¸æ ‡é¢˜ç„é—´è·ă€‚在图表标签ç„å‚数中,\#1ä¸\#2分别代表编å·å’Œæ ‡é¢˜ï¼Œä»£ç æ ‡ç­¾ç„ç¼–å·å’Œæ ‡é¢˜åˆ™æ˜¯ \tn{thelstlisting} å’Œ \tn{lst@@caption},标签中还å¯åŒ…å«æ ‡ç­¾å称,默认标签å称ä¸å›¾ă€è¡¨å’Œä»£ç ç¯å¢ƒç„标题åç§°ä¸€è‡´ă€‚ä¸‹é¢ä¸¾ä¸ªè®¾ç½®æ ‡ç­¾ç„ä¾‹å­ +% \opt{lolskip} 是代ç ç›®å½•ä¸­ç« ä¹‹é—´ç„代ç æ ‡é¢˜ç„è·ç¦»ï¼Œä¸\CTeX ç„表格目录和图片目录中章之间ç„标题è·ç¦»é€‰é¡¹ \opt{lotskip} å’Œ \opt{lofskip} 类似,它们ç„值å‡é»˜è®¤0.8 pc,在 \opt{article} 模å¼ä¸­æ­¤é€‰é¡¹å¤±æ•ˆă€‚目录标签整体使用 \opt{tocline} 设置,也å¯ä½¿ç”¨å°è‚ \ref{subsec:page margins} ç„ \opt{list-labelsep} 选项åªè®¾ç½®ç¼–å·ä¸æ ‡é¢˜ç„é—´è·ă€‚在图表标签ç„å‚数中,\#1ä¸\#2分别代表编å·å’Œæ ‡é¢˜ï¼Œä»£ç æ ‡ç­¾ç„ç¼–å·å’Œæ ‡é¢˜åˆ™æ˜¯ \tn{thelstlisting} å’Œ \tn{lstcaption},标签中还å¯åŒ…å«æ ‡ç­¾å称,默认标签å称ä¸å›¾ă€è¡¨å’Œä»£ç ç¯å¢ƒç„标题åç§°ä¸€è‡´ă€‚\opt{line-align} 选项å¯ä»¥ä½¿ç›®å½•å¼•å¯¼çº¿å³è¾¹å¯¹é½å¹¶ä¸é¡µç ä¿æŒä¸€å®é—´é™ï¼Œå¦åˆ™ä¼ä¸é¡µç è¿æ¥ă€‚下é¢ä¸¾ä¸ªè®¾ç½®æ ‡ç­¾ç„ä¾‹å­ % \begin{ctexexam} % \tocset % { -% lists/labelname-fig = 图#1\hspace{\ccwd}#2 -% lists/labelname-lst = 代ç \thelstlisting\hspace{\ccwd}\lst@@caption +% tocline-fig = 图#1\hspace{\ccwd}#2 +% tocline-lst = 代ç \thelstlisting\hspace{\ccwd}\lstcaption % } % \end{ctexexam} % % \opt{belowoffset} 选项为主目录标题 \tn{contentsname} åç„é—´è·è¡¥å¿ï¼Œä¸€èˆ¬ä¸ºè´Ÿå€¼ï¼Œç”¨äºæµæ¶ˆ \opt{format} 中设置ç„å‚ç›´é—´è·ă€‚\opt{lists} ä¸­ç„ \opt{belowoffset} ä¸ä¹‹æ„义类似,但是一般为正值,å¯ä»¥åœ¨ \opt{article} 模å¼ä¸­ä½¿ç”¨ă€‚建议 \opt{lists/lolskip(0.8pc) + lists/format/addvspace(0.2pc) + lists/belowoffset(0pc) = belowoffset(-1pc)}。 -% \changes{v1.24e}{2021/04/05}{å¯ä»¥è®¾ç½®å›¾ă€è¡¨å’Œä»£ç ç›®å½•ç„æ ‡ç­¾ă€‚} +% \changes{v1.24f}{2021/04/05}{å¯ä»¥è®¾ç½®å›¾ă€è¡¨å’Œä»£ç ç›®å½•ç„æ ‡ç­¾ă€‚} +% \changes{v1.24f}{2021/04/06}{å¢å ç›®å½•å¼•å¯¼çº¿å³è¾¹å¯¹é½æ–¹å¼ă€‚} % \end{function} % -% \begin{function}[added = 2021-01-13,updated = 2021-01-15]{\tocrule} +% \begin{function}[added = 2021-01-13,updated = 2021-04-06]{\tocrule} % \begin{syntax} -% \tn{tocrule} = \oarg{引导点间è·|(0.7pc)}\parg{引导点大å°|(1.2)}\marg{引导点}\oarg{页ç æ ¼å¼} +% \tn{tocrule}*\oarg{引导点间è·|(0.7pc)}\parg{引导点大å°|(1.2)}\marg{引导点}\oarg{页ç æ ¼å¼} % \end{syntax} -% \tn{tocrule} 命令生æˆç›®å½•å¼•å¯¼çº¿ï¼Œéœ€è¦åœ¨ \opt{rule} 选项中使用,其中引导线间è·éœ€å¸¦æœ‰é•¿åº¦å•ä½ï¼Œå¼•å¯¼ç‚¹å¤§å°ä¸å¸¦å•ä½ï¼Œä¸ºå¼•å¯¼ç‚¹ç¬¦å·æ­£å¸¸å¤§å°ç„å€æ•°ï¼Œå¼•å¯¼ç‚¹ä¸€èˆ¬ä¸ºè‹±æ–‡å¥å·æˆ– \tn{cdot} 中心点符å·ă€‚页ç æ ¼å¼ç„内容ä½äºé¡µç å‰é¢ï¼Œå¯ä»¥è®¾ç½®é¡µç å­—体ă€è·ç¦»ă€‚ +% \tn{tocrule} 命令生æˆç›®å½•å¼•å¯¼çº¿ï¼Œéœ€è¦åœ¨ \opt{rule} é€‰é¡¹ä¸­ä½¿ç”¨ă€‚å¸¦æœ‰æ˜Ÿå·ç„命令ä¼ä½¿å½“å‰çº§åˆ«ç„目录引导线å³è¾¹ä¸é¡µç è¿æ¥è€Œä¸æ˜¯å¯¹é½ă€‚引导点间è·éœ€å¸¦æœ‰é•¿åº¦å•ä½ï¼Œå¼•å¯¼ç‚¹å¤§å°ä¸å¸¦å•ä½ï¼Œä¸ºå¼•å¯¼ç‚¹ç¬¦å·æ­£å¸¸å¤§å°ç„å€æ•°ï¼Œå¼•å¯¼ç‚¹ä¸€èˆ¬ä¸ºè‹±æ–‡å¥å·æˆ– \tn{cdot} 中心点符å·ă€‚页ç æ ¼å¼ç„内容ä½äºé¡µç å‰é¢ï¼Œå¯ä»¥è®¾ç½®é¡µç å­—体ă€è·ç¦»ă€‚ % \begin{ctexexam} % \tocset % { @@ -801,7 +803,7 @@ The latest version of this license is in %<*class> \NeedsTeXFormat{LaTeX2e}[2020/10/01] \RequirePackage{l3keys2e} -\ProvidesExplClass{easybook}{2021/04/05}{1.24e}{beta} +\ProvidesExplClass{easybook}{2021/04/06}{1.24f}{beta} \cs_generate_variant:Nn \keys_define:nn {nx} \cs_generate_variant:Nn \int_to_arabic:n {v} @@ -1146,7 +1148,7 @@ The latest version of this license is in \easyhead[OC]{\color{ctex@frame}\kaishu\rightmark} \easyhead[EL,OR]{\color{ctex@frame}\thepage} }, - chap-mark .tl_set:N = \l__fancyhf_chap_mark_tl, + chap-mark .cs_set:Np = \__fancyhf_chap_mark:n #1, chap-mark .initial:n = { \int_compare:nT {\c@secnumdepth > -1} @@ -1156,9 +1158,9 @@ The latest version of this license is in \CTEXthechapter\hspace{\ccwd} \fi \fi - } + }#1 }, - sec-mark .tl_set:N = \l__fancyhf_sec_mark_tl, + sec-mark .cs_set:Np = \__fancyhf_sec_mark:n #1, sec-mark .initial:n = { \int_compare:nT {\c@secnumdepth > 0} @@ -1166,7 +1168,7 @@ The latest version of this license is in \ifodd\CTEX@section@numbering \CTEXthesection\hspace{0.5\ccwd} \fi - } + }#1 }, headrule .tl_gset:N = \headrule, headrule .initial:n = @@ -1188,6 +1190,12 @@ The latest version of this license is in \group_end: } } +\cs_new_protected:Npn \__ifuppercase_chapmark_set:n #1 + { + \bool_if:NTF \l__uppercase_bool + {\text_uppercase:n {\__fancyhf_chap_mark:n {#1}}} + {\text_titlecase_first:n {\__fancyhf_chap_mark:n {#1}}} + } \ctex_at_end_preamble:n { \exp_args:NV \geometry\g__geometry_clist @@ -1198,28 +1206,14 @@ The latest version of this license is in \cs_gset:Npn \chaptermark#1 { \markboth - { - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {\l__fancyhf_chap_mark_tl#1}} - {\text_titlecase_first:n {\l__fancyhf_chap_mark_tl#1}} - }{ - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {\l__fancyhf_chap_mark_tl#1}} - {\text_titlecase_first:n {\l__fancyhf_chap_mark_tl#1}} - } + {\__ifuppercase_chapmark_set:n {#1}} + {\__ifuppercase_chapmark_set:n {#1}} } \l__fancyhf_content_tl \cs_gset_eq:NN \ps@plain\ps@empty }{ \cs_gset:Npn \chaptermark#1 - { - \markboth - { - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {\l__fancyhf_chap_mark_tl#1}} - {\text_titlecase_first:n {\l__fancyhf_chap_mark_tl#1}} - }{} - } + {\markboth{\__ifuppercase_chapmark_set:n {#1}}{}} \l__fancyhf_content_tl \cs_gset_eq:NN \ps@plain\ps@empty } @@ -1228,8 +1222,8 @@ The latest version of this license is in \markright { \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {\l__fancyhf_sec_mark_tl#1}} - {\text_titlecase_first:n {\l__fancyhf_sec_mark_tl#1}} + {\text_uppercase:n {\__fancyhf_sec_mark:n {#1}}} + {\text_titlecase_first:n {\__fancyhf_sec_mark:n {#1}}} } } \bool_if:NT \l__draft_bool @@ -1255,25 +1249,28 @@ The latest version of this license is in } \__ctex_define:nn {tocset} { - lists/lolskip .skip_set:N = \l__toc_lolskip_skip, - lists/lolskip .initial:n = 0.8pc, - lists/belowoffset .dim_set:N = \l__toc_listsoffset_dim, - lists/belowoffset .initial:n = 0pc, - lists/labelname-fig .cs_set:Np = \labelname@lof#1#2, - lists/labelname-fig .initial:n = + lists/lolskip .skip_set:N = \l__toc_lolskip_skip, + lists/lolskip .initial:n = 0.8pc, + lists/belowoffset .dim_set:N = \l__toc_listsoffset_dim, + lists/belowoffset .initial:n = 0pc, + tocline-fig .cs_set:Np = \labelname@lof#1#2, + tocline-fig .initial:n = {\figurename\space#1\hspace{\list@labelsep}#2}, - lists/labelname-tab .cs_set:Np = \labelname@lot#1#2, - lists/labelname-tab .initial:n = + tocline-tab .cs_set:Np = \labelname@lot#1#2, + tocline-tab .initial:n = {\tablename\space#1\hspace{\list@labelsep}#2}, - lists/labelname-lst .tl_set:N = \labelname@lol, - lists/labelname-lst .initial:n = + tocline-lst .tl_set:N = \labelname@lol, + tocline-lst .initial:n = { \lstlistingname\space \thelstlisting\hspace{\list@labelsep} - \lst@@caption + \lstcaption }, - belowoffset .dim_set:N = \l__toc_offset_dim, - belowoffset .initial:n = -1pc + belowoffset .dim_set:N = \l__toc_offset_dim, + belowoffset .initial:n = -1pc, + line-align .bool_set:N = \l__toc_line_align_bool, + line-align .default:n = true, + line-align .initial:n = true } \ctex_set:nn {tocset} { @@ -1298,10 +1295,16 @@ The latest version of this license is in lists/rule = \tocrule{$\cdot$} } -\NewDocumentCommand{\tocrule}{O{0.7pc}D(){1.2}mO{}} +\NewDocumentCommand{\tocrule}{sO{0.7pc}D(){1.2}mO{}} { \normalsize\normalfont - \titlerule*[#1]{\scalebox{#2}{#3}}#4\contentspage + \titlerule*[#2]{\scalebox{#3}{#4}}#5 + \IfBooleanTF{#1} + {\thecontentspage} + { + \bool_if:NTF \l__toc_line_align_bool + {\contentspage}{\thecontentspage} + } } \cs_new_protected:Npn \__titlecontents_set:nn #1#2 { @@ -1321,6 +1324,7 @@ The latest version of this license is in {table}{lists}, {lstlisting}{lists} }{\__titlecontents_set:nn #1} + \prop_new:N \l_label_name_prop \prop_set_from_keyval:Nn \l_label_name_prop { @@ -1336,7 +1340,10 @@ The latest version of this license is in { \addcontentsline{lol}{lstlisting} {\protect\numberline{\thelstlisting}\lst@@caption} - }{\addcontentsline{lol}{lstlisting}{\labelname@lol}} + }{ + \let\lstcaption\lst@@caption + \addcontentsline{lol}{lstlisting}{\labelname@lol} + } \__appto_cmd:Nn \@chapter { \skip_if_eq:nnF {\l__toc_lolskip_skip}{\c_zero_skip} @@ -1358,28 +1365,20 @@ The latest version of this license is in The~\string\chapter\space~command~will~not~be~used. } +\cs_new_protected:Npn \__ifuppercase_set:n #1 + { + \bool_if:NTF \l__uppercase_bool + {\text_uppercase:n {#1}} + {\text_titlecase_first:n {#1}} + } \cs_new_protected:Npn \__markboth:n #1 { \bool_if:NTF \l__page_twoside_bool { \markboth - { - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {#1}} - {\text_titlecase_first:n {#1}} - }{ - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {#1}} - {\text_titlecase_first:n {#1}} - } - }{ - \markboth - { - \bool_if:NTF \l__uppercase_bool - {\text_uppercase:n {#1}} - {\text_titlecase_first:n {#1}} - }{} - } + {\__ifuppercase_set:n {#1}} + {\__ifuppercase_set:n {#1}} + }{\markboth{\__ifuppercase_set:n {#1}}{}} } \tl_set:Nn \l__toc_type_tl{book} diff --git a/macros/latex/contrib/texshade/README b/macros/latex/contrib/texshade/README index 71e52fa0c2..fe67201661 100644 --- a/macros/latex/contrib/texshade/README +++ b/macros/latex/contrib/texshade/README @@ -1,7 +1,6 @@ - TeXshade v1.25 + TeXshade v1.26 >> - >> A LaTeX package for setting nucleotide and peptide alignments, - >> fingerprints, as well as sequence and subfamily logos. + >> A LaTeX package for setting nucleotide and peptide alignments. >> >> Setting alignments of nucleotides and peptides for publication >> or presentation purposes is usually a time consuming two-step @@ -27,7 +26,7 @@ >> ding modes. TeXshade combines highest flexibility and the >> habitual TeX output quality--with reasonable time expenditure. >> - Copyright (C) 1999 - 2018 Eric Beitz + Copyright (C) 1999 - 2021 Eric Beitz @@ -42,8 +41,7 @@ texshade.ins Batch file, run through LaTeX texshade.dtx Docstrip archive, run twice through LaTeX - tsfaq.tex Frequently asked questions about TeXshade - texshade.txt This file + README This file (a) FILES THAT WILL BE GENERATED FROM TEXSHADE.INS @@ -58,6 +56,10 @@ AQP1.phd Example PHD secondary structure file AQP1_HMM.sgl Example HMMTOP topology data (single line format) AQP1_HMM.ext Example HMMTOP topology data (extended format) + AQP_sequence_logo_1FX8.cmd + Example structure meme file + AQP_subfamily_logo_1FX8.cmd + Example structure meme file Standard.cod Standard genetic code definitions Ciliate.cod Ciliate macronuclear genetic code definitions @@ -65,6 +67,8 @@ (b) FILE THAT WILL BE GENERATED FROM TEXSHADE.DTX texshade.dvi Package documentation + or + texshade.pdf Package documentation @@ -89,17 +93,13 @@ TeXshade needs lots of TeX's memory, so adjust your parameter set- tings to make TeXshade feel comfortable. The documentation is a - good test for this. (If you encounter problems texing the doc, you - should tex and read section A of the FAQ-list (see d below) or - download an on-line version [PDF-, DVI-, or PostScript format] at - http://homepages.uni-tuebingen.de/beitz/) - + good test for this. + The resulting file "texshade.dvi" can be viewed and printed using a DVI-viewer which is able to display embedded PostScript. Another possibility is to run "texshade.dvi" through DVIPS, a DVI to Post- Script converter, and finally view and print the converted file - which will be most likely "texshade.ps" with GhostView from the GNU - free software foundation. + which will be most likely "texshade.ps" with GhostView from the GNU free software foundation. TeXshade makes use of "color.sty" by David Carlisle. This style is part of the Standard LaTeX Graphics Bundle. Usually, the bundle is @@ -118,18 +118,11 @@ the files together. - (d) THE FAQ LIST - - The FAQ list contains frequently asked questions about the package. - Use it as a helpful source for solving problems with TeXshade. You - get the list by simply running "tsfaq.tex" through LaTeX once. - - 3 - CONTACT E-Mail: ebeitz@pharmazie.uni-kiel.de - WWW: http://www.pharmazie.uni-kiel.de/chem/ + WWW: https://www.pharmazie.uni-kiel.de/en/pharmceitica/ (On-line documentation and updates) Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry, Gutenbergstrasse 76, D-24118 Kiel (Germany) diff --git a/macros/latex/contrib/texshade/texshade.dtx b/macros/latex/contrib/texshade/texshade.dtx index adf4e661c3..2f2f4da380 100644 --- a/macros/latex/contrib/texshade/texshade.dtx +++ b/macros/latex/contrib/texshade/texshade.dtx @@ -10,7 +10,7 @@ % `README.txt' for further information! % % -% Copyright (C) 1999-2018 Eric Beitz +% Copyright (C) 1999-2021 Eric Beitz % See the file texshade.txt % % \fi @@ -393,11 +393,24 @@ % Postscript color samples are shown in the manual. % } % -% \changes{1.25}{2011-12-01}{% +% \changes{1.25}{2018-12-01}{% % Corrections: aligments with many seqs produced wrong calculation % of threshold shading, corrected. % Introduction: new feature style |S-S| for disulfide bridges; -% hooks in top feature lines can be drawn down to alignment. +% hooks in top feature lines can be drawn down to alignment +% by adding an underscore in the definition, e.g. |{_,-,}|. +% } +% +% \changes{1.26}{2021-04-01}{% +% Corrections: minor fixes; +% Introduction: Chimera command file export for 'structure memes', +% i.e. mapping of sequence logo and subfamily logo data +% onto 3D protein structures; +% new commands `structurememe', `chimeraballScale', +% `chimeraaxisdistance', `memeRed', `memeBlue', +% `memeYellow', `memeBlack', `memeWhite', +% `memeStandardcolors', `chimerachain', +% `memelabelcutoff', `echostructurefile'. % } % % @@ -440,7 +453,7 @@ % 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 v1.25; 2018/01/17\\[2pt]} +% \date{\small v1.26; 2021/04/01\\[2pt]} % \maketitle % \begin{abstract} % Setting alignments of nucleotides and peptides for publication @@ -504,6 +517,10 @@ % HMMTOP-format)\\ % \quad|AQP1_HMM.ext|\> topology information (extended, % HMMTOP-format)\\ +% \quad|AQP_sequence_logo_1FX8.cmd|\\ \> Chimera structure meme file +% \\ +% \quad|AQP_subfamily_logo_1FX8.cmd|\\ \> Chimera structure meme file +% \\ % \quad|standard.cod|\> standard genetic code definitions\\ % \quad|ciliate.cod|\> ciliate macronuclear genetic code\\ % \end{tabbing} @@ -518,6 +535,22 @@ % % % \subsection{Version History} +% +% \textbf{v1.26 2021/04/01} +% \medskip +% +% \emph{Introductions:} +% Chimera command file export option for 'structure memes' +% was introduced, +% i.e. mapping of sequence logo and subfamily logo data +% onto 3D protein structures. +% The new commands |\structurememe|, +% |\memeRed|, |\memeBlue|, +% |\memeYellow|, |\memeBlack|, |\memeWhite|, +% |\memeStandardcolors|, |\chimeraaxisdistance|, |\chimerachain|, |\chimeraballScale|, +% |\memelabelcutoff|, and |\echostructurefile| +% handle the new feature. +% \medskip % % \textbf{v1.25 2018/01/17} % \medskip @@ -526,7 +559,8 @@ % of threshold shading,\footnote{Noted by Kathryn Parker.} corrected; minor bug fixes. % % \emph{Introduction}: A new feature style |S-S| for disulfide bridges is -% implemented; hooks in top feature lines can be drawn down to alignment. +% implemented; hooks in top feature lines can be drawn down to alignment +% by adding an underscore in the definition, e.g. |{_,-,}|. % \medskip % % \textbf{v1.24 2011/12/01} @@ -1950,6 +1984,20 @@ % \end{texshade} % \end{verbatim}} % +% +% +% \subsection{Structure memes} +% +% The calculated sequence logo and subfamily logo data can +% be used to generate \emph{Structure memes}. This a type of 3D protein +% display that visualizes the residue composition and frequency and the +% information content of each sequence position. Therefore, in the structure file, +% a color code is projected onto a sphere at the $\alpha$-carbon position, +% which is scaled according to the information content. \TeXshade\ +% generates an output file for the molecular structure display software +% Chimera. See the files |AQP_sequence_logo_1FX8.cmd| and +% |AQP_subfamily_logo_1FX8.cmd| generated from |texshade.dtx|. +% % % % @@ -3025,6 +3073,54 @@ % |\showrelevance[Blue]{$\nabla$}|. The symbol will be hidden with % |\hiderelevance|. % +% +% +% \subsubsection{Structure memes} +% +% \label{Lmemes} +% +% Structure memes combine sequence logo and subfamily logo +% information with 3D protein structure data. \TeXshade{} generates +% a `command file' output that can be loaded into the molecular +% structure display software Chimera. +% +% A sequence logo or subfamily logo must be calculated as described in +% the two subsections above. Then, the command +% |\structurememe[|\meta{seqref}|]{|\meta{filename}|}| generates an +% Chimera output file (use the ending |.cmd| or |.com|) with +% \meta{seqref} as the reference sequence for which a protein structure +% file must be available for display. Two example files are distributed with +% this \TeXshade{} version to load into Chimera; the PDB file 1FX8 must +% be used for the structure meme. +% +% The |\memeStandardcolors| are: |DE| (Red), |CGNQSTY| (Yellow), +% |HKR| (Blue), |APV| (White), |FILMW| (Black). +% +% The color grouping can be changed using |\memeRed{|\meta{residues}|}|, +% and accordingly |\memeYellow|, |\memeBlue|, +% |\memeWhite|, and |\memeBlack|. If a 3D structure file contains +% more than one chain, the structure meme display can be +% restricted to one chain using |\chimerachain{|\meta{chainlabel}|}| with +% \meta{chainlabel} typically being a letter e.g. |{A}|. For the radius of the +% $\alpha$-carbon spheres the logo information bit-value is used, which can +% be scaled using |\chimeraballScale{|\meta{factor}|}| with \meta{factor} +% from 0--1. The residue composition at a sequence position is stored in +% a name label of the command file and will be visible in Chimera when +% pointing to it. To eliminate irrelevant residues a cut-off bit-value can be +% set |\memelabelcutoff{|\meta{bit-value}|}|. The symbols |>| |:| and |.| +% indicate the 3, 2, and 1 bit levels. +% +% Structure memes from subfamily logos will duplicate the structure model +% and shift it by 40 \AA{} along the x-axis to achieve a side-by-side arrangement. +% The translational direction can be changed using +% |\chimeraxisdistance{|\meta{x-dist}|}{|\meta{y-dist}|}{|\meta{z-dist}|}| in +% \AA{}ngstr\o{}m. +% +% Eventually, with |\echostructurefile{|\meta{strucref}|}| a reference to a +% suitable structure file, e.g. from the PDB, can be named, which will be put +% into the command file and which will appear when Chimera asks for a +% structure file in a load dialog window. +% % \subsection{Appearance of the sequence lines} % % \label{seqlines} @@ -3875,6 +3971,9 @@ % (|-=<',|$\vert$o), the middle-characters (|-=|), % and the right-end-characters (|-=>',|$\vert$o) are % allowed and produce the desired arrow or bar. +% Adding an underscore in the definition for top feature hooks, +% e.g. |{_,-,}| makes the hooks +% fully reach down to the alignment. % The color is changed as described above. % \label{Lfeaturerule} The thickness can be generally % set by the separate command |\featurerule{|\meta{length}|}| @@ -5795,6 +5894,50 @@ % \quad|\hiderelevance| % \hfill[\pageref{Lhiderelevance}] % +% +% +% \vspace{1.5\baselineskip} +% +% \textbf{Structure memes} +% \medskip +% +% \quad|\structurememe[|\meta{seqref}|]{|\meta{filename}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeStandardcolors| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeRed{|\meta{residues}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeYellow{|\meta{residues}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeBlue{|\meta{residues}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeWhite{|\meta{residues}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memeBlack{|\meta{residues}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\chimerachain{|\meta{chainlabel}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\chimeraballScale{|\meta{factor}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\memelabelcutoff{|\meta{bit-value}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\chimeraxisdistance{|\meta{x-dist}|}{|\meta{y-dist}|}{|\meta{z-dist}|}| +% \hfill[\pageref{Lmemes}] +% +% \quad|\echostructurefile{|\meta{strucref}|}| +% \hfill[\pageref{Lmemes}] +% +% % % \vspace{1.5\baselineskip} % @@ -6159,7 +6302,7 @@ % % \vspace{1.5\baselineskip} % -% \newpage +% % % \textbf{Including secondary structure information} % \medskip @@ -6437,8 +6580,8 @@ % \begin{macrocode} %<*texshade> \NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)] -\message{Package `texshade', Version 1.25 of 2018/01/17.} +\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)] +\message{Package `texshade', Version 1.26 of 2021/04/01.} \PassOptionsToPackage{dvips}{color} \PassOptionsToPackage{dvips}{graphicx} @@ -6480,6 +6623,7 @@ \newread\structurefile \newwrite\featurefile \newread\alignfile \newread\sublogofile \newwrite\exp@rtfile +\newwrite\exp@rt@chimerafile \expandafter\ifx\csname blacktriangleright\endcsname\relax \openin\structurefile = amssymb.sty @@ -7104,6 +7248,16 @@ \xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N} \xdef\HydroY{9} \xdef\HydroZ{N} +\xdef\hardnessA{98} \xdef\hardnessB{0} \xdef\hardnessC{37} +\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48} +\xdef\hardnessG{92} \xdef\hardnessH{50} \xdef\hardnessI{98} +\xdef\hardnessJ{86} \xdef\hardnessK{73} \xdef\hardnessL{98} +\xdef\hardnessM{25} \xdef\hardnessN{86} \xdef\hardnessO{0} +\xdef\hardnessP{91} \xdef\hardnessQ{95} \xdef\hardnessR{69} +\xdef\hardnessS{94} \xdef\hardnessT{98} \xdef\hardnessU{-34} +\xdef\hardnessV{98} \xdef\hardnessW{0} \xdef\hardnessX{0} +\xdef\hardnessY{28} \xdef\hardnessZ{0} + \xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0} @@ -9327,8 +9481,17 @@ \funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up} \funcgroup{Pro}{P}{Apricot}{White}{upper}{up} \else + \xdef\second@{hardness} + \ifx\temp@\second@ + \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up} + \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up} + \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up} + \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up} + \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up} + \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up} + \else \message{} - \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@{% @@ -12836,7 +12999,17 @@ \logocolor{EQ}{RoyalPurple} \logocolor{R}{RedViolet} \logocolor{K}{Black} - \fi\fi\fi\fi\fi\fi\fi + \else + \xdef\second@{hardness} + \ifx\first@\second@ + \clearlogocolors + \logocolor{ADEGILPQSTV}{BlueRed5} + \logocolor{KN}{BlueRed20} + \logocolor{R}{BlueRed40} + \logocolor{CFH}{BlueRed60} + \logocolor{MY}{BlueRed80} + \logocolor{W}{BlueRed100} + \fi\fi\fi\fi\fi\fi\fi\fi } \newcommand\findsubfamily[2][n]{% \xdef\first@{#1} @@ -16898,6 +17071,7 @@ \fi \fi \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} + \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi \ifnum\loopcount=\rule@num\relax \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens @@ -17041,6 +17215,7 @@ \the\innerloopcount} \else \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi + \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi \ifx\collect@valtop\yes \ifnum\v@lseqtop=\loopcount \xdef\v@ltop{\v@ltop,N} @@ -19324,9 +19499,628 @@ \divide\loopcount by 100 % \xdef\third@{\the\loopcount}% } +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%% Chimera export routines %%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}} +\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}} +\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}} +\def\memelabelcutoff#1{% + \xdef\label@threshold@lower{#1} + \setlength\temp@@length{1000sp} + \setlength\temp@@length{\label@threshold@lower\temp@@length} + \loopcount=\temp@@length + \xdef\label@threshold@lowerIOOO{\the\loopcount} + \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount} +} +\def\chimera@color@get#1#2@{% + \xdef\first@{#1}\xdef\third@{#2@} + \ifx\first@\ampers@nd + \else + \ifnum`#1>96 \make@upper\fi + \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi + \expandafter\chimera@color@get\third@ + \fi +} +\def\memered#1{% + \xdef\third@{#1&@} + \xdef\second@{red} + \expandafter\chimera@color@get\third@ +} +\def\memeblue#1{% + \xdef\third@{#1&@} + \xdef\second@{blue} + \expandafter\chimera@color@get\third@ +} +\def\memeyellow#1{% + \xdef\third@{#1&@} + \xdef\second@{yellow} + \expandafter\chimera@color@get\third@ +} +\def\memeblack#1{% + \xdef\third@{#1&@} + \xdef\second@{black} + \expandafter\chimera@color@get\third@ +} +\def\memewhite#1{% + \xdef\third@{#1&@} + \xdef\second@{white} + \expandafter\chimera@color@get\third@ +} +\def\memenone#1{% + \xdef\third@{#1&@} + \xdef\second@{none} + \expandafter\chimera@color@get\third@ +} +\def\memeRed#1{\memered{#1}} +\def\memeBlue#1{\memeblue{#1}} +\def\memeYellow#1{\memeyellow{#1}} +\def\memeBlack#1{\memeblack{#1}} +\def\memeWhite#1{\memewhite{#1}} +\def\memeNone#1{\memenone{#1}} +\def\chimera@colors#1#2@{% + \xdef\first@{#1}\xdef\third@{#2@} + \ifx\first@\ampers@nd + \else + \xdef\second@{\csname chimera@col@\first@\endcsname} + \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@} + \expandafter\chimera@colors\third@ + \fi +} +\def\memeStandardcolors{% + \xdef\chimera@col@A{white} + \xdef\chimera@col@B{none} + \xdef\chimera@col@C{yellow} + \xdef\chimera@col@D{red} + \xdef\chimera@col@E{red} + \xdef\chimera@col@F{black} + \xdef\chimera@col@G{yellow} + \xdef\chimera@col@H{blue} + \xdef\chimera@col@I{black} + \xdef\chimera@col@J{none} + \xdef\chimera@col@K{blue} + \xdef\chimera@col@L{black} + \xdef\chimera@col@M{black} + \xdef\chimera@col@N{yellow} + \xdef\chimera@col@O{none} + \xdef\chimera@col@P{white} + \xdef\chimera@col@Q{yellow} + \xdef\chimera@col@R{blue} + \xdef\chimera@col@S{yellow} + \xdef\chimera@col@T{yellow} + \xdef\chimera@col@U{none} + \xdef\chimera@col@V{white} + \xdef\chimera@col@W{black} + \xdef\chimera@col@X{none} + \xdef\chimera@col@Y{yellow} + \xdef\chimera@col@Z{none} +} +\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}} +\def\chimerachain#1{\xdef\chimerach@in{.#1}} +\catcode`\"=6 \catcode`\#=12 \catcode`\~=12 +\newcommand{\structurememe}[2][chimera.cmd]{% + \ifx\exp@rt@chimera\n@ + \xdef\first@{"2 @} \expandafter\check@letter\first@ + \xdef\first@{"2} \ifletter \get@name@number \fi + \xdef\chimera@seqnum{\first@} + \xdef\exp@rt@chimera{y} + \xdef\first@{"1} + \immediate\openout\exp@rt@chimerafile = \first@ + \fi +} +\def\init@chimera@file{% + \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{} + \xdef\chimera@list@none{} + \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@} + \expandafter\chimera@colors\first@ + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O ¡ o STRUCTURE MEME ¡ . O o} + \immediate\write\exp@rt@chimerafile{###} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix} + \immediate\write\exp@rt@chimerafile{###} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename} + \immediate\write\exp@rt@chimerafile{###} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{close session; background solid white;} + \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename} + \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface} + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale #0' below,} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0} + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca} + \immediate\write\exp@rt@chimerafile{} + \ifshow@sublogo + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move 1 models #1' below,} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{combine #0} + \ifnum\chimera@xdist@nce>0 + \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1} + \fi + \ifnum\chimera@ydist@nce>0 + \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1} + \fi + \ifnum\chimera@zdist@nce>0 + \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1} + \fi + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{wait; focus #0#1} + \ifx\sublogo@name@user\ampers@nd + \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0} + \else + \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0} + \fi + \xdef\first@{\sublogo@name@neg &} + \ifx\first@\ampers@nd + \immediate\write\exp@rt@chimerafile{setattr m name remaining #1} + \else + \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1} + \fi + \else + \immediate\write\exp@rt@chimerafile{\string ############################################################} + \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model} + \immediate\write\exp@rt@chimerafile{\string ############################################################} + \ifx\logo@name@user\ampers@nd + \immediate\write\exp@rt@chimerafile{setattr m name logo #0} + \else + \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0} + \fi + \fi + \immediate\write\exp@rt@chimerafile{} + \immediate\write\exp@rt@chimerafile{############################################################} + \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data} + \immediate\write\exp@rt@chimerafile{############################################################} +} +\def\make@HEX{% + \xdef\sixth@{\the\loopcount}% + \divide\loopcount by 4096\relax% + \ifnum\loopcount=10\relax% + \xdef\seventh@{A}% + \else% + \ifnum\loopcount=11\relax% + \xdef\seventh@{B}% + \else% + \ifnum\loopcount=12\relax% + \xdef\seventh@{C}% + \else% + \ifnum\loopcount=13\relax% + \xdef\seventh@{D}% + \else% + \ifnum\loopcount=14\relax% + \xdef\seventh@{E}% + \else% + \ifnum\loopcount>14\relax% + \xdef\seventh@{F}% + \else% + \xdef\seventh@{\the\loopcount}% + \fi\fi\fi\fi\fi\fi% + \multiply\loopcount by -4096\relax% + \advance\loopcount by \sixth@% + \xdef\sixth@{\the\loopcount}% + \divide\loopcount by 256\relax% + \ifnum\loopcount=10 \relax% + \xdef\eighth@{A}% + \else% + \ifnum\loopcount=11 \relax% + \xdef\eighth@{B}% + \else% + \ifnum\loopcount=12 \relax% + \xdef\eighth@{C}% + \else% + \ifnum\loopcount=13 \relax% + \xdef\eighth@{D}% + \else% + \ifnum\loopcount=14 \relax% + \xdef\eighth@{E}% + \else% + \ifnum\loopcount>14 \relax% + \xdef\eighth@{F}% + \else% + \xdef\eighth@{\the\loopcount}% + \fi\fi\fi\fi\fi\fi% + \xdef\seventh@{\seventh@\eighth@}% + \multiply\loopcount by -256\relax% + \advance\loopcount by \sixth@% + \xdef\sixth@{\the\loopcount}% + \divide\loopcount by 16\relax% + \ifnum\loopcount=10\relax% + \xdef\eighth@{A}% + \else% + \ifnum\loopcount=11\relax% + \xdef\eighth@{B}% + \else% + \ifnum\loopcount=12\relax% + \xdef\eighth@{C}% + \else% + \ifnum\loopcount=13\relax% + \xdef\eighth@{D}% + \else% + \ifnum\loopcount=14\relax% + \xdef\eighth@{E}% + \else% + \ifnum\loopcount>14\relax% + \xdef\eighth@{F}% + \else% + \xdef\eighth@{\the\loopcount}% + \fi\fi\fi\fi\fi\fi% + \xdef\seventh@{\seventh@\eighth@}% + \multiply\loopcount by -16\relax% + \advance\loopcount by \sixth@\relax% + \ifnum\loopcount=10\relax% + \xdef\eighth@{A}% + \else% + \ifnum\loopcount=11\relax% + \xdef\eighth@{B}% + \else% + \ifnum\loopcount=12\relax% + \xdef\eighth@{C}% + \else% + \ifnum\loopcount=13\relax% + \xdef\eighth@{D}% + \else% + \ifnum\loopcount=14\relax% + \xdef\eighth@{E}% + \else% + \ifnum\loopcount>14\relax% + \xdef\eighth@{F}% + \else% + \xdef\eighth@{\the\loopcount}% + \fi\fi\fi\fi\fi\fi% + \xdef\seventh@{\seventh@\eighth@}% +} +\def\write@chimera@data{% + \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi% + \loopcount=\temp@count% + \xdef\fourth@{\the\loopcount @}% + \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% + \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% + \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% + \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% + \expandafter\decimal@E\fourth@% + \fi\fi\fi\fi% + \loopcount=\chimera@subfamily@col@black% + \multiply\loopcount by 65535\relax% + \divide\loopcount by \temp@count% + \xdef\chimera@subfamily@col@black{\the\loopcount}% + \loopcount=65535\relax% + \advance\loopcount by -\chimera@subfamily@col@black% + \xdef\temp@@{\the\loopcount}% +%%%%%%%%%%%%%% +% * This code was taken from: +% * +% * Color Space - A RGB to RYB converter. +% * +% * Copyright (C) 2013 Joshua Gentry +% * +% * This program is free software: you can redistribute it and/or modify +% * it under the terms of the GNU Affero General Public License as +% * published by the Free Software Foundation, either version 3 of the +% * License, or (at your option) any later version. +%. * +% * This program is distributed in the hope that it will be useful, +% * but WITHOUT ANY WARRANTY; without even the implied warranty of +% * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% * GNU Affero General Public License for more details. +%. * +% * You should have received a copy of the GNU Affero General Public License +% * along with this program. If not, see . +% */ +% RgbRyb.prototype.setRyb = function(iRed, iYellow, iBlue) +% { +% //----------------------------------------------------------------------------------------- +% // Validate the arguments. +% VALIDATOR.validate(E10002, "setRyb", arguments, [ +% {type: "number", max: 255, min: 0, arrayType: "int"}, +% {type: "number", max: 255, min: 0, arrayType: "int"}, +% {type: "number", max: 255, min: 0, arrayType: "int"} +% ]); +% +% //----------------------------------------------------------------------------------------- +% // Save the RYB +% this.pRyb = [iRed, iYellow, iBlue]; +% +% // Remove the whiteness from the color. +% var iWhite = Math.min(iRed, iYellow, iBlue); +% +% iRed -= iWhite; +% iYellow -= iWhite; +% iBlue -= iWhite; +% +% var iMaxYellow = Math.max(iRed, iYellow, iBlue); +% +% // Get the green out of the yellow and blue +% var iGreen = Math.min(iYellow, iBlue); +% +% iYellow -= iGreen; +% iBlue -= iGreen; +% +% if (iBlue > 0 && iGreen > 0) +% { +% iBlue *= 2.0; +% iGreen *= 2.0; +% } +% +% // Redistribute the remaining yellow. +% iRed += iYellow; +% iGreen += iYellow; +% +% // Normalize to values. +% var iMaxGreen = Math.max(iRed, iGreen, iBlue); +% +% if (iMaxGreen > 0) +% { +% var iN = iMaxYellow / iMaxGreen; +% +% iRed *= iN; +% iGreen *= iN; +% iBlue *= iN; +% } +% +% // Add the white back in. +% iRed += iWhite; +% iGreen += iWhite; +% iBlue += iWhite; +% +% // Save the RGB +% this.pRgb = [Math.floor(iRed), Math.floor(iGreen), Math.floor(iBlue)]; +% } +%%%%%%%%%%%%%% + \loopcount=\chimera@subfamily@col@blue\relax% + \ifnum\chimera@subfamily@col@yellow>\loopcount\relax% + \loopcount=\chimera@subfamily@col@yellow\relax% + \else% + \ifnum\chimera@subfamily@col@red>\loopcount\relax% + \loopcount=\chimera@subfamily@col@red\relax% + \fi% + \fi% + \xdef\max@yellow{\the\loopcount}% + \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax% + \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}% + \else% + \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}% + \fi% + \loopcount=\chimera@subfamily@col@yellow\relax% + \advance\loopcount by -\chimera@subfamily@col@green% + \xdef\chimera@subfamily@col@yellow{\the\loopcount}% + \loopcount=\chimera@subfamily@col@blue\relax% + \advance\loopcount by -\chimera@subfamily@col@green% + \xdef\chimera@subfamily@col@blue{\the\loopcount}% + \ifnum\chimera@subfamily@col@blue>0\relax% + \ifnum\chimera@subfamily@col@green>0\relax% + \loopcount=\chimera@subfamily@col@blue\relax% + \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}% + \loopcount=\chimera@subfamily@col@green\relax% + \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}% + \fi% + \fi% + \loopcount=\chimera@subfamily@col@green\relax% + \advance\loopcount by \chimera@subfamily@col@yellow% + \xdef\chimera@subfamily@col@green{\the\loopcount}% + \loopcount=\chimera@subfamily@col@red\relax% + \advance\loopcount by \chimera@subfamily@col@yellow% + \xdef\chimera@subfamily@col@red{\the\loopcount}% + \loopcount=\chimera@subfamily@col@blue\relax% + \ifnum\chimera@subfamily@col@green>\loopcount\relax% + \loopcount=\chimera@subfamily@col@green\relax% + \else% + \ifnum\chimera@subfamily@col@red>\loopcount\relax% + \loopcount=\chimera@subfamily@col@red\relax% + \fi% + \fi% + \xdef\max@green{\the\loopcount}% + \loopcount=\chimera@subfamily@col@blue% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@subfamily@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@}% + \loopcount=\chimera@subfamily@col@green% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@subfamily@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@\nineth@}% + \loopcount=\chimera@subfamily@col@red% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@subfamily@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@\nineth@}% + \ifx\chimera@labelOne@set\n@% + \xdef\chimera@labelOne@set{y}% + \xdef\chimera@label@subfamily{.\chimera@label@subfamily}% + \fi% + \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}% + \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}% + \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}% + \ifshow@sublogo + \ifnum\temp@@count>0 \else\temp@@count=1\fi% + \loopcount=\temp@@count% + \xdef\fourth@{\the\loopcount @}% + \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% + \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% + \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% + \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% + \expandafter\decimal@E\fourth@% + \fi\fi\fi\fi% + \loopcount=-\chimera@remaining@col@red\relax% + \xdef\chimera@remaining@col@red{\the\loopcount}% + \loopcount=-\chimera@remaining@col@yellow\relax% + \xdef\chimera@remaining@col@yellow{\the\loopcount}% + \loopcount=-\chimera@remaining@col@blue\relax% + \xdef\chimera@remaining@col@blue{\the\loopcount}% + \loopcount=-\chimera@remaining@col@white\relax% + \xdef\chimera@remaining@col@white{\the\loopcount}% + \loopcount=-\chimera@remaining@col@black% + \multiply\loopcount by 65535\relax% + \divide\loopcount by \temp@count% + \xdef\chimera@remaining@col@black{\the\loopcount}% + \loopcount=65535\relax% + \advance\loopcount by -\chimera@remaining@col@black% + \xdef\temp@@{\the\loopcount}% + \loopcount=\chimera@remaining@col@blue\relax% + \ifnum\chimera@remaining@col@yellow>\loopcount\relax% + \loopcount=\chimera@remaining@col@yellow\relax% + \else% + \ifnum\chimera@remaining@col@red>\loopcount\relax% + \loopcount=\chimera@remaining@col@red\relax% + \fi% + \fi% + \xdef\max@yellow{\the\loopcount}% + \ifnum\chimera@remaining@col@blue<\chimera@remaining@col@yellow\relax% + \xdef\chimera@remaining@col@green{\chimera@remaining@col@blue}% + \else% + \xdef\chimera@remaining@col@green{\chimera@remaining@col@yellow}% + \fi% + \loopcount=\chimera@remaining@col@yellow\relax% + \advance\loopcount by -\chimera@remaining@col@green% + \xdef\chimera@remaining@col@yellow{\the\loopcount}% + \loopcount=\chimera@remaining@col@blue\relax% + \advance\loopcount by -\chimera@remaining@col@green% + \xdef\chimera@remaining@col@blue{\the\loopcount}% + \ifnum\chimera@remaining@col@blue>0\relax% + \ifnum\chimera@remaining@col@green>0\relax% + \loopcount=\chimera@remaining@col@blue\relax% + \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@blue{\the\loopcount}% + \loopcount=\chimera@remaining@col@green\relax% + \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@green{\the\loopcount}% + \fi% + \fi% + \loopcount=\chimera@remaining@col@green\relax% + \advance\loopcount by \chimera@remaining@col@yellow% + \xdef\chimera@remaining@col@green{\the\loopcount}% + \loopcount=\chimera@remaining@col@red\relax% + \advance\loopcount by \chimera@remaining@col@yellow% + \xdef\chimera@remaining@col@red{\the\loopcount}% + \loopcount=\chimera@remaining@col@blue\relax% + \ifnum\chimera@remaining@col@green>\loopcount\relax% + \loopcount=\chimera@remaining@col@green\relax% + \else% + \ifnum\chimera@remaining@col@red>\loopcount\relax% + \loopcount=\chimera@remaining@col@red\relax% + \fi% + \fi% + \xdef\max@green{\the\loopcount}% + \loopcount=\chimera@remaining@col@blue% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@remaining@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@}% + \loopcount=\chimera@remaining@col@green% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@remaining@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@\nineth@}% + \loopcount=\chimera@remaining@col@red% + \ifnum\max@green>0\relax% + \multiply\loopcount by \max@yellow% + \divide\loopcount by \max@green% + \fi% + \advance\loopcount by \chimera@remaining@col@white% + \multiply\loopcount by \temp@@% + \divide\loopcount by \temp@count% + \make@HEX% + \xdef\nineth@{\seventh@\nineth@}% + \ifx\chimera@label@remainingOne@set\n@% + \xdef\chimera@label@remainingOne@set{y}% + \xdef\chimera@label@remaining{.\chimera@label@remaining}% + \fi% + \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}% + \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}% + \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@remaining' #1:\chimera@res@num\chimerach@in @ca}% + \fi% +} +\catcode`\"=12 \catcode`\#=6 \catcode`\~=13 +\def\get@chimera@res@num#1,#2@{\xdef\chimera@res@num{#1}\xdef\chimera@stack{#2}} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%% Chimera export routines end %%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \def\next@logo#1:#2,#3@{% \xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}% \ifx\first@\ampers@nd% + \ifx\exp@rt@chimera\y@% + \xdef\chimera@stack{\chimera@stack @}% + \expandafter\get@chimera@res@num\chimera@stack% + \ifx\chimera@res@num\ampers@nd% + \else% + \write@chimera@data% + \fi% + \xdef\chimera@label@subfamily{}% + \xdef\chimera@label@remaining{}% + \xdef\chimera@subfamily@col@red{0}% + \xdef\chimera@subfamily@col@blue{0}% + \xdef\chimera@subfamily@col@yellow{0}% + \xdef\chimera@subfamily@col@black{0}% + \xdef\chimera@subfamily@col@white{0}% + \xdef\chimera@remaining@col@red{0}% + \xdef\chimera@remaining@col@blue{0}% + \xdef\chimera@remaining@col@yellow{0}% + \xdef\chimera@remaining@col@black{0}% + \xdef\chimera@remaining@col@white{0}% + \xdef\chimera@labelOne@set{n}% + \xdef\chimera@labelTwo@set{n}% + \xdef\chimera@labelThree@set{n}% + \xdef\chimera@label@remainingOne@set{n}% + \xdef\chimera@label@remainingTwo@set{n}% + \xdef\chimera@label@remainingThree@set{n}% + \fi% \ifx\clear@logo\n@% \ifx\hide@sig\n@% \expandafter\firstchar@get\sublogo@sig% @@ -19348,12 +20142,10 @@ \fi% \fi% \temp@count=0% + \temp@@count=0% \kern\box@width% \advance\outerloopcount by 1 % \else% - \ifnum#2=1% - \temp@count=0% - \else% \if\seq@type N% \loopcount=\second@% \multiply\loopcount by 2% @@ -19389,7 +20181,7 @@ \fi\fi\fi\fi% \xdef\third@{\fl@g\temp@}% \ifnum\temp@count<0 % - \ifnum\second@<0 \else\temp@count=0 \fi% + \ifnum\second@<0 \else\temp@@count=-\temp@count\relax\temp@count=0 \fi% \fi% \ifnum\temp@count>0 % \loopcount=\temp@count \xdef\fl@g{}% @@ -19416,7 +20208,64 @@ \kern-\box@width% \fi% \advance\temp@count by \second@% - \fi% + \xdef\temp@{\the\temp@count}% + \ifx\exp@rt@chimera\y@% + \xdef\temp@@{\csname chimera@col@\first@\endcsname}% + \ifnum\second@<0 % + \xdef\temp@@@{\csname chimera@remaining@col@\temp@@\endcsname}% + \temp@count=\temp@@@% + \advance\temp@count by \second@% + \expandafter\xdef\csname chimera@remaining@col@\temp@@\endcsname{\the\temp@count}% + \ifnum\second@<\label@threshold@lowerremainingIOOO% + \ifnum\second@<-999% + \ifx\chimera@label@remainingOne@set\n@% + \xdef\chimera@label@remainingOne@set{y}% + \xdef\chimera@label@remaining{.\chimera@label@remaining}% + \fi% + \fi% + \ifnum\second@<-1999% + \ifx\chimera@label@remainingTwo@set\n@% + \xdef\chimera@label@remainingTwo@set{y}% + \xdef\chimera@label@remaining{:\chimera@label@remaining}% + \fi% + \fi% + \ifnum\second@<-2999% + \ifx\chimera@label@remainingThree@set\n@% + \xdef\chimera@label@remainingThree@set{y}% + \xdef\chimera@label@remaining{>\chimera@label@remaining}% + \fi% + \fi% + \xdef\chimera@label@remaining{\first@\chimera@label@remaining}% + \fi% + \else% + \xdef\temp@@@{\csname chimera@subfamily@col@\temp@@\endcsname}% + \temp@count=\temp@@@% + \advance\temp@count by \second@% + \expandafter\xdef\csname chimera@subfamily@col@\temp@@\endcsname{\the\temp@count}% + \ifnum\second@>\label@threshold@lowerIOOO% + \ifnum\second@>999% + \ifx\chimera@labelOne@set\n@% + \xdef\chimera@labelOne@set{y}% + \xdef\chimera@label@subfamily{.\chimera@label@subfamily}% + \fi% + \fi% + \ifnum\second@>1999% + \ifx\chimera@labelTwo@set\n@% + \xdef\chimera@labelTwo@set{y}% + \xdef\chimera@label@subfamily{:\chimera@label@subfamily}% + \fi% + \fi% + \ifnum\second@>2999% + \ifx\chimera@labelThree@set\n@% + \xdef\chimera@labelThree@set{y}% + \xdef\chimera@label@subfamily{>\chimera@label@subfamily}% + \fi% + \fi% + \xdef\chimera@label@subfamily{\first@\chimera@label@subfamily}% + \fi% + \fi% + \fi% + \temp@count=\temp@% \fi% \xdef\temp@{\last@.}% \ifx\temp@\d@t% @@ -19926,8 +20775,7 @@ \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% -% \vspace{-\bar@length}%%%%%%%%%%%%%%%%%%%%%%% - \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%% + \setlength{\bar@length}{0pt}% \put@feature% \temp@@count=\b@feature@count% \advance\temp@@count by 1% @@ -20680,6 +21528,7 @@ \fi \ifshow@sublogo \closein\sublogofile \fi \ifx\exp@rt\y@ \closeout\exp@rtfile \fi + \ifx\exp@rt@chimera\y@ \closeout\exp@rt@chimerafile \fi% \closein\alignfile \message{)} } @@ -20832,8 +21681,6 @@ \ifnum\loopcount<\seq@count \repeat \xdef\seq@order{\seq@order,@} \killseq@count=\seq@count -% \seq@percent=100 -% \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi \fi \fi } @@ -21105,6 +21952,14 @@ \xdef\thresh@ld@{\the\loopcount} \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 \xdef\all@thresh@ld@{\the\loopcount} + \if\exp@rt@chimera\y@% + \ifshow@logo% + \init@chimera@file% + \else% + \ifshow@sublogo% + \init@chimera@file% + \fi\fi% + \fi% \bgroup \ifx\out@put\y@\bigskip\fi \iffuncmode \show@consfalse \fi @@ -21262,6 +22117,32 @@ \expandafter\xdef\csname group@num1\endcsname{0} \expandafter\xdef\csname group@num2\endcsname{0} \xdef\exp@rt@num{0} \xdef\exp@rt{n} +\xdef\exp@rt@chimera@num{1} \xdef\exp@rt@chimera{n} \xdef\chimera@stack{} +\xdef\chimerab@llSc@le{1.0} +\memelabelcutoff{0.1} +\xdef\chimera@labelOne@set{n} +\xdef\chimera@labelTwo@set{n} +\xdef\chimera@labelThree@set{n} +\xdef\chimera@labelOne@remaining@set{n} +\xdef\chimera@labelTwo@remaining@set{n} +\xdef\chimera@labelThree@remaining@set{n} +\xdef\chimera@xdist@nce{0} \xdef\chimera@ydist@nce{40} \xdef\chimera@zdist@nce{0} +\xdef\chimerach@in{} \xdef\chimera@seqnum{0} +\xdef\chimera@label@subfamily{} \xdef\chimera@label@remaining{} +\memeStandardcolors +\xdef\chimera@subfamily@col@red{0}% +\xdef\chimera@subfamily@col@blue{0}% +\xdef\chimera@subfamily@col@yellow{0}% +\xdef\chimera@subfamily@col@black{0}% +\xdef\chimera@subfamily@col@white{0}% +\xdef\chimera@subfamily@col@none{0}% +\xdef\chimera@remaining@col@red{0}% +\xdef\chimera@remaining@col@blue{0}% +\xdef\chimera@remaining@col@yellow{0}% +\xdef\chimera@remaining@col@black{0}% +\xdef\chimera@remaining@col@white{0}% +\xdef\chimera@remaining@col@none{0}% +\xdef\echo@filename{} \xdef\divref@{0} \xdef\all@thresh@ld{100} \all@shadefalse \hidefeaturenames \hidefeaturestylenames @@ -24118,6 +24999,2606 @@ cons 301 23322--32222222223--3222223233322122-111112221------223 355 % % \end{macrocode} % \begin{macrocode} +%<*AQPlogo> +############################################################ +### +### . O ¡ o STRUCTURE MEME ¡ . O o +### +### Chimera command file generated from TeXshade logo data +### use '.cmd' or '.com' suffix +### +### Reference sequence: 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8 +### +############################################################ + +############################################################ +### residue colors: (set with \memeRed{residues} etc.) +### DE (Red) +### HKR (Blue) +### CGNQSTY (Yellow) +### FILMW (Black) +### APV (White) +############################################################ + +############################################################ +### residues in labels: (\memelabelcutoff{bit-value}) +### 0.1 bit required to appear +### > : . indicate 3, 2, and 1 bit levels +############################################################ + +############################################################ +### initialize & load structure +############################################################ +close session; background solid white; +echo load structure file for 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8 +open #0; ~ribbon; ~surface + +############################################################ +### to set ball scale, change factor ]0.0 - 1.0] +### in 'setattr m ballScale #0' below, +### or use the \chimeraballScale{factor} command +############################################################ +setattr m ballScale 1.0 #0 + +############################################################ +### display alpha-carbons only +############################################################ +represent bs @ca; show @ca + +############################################################ +### name structure model +############################################################ +setattr m name logo #0 + +############################################################ +### logo data +############################################################ +setattr a radius 1.473 #0:7@ca +setattr a color #0CC010570517 #0:7@ca +setattr a name '|| .FLS' #0:7@ca +setattr a radius 1.061 #0:8@ca +setattr a color #22962541099F #0:8@ca +setattr a name '|| .WYLF' #0:8@ca +setattr a radius 2.096 #0:9@ca +setattr a color #09032F7DC2EF #0:9@ca +setattr a name '|| R.KQ' #0:9@ca +setattr a radius 2.178 #0:10@ca +setattr a color #CA40C889AC09 #0:10@ca +setattr a name '|| A.EKQ' #0:10@ca +setattr a radius 1.232 #0:11@ca +setattr a color #8A718A714538 #0:11@ca +setattr a name '|| .VGAYLF' #0:11@ca +setattr a radius 1.913 #0:12@ca +setattr a color #09F109F105D4 #0:12@ca +setattr a name '|| .ILFV' #0:12@ca +setattr a radius 3.112 #0:13@ca +setattr a color #FC8DFC8DCC2F #0:13@ca +setattr a name '|| A:.GSV' #0:13@ca +setattr a radius 4.322 #0:14@ca +setattr a color #FFFF00000000 #0:14@ca +setattr a name '|| E>:.' #0:14@ca +setattr a radius 3.440 #0:15@ca +setattr a color #016B016B0083 #0:15@ca +setattr a name '|| F:.LC' #0:15@ca +setattr a radius 2.230 #0:16@ca +setattr a color #075807A505D3 #0:16@ca +setattr a name '|| .LIVF' #0:16@ca +setattr a radius 2.657 #0:17@ca +setattr a color #FFFFFFFF783D #0:17@ca +setattr a name '|| A.GS' #0:17@ca +setattr a radius 3.773 #0:18@ca +setattr a color #D7E8D7E80000 #0:18@ca +setattr a name '|| T>:.M' #0:18@ca +setattr a radius 2.097 #0:19@ca +setattr a color #088A088A0420 #0:19@ca +setattr a name '|| .LFA' #0:19@ca +setattr a radius 2.481 #0:20@ca +setattr a color #00F200F200BD #0:20@ca +setattr a name '|| L.IFVW' #0:20@ca +setattr a radius 3.057 #0:21@ca +setattr a color #004A004A000E #0:21@ca +setattr a name '|| F.L' #0:21@ca +setattr a radius 2.701 #0:22@ca +setattr a color #3BC23BC23BC2 #0:22@ca +setattr a name '|| V.LI' #0:22@ca +setattr a radius 2.024 #0:23@ca +setattr a color #1ECB1ECB069F #0:23@ca +setattr a name '|| .FYLV' #0:23@ca +setattr a radius 1.768 #0:24@ca +setattr a color #1B441B441476 #0:24@ca +setattr a name '|| .IFALV' #0:24@ca +setattr a radius 2.841 #0:25@ca +setattr a color #FFFFFFFF08A6 #0:25@ca +setattr a name '|| G.TS' #0:25@ca +setattr a radius 1.326 #0:26@ca +setattr a color #879582864490 #0:26@ca +setattr a name '|| .VILC' #0:26@ca +setattr a radius 2.916 #0:27@ca +setattr a color #9F8A9F8A175B #0:27@ca +setattr a name '|| G.LA' #0:27@ca +setattr a radius 2.371 #0:28@ca +setattr a color #EF03EF032197 #0:28@ca +setattr a name '|| S.TAVC' #0:28@ca +setattr a radius 2.180 #0:29@ca +setattr a color #E860E860B33C #0:29@ca +setattr a name '|| V.AGC' #0:29@ca +setattr a radius 1.761 #0:30@ca +setattr a color #1CBC1CBC1779 #0:30@ca +setattr a name '|| .IMALV' #0:30@ca +setattr a radius 1.470 #0:31@ca +setattr a color #C42ECDFE4527 #0:31@ca +setattr a name '|| .GAQN' #0:31@ca +setattr a radius 1.181 #0:32@ca +setattr a color #5DEA64CE3980 #0:32@ca +setattr a name '|| .VYFWA' #0:32@ca +setattr a radius 0.902 #0:33@ca +setattr a color #75B6A8AB46D8 #0:33@ca +setattr a name '|| .KNV' #0:33@ca +setattr a radius 0.889 #0:34@ca +setattr a color #10BD5883373D #0:34@ca +setattr a name '|| .KLR' #0:34@ca +setattr a radius 0.906 #0:35@ca +setattr a color #74E177B12C96 #0:35@ca +setattr a name '|| .SLA' #0:35@ca +setattr a radius 0.623 #0:36@ca +setattr a color #83EF89E63287 #0:36@ca +setattr a name '|| .T' #0:36@ca +setattr a radius 0.820 #0:37@ca +setattr a color #D292B0543AE0 #0:37@ca +setattr a name '|| .SA' #0:37@ca +setattr a radius 0.623 #0:38@ca +setattr a color #925787241E9C #0:38@ca +setattr a name '|| .S' #0:38@ca +setattr a radius 0.436 #0:39@ca +setattr a color #4EE56E191F33 #0:39@ca +setattr a name '|| .' #0:39@ca +setattr a radius 0.550 #0:40@ca +setattr a color #B86FC42D53F3 #0:40@ca +setattr a name '|| .GA' #0:40@ca +setattr a radius 0.420 #0:41@ca +setattr a color #19491949024C #0:41@ca +setattr a name '|| .W' #0:41@ca +setattr a radius 0.498 #0:42@ca +setattr a color #01D201360000 #0:42@ca +setattr a name '|| .LI' #0:42@ca +setattr a radius 0.312 #0:43@ca +setattr a color #CCB5A5D24091 #0:43@ca +setattr a name '|| .' #0:43@ca +setattr a radius 2.906 #0:44@ca +setattr a color #1B971B971B0A #0:44@ca +setattr a name '|| I.VA' #0:44@ca +setattr a radius 2.647 #0:45@ca +setattr a color #FC87FC87A050 #0:45@ca +setattr a name '|| A.SN' #0:45@ca +setattr a radius 1.815 #0:46@ca +setattr a color #04BD04BD0447 #0:46@ca +setattr a name '|| .LWIVF' #0:46@ca +setattr a radius 2.362 #0:47@ca +setattr a color #E816E81695BC #0:47@ca +setattr a name '|| A.GCST' #0:47@ca +setattr a radius 2.672 #0:48@ca +setattr a color #006602D30BD3 #0:48@ca +setattr a name '|| F.HW' #0:48@ca +setattr a radius 3.512 #0:49@ca +setattr a color #FFFFFFFF284F #0:49@ca +setattr a name '|| G:.A' #0:49@ca +setattr a radius 2.212 #0:50@ca +setattr a color #142D142D00F9 #0:50@ca +setattr a name '|| .LGFI' #0:50@ca +setattr a radius 2.009 #0:51@ca +setattr a color #8C0F8C0F44B5 #0:51@ca +setattr a name '|| .AMGS' #0:51@ca +setattr a radius 2.611 #0:52@ca +setattr a color #1CAF1CAF1AFA #0:52@ca +setattr a name '|| I.VL' #0:52@ca +setattr a radius 1.862 #0:53@ca +setattr a color #329F329F1E62 #0:53@ca +setattr a name '|| .FAGMTL' #0:53@ca +setattr a radius 1.664 #0:54@ca +setattr a color #760E760E49F7 #0:54@ca +setattr a name '|| .VTAMILF' #0:54@ca +setattr a radius 1.938 #0:55@ca +setattr a color #3AB33AB324F0 #0:55@ca +setattr a name '|| .LAGM' #0:55@ca +setattr a radius 2.923 #0:56@ca +setattr a color #A74DA74DA74D #0:56@ca +setattr a name '|| V.IA' #0:56@ca +setattr a radius 1.937 #0:57@ca +setattr a color #BBE9C06E0F4D #0:57@ca +setattr a name '|| .YQSAL' #0:57@ca +setattr a radius 1.734 #0:58@ca +setattr a color #BF91BF91517A #0:58@ca +setattr a name '|| .CAVSIT' #0:58@ca +setattr a radius 1.519 #0:59@ca +setattr a color #94C794C73679 #0:59@ca +setattr a name '|| .TAVLGFS' #0:59@ca +setattr a radius 2.729 #0:60@ca +setattr a color #E1A0E1A074F3 #0:60@ca +setattr a name '|| AG.' #0:60@ca +setattr a radius 1.939 #0:61@ca +setattr a color #7125B8920DDC #0:61@ca +setattr a name '|| .GHN' #0:61@ca +setattr a radius 2.932 #0:62@ca +setattr a color #102110210EDC #0:62@ca +setattr a name '|| I.VL' #0:62@ca +setattr a radius 4.044 #0:63@ca +setattr a color #F914F91401AF #0:63@ca +setattr a name '|| S>:.' #0:63@ca +setattr a radius 0.728 #0:64@ca +setattr a color #FFFFFFFF20B3 #0:64@ca +setattr a name '|| .G' #0:64@ca +setattr a radius 3.132 #0:65@ca +setattr a color #FFFFFFFF5555 #0:65@ca +setattr a name '|| GA.' #0:65@ca +setattr a radius 3.981 #0:66@ca +setattr a color #06F10C37FAC9 #0:66@ca +setattr a name '|| H>:.A' #0:66@ca +setattr a radius 2.420 #0:67@ca +setattr a color #06C906C906C9 #0:67@ca +setattr a name '|| I.LVF' #0:67@ca +setattr a radius 4.322 #0:68@ca +setattr a color #FFFFFFFF0000 #0:68@ca +setattr a name '|| N>:.' #0:68@ca +setattr a radius 4.218 #0:69@ca +setattr a color #FFFFFFFFFFFF #0:69@ca +setattr a name '|| P>:.' #0:69@ca +setattr a radius 4.264 #0:70@ca +setattr a color #FFFFFFFFFE41 #0:70@ca +setattr a name '|| A>:.' #0:70@ca +setattr a radius 3.811 #0:71@ca +setattr a color #DB83DB83DB83 #0:71@ca +setattr a name '|| V>:.I' #0:71@ca +setattr a radius 3.595 #0:72@ca +setattr a color #FFFFFFFF01B5 #0:72@ca +setattr a name '|| T:.S' #0:72@ca +setattr a radius 2.524 #0:73@ca +setattr a color #03D603D603A0 #0:73@ca +setattr a name '|| F.LIV' #0:73@ca +setattr a radius 2.925 #0:74@ca +setattr a color #EF21EF214BCA #0:74@ca +setattr a name '|| G.A' #0:74@ca +setattr a radius 2.254 #0:75@ca +setattr a color #0D920D920731 #0:75@ca +setattr a name '|| L.MAFC' #0:75@ca +setattr a radius 1.789 #0:76@ca +setattr a color #2518251817DB #0:76@ca +setattr a name '|| .FLACW' #0:76@ca +setattr a radius 1.947 #0:77@ca +setattr a color #226A230D1A05 #0:77@ca +setattr a name '|| .LVI' #0:77@ca +setattr a radius 1.627 #0:78@ca +setattr a color #B633B9314FD0 #0:78@ca +setattr a name '|| .AGSF' #0:78@ca +setattr a radius 2.199 #0:79@ca +setattr a color #50ACA8551176 #0:79@ca +setattr a name '|| .GRCAS' #0:79@ca +setattr a radius 1.325 #0:80@ca +setattr a color #17719FE59351 #0:80@ca +setattr a name '|| .KRQHN' #0:80@ca +setattr a radius 2.039 #0:81@ca +setattr a color #0B5509E10989 #0:81@ca +setattr a name '|| 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'|| G>:.A' #0:243@ca +setattr a radius 3.083 #0:244@ca +setattr a color #FFFFFFFF924E #0:244@ca +setattr a name '|| AG.S' #0:244@ca +setattr a radius 1.637 #0:245@ca +setattr a color #82C582C559C0 #0:245@ca +setattr a name '|| .AGVIL' #0:245@ca +setattr a radius 2.327 #0:246@ca +setattr a color #0B420B42097B #0:246@ca +setattr a name '|| L.IAV' #0:246@ca +setattr a radius 3.218 #0:247@ca +setattr a color #F5EAF5EAB6C2 #0:247@ca +setattr a name '|| A:.G' #0:247@ca +setattr a radius 2.479 #0:248@ca +setattr a color #F258F25887A4 #0:248@ca +setattr a name '|| A.GVS' #0:248@ca +setattr a radius 1.773 #0:249@ca +setattr a color #0F440F4409C4 #0:249@ca +setattr a name '|| .LIFAV' #0:249@ca +setattr a radius 1.935 #0:250@ca +setattr a color #445F445F1DAC #0:250@ca +setattr a name '|| .IYVL' #0:250@ca +setattr a radius 2.590 #0:251@ca +setattr a color #501E8C4C048C #0:251@ca +setattr a name '|| Y.HWF' #0:251@ca +setattr a radius 0.903 #0:252@ca +setattr a color #92D47EB2186D #0:252@ca +setattr a name '|| .QE' #0:252@ca +setattr a radius 1.003 #0:253@ca +setattr a color #46EF47CA1A99 #0:253@ca +setattr a name '|| .FYVL' #0:253@ca +setattr a radius 1.957 #0:254@ca +setattr a color #2F9A30592D5E #0:254@ca +setattr a name '|| .VLIFM' #0:254@ca +setattr a radius 1.931 #0:255@ca +setattr a color #04C505050243 #0:255@ca +setattr a name '|| .LIF' #0:255@ca +setattr a radius 0.984 #0:256@ca +setattr a color #192B52294732 #0:256@ca +setattr a name '|| .RI' #0:256@ca +setattr a radius 1.032 #0:257@ca +setattr a color #BC94BC948612 #0:257@ca +setattr a name '|| .AP' #0:257@ca +setattr a radius 0.726 #0:258@ca +setattr a color #501D60C71220 #0:258@ca +setattr a name '|| .SI' #0:258@ca +setattr a radius 0.319 #0:259@ca +setattr a color #115914170EEA #0:259@ca +setattr a name '|| .L' #0:259@ca +setattr a radius 0.267 #0:260@ca +setattr a color #D5CFB5356B62 #0:260@ca +setattr a name '|| .P' #0:260@ca +setattr a radius 0.155 #0:261@ca +setattr a color #BD3DB2331614 #0:261@ca +setattr a name '|| .' #0:261@ca +setattr a radius 0.220 #0:262@ca +setattr a color #A69CA69C854A #0:262@ca +setattr a name '|| .' #0:262@ca +setattr a radius 0.231 #0:263@ca +setattr a color #B9C28208662A #0:263@ca +setattr a name '|| .' #0:263@ca +setattr a radius 0.215 #0:264@ca +setattr a color #A565AD6A4F30 #0:264@ca +setattr a name '|| .' #0:264@ca +setattr a radius 0.120 #0:265@ca +setattr a color #8C0082AA2555 #0:265@ca +setattr a name '|| .' #0:265@ca +setattr a radius 0.133 #0:266@ca +setattr a color #6CD88C653BF1 #0:266@ca +setattr a name '|| .' #0:266@ca +setattr a radius 0.684 #0:267@ca +setattr a color #CCC3A7885B01 #0:267@ca +setattr a name '|| .PA' #0:267@ca +setattr a radius 0.598 #0:268@ca +setattr a color #215145631FCA #0:268@ca +setattr a name '|| .F' #0:268@ca +setattr a radius 0.897 #0:269@ca +setattr a color #3ED96AAF3F60 #0:269@ca +setattr a name '|| .KE' #0:269@ca +setattr a radius 0.771 #0:270@ca +setattr a color #7DFB8C3642F1 #0:270@ca +setattr a name '|| .SLPA' #0:270@ca +setattr a radius 0.412 #0:271@ca +setattr a color #62D273CCB108 #0:271@ca +setattr a name '|| .K' #0:271@ca +setattr a radius 0.237 #0:272@ca +setattr a color #EEB6E6125BD0 #0:272@ca +setattr a name '|| .' #0:272@ca +setattr a radius 0.254 #0:273@ca +setattr a color #CAABA0853237 #0:273@ca +setattr a name '|| .' #0:273@ca +setattr a radius 0.262 #0:274@ca +setattr a color #4A0258CF3B35 #0:274@ca +setattr a name '|| .' #0:274@ca +setattr a radius 0.253 #0:275@ca +setattr a color #841384135601 #0:275@ca +setattr a name '|| .' #0:275@ca +setattr a radius 0.200 #0:276@ca +setattr a color #49027CD3A992 #0:276@ca +setattr a name '|| .' #0:276@ca +setattr a radius 0.300 #0:277@ca +setattr a color #C28EAE1351EB #0:277@ca +setattr a name '|| .' #0:277@ca +setattr a radius 0.264 #0:278@ca +setattr a color #22614CB10DE2 #0:278@ca +setattr a name '|| .' #0:278@ca +setattr a radius 0.288 #0:279@ca +setattr a color #434B36849955 #0:279@ca +setattr a name '|| .K' #0:279@ca +setattr a radius 0.192 #0:280@ca +setattr a color #558E6CE37C71 #0:280@ca +setattr a name '|| .' #0:280@ca +setattr a radius 0.232 #0:281@ca +setattr a color #2E471A71358C #0:281@ca +setattr a name '|| .' #0:281@ca +% +% \end{macrocode} +% \begin{macrocode} +%<*AQPsublogo> +############################################################ +### +### . O ¡ o STRUCTURE MEME ¡ . O o +### +### Chimera command file generated from TeXshade logo data +### use '.cmd' or '.com' suffix +### +### Reference sequence: 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8 +### +############################################################ + +############################################################ +### residue colors: (set with \memeRed{residues} etc.) +### DE (Red) +### HKR (Blue) +### CGNQSTY (Yellow) +### FILMW (Black) +### APV (White) +############################################################ + +############################################################ +### residues in labels: (\memelabelcutoff{bit-value}) +### 0.1 bit required to appear +### > : . indicate 3, 2, and 1 bit levels +############################################################ + +############################################################ +### initialize & load structure +############################################################ +close session; background solid white; +echo load structure file for 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8 +open #0; ~ribbon; ~surface + +############################################################ +### to set ball scale, change factor ]0.0 - 1.0] +### in 'setattr m ballScale #0' below, +### or use the \chimeraballScale{factor} command +############################################################ +setattr m ballScale 1.0 #0 + +############################################################ +### display alpha-carbons only +############################################################ +represent bs @ca; show @ca + +############################################################ +### duplicate structure; +### to alter direction or Angstrom distance, set +### 'move 1 models #1' below, +### or use the \chimeraaxisdistance{x}{y}{z} command +############################################################ +combine #0 +move x 1 40 models #1 + +############################################################ +### focus view and name structure models +############################################################ +wait; focus #0#1 +setattr m name subfamily #0 +setattr m name remaining #1 + +############################################################ +### logo data +############################################################ +setattr a radius 1.413 #0:7@ca +setattr a color #017A017A046F #0:7@ca +setattr a name '|| .LWMK' #0:7@ca +setattr a radius 1.408 #1:7@ca +setattr a color #17361752081A #1:7@ca +setattr a name '|| FSA' #1:7@ca +setattr a radius 0.795 #0:8@ca +setattr a color #368759C23733 #0:8@ca +setattr a name '|| .MKVA' #0:8@ca +setattr a radius 0.799 #1:8@ca +setattr a color #26AC26AC0000 #1:8@ca +setattr a name '|| .WY' #1:8@ca +setattr a radius 1.377 #0:9@ca +setattr a color #BB08AF463B97 #0:9@ca +setattr a name '|| .VSGTAN' #0:9@ca +setattr a radius 1.386 #1:9@ca +setattr a color #00000137DFF9 #1:9@ca +setattr a name '|| .RK' #1:9@ca +setattr a radius 2.223 #0:10@ca +setattr a color #A97E52390E6C #0:10@ca +setattr a name '|| .EQKWND' #0:10@ca +setattr a radius 2.225 #1:10@ca +setattr a color #F078F5B6E5FC #1:10@ca +setattr a name '|| A:.' #1:10@ca +setattr a radius 0.931 #0:11@ca +setattr a color #33DA33DA03B6 #0:11@ca +setattr a name '|| .FCT' #0:11@ca +setattr a radius 0.930 #1:11@ca +setattr a color #ABB8ABB867E3 #1:11@ca +setattr a name '|| .VGL' #1:11@ca +setattr a radius 0.906 #0:12@ca +setattr a color #02C102C10000 #0:12@ca +setattr a name '|| .L' #0:12@ca +setattr a radius 0.907 #1:12@ca +setattr a color #51EA51EA37E3 #1:12@ca +setattr a name '|| .IVT' #1:12@ca +setattr a radius 1.929 #0:13@ca +setattr a color #E361E3610000 #0:13@ca +setattr a name '|| .GSTM' #0:13@ca +setattr a radius 1.931 #1:13@ca +setattr a color #F042F042F042 #1:13@ca +setattr a name '|| A.V' #1:13@ca +setattr a radius 0.001 #0:14@ca +setattr a color #FFFF00000000 #0:14@ca +setattr a name '|| .' #0:14@ca +setattr a radius 0.001 #1:14@ca +setattr a color #000000000000 #1:14@ca +setattr a name '|| .' #1:14@ca +setattr a radius 0.947 #0:15@ca +setattr a color #DA0DDA0D2AE9 #0:15@ca +setattr a name '|| .CVTG' #0:15@ca +setattr a radius 0.949 #1:15@ca +setattr a color #000000000000 #1:15@ca +setattr a name '|| .F' #1:15@ca +setattr a radius 1.205 #0:16@ca +setattr a color #008300830000 #0:16@ca +setattr a name '|| L.' #0:16@ca +setattr a radius 1.201 #1:16@ca +setattr a color #23C025AE1D9F #1:16@ca +setattr a name '|| .IV' #1:16@ca +setattr a radius 2.268 #0:17@ca +setattr a color #FFFFFFFF0000 #0:17@ca +setattr a name '|| G:.' #0:17@ca +setattr a radius 2.265 #1:17@ca +setattr a color #FFA8FFA8D161 #1:17@ca +setattr a name '|| A.S' #1:17@ca +setattr a radius 0.610 #0:18@ca +setattr a color #FFFFFFFF0000 #0:18@ca +setattr a name '|| .T' #0:18@ca +setattr a radius 0.610 #1:18@ca +setattr a color #0A3D0A3D0000 #1:18@ca +setattr a name '|| .MS' #1:18@ca +setattr a radius 1.223 #0:19@ca +setattr a color #B26AB26A77B3 #0:19@ca +setattr a name '|| .AMYG' #0:19@ca +setattr a radius 1.224 #1:19@ca +setattr a color #00C100C10000 #1:19@ca +setattr a name '|| .LFI' #1:19@ca +setattr a radius 1.021 #0:20@ca +setattr a color #3F1F3F1F3F1F #0:20@ca +setattr a name '|| .IV' #0:20@ca +setattr a radius 1.016 #1:20@ca +setattr a color #00BA00BA0000 #1:20@ca +setattr a name '|| .LWM' #1:20@ca +setattr a radius 3.234 #0:21@ca +setattr a color #004900490049 #0:21@ca +setattr a name '|| L:.MV' #0:21@ca +setattr a radius 3.235 #1:21@ca +setattr a color #006A006A0000 #1:21@ca +setattr a name '|| F>:.Y' #1:21@ca +setattr a radius 2.123 #0:22@ca +setattr a color #000000000000 #0:22@ca +setattr a name '|| I.M' #0:22@ca +setattr a radius 2.122 #1:22@ca +setattr a color #503B503B503B #1:22@ca +setattr a name '|| V.L' #1:22@ca +setattr a radius 1.631 #0:23@ca +setattr a color #198619861986 #0:23@ca +setattr a name '|| .IVLMA' #0:23@ca +setattr a radius 1.630 #1:23@ca +setattr a color #494249420000 #1:23@ca +setattr a name '|| .YF' #1:23@ca +setattr a radius 1.693 #0:24@ca +setattr a color #005A005A0000 #0:24@ca +setattr a name '|| .FL' #0:24@ca +setattr a radius 1.691 #1:24@ca +setattr a color #47B447B4371E #1:24@ca +setattr a name '|| .IAVG' #1:24@ca +setattr a radius 1.749 #0:25@ca +setattr a color #FFFFFFFF0000 #0:25@ca +setattr a name '|| G.' #0:25@ca +setattr a radius 1.746 #1:25@ca +setattr a color #FF8EFF8E163F #1:25@ca +setattr a name '|| T.SA' #1:25@ca +setattr a radius 0.938 #0:26@ca +setattr a color #FFFFFFFF26C1 #0:26@ca +setattr a name '|| .NCAGT' #0:26@ca +setattr a radius 0.936 #1:26@ca +setattr a color #849179BF529B #1:26@ca +setattr a name '|| .VIS' #1:26@ca +setattr a radius 1.511 #0:27@ca +setattr a color #FFFFFFFF0000 #0:27@ca +setattr a name '|| G.S' #0:27@ca +setattr a radius 1.507 #1:27@ca +setattr a color #201720172017 #1:27@ca +setattr a name '|| .LAV' #1:27@ca +setattr a radius 1.494 #0:28@ca +setattr a color #FFFFFFFF8BA6 #0:28@ca +setattr a name '|| .VCA' #0:28@ca +setattr a radius 1.496 #1:28@ca +setattr a color #FA8BFA8B0000 #1:28@ca +setattr a name '|| .TS' #1:28@ca +setattr a radius 1.126 #0:29@ca +setattr a color #9E249E24761D #0:29@ca +setattr a name '|| .VIC' #0:29@ca +setattr a radius 1.125 #1:29@ca +setattr a color #FFC4FFC4C29C #1:29@ca +setattr a name '|| .ATG' #1:29@ca +setattr a radius 1.985 #0:30@ca +setattr a color #FFFFFFFFF274 #0:30@ca +setattr a name '|| A.' #0:30@ca +setattr a radius 1.980 #1:30@ca +setattr a color #055E055E033D #1:30@ca +setattr a name '|| .IMLV' #1:30@ca +setattr a radius 0.860 #0:31@ca +setattr a color #73229C7B0000 #0:31@ca +setattr a name '|| .QHM' #0:31@ca +setattr a radius 0.853 #1:31@ca +setattr a color #90879CBE1EEE #1:31@ca +setattr a name '|| .G' #1:31@ca +setattr a radius 0.902 #0:32@ca +setattr a color #6306630650D8 #0:32@ca +setattr a name '|| .VLMT' #0:32@ca +setattr a radius 0.905 #1:32@ca +setattr a color #2A49355B0000 #1:32@ca +setattr a name '|| .YWF' #1:32@ca +setattr a radius 0.680 #0:33@ca +setattr a color #E7C0CD29A547 #0:33@ca +setattr a name '|| .VT' #0:33@ca +setattr a radius 0.675 #1:33@ca +setattr a color #B909CA8F530E #1:33@ca +setattr a name '|| .ASG' #1:33@ca +setattr a radius 1.038 #0:34@ca +setattr a color #07C807C807C8 #0:34@ca +setattr a name '|| .LV' #0:34@ca +setattr a radius 1.025 #1:34@ca +setattr a color #038A7C8944CB #1:34@ca +setattr a name '|| .KRS' #1:34@ca +setattr a radius 0.578 #0:35@ca +setattr a color #0D49A28B664F #0:35@ca +setattr a name '|| .K' #0:35@ca +setattr a radius 0.576 #1:35@ca +setattr a color #292A184A076A #1:35@ca +setattr a name '|| .L' #1:35@ca +setattr a radius 0.646 #0:36@ca +setattr a color #00008D9294F1 #0:36@ca +setattr a name '|| .KGR' #0:36@ca +setattr a radius 0.640 #1:36@ca +setattr a color #B433A77E4332 #1:36@ca +setattr a name '|| .TP' #1:36@ca +setattr a radius 0.452 #0:37@ca +setattr a color #9ECE9ECE1FAB #0:37@ca +setattr a name '|| .TG' #0:37@ca +setattr a radius 0.450 #1:37@ca +setattr a color #CD8F816D2FDB #1:37@ca +setattr a name '|| .DN' #1:37@ca +setattr a radius 0.422 #0:38@ca +setattr a color #0D429CCA926A #0:38@ca +setattr a name '|| .KS' #0:38@ca +setattr a radius 0.418 #1:38@ca +setattr a color #D4E6630C3B33 #1:38@ca +setattr a name '|| .DP' #1:38@ca +setattr a radius 0.356 #0:39@ca +setattr a color #31ED4EDB2A76 #0:39@ca +setattr a name '|| .F' #0:39@ca +setattr a radius 0.356 #1:39@ca +setattr a color #1C6865342C63 #1:39@ca +setattr a name '|| .KT' #1:39@ca +setattr a radius 0.518 #0:40@ca +setattr a color #A11CBD470000 #0:40@ca +setattr a name '|| .G' #0:40@ca +setattr a radius 0.521 #1:40@ca +setattr a color #CCF6CCF6B3D6 #1:40@ca +setattr a name '|| .A' #1:40@ca +setattr a radius 0.325 #0:41@ca +setattr a color #406540650587 #0:41@ca +setattr a name '|| .' #0:41@ca +setattr a radius 0.330 #1:41@ca +setattr a color #000000000000 #1:41@ca +setattr a name '|| .W' #1:41@ca +setattr a radius 0.588 #0:42@ca +setattr a color #020001590000 #0:42@ca +setattr a name '|| .LI' #0:42@ca +setattr a radius 0.593 #1:42@ca +setattr a color #000000000000 #1:42@ca +setattr a name '|| .F' #1:42@ca +setattr a radius 0.355 #0:43@ca +setattr a color #D53DA87C33FE #0:43@ca +setattr a name '|| .T' #0:43@ca +setattr a radius 0.364 #1:43@ca +setattr a color #379937993799 #1:43@ca +setattr a name '|| .FA' #1:43@ca +setattr a radius 0.566 #0:44@ca +setattr a color #000000000000 #0:44@ca +setattr a name '|| .IL' #0:44@ca +setattr a radius 0.564 #1:44@ca +setattr a color #FF17FF17F185 #1:44@ca +setattr a name '|| .AVP' #1:44@ca +setattr a radius 1.724 #0:45@ca +setattr a color #FFFFFFFF2A2B #0:45@ca +setattr a name '|| N.TV' #0:45@ca +setattr a radius 1.728 #1:45@ca +setattr a color #F855F855F855 #1:45@ca +setattr a name '|| A.' #1:45@ca +setattr a radius 0.698 #0:46@ca +setattr a color #22F922F9119F #0:46@ca +setattr a name '|| .FA' #0:46@ca +setattr a radius 0.703 #1:46@ca +setattr a color #01CB01CB01CB #1:46@ca +setattr a name '|| .WL' #1:46@ca +setattr a radius 2.055 #0:47@ca +setattr a color #932593250000 #0:47@ca +setattr a name '|| G.IM' #0:47@ca +setattr a radius 2.056 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#F4FD00000000 #1:279@ca +setattr a name '|| .D' #1:279@ca +setattr a radius 0.204 #0:280@ca +setattr a color #4A097FFF5B9B #0:280@ca +setattr a name '|| .' #0:280@ca +setattr a radius 0.202 #1:280@ca +setattr a color #43B843B847BE #1:280@ca +setattr a name '|| .' #1:280@ca +setattr a radius 0.286 #0:281@ca +setattr a color #11C61D553638 #0:281@ca +setattr a name '|| .L' #0:281@ca +setattr a radius 0.289 #1:281@ca +setattr a color #B50400000000 #1:281@ca +setattr a name '|| .D' #1:281@ca +% +% \end{macrocode} +% \begin{macrocode} %<*Standard> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% diff --git a/macros/latex/contrib/texshade/texshade.ins b/macros/latex/contrib/texshade/texshade.ins index 73f08c8f6d..c29495fa68 100644 --- a/macros/latex/contrib/texshade/texshade.ins +++ b/macros/latex/contrib/texshade/texshade.ins @@ -1,7 +1,7 @@ %% %% docstrip install file for texshade.sty %% -%% Copyright 1999-2011 Eric Beitz +%% Copyright 1999-2021 Eric Beitz %% \def\batchfile{texshade.ins} @@ -14,7 +14,7 @@ LaTeX package for typesetting nucleotide and peptide alignments -Copyright (C) 1999-2011 Eric Beitz +Copyright (C) 1999-2021 Eric Beitz See the file texshade.txt \endpreamble @@ -32,6 +32,8 @@ See the file texshade.txt \file{AQP_HMM.sgl}{\from{texshade.dtx}{AQPHMMsgl}} \file{AQP_HMM.ext}{\from{texshade.dtx}{AQPHMMext}} \file{AQP_TC.asc}{\from{texshade.dtx}{TCoffee}} + \file{AQP_sequence_logo_1FX8.cmd}{\from{texshade.dtx}{AQPlogo}} + \file{AQP_subfamily_logo_1FX8.cmd}{\from{texshade.dtx}{AQPsublogo}} \file{standard.cod}{\from{texshade.dtx}{Standard}} \file{ciliate.cod}{\from{texshade.dtx}{Ciliate}}} diff --git a/macros/latex/contrib/texshade/texshade.pdf b/macros/latex/contrib/texshade/texshade.pdf index f423a08595..53941cff68 100644 Binary files a/macros/latex/contrib/texshade/texshade.pdf and b/macros/latex/contrib/texshade/texshade.pdf differ diff --git a/macros/latex/contrib/texshade/tsfaq.pdf b/macros/latex/contrib/texshade/tsfaq.pdf deleted file mode 100644 index 53b9b89528..0000000000 Binary files a/macros/latex/contrib/texshade/tsfaq.pdf and /dev/null differ diff --git a/macros/latex/contrib/texshade/tsfaq.tex b/macros/latex/contrib/texshade/tsfaq.tex deleted file mode 100644 index 0ab7a0ec37..0000000000 --- a/macros/latex/contrib/texshade/tsfaq.tex +++ /dev/null @@ -1,432 +0,0 @@ -\documentclass[12pt]{article} - - -\begin{document} - - -\noindent -Eric Beitz \hfill March 2005 - -\section*{\TeX{}shade: frequently asked questions } -\bigskip - -This is the sixth update of the FAQ list for \TeX{}shade. Feel free to -contact me if you have problems, questions or suggestions about the -package. I will post them and provide hopefully helpful hints in -future issues of this list. -\bigskip - -\noindent -\qquad email: \texttt{eric.beitz@uni-tuebingen.de} -\smallskip - -\noindent -\TeX{}shade: -\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} - - -\subsection*{A. Increasing \TeX{}'s memory settings} -\medskip - - If you are using \TeX{}shade to align several large sequences (about 1000 - residues/sequence), LaTeX will probably stop compiling and quit with one - of the following messages: - \texttt{!\ TeX capacity exceeded, sorry [main memory size=384000]} or - \texttt{!\ TeX capacity exceeded, sorry [stack size=300]}. - -Due to several requests I want to start a list of protocols how -to increase the standard \TeX{} memory settings for bigger -alignments. Please contribute to this list by sending me the -procedure for your particular system. - -\begin{enumerate} - - \item - - \textbf{Oz\TeX{} 4.0 for the Macintosh:} - - Find the file `OzTeX:TeX:Configs:Default'. This file contains - all memory settings. Look for the section - `\% TeX parameters' and increase the values that \TeX{} complains - about during the run. You will have to restart Oz\TeX{} before the - changes are active. - - For older versions of Oz\TeX{} the configuration file has the - same name but the path is somewhat different. - - - \item - - \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn) - - Find the file: `/usr/share/texmf/web2c/texmf.cnf' or - - use \verb|locate texmf.cnf| at the command prompt to find it. - - Login as super user. Backup `texmf.cnf' in case you destroy something and - then open the `texmf.cnf' file in your favorite text editor and use its - search function to locate \verb|main_memory|. This variable is set to 384000. - Change this to some higher value, i.e. 4000000 (works fine for me!). The - total amount of memory should not exceed 8000000, so check the other - values in that section. - - Next, you want to change the stack size. Search for \verb|stack_size|. This - will be set to 300. I changed it to 4000 and it works fine. - - There might be complains by \TeX{} about further specific parameters such - as \verb|stack_size|. You find all those in the same file. - - After this you have to run `texconfig init'. - - Logout as root. - - After this all should be set for large alignments. Happy \TeX{}ing! - - The information on how to achieve this was derived from a mail in the - te\TeX{} mail archive. The original question was posted by Pascal Francq and - answered by Rolf Nieprasch. - - - \item - - \textbf{MiK\TeX{} for Windows:} - - The MiK\TeX{} documentation describes very detailed how the memory - settings can be changed. In brief, you must locate the - configuration file `miktex/config/miktex.ini'. In the [MiKTeX] - section of this file you find all the parameters you need, e.\,g.\ - \verb|mem_min|, \verb|mem_max|, \verb|buf_size|, \verb|stack_size| etc. - - It appears, that the standard settings of MiK\TeX{} are bigger - than that of other \TeX{} installations, so it may not always be necessary - to increase the values. - - -\end{enumerate} - - -\subsection*{B. Problems using \TeX{}shade} -\medskip - -\begin{enumerate} - - \item - - \textbf{I cannot \TeX{} the manual because I get the error - message `\texttt{!\ TeX capacity exceeded, sorry \ldots}'.} - - \TeX{}shade needs a lot of memory for setting and shading - alignments. The manual is a good test for your memory settings - because it uses many alignments and fingerprints, which are - in particular memory consuming. If you do not know how to increase - \TeX's memory settings, and you do not know a \TeX{} wizard either, then - visit the \TeX{}shade homepage at - \texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} for - downloading the manual in either of three formats: DVI, PDF or - PostScript. - - - \item - - \textbf{I can set my alignment only when I reduce the number of - base-pairs by about 11,000. Otherwise I get the `\texttt{!\ TeX - capacity exceeded, sorry \ldots}' error.} - - There are several parameters defining \TeX's - usable space. If you are a \TeX{} wizard (or you know one) - increase the values that - \TeX{}shade complains about during the run in order to set - bigger alignments. But do not be disappointed when your \TeX{} - system will not set an alignment containing thousands of residues. - There is definitely an upper limit (probably the new \LaTeX3 will - allow you to use even more memory). Setting alignments is a big job for a - typesetting system! - - - \item - - \textbf{I want to align 80 sequences but I get the - `\texttt{!\ No room for a new count}' message.} - - For each sequence two counter variables are used by \TeX{}shade, - further 14 counters for other purposes are needed (and \TeX{} - can handle only 255 counters). This limits the amount of sequences - to about 100 in theory. But \LaTeX{} itself and each of - the loaded packages allocates more counters further reducing the maximum - number of sequences. - - - \item - - \textbf{I receive error messages `\texttt{!\ Missing \$ inserted}' - when \TeX{}ing my alignment. What is wrong?} - - At least one of the sequence names in the alignment file contains an - underscore `\_' symbol. This makes \TeX{} to believe you missed to - enter math mode because subscript initiated by an underscore is - only allowed in math. You need to change the sequence name(s) either in the - alignment file using the `find \& replace' option of your editor or - by using the \verb|\nameseq| command in the \TeX{}shade environment. - Nevertheless, subscript and superscript are permitted in sequence names, - e.\,g. \verb|\nameseq{1}{Name$_{sub}^{super}$}| will result in - Name$_{sub}^{super}$. - - Since v1.3b \TeX{}shade{} is much more tolerant concering special - characters. Get it and read the section about sequence names. - - - \item - - \textbf{My sequence names start out with a number in the - alignment file. Why are they ignored by \TeX{}shade?} - - \TeX{}shade analyzes the first character of each line in the - alignment file in order to decide whether it is a comment, a - ruler or a sequence line etc. All lines starting out with a - non-letter character are interpreted as non-sequence lines. Hence, - you have to change those names in the alignment file. If you - want to have sequence names starting with a number you can - use the \verb|\nameseq| command in the \TeX{}shade environment to - introduce the number, e.\,g. \verb|\nameseq{1}{57th sequence}|. - - - \item - - \textbf{Only a fraction of the residues which are supposed to be - shaded actually are. Why?} - - Make sure that \TeX{}shade knows when protein sequences are to be - set. Align\-ments in the ALN-format do not contain information about the - sequence type (DNA or protein). In such cases DNA sequences are - assumed by \TeX{}shade leading to a shading of only A's, C's, G's, - R's, T's and Y's. A simple solution is to say \verb|\seqtype{P}| in the - \verb|texshade| environment. - - - \item - - \textbf{Functional shading does not work and I get an error message. Why?} - - Same problem as discussed in the point before this one. Functional - shading is permitted only on protein sequences. So, tell \TeX{}shade - that you are using a protein alignment. - - - \item - - \textbf{There is an incompatiblity between \TeX{}shade (v1.2) - and the multi-language package `\texttt{babel}'!} - - You are right! The command \verb|\language| is defined in both - packages which leads to error messages. This bug is fixed since - the release of \TeX{}shade version 1.3 from March 2000. In this - version \verb|\language| is replaced by two commands: - \verb|\germanlanguage| and \verb|\englishlanguage|. - - \item - - \textbf{\TeX{}shade crashes when dashes ``-'' are used as gap - symbols in alignment input files.} - - Yes. Be careful with all kinds of characters that are ``active'' - in \TeX{}, such as \verb|$ _ ^ & % " \|. The dash is not really active - but two or three consecutive dashes are amalgamated to one longer - dash in \TeX. Having those characters in an input file might result - in unforeseen errors or even crashes. - - \item - - \textbf{I have problems using PHD predictions in \TeX{}shade. An - empty \texttt{.top} or \texttt{.sec} file is created.} - - When you do the PHD run do not restrict the calculation to either - secondary structure or topology prediction. Turn on everything. - Otherwise the output will have some ambiguous lines which can not - be interpreted by \TeX{}shade. Result is an empty - \texttt{.top} or \texttt{.sec} file. - -\end{enumerate} - - - -\subsection*{C. Changing the output} -\medskip - -\begin{enumerate} - - \item - - \textbf{How can I force \TeX{}shade to print more residues per line?} - - Use the \verb|\residuesperline*| command with the `\verb|*|' extension. - This will allow you to set any number of residues per line that is - desired, e.\,g. \verb|\residuesperline*{97}|. But then expect numerous - `\texttt{!\ Overfull hbox}' errors due to printing lines that - are broader than the preset \verb|\textwidth|. The same command - without the `\verb|*|' will calculate the highest number of residues - fitting in one line and round it to be divisible by five. - - - \item - - \textbf{Is it possible to add a caption to the \TeX{}shade output?} - - Yes, it is. Since \TeX{}shade v1.5 the \verb|\showcaption| - command is - available to add captions on the top or the bottom of the - alignment. The caption behaves exactly as a figure caption - including the style, numbering and appearance in the list of - figures. - \medskip - - Example: \verb|\showcaption{Nice alignment!}|. - - - \item - - \textbf{I want a short version of the caption for the `List of - Figures'. Is this possible?} - - Yes, with \TeX{}shade v1.9 short captions have been introduced. - In addition to \verb|showcaption| use the command - \verb|shortcaption{|\emph{text}\verb|}|. - \medskip - - Example: \verb|\showcaption{Nice alignment!}|\ - \verb|\shortcaption{Nice}|. - - - \item - - \textbf{My alignment file contains the letters `B' and `Z' for - Asx and Glx, respectively. How can I apply a special shading for - these?} - - Use \verb|\funcgroup| to define `B' and `Z' as functional groups - and assign the colors and the printing style, e.\,g. - \medskip - - \verb|\funcgroup{B}{White}{Blue}{upper}{up}| - \smallskip - - \verb|\funcgroup{Z}{White}{Red}{upper}{up}| - \medskip - - or add the new residues to an existing group, e.\,g. - \medskip - - \verb|\funcgroup{acidic/amide}{DENQBZ}{Black}{Green}{upper}{up}|. - - - \item - - \textbf{How can I build a legend using the `\texttt{shadebox}' - command?} - - The \verb|\shadebox| command simply prints a color-filled box at - the very location it occurs in the text. This means you have to - use \verb|\shadebox| in the normal text after the \TeX{}shade environment - or inside the caption. You find a minimal example below: - \medskip - - \qquad\vbox{% - \verb|\begin{texshade}{alignmentfile.MSF}| - \medskip - - \qquad \verb|\showcpation{Red box: \shadebox{Red}}| - \medskip - - \qquad \emph{further commands, if needed} - \medskip - - \verb|\end{texshade}| - } - - \medskip - - Legend: - - \qquad\verb|\shadebox{conserved}|: conserved residues - - \qquad\verb|\shadebox{White}|: boring residues - - \qquad\verb|\shadebox{Red}|: exciting residues - - - - \item - - \textbf{I do not like the spacing between the feature lines. How - can I change it?} - - Employ the respective space controlling command from the - following list \verb|\ttopspace|, - \verb|\topspace|, \verb|\bottomspace|, \verb|\bbottomspace|. - Those are available since \TeX{}shade v1.5 (see manual). - - - - \item - - \textbf{How can I change gap and match symbols in diverse mode?} - - Since \TeX{}shade version 1.7, standard definitions for \verb|diverse| - mode are: - - \begin{verbatim} - \nomatchresidues{Black}{White}{lower}{up} - \similarresidues{Black}{White}{lower}{up} - \conservedresidues{Black}{White}{{.}}{up} - \allmatchresidues{Black}{White}{{.}}{up} - \gapchar{-} - \end{verbatim} - - After calling \verb|\shadingmode{diverse}| these commands can be - used to redefine the \verb|diverse| mode settings (mind the double - curly braces around the dot-symbol!). - - - - \item - - \textbf{I want to rotate the alignment on the page. Is this possible?} - - Yes. Stefan Vogt has found this solution: use pdflscape.sty and - activate it in the preamble with \verb|\usepackage{pdflscape}|. Then - put your \TeX{}shade environment inside a \verb|landscape|-environment. - You also need to adjust the number of residues per line with - \verb|\residuesperline*{number}| to make them fill the rotated page. - \medskip - - \qquad\vbox{% - \verb|\begin{landscape}| - - \verb|\centering| - - \qquad \verb|\begin{texshade}{alignmentfile.MSF}| - - \qquad \verb|\residuesperline*{|\emph{number}\verb|}| - \medskip - - \qquad \qquad \emph{further commands, if needed} - \medskip - - \qquad \verb|\end{texshade}| - - \verb|\end{landscape}| - } - - - - \item - - \textbf{I want use the \TeX{}shade and \TeX{}topo logos in my text. How?} - - Use the commands: \verb|\TeXshade| and \verb|\TeXtopo|. - - -\end{enumerate} - - - -\end{document} \ No newline at end of file diff --git a/support/latexindent/LatexIndent/Verbatim.pm b/support/latexindent/LatexIndent/Verbatim.pm index d115bf078f..6149ca5236 100644 --- a/support/latexindent/LatexIndent/Verbatim.pm +++ b/support/latexindent/LatexIndent/Verbatim.pm @@ -41,7 +41,7 @@ sub find_noindent_block{ ( (?!<\\) % - \h* # possible horizontal spaces + (?:\h|(?!<\\)%)* # possible horizontal spaces \\begin\{ $noIndentBlockSpec # environment name captured into $2 \} # % \begin{noindentblock} statement @@ -52,7 +52,7 @@ sub find_noindent_block{ ( (?!<\\) % # % - \h* # possible horizontal spaces + (?:\h|(?!<\\)%)* # possible horizontal spaces \\end\{$noIndentBlockSpec\} # \end{noindentblock} ) # % \end{} statement /sx; diff --git a/support/latexindent/LatexIndent/Version.pm b/support/latexindent/LatexIndent/Version.pm index 170b08f58f..3751a17adb 100644 --- a/support/latexindent/LatexIndent/Version.pm +++ b/support/latexindent/LatexIndent/Version.pm @@ -19,6 +19,6 @@ use warnings; use Exporter qw/import/; our @EXPORT_OK = qw/$versionNumber $versionDate/; -our $versionNumber = '3.9.1'; -our $versionDate = '2021-03-21'; +our $versionNumber = '3.9.2'; +our $versionDate = '2021-04-06'; 1 diff --git a/support/latexindent/README b/support/latexindent/README index a8b0e8e182..3d68267b28 100644 --- a/support/latexindent/README +++ b/support/latexindent/README @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - latexindent.pl, version 3.9.1, 2021-03-21 + latexindent.pl, version 3.9.2, 2021-04-06 PERL script to indent code within environments, and align delimited environments in .tex files. diff --git a/support/latexindent/defaultSettings.yaml b/support/latexindent/defaultSettings.yaml index a794364f93..a102896111 100644 --- a/support/latexindent/defaultSettings.yaml +++ b/support/latexindent/defaultSettings.yaml @@ -1,4 +1,4 @@ -# defaultSettings.yaml for latexindent.pl, version 3.9.1, 2021-03-21 +# defaultSettings.yaml for latexindent.pl, version 3.9.2, 2021-04-06 # a script that aims to # beautify .tex, .sty, .cls files # diff --git a/support/latexindent/documentation/cmhlistings.tex b/support/latexindent/documentation/cmhlistings.tex index 5d44a59803..1f058616d6 100644 --- a/support/latexindent/documentation/cmhlistings.tex +++ b/support/latexindent/documentation/cmhlistings.tex @@ -26,8 +26,3 @@ #1^^J .. endproof:example::^^J } -\newcommand{\cmhindex}[1]{ - -:index:@#1@ - -} diff --git a/support/latexindent/documentation/latexindent.pdf b/support/latexindent/documentation/latexindent.pdf index dcb5eb21a0..9aff38414b 100644 Binary files a/support/latexindent/documentation/latexindent.pdf and b/support/latexindent/documentation/latexindent.pdf differ diff --git a/support/latexindent/documentation/sec-default-user-local.tex b/support/latexindent/documentation/sec-default-user-local.tex index 411461e3e5..5e04637ea3 100644 --- a/support/latexindent/documentation/sec-default-user-local.tex +++ b/support/latexindent/documentation/sec-default-user-local.tex @@ -152,6 +152,8 @@ copy myfile.bak4 to myfile.bak3 %(*@@*)\end{noindent} \end{cmhlistings} + Important note: it is assumed that the \texttt{noindent} block statements appear on their own line. + \yamltitle{removeTrailingWhitespace}*{fields}\label{yaml:removeTrailingWhitespace} Trailing white space can be removed both \emph{before} and diff --git a/support/latexindent/documentation/title.tex b/support/latexindent/documentation/title.tex index 5df477ecad..cd892f1348 100644 --- a/support/latexindent/documentation/title.tex +++ b/support/latexindent/documentation/title.tex @@ -8,13 +8,14 @@ sharp corners, enhanced, overlay={\node[anchor=north east,outer sep=2pt] at ([xshift=3cm,yshift=4mm]frame.north east) {\includegraphics[width=3cm]{logo}}; }] - \centering\ttfamily\bfseries latexindent.pl\\[1cm] Version 3.9.1 + \centering\ttfamily\bfseries latexindent.pl\\[1cm] Version 3.9.2 \end{tcolorbox} } \author{Chris Hughes \thanks{and contributors! See \vref{sec:contributors}. For all communication, please visit \cite{latexindent-home}.}} +\date{2021-04-06} \maketitle \begin{adjustwidth}{1cm}{1cm} \small diff --git a/support/latexindent/latexindent.pl b/support/latexindent/latexindent.pl index 2c6dc044b8..f339ec591b 100755 --- a/support/latexindent/latexindent.pl +++ b/support/latexindent/latexindent.pl @@ -1,5 +1,5 @@ #!/usr/bin/env perl -# latexindent.pl, version 3.9.1, 2021-03-21 +# latexindent.pl, version 3.9.2, 2021-04-06 # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/support/texlive/texlive-dummy/openSUSE/README.md b/support/texlive/texlive-dummy/openSUSE/README.md index b8d0ee83f1..89de73a559 100644 --- a/support/texlive/texlive-dummy/openSUSE/README.md +++ b/support/texlive/texlive-dummy/openSUSE/README.md @@ -7,13 +7,10 @@ makes it possible to install the original TeX Live distribution (http://www.tug.org/texlive/) without the overhead of the openSUSE packages. The "dummy-package" provides scripts in "/etc/profile.d/" for setting the correct paths of the TeX Live binaries (assuming -the installation path "/usr/local/texlive"). - -After installing a new-year "dummy-package", uninstall the previous -one. +the installation path "/usr/local/texlive"). Permission is granted to copy, distribute and/or modify this software under the terms of the LaTeX Project Public License (LPPL), version 1.3. The LPPL maintenance status of this software is "maintained". -Rolf Niepraschk, Rolf.Niepraschk@gmx.de, 2020/04/15 +Rolf Niepraschk, 2021/04/06 diff --git a/systems/mac/mactex/ExtrasFolder.pdf b/systems/mac/mactex/ExtrasFolder.pdf index 5a4e539924..f6f55a5b31 100644 Binary files a/systems/mac/mactex/ExtrasFolder.pdf and b/systems/mac/mactex/ExtrasFolder.pdf differ diff --git a/systems/mac/mactex/Licenses.txt b/systems/mac/mactex/Licenses.txt index 99ab664710..ab6c179cb8 100644 --- a/systems/mac/mactex/Licenses.txt +++ b/systems/mac/mactex/Licenses.txt @@ -1,6 +1,6 @@ $Id: Licenses.txt,v 1.14 2007/02/28 14:23:19 herbs Exp $ -Brief summary of the licensing of the various applications included as of 2021/03/22 +Brief summary of the licensing of the various applications included as of 2021/04/06 Aquamacs Emacs (Intel) - 3.5 - gpl - http://aquamacs.org/ Aquatkbibtex - 1.3 - gpl - http://aquatkbibtex.sourceforge.net/ @@ -11,10 +11,10 @@ CocoAspell (10.11+) - 2.5 - free? - http://people.ict.usc.edu/~l Excalibur - 4.0.7 - gpl - http://excalibur.sourceforge.net/ JabRef - 5.0 - gpl - http://jabref.sourceforge.net/ LaTeXiT (10.9+) - 2.16.1 - free? - http://ktd.club.fr/programmation/latexit_en.php -Lyx (10.6+) - 2.3.4.2 - gpl - http://wiki.lyx.org/Mac/Mac +Lyx (10.6+) - 2.3.6.2 - gpl - http://wiki.lyx.org/Mac/Mac PrĂ©sentation - 2.2 - gpl - http://iihm.imag.fr/blanch/software/osx-presentation/ SimpleTeX4ht - 3.3 - gpl - http://www.simpletex4ht.free.fr/ -Skim (10.10+) - 1.6.2 - bsd - http://skim-app.sourceforge.net/ +Skim (10.10+) - 1.6.3 - bsd - http://skim-app.sourceforge.net/ Symbols Widget - 1.4.3 - gpl - http://vocaro.com/trevor/software/widgets/ TeX FoG (10.4+) - 1.3.2 - gpl - http://homepage.mac.com/marco_coisson/TeXFoG/ TeX Live Utility (10.9+) - 1.49 - bsd - https://github.com/amaxwell/tlutility/releases diff --git a/systems/texlive/tlnet/tlpkg/TeXLive/TLWinGoo.pm b/systems/texlive/tlnet/tlpkg/TeXLive/TLWinGoo.pm index 35e92c7300..38b23d34b4 100644 --- a/systems/texlive/tlnet/tlpkg/TeXLive/TLWinGoo.pm +++ b/systems/texlive/tlnet/tlpkg/TeXLive/TLWinGoo.pm @@ -1,4 +1,4 @@ -# $Id: TLWinGoo.pm 58646 2021-03-23 03:34:22Z preining $ +# $Id: TLWinGoo.pm 58768 2021-04-06 10:39:46Z siepo $ # TeXLive::TLWinGoo.pm - Windows goop. # Copyright 2008-2018 Siep Kroonenberg, Norbert Preining # This file is licensed under the GNU General Public License version 2 @@ -11,7 +11,7 @@ package TeXLive::TLWinGoo; -my $svnrev = '$Revision: 58646 $'; +my $svnrev = '$Revision: 58768 $'; my $_modulerevision; if ($svnrev =~ m/: ([0-9]+) /) { $_modulerevision = $1; @@ -32,8 +32,6 @@ C -- Additional utilities for Windows =head2 DIAGNOSTICS - TeXLive::TLWinGoo::is_vista; - TeXLive::TLWinGoo::is_seven; TeXLive::TLWinGoo::is_ten; TeXLive::TLWinGoo::admin; TeXLive::TLWinGoo::non_admin; @@ -161,22 +159,18 @@ sub reg_debug { my $is_win = ($^O =~ /^MSWin/i); -# Win32: import some wrappers for API functions -# failed to get Win32::API::More to work with raw API functions; +# Win32: import wrappers for some horrible API functions # import failures return a null result; # call imported functions only if true/non-null my $SendMessage = 0; my $update_fu = 0; -my $getlang = 0; if ($is_win) { - $SendMessage = new Win32::API('user32', 'SendMessageTimeout', 'LLPPLLP', 'L'); + $SendMessage = Win32::API::More->new('user32', 'SendMessageTimeout', 'LLPPLLP', 'L'); debug ("Import failure SendMessage\n") unless $SendMessage; - $update_fu = new Win32::API('shell32', 'SHChangeNotify', 'LIPP', 'V'); + $update_fu = Win32::API::More->new('shell32', 'SHChangeNotify', 'LIPP', 'V'); debug ("Import failure assoc_notify\n") unless $update_fu; - $getlang = Win32::API::More->new('kernel32', 'long GetUserDefaultLangID()'); - debug ("Import failure GetUserDefaultLangID\n") unless $getlang; } =pod @@ -198,9 +192,6 @@ my $windows_version = 0; my $windows_subversion = 0; if ($is_win) { - #my @osver = Win32::GetOSVersion(); # deprecated - #$windows_version = $osver[1]; - #debug "Windows version $osver[0], major version $osver[1]\n"; my $ver = `ver`; chomp $ver; $ver =~ s/^[^0-9]*//; @@ -210,25 +201,6 @@ if ($is_win) { $windows_subversion =~ s/\..*$//; } -=item C - -C returns 1 if windows version is >= 6.0, otherwise 0. - -=cut - -sub is_vista { return $windows_version >= 6; } - -=item C - -C returns 1 if windows version is >= 6.1, otherwise 0. - -=cut - -sub is_seven { - return (($windows_version == 6 && $windows_subversion >= 1) || - ($windows_version > 6)); -} - =item C C returns 1 if windows version is >= 10.0, otherwise 0. @@ -272,7 +244,7 @@ to the system environment. =cut -# during processing of this source, $is_admin will get its correct value +# $is_admin has already got its correct value sub admin { return $is_admin; } @@ -307,16 +279,9 @@ Two-letter country code representing the locale of the current user =cut sub reg_country { - my $value = 0; - if ($getlang) {$value = $getlang->Call();} - return unless $value; - $value = sprintf ("%04x", $value); - my $lmkey = $Registry -> Open("HKEY_CLASSES_ROOT/MIME/Database/Rfc1766/", - {Access => KEY_READ()}); - return unless $lmkey; - $lm = $lmkey->{"/$value"}; + my $lm = cu_root()->{"Control Panel/international//localename"}; return unless $lm; - debug("found lang codes value = $value, lm = $lm...\n"); + debug("found lang code lm = $lm...\n"); if ($lm) { if ($lm =~ m/^zh-(tw|hk)$/i) { return ("zh", "tw"); @@ -330,6 +295,7 @@ sub reg_country { return($lang, $area); } } + # otherwise undef will be returned } @@ -389,8 +355,7 @@ sub is_a_texdir { =item C -Returns unexpanded system path, as stored in the registry, but with -forward slashes. +Returns unexpanded system path, as stored in the registry. =cut @@ -406,9 +371,8 @@ sub get_system_path { =item C -Returns unexpanded user path, as stored in the registry, but with -forward slashes. The user path often does not exist, and is rarely -expandable. +Returns unexpanded user path, as stored in the registry. The user +path often does not exist, and is rarely expandable. =cut @@ -1034,15 +998,15 @@ sub unregister_file_type { =item C Broadcasts system message that enviroment has changed. This only has -an effect on newly-started programs, not on running programs and the +an effect on newly-started programs, not on running programs or the processes they spawn. =cut sub broadcast_env() { if ($SendMessage) { - use constant HWND_BROADCAST => 0xffff; - use constant WM_SETTINGCHANGE => 0x001A; + use constant HWND_BROADCAST => 0xffff; + use constant WM_SETTINGCHANGE => 0x001A; my $result = ""; my $ans = "12345678"; # room for dword $result = $SendMessage->Call(HWND_BROADCAST, WM_SETTINGCHANGE, @@ -1062,12 +1026,16 @@ Notifies the system that filetypes have changed. =cut sub update_assocs() { - use constant SHCNE_ASSOCCHANGED => 0x8000000; - use constant SHCNF_IDLIST => 0; + use constant SHCNE_ASSOCCHANGED => 0x8000000; + use constant SHCNF_IDLIST => 0; if ($update_fu) { debug("Notifying changes in filetypes...\n"); - $update_fu->Call (SHCNE_ASSOCCHANGED, SHCNF_IDLIST, 0, 0); - debug("Done notifying\n"); + my $result = $update_fu->Call(SHCNE_ASSOCCHANGED, SHCNF_IDLIST, 0, 0); + if ($result) { + debug("Done notifying filetype changes\n"); + } else{ + debug("Failure notifying filetype changes\n"); + } } else { debug("No update_fu\n"); } diff --git a/systems/texlive/tlnet/tlpkg/installer/install-tl-gui.tcl b/systems/texlive/tlnet/tlpkg/installer/install-tl-gui.tcl index 455641f4db..66ba9a0252 100755 --- a/systems/texlive/tlnet/tlpkg/installer/install-tl-gui.tcl +++ b/systems/texlive/tlnet/tlpkg/installer/install-tl-gui.tcl @@ -1644,6 +1644,7 @@ proc run_menu {} { ttk::checkbutton .srcb -variable ::vars(tlpdbopt_install_srcfiles) \ -command {update_vars; show_stats} pgrid .srcb -in $curf -row $rw -column 2 -sticky e + puts stderr [bindtags .srcb] } } @@ -1698,14 +1699,9 @@ proc run_menu {} { pgrid [ttk::label .texwl -text [__ "Install TeXworks front end"]] \ -in $curf -row $rw -column 0 -columnspan 2 -sticky w ttk::checkbutton .texwb -variable ::vars(collection-texworks) + .texwb configure -command \ + {set ::vars(selected_scheme) "scheme-custom"; update_vars; show_stats} pgrid .texwb -in $curf -row $rw -column 2 -sticky e - bind .texwb {+ - set ::vars(selected_scheme) "scheme-custom"; update_vars; show_stats} - bind .texwb {+ - set ::vars(selected_scheme) "scheme-custom"; update_vars; show_stats} - bind .texwb {+ - set ::vars(selected_scheme) "scheme-custom"; update_vars; show_stats} - } else { if $::advanced { # instopt_adjustpath, unix edition: symlinks diff --git a/systems/texlive/tlnet/tlpkg/texlive.tlpdb b/systems/texlive/tlnet/tlpkg/texlive.tlpdb index 378e17cf99..1009b44dc0 100644 --- a/systems/texlive/tlnet/tlpkg/texlive.tlpdb +++ b/systems/texlive/tlnet/tlpkg/texlive.tlpdb @@ -26,11 +26,11 @@ depend container_split_src_files/1 depend frozen/0 depend minrelease/2016 depend release/2021 -depend revision/58764 +depend revision/58778 name 00texlive.image category TLCore -revision 58759 +revision 58777 shortdesc TeX Live files only in the source repository longdesc The files here are not copied by the installer and containers longdesc are not built for them; they exist only in the source @@ -689,6 +689,7 @@ runfiles size=13859 tlpkg/tlpsrc/beamertheme-saintpetersburg.tlpsrc tlpkg/tlpsrc/beamertheme-upenn-bc.tlpsrc tlpkg/tlpsrc/beamerthemejltree.tlpsrc + tlpkg/tlpsrc/beamerthemelalic.tlpsrc tlpkg/tlpsrc/beamerthemenirma.tlpsrc tlpkg/tlpsrc/beamerthemenord.tlpsrc tlpkg/tlpsrc/bearwear.tlpsrc @@ -1369,6 +1370,7 @@ runfiles size=13859 tlpkg/tlpsrc/diffcoeff.tlpsrc tlpkg/tlpsrc/digiconfigs.tlpsrc tlpkg/tlpsrc/dijkstra.tlpsrc + tlpkg/tlpsrc/dimnum.tlpsrc tlpkg/tlpsrc/din1505.tlpsrc tlpkg/tlpsrc/dinat.tlpsrc tlpkg/tlpsrc/dinbrief.tlpsrc @@ -4367,7 +4369,7 @@ depend setting_available_architectures:aarch64-linux amd64-freebsd amd64-netbsd name 00texlive.installer category TLCore -revision 58742 +revision 58767 shortdesc TeX Live standalone installer package longdesc This package defines the files to go into the installer longdesc archives (install-tl-unx.tar.gz, install-tl.zip) built by the @@ -29572,20 +29574,21 @@ catalogue-version 1.2s name babel-romanian category Package -revision 30285 +revision 58776 shortdesc Babel support for Romanian relocated 1 longdesc The package provides the language definition file for support longdesc of Romanian in babel. Translations to Romanian of standard longdesc "LaTeX names" are provided. -containersize 2176 -containerchecksum d2aca8f17ae173c36185d6d3514b0b09f76233e44f30177a50240ef0cf0f25f85767a6fc5ee0f94e2eff0df0b94fbca08eb048e95b35a631b7d30a1fbf6c23e6 -doccontainersize 113084 -doccontainerchecksum 876a8cd9e515ecad570ce23686b71e896fa377ce8fb4840e511430aabb05e9cb03f614167fa2abd13328d0ea7f4eebf7044a65db584b95ce4c64bd37d2602b2e -docfiles size=28 +containersize 2124 +containerchecksum ca6318ca8453dae2286b305766c6ced299f18f390c0d0f44e77ddf8eb4b05c31c7a2b01ed52e271f68acd6b127650b370d15ea9bcb3b591fd01e5d3a50b17db5 +doccontainersize 113056 +doccontainerchecksum 73ff361e7e03499427529824b83ea584a5ca190aae3d1ef9a5f4a5adf52cc8ab02f5652c92c1464a702f581e29626fa9cd14d4ee84f6cdde69b38af9d10b20ee +docfiles size=29 + RELOC/doc/generic/babel-romanian/README.md RELOC/doc/generic/babel-romanian/romanian.pdf details="Package documentation" -srccontainersize 4340 -srccontainerchecksum 493834afa2339a8a63c017ca880ec07626a62b88f76688192253985bb5b254412409c1128714a2ce8a7f7a296cef6ad9ae67b32a276372c811933df8d2929e2b +srccontainersize 4308 +srccontainerchecksum 0e4aef9bf20e6602dd946e2ad2856c7ee7849b492d4b66334450b450faed146eef83d2b7f13506eac6f34507bfec4ae735ae9845d3a21c36d98105bb353166c8 srcfiles size=5 RELOC/source/generic/babel-romanian/romanian.dtx RELOC/source/generic/babel-romanian/romanian.ins @@ -29594,7 +29597,7 @@ runfiles size=1 catalogue-ctan /macros/latex/contrib/babel-contrib/romanian catalogue-license lppl1.3 catalogue-topics romanian -catalogue-version 1.2l +catalogue-version 1.2m name babel-romansh category Package @@ -33770,6 +33773,36 @@ catalogue-license gpl catalogue-topics presentation catalogue-version 1.1 +name beamerthemelalic +category Package +revision 58777 +shortdesc A beamer theme for LALIC +relocated 1 +longdesc This package provides the beamer theme for LALIC (Laboratorio +longdesc de Linguistica e Inteligencia Computacional of the Federal +longdesc University of Sao Carlos, Brazil). +containersize 2924 +containerchecksum 70d789b4490e5ceb9d578be03f815eea97706fc89e41756908d41f1953c2b4cee4ce7c142406a0abef0497b89b74dfb2dc6d2a841898996f32025f53626a8548 +doccontainersize 224372 +doccontainerchecksum b79c55da51785c42c68a2bd5f7a386b21fbb36948df8b5e87e60b9eab263e43592b7265902b6f3a2d3bd214dce122fcf0d504ff807a7bee0ebccf7241fa8e1fd +docfiles size=65 + RELOC/doc/latex/beamerthemelalic/LICENSE + RELOC/doc/latex/beamerthemelalic/README.md details="Readme" + RELOC/doc/latex/beamerthemelalic/beamerthemelalic-exemplo.pdf details="Package documentation" + RELOC/doc/latex/beamerthemelalic/beamerthemelalic-exemplo.tex +runfiles size=5 + RELOC/tex/latex/beamerthemelalic/beamercolorthemelalic.sty + RELOC/tex/latex/beamerthemelalic/beamerfontthemelalic.sty + RELOC/tex/latex/beamerthemelalic/beamerinnerthemelalic.sty + RELOC/tex/latex/beamerthemelalic/beamerouterthemelalic.sty + RELOC/tex/latex/beamerthemelalic/beamerthemelalic.sty +catalogue-contact-bugs https://github.com/jandermoreira/temabeamerlalic/issues +catalogue-contact-repository https://github.com/jandermoreira/temabeamerlalic +catalogue-ctan /macros/latex/contrib/beamer-contrib/themes/beamerthemelalic +catalogue-license gpl3+ +catalogue-topics presentation +catalogue-version 1.0 + name beamerthemenirma category Package revision 20765 @@ -51889,7 +51922,7 @@ catalogue-version 1.0c name changes category Package -revision 57756 +revision 58773 shortdesc Manual change markup relocated 1 longdesc The package allows the user to manually markup changes of text, @@ -51900,10 +51933,10 @@ longdesc package allows free definition of additional authors and their longdesc associated color. It also allows you to change the markup of longdesc changes, authors, highlights or comments. 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RELOC/doc/latex/changes/userdoc/usepackage_ulem_changes_in.tex RELOC/doc/latex/changes/userdoc/usepackage_xcolor_changes_ex.tex RELOC/doc/latex/changes/userdoc/usepackage_xcolor_changes_in.tex -srccontainersize 16892 -srccontainerchecksum 0f6f50d6b3a49ca612ab0e7bbf93acb55b3100b8e7e89563459fe9b530786f2260b5b25b94ee374a062b04c56e0a2f78380b95b91880c8da31790df83a1d355e +srccontainersize 16908 +srccontainerchecksum a74ee0bd131301f12a674155d87ffec87b88916e242e80a4daa18fca251d8479e05dc8ddd343943c96055cb3c54fdaa37f91198c8daab1a0c85eb8029d8f9f9b srcfiles size=27 RELOC/source/latex/changes/changes.drv RELOC/source/latex/changes/changes.dtx @@ -52161,7 +52194,7 @@ catalogue-contact-support https://gitlab.com/ekleinod/changes/issues catalogue-ctan /macros/latex/contrib/changes catalogue-license lppl1.3 catalogue-topics editorial doc-tool -catalogue-version 4.0.1 +catalogue-version 4.0.2 name chappg category Package @@ -66804,7 +66837,7 @@ containerchecksum 0568a3251d71fb3106fbb3961427200419ae1df22d39b5e72c608e2d94fc35 name collection-latexextra category Collection -revision 58593 +revision 58777 shortdesc LaTeX additional packages relocated 1 longdesc A very large collection of add-on packages for LaTeX. @@ -66894,6 +66927,7 @@ depend beamertheme-pure-minimalistic depend beamertheme-saintpetersburg depend beamertheme-upenn-bc depend beamerthemejltree +depend beamerthemelalic depend beamerthemenirma depend beamerthemenord depend bearwear @@ -67125,6 +67159,7 @@ depend diagbox depend diagnose depend dialogl depend dichokey +depend dimnum depend dinbrief depend directory depend dirtytalk @@ -68169,8 +68204,8 @@ depend ziffer depend zref depend zwgetfdate depend zwpagelayout -containersize 6308 -containerchecksum 6fe09261d6e4428f0244b87eba97f8e483f3c4a11b3531698486f9e86807712357f5231df5104a123c6a0abccb42d8d05ad559a729f4b20ad35652ea024f086b +containersize 6316 +containerchecksum 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Add figchild. +(10) web2c-w32.tar.xz + Update tie.exe. +(11) xetex-w32.tar.xz + Update HarfBuzz (2.8.0) in xetex.dll. +(12) win64/cweb-w64.tar.xz + Update ctie.exe. +(13) win64/luajittex-dev-w64.tar.xz + Update HarfBuzz (2.8.0) in luajithbtex.dll. +(14) win64/luatex-exp-w64.tar.xz + Update HarfBuzz (2.8.0) in luajithbtex.dll. +(15) win64/luatex-w64.tar.xz + Update HarfBuzz (2.8.0) in luajithbtex.dll. +(16) win64/luatex-dev-w64.tar.xz + Update HarfBuzz (2.8.0) in luahbtex.dll. +(17) win64/luatex-exp-w64.tar.xz + Update HarfBuzz (2.8.0) in luahbtex.dll. +(18) win64/luatex-w64.tar.xz + Update HarfBuzz (2.8.0) in luahbtex.dll. +(19) win64/web2c-w64.tar.xz + Update tie.exe. +(20) win64/xetex-w64.tar.xz + Update HarfBuzz (2.8.0) in xetex.dll. + +[2021/04/04] +(01) biblatex-biber.tar.xz + Update biblatex-gb7714-2015. +(02) ltxpkgs.tar.xz + Add fontawesome and fontawesome5 fonts. +(03) ptex-ng-w32.tar.xz + Rebuild ptex-ng.exe. +(04) uptex-w32.tar.xz + Update gckanbun. +(05) web2c-w32.tar.xz + Update updmap.cfg. +(06) win64/ptex-ng-w64.tar.xz + Rebuild ptex-ng.exe. + +[2021/04/03] +(01) cweb-w32.tar.xz + Update ctie.exe. +(02) dvipdfm-w32.tar.xz + Rebuild dvipdfmx.dll. +(03) latex-dev.tar.xz + Update lualatex-dev.fmt. +(04) luajittex-dev-w32.tar.xz + Update luajittex.dll and luajithbtex.dll (1.13.1). +(05) luatex-exp-w32.tar.xz + Update luajittex.dll and luajithbtex.dll. +(06) luatex-w32.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(07) luatex-dev-w32.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(08) luatex-exp-w32.tar.xz + Update luajittex.dll and luajithbtex.dll. +(09) luatex-w32.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(10) ptex-w32.tar.xz + Update pmpost.dll. +(11) uptex-w32.tar.xz + Update upmpost.dll. +(12) web2c-w32.tar.xz + Update mpost.dll. +(13) xetex-w32.tar.xz + Rebuild dvipdfmx.dll. +(14) win64/cweb-w64.tar.xz + Update ctie.exe. +(15) win64/dvipdfm-w64.tar.xz + Rebuild dvipdfmx.dll. +(16) win64/luajittex-dev-w64.tar.xz + Update luajittex.dll and luajithbtex.dll (1.13.1). +(17) win64/luatex-exp-w64.tar.xz + Update luajittex.dll and luajithbtex.dll. +(18) win64/luatex-w64.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(19) win64/luatex-dev-w64.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(20) win64/luatex-exp-w64.tar.xz + Update luajittex.dll and luajithbtex.dll. +(21) win64/luatex-w64.tar.xz + Update luatex.dll and luahbtex.dll (1.13.1). +(22) win64/ptex-w64.tar.xz + Update pmpost.dll. +(23) win64/uptex-w64.tar.xz + Update upmpost.dll. +(24) win64/web2c-w64.tar.xz + Update mpost.dll. +(25) win64/xetex-w64.tar.xz + Rebuild dvipdfmx.dll. + +[2021/04/02] +(01) extractpdfmark-w32.tar.xz + Update poppler (21.04.0) in extractpdfmark.exe. +(02) pdftex-w32.tar.xz + Update poppler (21.04.0) in poppler utilities. +(03) web2c-w32.tar.xz + Update fontools. +(04) win64/extractpdfmark-w64.tar.xz + Update poppler (21.04.0) in extractpdfmark.exe. +(05) win64/pdftex-w64.tar.xz + Update poppler (21.04.0) in poppler utilities. + +[2021/04/01] +(01) context.tar.xz + ConTeXt version: 2021.03.31 18:00. + Update curl.exe (7.76.0). +(02) ltxpkgs.tar.xz + Update knowledge. +(03) pgfcontrib.tar.xz + Update dynkin-diagrams. +(04) win64/context-w64.tar.xz + Update mtxrun.lua and curl.exe (7.76.0). + [2021/03/31] (01) pstricks.tar.xz Update pstricks-base. diff --git a/timestamp b/timestamp index 8e0591b2af..8df3043216 100644 --- a/timestamp +++ b/timestamp @@ -2,4 +2,4 @@ # The source CTAN of this site's material: dante.ctan.org # The year-month-day-hour-minute of this site's material: -2021-04-06-02-02 +2021-04-07-02-02 -- cgit v1.2.3