UBod authored on 24/06/2022 17:41:17
| ... | ... |
@@ -8,13 +8,13 @@ |
| 8 | 8 |
%% |
| 9 | 9 |
%% LaTeX package for typesetting nucleotide and peptide alignments |
| 10 | 10 |
%% |
| 11 |
-%% Copyright (C) 1999-2011 Eric Beitz |
|
| 11 |
+%% Copyright (C) 1999-2021 Eric Beitz |
|
| 12 | 12 |
%% See the file texshade.txt |
| 13 | 13 |
%% |
| 14 | 14 |
|
| 15 | 15 |
\NeedsTeXFormat{LaTeX2e}
|
| 16 |
-\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.24)]
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|
| 17 |
-\message{Package `texshade', Version 1.24 of 2011/12/01.}
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|
| 16 |
+\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)]
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|
| 17 |
+\message{Package `texshade', Version 1.26 of 2021/04/01.}
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|
| 18 | 18 |
|
| 19 | 19 |
\PassOptionsToPackage{dvips}{color}
|
| 20 | 20 |
\PassOptionsToPackage{dvips}{graphicx}
|
| ... | ... |
@@ -56,6 +56,7 @@ |
| 56 | 56 |
\newread\structurefile \newwrite\featurefile |
| 57 | 57 |
\newread\alignfile \newread\sublogofile |
| 58 | 58 |
\newwrite\exp@rtfile |
| 59 |
+\newwrite\exp@rt@chimerafile |
|
| 59 | 60 |
|
| 60 | 61 |
\expandafter\ifx\csname blacktriangleright\endcsname\relax |
| 61 | 62 |
\openin\structurefile = amssymb.sty |
| ... | ... |
@@ -94,6 +95,7 @@ |
| 94 | 95 |
\newlength\equal@height \newlength\temp@@length |
| 95 | 96 |
\newlength\vspace@legend |
| 96 | 97 |
\newlength\hspace@legend |
| 98 |
+\newlength\bar@length |
|
| 97 | 99 |
|
| 98 | 100 |
\newif\ifletter \newif\ifnumber |
| 99 | 101 |
\newif\ifnewres \newif\ifall@shade |
| ... | ... |
@@ -151,7 +153,12 @@ |
| 151 | 153 |
\def\resn@m@tch{upper} \def\ressimm@tch{upper}
|
| 152 | 154 |
\def\resm@tch{upper} \def\res@llm@tch{upper}
|
| 153 | 155 |
\def\tr@ns{translate} \def\gr@ydef@ult{GrayDefault}
|
| 154 |
-\xdef\par@{\expandafter\string\par}
|
|
| 156 |
+%%%%REMOVED FOLLOWING LINE: |
|
| 157 |
+%%%%\xdef\par@{\expandafter\string\par}
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|
| 158 |
+%%%%ADDED FOLLOWING TWO LINES (according to https://ctan.org/pkg/texshade) |
|
| 159 |
+\xdef\par@{\par}
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|
| 160 |
+\xdef\par@{\expandafter\string\par@}
|
|
| 161 |
+%%%% |
|
| 155 | 162 |
\expandafter\def\csname fg@textcolor/\endcsname{White}
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| 156 | 163 |
\expandafter\def\csname fg@color/\endcsname{White}
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| 157 | 164 |
\expandafter\def\csname func@style/\endcsname{\csname textup\endcsname}
|
| ... | ... |
@@ -678,6 +685,16 @@ |
| 678 | 685 |
\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N}
|
| 679 | 686 |
\xdef\HydroY{9} \xdef\HydroZ{N}
|
| 680 | 687 |
|
| 688 |
+\xdef\hardnessA{98} \xdef\hardnessB{0} \xdef\hardnessC{37}
|
|
| 689 |
+\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48}
|
|
| 690 |
+\xdef\hardnessG{92} \xdef\hardnessH{50} \xdef\hardnessI{98}
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|
| 691 |
+\xdef\hardnessJ{86} \xdef\hardnessK{73} \xdef\hardnessL{98}
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|
| 692 |
+\xdef\hardnessM{25} \xdef\hardnessN{86} \xdef\hardnessO{0}
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|
| 693 |
+\xdef\hardnessP{91} \xdef\hardnessQ{95} \xdef\hardnessR{69}
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|
| 694 |
+\xdef\hardnessS{94} \xdef\hardnessT{98} \xdef\hardnessU{-34}
|
|
| 695 |
+\xdef\hardnessV{98} \xdef\hardnessW{0} \xdef\hardnessX{0}
|
|
| 696 |
+\xdef\hardnessY{28} \xdef\hardnessZ{0}
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|
| 697 |
+ |
|
| 681 | 698 |
\xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0}
|
| 682 | 699 |
\expandafter\xdef\csname consC?\endcsname{0}
|
| 683 | 700 |
|
| ... | ... |
@@ -2593,7 +2610,6 @@ |
| 2593 | 2610 |
\expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
|
| 2594 | 2611 |
\ifnum\first@=\cons@num \xdef\cons@num{0} \fi
|
| 2595 | 2612 |
\advance\killseq@count by -1 |
| 2596 |
- \seq@percent=100 \divide\seq@percent by \killseq@count |
|
| 2597 | 2613 |
\fi |
| 2598 | 2614 |
\fi\fi |
| 2599 | 2615 |
\xdef\first@{\first@@ @}
|
| ... | ... |
@@ -2612,7 +2628,6 @@ |
| 2612 | 2628 |
\expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
|
| 2613 | 2629 |
\ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
|
| 2614 | 2630 |
\advance\killseq@count by -1 |
| 2615 |
- \seq@percent=100 \divide\seq@percent by \killseq@count |
|
| 2616 | 2631 |
\fi |
| 2617 | 2632 |
\fi\fi |
| 2618 | 2633 |
\killseq@ |
| ... | ... |
@@ -2893,8 +2908,17 @@ |
| 2893 | 2908 |
\funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
|
| 2894 | 2909 |
\funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
|
| 2895 | 2910 |
\else |
| 2911 |
+ \xdef\second@{hardness}
|
|
| 2912 |
+ \ifx\temp@\second@ |
|
| 2913 |
+ \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up}
|
|
| 2914 |
+ \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up}
|
|
| 2915 |
+ \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up}
|
|
| 2916 |
+ \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up}
|
|
| 2917 |
+ \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
|
|
| 2918 |
+ \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
|
|
| 2919 |
+ \else |
|
| 2896 | 2920 |
\message{<Unknown shading mode - clearing `funcgroups'>}
|
| 2897 |
- \fi\fi\fi\fi\fi\fi\fi |
|
| 2921 |
+ \fi\fi\fi\fi\fi\fi\fi\fi |
|
| 2898 | 2922 |
} |
| 2899 | 2923 |
\def\shadeallresidues{\all@fshadetrue}
|
| 2900 | 2924 |
\def\get@fromstack#1;#2;#3;#4;#5@{%
|
| ... | ... |
@@ -3114,22 +3138,33 @@ |
| 3114 | 3138 |
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
|
| 3115 | 3139 |
} |
| 3116 | 3140 |
\def\getarrow@shape#1#2#3#4&{%
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| 3117 |
- \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
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|
| 3118 |
- \if\first@@ v |
|
| 3119 |
- \if\second@@ = |
|
| 3120 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
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|
| 3141 |
+ \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
|
|
| 3142 |
+ \ifx\temp@@\y@ |
|
| 3143 |
+ \if\first@@ ` \xdef\first@@{a} \else
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|
| 3144 |
+ \if\first@@ ' \xdef\first@@{a} \else
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|
| 3145 |
+ \if\first@@ , \xdef\first@@{b} \else
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|
| 3146 |
+ \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
|
|
| 3147 |
+ \fi\fi\fi\fi |
|
| 3148 |
+ \if\third@@ ` \xdef\third@@{a} \else
|
|
| 3149 |
+ \if\third@@ ' \xdef\third@@{a} \else
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|
| 3150 |
+ \if\third@@ , \xdef\third@@{b} \else
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|
| 3151 |
+ \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
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|
| 3152 |
+ \fi\fi\fi\fi |
|
| 3153 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
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|
| 3154 |
+ \fi |
|
| 3155 |
+ \if\first@@ S |
|
| 3156 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
|
|
| 3121 | 3157 |
\else |
| 3122 | 3158 |
\if\first@@ v |
| 3123 | 3159 |
\if\second@@ = |
| 3124 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3160 |
+ \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
|
|
| 3125 | 3161 |
\else |
| 3126 |
- \if\third@@ v |
|
| 3127 |
- \if\second@@ = |
|
| 3128 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3162 |
+ \if\third@@ S |
|
| 3163 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
|
|
| 3129 | 3164 |
\else |
| 3130 | 3165 |
\if\third@@ v |
| 3131 | 3166 |
\if\second@@ = |
| 3132 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3167 |
+ \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
|
|
| 3133 | 3168 |
\fi\fi\fi\fi |
| 3134 | 3169 |
} |
| 3135 | 3170 |
\def\get@shape#1#2#3{%
|
| ... | ... |
@@ -5894,7 +5929,11 @@ |
| 5894 | 5929 |
\fi |
| 5895 | 5930 |
\xdef\style@{cons[color]:cons[\f@color][0]}
|
| 5896 | 5931 |
\else |
| 5897 |
- \xdef\style@{#4} \expandafter\getarrow@shape\temp@
|
|
| 5932 |
+ \xdef\style@{#4} \xdef\temp@@{n}
|
|
| 5933 |
+ \expandafter\get@firstfill\temp@ |
|
| 5934 |
+ \if\second@@ ^ \xdef\second@@{_} \fi
|
|
| 5935 |
+ \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
|
|
| 5936 |
+ \expandafter\getarrow@shape\temp@ |
|
| 5898 | 5937 |
\fi |
| 5899 | 5938 |
\fi |
| 5900 | 5939 |
\fi |
| ... | ... |
@@ -6382,7 +6421,17 @@ |
| 6382 | 6421 |
\logocolor{EQ}{RoyalPurple}
|
| 6383 | 6422 |
\logocolor{R}{RedViolet}
|
| 6384 | 6423 |
\logocolor{K}{Black}
|
| 6385 |
- \fi\fi\fi\fi\fi\fi\fi |
|
| 6424 |
+ \else |
|
| 6425 |
+ \xdef\second@{hardness}
|
|
| 6426 |
+ \ifx\first@\second@ |
|
| 6427 |
+ \clearlogocolors |
|
| 6428 |
+ \logocolor{ADEGILPQSTV}{BlueRed5}
|
|
| 6429 |
+ \logocolor{KN}{BlueRed20}
|
|
| 6430 |
+ \logocolor{R}{BlueRed40}
|
|
| 6431 |
+ \logocolor{CFH}{BlueRed60}
|
|
| 6432 |
+ \logocolor{MY}{BlueRed80}
|
|
| 6433 |
+ \logocolor{W}{BlueRed100}
|
|
| 6434 |
+ \fi\fi\fi\fi\fi\fi\fi\fi |
|
| 6386 | 6435 |
} |
| 6387 | 6436 |
\newcommand\findsubfamily[2][n]{%
|
| 6388 | 6437 |
\xdef\first@{#1}
|
| ... | ... |
@@ -7793,9 +7842,8 @@ |
| 7793 | 7842 |
\advance\pos@sum by 1 \fi |
| 7794 | 7843 |
\ifnum\innerloopcount<\seq@count \repeat |
| 7795 | 7844 |
|
| 7796 |
- \multiply\pos@sum by \seq@percent |
|
| 7797 | 7845 |
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
|
| 7798 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld |
|
| 7846 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ |
|
| 7799 | 7847 |
\else |
| 7800 | 7848 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x |
| 7801 | 7849 |
\xdef\m@x{\csname pos\the\loopcount\endcsname}
|
| ... | ... |
@@ -7843,13 +7891,12 @@ |
| 7843 | 7891 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count |
| 7844 | 7892 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
|
| 7845 | 7893 |
\else |
| 7846 |
- \multiply\pos@sum by \seq@percent |
|
| 7847 | 7894 |
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
|
| 7848 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld |
|
| 7895 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ |
|
| 7849 | 7896 |
\else |
| 7850 | 7897 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x |
| 7851 | 7898 |
\xdef\m@x{\csname pos\the\loopcount\endcsname}
|
| 7852 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld |
|
| 7899 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@ |
|
| 7853 | 7900 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
|
| 7854 | 7901 |
\else |
| 7855 | 7902 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
|
| ... | ... |
@@ -10431,6 +10478,7 @@ |
| 10431 | 10478 |
\fi |
| 10432 | 10479 |
\fi |
| 10433 | 10480 |
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
|
| 10481 |
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi
|
|
| 10434 | 10482 |
\ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
|
| 10435 | 10483 |
\ifnum\loopcount=\rule@num\relax |
| 10436 | 10484 |
\expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens |
| ... | ... |
@@ -10574,6 +10622,7 @@ |
| 10574 | 10622 |
\the\innerloopcount} |
| 10575 | 10623 |
\else |
| 10576 | 10624 |
\ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
|
| 10625 |
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi
|
|
| 10577 | 10626 |
\ifx\collect@valtop\yes |
| 10578 | 10627 |
\ifnum\v@lseqtop=\loopcount |
| 10579 | 10628 |
\xdef\v@ltop{\v@ltop,N}
|
| ... | ... |
@@ -11373,7 +11422,7 @@ |
| 11373 | 11422 |
\textcolor{\legend@fg}{%
|
| 11374 | 11423 |
\ifgerm@n\kern2ex\legend@size{nicht konserviert}%
|
| 11375 | 11424 |
\else\ifsp@nish\kern2ex\legend@size{no conservado}%
|
| 11376 |
- \else\kern2ex\legend@size{non conserved}\fi\fi}
|
|
| 11425 |
+ \else\kern2ex\legend@size{non-conserved}\fi\fi}
|
|
| 11377 | 11426 |
\newline\hbox{}\noindent%
|
| 11378 | 11427 |
\ifsimmode% |
| 11379 | 11428 |
\ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
|
| ... | ... |
@@ -11862,6 +11911,7 @@ |
| 11862 | 11911 |
\def\get@tripletfill#1#2#3#4&{%
|
| 11863 | 11912 |
\multiply\temp@count by -1% |
| 11864 | 11913 |
\def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
|
| 11914 |
+ |
|
| 11865 | 11915 |
\def\putfeature@style#1{%
|
| 11866 | 11916 |
\residues@size% |
| 11867 | 11917 |
\setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
|
| ... | ... |
@@ -11967,6 +12017,7 @@ |
| 11967 | 12017 |
\fontseries{\featurestyles@series}%
|
| 11968 | 12018 |
\fontshape{\featurestyles@shape}%
|
| 11969 | 12019 |
\selectfont% |
| 12020 |
+ \xdef\last@{bottom}%
|
|
| 11970 | 12021 |
\ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
|
| 11971 | 12022 |
\kern0.15\box@width% |
| 11972 | 12023 |
\loopcount=0\relax% |
| ... | ... |
@@ -12137,6 +12188,7 @@ |
| 12137 | 12188 |
\ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
|
| 12138 | 12189 |
\textcolor{\f@color}{%
|
| 12139 | 12190 |
\raisebox{\last@\arrow@height}{%
|
| 12191 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12140 | 12192 |
\if\first@@ ,% |
| 12141 | 12193 |
\rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
| 12142 | 12194 |
\else% |
| ... | ... |
@@ -12144,6 +12196,10 @@ |
| 12144 | 12196 |
\rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height%
|
| 12145 | 12197 |
\else% |
| 12146 | 12198 |
\if\first@@ `\xdef\first@@{'}\fi%
|
| 12199 |
+ \if\first@@ '% |
|
| 12200 |
+ \rule[\arrow@height]% |
|
| 12201 |
+ {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
|
| 12202 |
+ \else% |
|
| 12147 | 12203 |
\if\first@@ '% |
| 12148 | 12204 |
\rule[\arrow@height]% |
| 12149 | 12205 |
{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
| ... | ... |
@@ -12152,6 +12208,7 @@ |
| 12152 | 12208 |
\rule{0pt}{0pt}\kern-0.35\arrow@height%
|
| 12153 | 12209 |
\fi% |
| 12154 | 12210 |
\fi% |
| 12211 |
+ \fi% |
|
| 12155 | 12212 |
\fi% |
| 12156 | 12213 |
\fi% |
| 12157 | 12214 |
\if\third@@ v% |
| ... | ... |
@@ -12212,6 +12269,7 @@ |
| 12212 | 12269 |
\xdef\last@{-0.25}\fi\fi\fi\fi%
|
| 12213 | 12270 |
\textcolor{\f@color}{%
|
| 12214 | 12271 |
\raisebox{\last@\arrow@height}{%
|
| 12272 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12215 | 12273 |
\if\first@@ ,% |
| 12216 | 12274 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| 12217 | 12275 |
\kern-0.1\arrow@height% |
| ... | ... |
@@ -12220,7 +12278,8 @@ |
| 12220 | 12278 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
|
| 12221 | 12279 |
\kern-0.1\arrow@height% |
| 12222 | 12280 |
\else% |
| 12223 |
- \if\first@@ `\xdef\first@@{'}\fi%
|
|
| 12281 |
+ \if\first@@ a \xdef\first@@{'}\fi%
|
|
| 12282 |
+ \if\first@@ ` \xdef\first@@{'}\fi%
|
|
| 12224 | 12283 |
\if\first@@ '% |
| 12225 | 12284 |
\rule[0.4\arrow@height]% |
| 12226 | 12285 |
{0.1\arrow@height}{1.5\arrow@height}%
|
| ... | ... |
@@ -12245,6 +12304,7 @@ |
| 12245 | 12304 |
\rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
|
| 12246 | 12305 |
\kern-\width@tmp% |
| 12247 | 12306 |
\rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
|
| 12307 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12248 | 12308 |
\if\third@@ ,% |
| 12249 | 12309 |
\kern-0.05\arrow@height% |
| 12250 | 12310 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| ... | ... |
@@ -12253,10 +12313,16 @@ |
| 12253 | 12313 |
\kern-0.05\arrow@height% |
| 12254 | 12314 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
|
| 12255 | 12315 |
\else% |
| 12256 |
- \if\third@@ `\xdef\third@@{'}\fi%
|
|
| 12316 |
+ \if\first@@ a \xdef\first@@{'}\fi%
|
|
| 12317 |
+ \if\third@@ ` \xdef\third@@{'}\fi%
|
|
| 12257 | 12318 |
\if\third@@ '% |
| 12258 | 12319 |
\kern-0.05\arrow@height% |
| 12259 | 12320 |
\rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| 12321 |
+ \else% |
|
| 12322 |
+ \if\third@@ a% |
|
| 12323 |
+ \kern-0.05\arrow@height% |
|
| 12324 |
+ \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
|
| 12325 |
+ \fi% |
|
| 12260 | 12326 |
\fi% |
| 12261 | 12327 |
\fi% |
| 12262 | 12328 |
\fi% |
| ... | ... |
@@ -12268,9 +12334,25 @@ |
| 12268 | 12334 |
\advance\width@tmp by -0.5\temp@@length% |
| 12269 | 12335 |
\if\first@@ o\xdef\first@@{O}\fi%
|
| 12270 | 12336 |
\if\third@@ o\xdef\third@@{O}\fi%
|
| 12337 |
+ \xdef\last@{bottom}%
|
|
| 12338 |
+ \ifx\fe@turep@s\last@% |
|
| 12339 |
+ \vspace{-20pt}\message{(((-20pt)))}%
|
|
| 12340 |
+ \fi% |
|
| 12271 | 12341 |
\textcolor{\f@color}{%
|
| 12272 | 12342 |
\if\first@@ ,% |
| 12273 |
- \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12343 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12344 |
+ \else% |
|
| 12345 |
+ \if\first@@ b% |
|
| 12346 |
+ \xdef\last@{bottom}%
|
|
| 12347 |
+ \ifx\fe@turep@s\last@% |
|
| 12348 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12349 |
+ \else |
|
| 12350 |
+ \xdef\shift@feature{y}%
|
|
| 12351 |
+ \kern-\temp@@length% |
|
| 12352 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12353 |
+ \kern-\temp@@length% |
|
| 12354 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12355 |
+ \fi |
|
| 12274 | 12356 |
\else% |
| 12275 | 12357 |
\if\first@@ |% |
| 12276 | 12358 |
\rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
|
| ... | ... |
@@ -12278,6 +12360,52 @@ |
| 12278 | 12360 |
\if\first@@ O% |
| 12279 | 12361 |
\raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
|
| 12280 | 12362 |
\rule[\width@tmp]{0.65ex}{\temp@@length}%
|
| 12363 |
+ \else% |
|
| 12364 |
+ \if\first@@ S% |
|
| 12365 |
+ \xdef\last@{bottom}%
|
|
| 12366 |
+ \ifx\fe@turep@s\last@% |
|
| 12367 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12368 |
+ \kern0.5\box@width% |
|
| 12369 |
+ \kern-2\temp@@length% |
|
| 12370 |
+ \rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12371 |
+ \advance\width@tmp by -0.5\temp@@length% |
|
| 12372 |
+ \kern-\temp@@length% |
|
| 12373 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12374 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12375 |
+ \else% |
|
| 12376 |
+ \kern0.5\box@width% |
|
| 12377 |
+ \kern-2\temp@@length% |
|
| 12378 |
+ \rule{\temp@@length}{\arrow@height}%
|
|
| 12379 |
+ \kern-\temp@@length% |
|
| 12380 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12381 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12382 |
+ \fi% |
|
| 12383 |
+ \else% |
|
| 12384 |
+ \if\first@@ c% |
|
| 12385 |
+ \xdef\last@{bottom}%
|
|
| 12386 |
+ \ifx\fe@turep@s\last@% |
|
| 12387 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12388 |
+ \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12389 |
+ \kern0.5\box@width% |
|
| 12390 |
+ \kern-2\temp@@length% |
|
| 12391 |
+ \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12392 |
+ \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12393 |
+ \rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12394 |
+ \advance\width@tmp by -0.5\temp@@length% |
|
| 12395 |
+ \kern-\temp@@length% |
|
| 12396 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12397 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12398 |
+ \else% |
|
| 12399 |
+ \xdef\shift@feature{y}%
|
|
| 12400 |
+ \kern0.5\box@width% |
|
| 12401 |
+ \kern-2\temp@@length% |
|
| 12402 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12403 |
+ \kern-\temp@@length% |
|
| 12404 |
+ \rule{\temp@@length}{\arrow@height}%
|
|
| 12405 |
+ \kern-\temp@@length% |
|
| 12406 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12407 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12408 |
+ \fi% |
|
| 12281 | 12409 |
\else% |
| 12282 | 12410 |
\if\first@@ <% |
| 12283 | 12411 |
\raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
|
| ... | ... |
@@ -12290,13 +12418,20 @@ |
| 12290 | 12418 |
\fi% |
| 12291 | 12419 |
\fi% |
| 12292 | 12420 |
\fi% |
| 12421 |
+ \fi% |
|
| 12422 |
+ \fi% |
|
| 12293 | 12423 |
\fi% |
| 12294 | 12424 |
\fi% |
| 12425 |
+ \fi% |
|
| 12295 | 12426 |
\loopcount=\second@% |
| 12296 | 12427 |
\if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12297 | 12428 |
\if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12298 | 12429 |
\if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12299 | 12430 |
\if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12431 |
+ \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12432 |
+ \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12433 |
+ \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12434 |
+ \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12300 | 12435 |
\xdef\second@{\the\loopcount}%
|
| 12301 | 12436 |
\rule[\width@tmp]{\second@\box@width}{\temp@@length}%
|
| 12302 | 12437 |
\setbox1=\hbox{\residues@size{\fill@char}}%
|
| ... | ... |
@@ -12306,6 +12441,17 @@ |
| 12306 | 12441 |
\hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}%
|
| 12307 | 12442 |
\if\third@@ ,% |
| 12308 | 12443 |
\kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
| 12444 |
+ \else% |
|
| 12445 |
+ \if\third@@ b% |
|
| 12446 |
+ \xdef\last@{bottom}%
|
|
| 12447 |
+ \ifx\fe@turep@s\last@% |
|
| 12448 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12449 |
+ \else |
|
| 12450 |
+ \xdef\shift@feature{y}%
|
|
| 12451 |
+ \kern-\temp@@length% |
|
| 12452 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12453 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12454 |
+ \fi |
|
| 12309 | 12455 |
\else% |
| 12310 | 12456 |
\if\third@@ |% |
| 12311 | 12457 |
\kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
|
| ... | ... |
@@ -12313,6 +12459,31 @@ |
| 12313 | 12459 |
\if\third@@ O% |
| 12314 | 12460 |
\rule[\width@tmp]{0.65ex}{\temp@@length}%
|
| 12315 | 12461 |
\kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
|
| 12462 |
+ \else% |
|
| 12463 |
+ \if\third@@ S% |
|
| 12464 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12465 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12466 |
+ \xdef\last@{bottom}%
|
|
| 12467 |
+ \ifx\fe@turep@s\last@% |
|
| 12468 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12469 |
+ \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12470 |
+ \else |
|
| 12471 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12472 |
+ \fi% |
|
| 12473 |
+ \else% |
|
| 12474 |
+ \if\third@@ c% |
|
| 12475 |
+ \xdef\shift@feature{y}%
|
|
| 12476 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12477 |
+ \xdef\last@{bottom}%
|
|
| 12478 |
+ \ifx\fe@turep@s\last@% |
|
| 12479 |
+ \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12480 |
+ \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12481 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12482 |
+ \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12483 |
+ \else |
|
| 12484 |
+ \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12485 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12486 |
+ \fi% |
|
| 12316 | 12487 |
\else% |
| 12317 | 12488 |
\if\third@@ >% |
| 12318 | 12489 |
\kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
|
| ... | ... |
@@ -12324,7 +12495,10 @@ |
| 12324 | 12495 |
\fi% |
| 12325 | 12496 |
\fi% |
| 12326 | 12497 |
\fi% |
| 12327 |
- \fi |
|
| 12498 |
+ \fi% |
|
| 12499 |
+ \fi% |
|
| 12500 |
+ \fi% |
|
| 12501 |
+ \fi% |
|
| 12328 | 12502 |
\fi}% |
| 12329 | 12503 |
\fi |
| 12330 | 12504 |
\fi |
| ... | ... |
@@ -12731,9 +12905,550 @@ |
| 12731 | 12905 |
\divide\loopcount by 100 % |
| 12732 | 12906 |
\xdef\third@{\the\loopcount}%
|
| 12733 | 12907 |
} |
| 12908 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12909 |
+%%%% Chimera export routines %%%% |
|
| 12910 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12911 |
+\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}}
|
|
| 12912 |
+\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}}
|
|
| 12913 |
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}}
|
|
| 12914 |
+\def\memelabelcutoff#1{%
|
|
| 12915 |
+ \xdef\label@threshold@lower{#1}
|
|
| 12916 |
+ \setlength\temp@@length{1000sp}
|
|
| 12917 |
+ \setlength\temp@@length{\label@threshold@lower\temp@@length}
|
|
| 12918 |
+ \loopcount=\temp@@length |
|
| 12919 |
+ \xdef\label@threshold@lowerIOOO{\the\loopcount}
|
|
| 12920 |
+ \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount}
|
|
| 12921 |
+} |
|
| 12922 |
+\def\chimera@color@get#1#2@{%
|
|
| 12923 |
+ \xdef\first@{#1}\xdef\third@{#2@}
|
|
| 12924 |
+ \ifx\first@\ampers@nd |
|
| 12925 |
+ \else |
|
| 12926 |
+ \ifnum`#1>96 \make@upper\fi |
|
| 12927 |
+ \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi
|
|
| 12928 |
+ \expandafter\chimera@color@get\third@ |
|
| 12929 |
+ \fi |
|
| 12930 |
+} |
|
| 12931 |
+\def\memered#1{%
|
|
| 12932 |
+ \xdef\third@{#1&@}
|
|
| 12933 |
+ \xdef\second@{red}
|
|
| 12934 |
+ \expandafter\chimera@color@get\third@ |
|
| 12935 |
+} |
|
| 12936 |
+\def\memeblue#1{%
|
|
| 12937 |
+ \xdef\third@{#1&@}
|
|
| 12938 |
+ \xdef\second@{blue}
|
|
| 12939 |
+ \expandafter\chimera@color@get\third@ |
|
| 12940 |
+} |
|
| 12941 |
+\def\memeyellow#1{%
|
|
| 12942 |
+ \xdef\third@{#1&@}
|
|
| 12943 |
+ \xdef\second@{yellow}
|
|
| 12944 |
+ \expandafter\chimera@color@get\third@ |
|
| 12945 |
+} |
|
| 12946 |
+\def\memeblack#1{%
|
|
| 12947 |
+ \xdef\third@{#1&@}
|
|
| 12948 |
+ \xdef\second@{black}
|
|
| 12949 |
+ \expandafter\chimera@color@get\third@ |
|
| 12950 |
+} |
|
| 12951 |
+\def\memewhite#1{%
|
|
| 12952 |
+ \xdef\third@{#1&@}
|
|
| 12953 |
+ \xdef\second@{white}
|
|
| 12954 |
+ \expandafter\chimera@color@get\third@ |
|
| 12955 |
+} |
|
| 12956 |
+\def\memenone#1{%
|
|
| 12957 |
+ \xdef\third@{#1&@}
|
|
| 12958 |
+ \xdef\second@{none}
|
|
| 12959 |
+ \expandafter\chimera@color@get\third@ |
|
| 12960 |
+} |
|
| 12961 |
+\def\memeRed#1{\memered{#1}}
|
|
| 12962 |
+\def\memeBlue#1{\memeblue{#1}}
|
|
| 12963 |
+\def\memeYellow#1{\memeyellow{#1}}
|
|
| 12964 |
+\def\memeBlack#1{\memeblack{#1}}
|
|
| 12965 |
+\def\memeWhite#1{\memewhite{#1}}
|
|
| 12966 |
+\def\memeNone#1{\memenone{#1}}
|
|
| 12967 |
+\def\chimera@colors#1#2@{%
|
|
| 12968 |
+ \xdef\first@{#1}\xdef\third@{#2@}
|
|
| 12969 |
+ \ifx\first@\ampers@nd |
|
| 12970 |
+ \else |
|
| 12971 |
+ \xdef\second@{\csname chimera@col@\first@\endcsname}
|
|
| 12972 |
+ \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@}
|
|
| 12973 |
+ \expandafter\chimera@colors\third@ |
|
| 12974 |
+ \fi |
|
| 12975 |
+} |
|
| 12976 |
+\def\memeStandardcolors{%
|
|
| 12977 |
+ \xdef\chimera@col@A{white}
|
|
| 12978 |
+ \xdef\chimera@col@B{none}
|
|
| 12979 |
+ \xdef\chimera@col@C{yellow}
|
|
| 12980 |
+ \xdef\chimera@col@D{red}
|
|
| 12981 |
+ \xdef\chimera@col@E{red}
|
|
| 12982 |
+ \xdef\chimera@col@F{black}
|
|
| 12983 |
+ \xdef\chimera@col@G{yellow}
|
|
| 12984 |
+ \xdef\chimera@col@H{blue}
|
|
| 12985 |
+ \xdef\chimera@col@I{black}
|
|
| 12986 |
+ \xdef\chimera@col@J{none}
|
|
| 12987 |
+ \xdef\chimera@col@K{blue}
|
|
| 12988 |
+ \xdef\chimera@col@L{black}
|
|
| 12989 |
+ \xdef\chimera@col@M{black}
|
|
| 12990 |
+ \xdef\chimera@col@N{yellow}
|
|
| 12991 |
+ \xdef\chimera@col@O{none}
|
|
| 12992 |
+ \xdef\chimera@col@P{white}
|
|
| 12993 |
+ \xdef\chimera@col@Q{yellow}
|
|
| 12994 |
+ \xdef\chimera@col@R{blue}
|
|
| 12995 |
+ \xdef\chimera@col@S{yellow}
|
|
| 12996 |
+ \xdef\chimera@col@T{yellow}
|
|
| 12997 |
+ \xdef\chimera@col@U{none}
|
|
| 12998 |
+ \xdef\chimera@col@V{white}
|
|
| 12999 |
+ \xdef\chimera@col@W{black}
|
|
| 13000 |
+ \xdef\chimera@col@X{none}
|
|
| 13001 |
+ \xdef\chimera@col@Y{yellow}
|
|
| 13002 |
+ \xdef\chimera@col@Z{none}
|
|
| 13003 |
+} |
|
| 13004 |
+\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}}
|
|
| 13005 |
+\def\chimerachain#1{\xdef\chimerach@in{.#1}}
|
|
| 13006 |
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12 |
|
| 13007 |
+\newcommand{\structurememe}[2][chimera.cmd]{%
|
|
| 13008 |
+ \ifx\exp@rt@chimera\n@ |
|
| 13009 |
+ \xdef\first@{"2 @} \expandafter\check@letter\first@
|
|
| 13010 |
+ \xdef\first@{"2} \ifletter \get@name@number \fi
|
|
| 13011 |
+ \xdef\chimera@seqnum{\first@}
|
|
| 13012 |
+ \xdef\exp@rt@chimera{y}
|
|
| 13013 |
+ \xdef\first@{"1}
|
|
| 13014 |
+ \immediate\openout\exp@rt@chimerafile = \first@ |
|
| 13015 |
+ \fi |
|
| 13016 |
+} |
|
| 13017 |
+\def\init@chimera@file{%
|
|
| 13018 |
+ \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{}
|
|
| 13019 |
+ \xdef\chimera@list@none{}
|
|
| 13020 |
+ \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
|
|
| 13021 |
+ \expandafter\chimera@colors\first@ |
|
| 13022 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13023 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13024 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O � o STRUCTURE MEME � . O o}
|
|
| 13025 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13026 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
|
|
| 13027 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
|
|
| 13028 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13029 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
|
|
| 13030 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13031 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13032 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13033 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13034 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
|
|
| 13035 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)}
|
|
| 13036 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)}
|
|
| 13037 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)}
|
|
| 13038 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)}
|
|
| 13039 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)}
|
|
| 13040 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13041 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13042 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13043 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
|
|
| 13044 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear}
|
|
| 13045 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
|
|
| 13046 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13047 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13048 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13049 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
|
|
| 13050 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13051 |
+ \immediate\write\exp@rt@chimerafile{close session; background solid white;}
|
|
| 13052 |
+ \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
|
|
| 13053 |
+ \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface}
|
|
| 13054 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13055 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13056 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
|
|
| 13057 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
|
|
| 13058 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
|
|
| 13059 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13060 |
+ \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0}
|
|
| 13061 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13062 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13063 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
|
|
| 13064 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13065 |
+ \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca}
|
|
| 13066 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13067 |
+ \ifshow@sublogo |
|
| 13068 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13069 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
|
|
| 13070 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
|
|
| 13071 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
|
|
| 13072 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
|
|
| 13073 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13074 |
+ \immediate\write\exp@rt@chimerafile{combine #0}
|
|
| 13075 |
+ \ifnum\chimera@xdist@nce>0 |
|
| 13076 |
+ \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1}
|
|
| 13077 |
+ \fi |
|
| 13078 |
+ \ifnum\chimera@ydist@nce>0 |
|
| 13079 |
+ \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1}
|
|
| 13080 |
+ \fi |
|
| 13081 |
+ \ifnum\chimera@zdist@nce>0 |
|
| 13082 |
+ \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1}
|
|
| 13083 |
+ \fi |
|
| 13084 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13085 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13086 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
|
|
| 13087 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13088 |
+ \immediate\write\exp@rt@chimerafile{wait; focus #0#1}
|
|
| 13089 |
+ \ifx\sublogo@name@user\ampers@nd |
|
| 13090 |
+ \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0}
|
|
| 13091 |
+ \else |
|
| 13092 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0}
|
|
| 13093 |
+ \fi |
|
| 13094 |
+ \xdef\first@{\sublogo@name@neg &}
|
|
| 13095 |
+ \ifx\first@\ampers@nd |
|
| 13096 |
+ \immediate\write\exp@rt@chimerafile{setattr m name remaining #1}
|
|
| 13097 |
+ \else |
|
| 13098 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1}
|
|
| 13099 |
+ \fi |
|
| 13100 |
+ \else |
|
| 13101 |
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
|
|
| 13102 |
+ \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
|
|
| 13103 |
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
|
|
| 13104 |
+ \ifx\logo@name@user\ampers@nd |
|
| 13105 |
+ \immediate\write\exp@rt@chimerafile{setattr m name logo #0}
|
|
| 13106 |
+ \else |
|
| 13107 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0}
|
|
| 13108 |
+ \fi |
|
| 13109 |
+ \fi |
|
| 13110 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13111 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13112 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
|
|
| 13113 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13114 |
+} |
|
| 13115 |
+\def\make@HEX{%
|
|
| 13116 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13117 |
+ \divide\loopcount by 4096\relax% |
|
| 13118 |
+ \ifnum\loopcount=10\relax% |
|
| 13119 |
+ \xdef\seventh@{A}%
|
|
| 13120 |
+ \else% |
|
| 13121 |
+ \ifnum\loopcount=11\relax% |
|
| 13122 |
+ \xdef\seventh@{B}%
|
|
| 13123 |
+ \else% |
|
| 13124 |
+ \ifnum\loopcount=12\relax% |
|
| 13125 |
+ \xdef\seventh@{C}%
|
|
| 13126 |
+ \else% |
|
| 13127 |
+ \ifnum\loopcount=13\relax% |
|
| 13128 |
+ \xdef\seventh@{D}%
|
|
| 13129 |
+ \else% |
|
| 13130 |
+ \ifnum\loopcount=14\relax% |
|
| 13131 |
+ \xdef\seventh@{E}%
|
|
| 13132 |
+ \else% |
|
| 13133 |
+ \ifnum\loopcount>14\relax% |
|
| 13134 |
+ \xdef\seventh@{F}%
|
|
| 13135 |
+ \else% |
|
| 13136 |
+ \xdef\seventh@{\the\loopcount}%
|
|
| 13137 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13138 |
+ \multiply\loopcount by -4096\relax% |
|
| 13139 |
+ \advance\loopcount by \sixth@% |
|
| 13140 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13141 |
+ \divide\loopcount by 256\relax% |
|
| 13142 |
+ \ifnum\loopcount=10 \relax% |
|
| 13143 |
+ \xdef\eighth@{A}%
|
|
| 13144 |
+ \else% |
|
| 13145 |
+ \ifnum\loopcount=11 \relax% |
|
| 13146 |
+ \xdef\eighth@{B}%
|
|
| 13147 |
+ \else% |
|
| 13148 |
+ \ifnum\loopcount=12 \relax% |
|
| 13149 |
+ \xdef\eighth@{C}%
|
|
| 13150 |
+ \else% |
|
| 13151 |
+ \ifnum\loopcount=13 \relax% |
|
| 13152 |
+ \xdef\eighth@{D}%
|
|
| 13153 |
+ \else% |
|
| 13154 |
+ \ifnum\loopcount=14 \relax% |
|
| 13155 |
+ \xdef\eighth@{E}%
|
|
| 13156 |
+ \else% |
|
| 13157 |
+ \ifnum\loopcount>14 \relax% |
|
| 13158 |
+ \xdef\eighth@{F}%
|
|
| 13159 |
+ \else% |
|
| 13160 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13161 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13162 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13163 |
+ \multiply\loopcount by -256\relax% |
|
| 13164 |
+ \advance\loopcount by \sixth@% |
|
| 13165 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13166 |
+ \divide\loopcount by 16\relax% |
|
| 13167 |
+ \ifnum\loopcount=10\relax% |
|
| 13168 |
+ \xdef\eighth@{A}%
|
|
| 13169 |
+ \else% |
|
| 13170 |
+ \ifnum\loopcount=11\relax% |
|
| 13171 |
+ \xdef\eighth@{B}%
|
|
| 13172 |
+ \else% |
|
| 13173 |
+ \ifnum\loopcount=12\relax% |
|
| 13174 |
+ \xdef\eighth@{C}%
|
|
| 13175 |
+ \else% |
|
| 13176 |
+ \ifnum\loopcount=13\relax% |
|
| 13177 |
+ \xdef\eighth@{D}%
|
|
| 13178 |
+ \else% |
|
| 13179 |
+ \ifnum\loopcount=14\relax% |
|
| 13180 |
+ \xdef\eighth@{E}%
|
|
| 13181 |
+ \else% |
|
| 13182 |
+ \ifnum\loopcount>14\relax% |
|
| 13183 |
+ \xdef\eighth@{F}%
|
|
| 13184 |
+ \else% |
|
| 13185 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13186 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13187 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13188 |
+ \multiply\loopcount by -16\relax% |
|
| 13189 |
+ \advance\loopcount by \sixth@\relax% |
|
| 13190 |
+ \ifnum\loopcount=10\relax% |
|
| 13191 |
+ \xdef\eighth@{A}%
|
|
| 13192 |
+ \else% |
|
| 13193 |
+ \ifnum\loopcount=11\relax% |
|
| 13194 |
+ \xdef\eighth@{B}%
|
|
| 13195 |
+ \else% |
|
| 13196 |
+ \ifnum\loopcount=12\relax% |
|
| 13197 |
+ \xdef\eighth@{C}%
|
|
| 13198 |
+ \else% |
|
| 13199 |
+ \ifnum\loopcount=13\relax% |
|
| 13200 |
+ \xdef\eighth@{D}%
|
|
| 13201 |
+ \else% |
|
| 13202 |
+ \ifnum\loopcount=14\relax% |
|
| 13203 |
+ \xdef\eighth@{E}%
|
|
| 13204 |
+ \else% |
|
| 13205 |
+ \ifnum\loopcount>14\relax% |
|
| 13206 |
+ \xdef\eighth@{F}%
|
|
| 13207 |
+ \else% |
|
| 13208 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13209 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13210 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13211 |
+} |
|
| 13212 |
+\def\write@chimera@data{%
|
|
| 13213 |
+ \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi% |
|
| 13214 |
+ \loopcount=\temp@count% |
|
| 13215 |
+ \xdef\fourth@{\the\loopcount @}%
|
|
| 13216 |
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% |
|
| 13217 |
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% |
|
| 13218 |
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% |
|
| 13219 |
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% |
|
| 13220 |
+ \expandafter\decimal@E\fourth@% |
|
| 13221 |
+ \fi\fi\fi\fi% |
|
| 13222 |
+ \loopcount=\chimera@subfamily@col@black% |
|
| 13223 |
+ \multiply\loopcount by 65535\relax% |
|
| 13224 |
+ \divide\loopcount by \temp@count% |
|
| 13225 |
+ \xdef\chimera@subfamily@col@black{\the\loopcount}%
|
|
| 13226 |
+ \loopcount=65535\relax% |
|
| 13227 |
+ \advance\loopcount by -\chimera@subfamily@col@black% |
|
| 13228 |
+ \xdef\temp@@{\the\loopcount}%
|
|
| 13229 |
+%%%%%%%%%%%%%% |
|
| 13230 |
+%%%%%%%%%%%%%% |
|
| 13231 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13232 |
+ \ifnum\chimera@subfamily@col@yellow>\loopcount\relax% |
|
| 13233 |
+ \loopcount=\chimera@subfamily@col@yellow\relax% |
|
| 13234 |
+ \else% |
|
| 13235 |
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax% |
|
| 13236 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13237 |
+ \fi% |
|
| 13238 |
+ \fi% |
|
| 13239 |
+ \xdef\max@yellow{\the\loopcount}%
|
|
| 13240 |
+ \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax% |
|
| 13241 |
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}%
|
|
| 13242 |
+ \else% |
|
| 13243 |
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}%
|
|
| 13244 |
+ \fi% |
|
| 13245 |
+ \loopcount=\chimera@subfamily@col@yellow\relax% |
|
| 13246 |
+ \advance\loopcount by -\chimera@subfamily@col@green% |
|
| 13247 |
+ \xdef\chimera@subfamily@col@yellow{\the\loopcount}%
|
|
| 13248 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13249 |
+ \advance\loopcount by -\chimera@subfamily@col@green% |
|
| 13250 |
+ \xdef\chimera@subfamily@col@blue{\the\loopcount}%
|
|
| 13251 |
+ \ifnum\chimera@subfamily@col@blue>0\relax% |
|
| 13252 |
+ \ifnum\chimera@subfamily@col@green>0\relax% |
|
| 13253 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13254 |
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}%
|
|
| 13255 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13256 |
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}%
|
|
| 13257 |
+ \fi% |
|
| 13258 |
+ \fi% |
|
| 13259 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13260 |
+ \advance\loopcount by \chimera@subfamily@col@yellow% |
|
| 13261 |
+ \xdef\chimera@subfamily@col@green{\the\loopcount}%
|
|
| 13262 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13263 |
+ \advance\loopcount by \chimera@subfamily@col@yellow% |
|
| 13264 |
+ \xdef\chimera@subfamily@col@red{\the\loopcount}%
|
|
| 13265 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13266 |
+ \ifnum\chimera@subfamily@col@green>\loopcount\relax% |
|
| 13267 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13268 |
+ \else% |
|
| 13269 |
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax% |
|
| 13270 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13271 |
+ \fi% |
|
| 13272 |
+ \fi% |
|
| 13273 |
+ \xdef\max@green{\the\loopcount}%
|
|
| 13274 |
+ \loopcount=\chimera@subfamily@col@blue% |
|
| 13275 |
+ \ifnum\max@green>0\relax% |
|
| 13276 |
+ \multiply\loopcount by \max@yellow% |
|
| 13277 |
+ \divide\loopcount by \max@green% |
|
| 13278 |
+ \fi% |
|
| 13279 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13280 |
+ \multiply\loopcount by \temp@@% |
|
| 13281 |
+ \divide\loopcount by \temp@count% |
|
| 13282 |
+ \make@HEX% |
|
| 13283 |
+ \xdef\nineth@{\seventh@}%
|
|
| 13284 |
+ \loopcount=\chimera@subfamily@col@green% |
|
| 13285 |
+ \ifnum\max@green>0\relax% |
|
| 13286 |
+ \multiply\loopcount by \max@yellow% |
|
| 13287 |
+ \divide\loopcount by \max@green% |
|
| 13288 |
+ \fi% |
|
| 13289 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13290 |
+ \multiply\loopcount by \temp@@% |
|
| 13291 |
+ \divide\loopcount by \temp@count% |
|
| 13292 |
+ \make@HEX% |
|
| 13293 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13294 |
+ \loopcount=\chimera@subfamily@col@red% |
|
| 13295 |
+ \ifnum\max@green>0\relax% |
|
| 13296 |
+ \multiply\loopcount by \max@yellow% |
|
| 13297 |
+ \divide\loopcount by \max@green% |
|
| 13298 |
+ \fi% |
|
| 13299 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13300 |
+ \multiply\loopcount by \temp@@% |
|
| 13301 |
+ \divide\loopcount by \temp@count% |
|
| 13302 |
+ \make@HEX% |
|
| 13303 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13304 |
+ \ifx\chimera@labelOne@set\n@% |
|
| 13305 |
+ \xdef\chimera@labelOne@set{y}%
|
|
| 13306 |
+ \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
|
|
| 13307 |
+ \fi% |
|
| 13308 |
+ \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13309 |
+ \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13310 |
+ \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13311 |
+ \ifshow@sublogo |
|
| 13312 |
+ \ifnum\temp@@count>0 \else\temp@@count=1\fi% |
|
| 13313 |
+ \loopcount=\temp@@count% |
|
| 13314 |
+ \xdef\fourth@{\the\loopcount @}%
|
|
| 13315 |
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% |
|
| 13316 |
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% |
|
| 13317 |
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% |
|
| 13318 |
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% |
|
| 13319 |
+ \expandafter\decimal@E\fourth@% |
|
| 13320 |
+ \fi\fi\fi\fi% |
|
| 13321 |
+ \loopcount=-\chimera@remaining@col@red\relax% |
|
| 13322 |
+ \xdef\chimera@remaining@col@red{\the\loopcount}%
|
|
| 13323 |
+ \loopcount=-\chimera@remaining@col@yellow\relax% |
|
| 13324 |
+ \xdef\chimera@remaining@col@yellow{\the\loopcount}%
|
|
| 13325 |
+ \loopcount=-\chimera@remaining@col@blue\relax% |
|
| 13326 |
+ \xdef\chimera@remaining@col@blue{\the\loopcount}%
|
|
| 13327 |
+ \loopcount=-\chimera@remaining@col@white\relax% |
|