summaryrefslogtreecommitdiff
path: root/Master/texmf-dist/tex/latex/textopo/textopo.def
blob: 5034fcf422bb8c9f2d4305a13e96cff0b992fe25 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%                                                                      %%%%%
%%%%%     Default parameter settings for the LaTeX ``TeXtopo'' package     %%%%%
%%%%%                                                                      %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%                                                                      %%%%%
%%%%%   This example file contains all standard  settings of the TeXtopo   %%%%%
%%%%%   package. It can be used as a template for the creation of perso-   %%%%%
%%%%%   nal parameter files.  All TeXtopo user commands are  allowed and   %%%%%
%%%%%   functional when specified here.                                    %%%%%
%%%%%                                                                      %%%%%
%%%%%   To activate these settings for your topology plot load this file   %%%%%
%%%%%   by naming it as optional parameter  at the beginning of the tex-   %%%%%
%%%%%   topo environment, e.g.                                             %%%%%
%%%%%                                                                      %%%%%
%%%%%          \begin{textopo}[myparameterfile]                            %%%%%
%%%%%             .                                                        %%%%%
%%%%%             .                                                        %%%%%
%%%%%          \end{textopo}                                               %%%%%
%%%%%                                                                      %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\Nterm{intra}                       %  Assume N-terminus intracellular
\loopextent{30}                     %  Set loop extent to 30 residues
\shadingcolors{blues}               %  Use color scheme `blues' for shading
\showmembrane                       %  Show the membrane
\membranecolors{Black}{White}       %        as black lines w/o filling
\labeloutside{extra}                %  Label extracellular side with `extra'
\labelinside{intra}                 %  Label intracellular side with `intra'
\rulethickness{0.5pt}               %  Set thickness of label rules to 0.5pt
\countercolor{Red}                  %  Use red color for position counter
\helixstyle{perspective}            %  Draw helical wheels in perspective
\showbonds                          %  Show bonds on helical wheels
\hidemoment                         %  Do not show hydrophobic moment
\momentcolor{Lavender}              %  Lavender color for hydrophobic moment
\scalemoment{100}                   %  Moment rule length is 100%
\showwheelnumbering                 %  Show residue numbers on helical wheels
\scalewheel{100}                    %  Show full size helical wheel
\symbolsize{medium}                 %  Use medium sized symbols in wheels
\donotshadestartMet                 %  Do not shade the start methionine
\showNterm                          %  Show amino terminus as NH2
\showCterm                          %  Show carboxy terminus as COOH

\setfamily{labels}{sf}              %  Use sans serif family for labels
\setseries{labels}{md}              %  Use normal series for labels
\setshape {labels}{up}              %  Use upright shape for labels
\setfamily{membranelabels}{sf}      %  Use sans serif for membrane labels
\setseries{membranelabels}{md}      %  Use normal series for membrane labels
\setshape {membranelabels}{up}      %  Use upright shape for membrane labels
\setfamily{looplabels}{sf}          %  Use sans serif for loop labels
\setseries{looplabels}{bf}          %  Use bold face for loop labels
\setshape {looplabels}{up}          %  Use upright shape for loop labels
\looplabelcolor{Red}                %  Set loop label color to `Red'
\setfamily{TMlabels}{sf}            %  Use sans serif for TM labels
\setseries{TMlabels}{bf}            %  Use bold face for TM labels
\setshape {TMlabels}{up}            %  Use upright shape for TM labels
\TMlabelcolor{Blue}                 %  Set TM label color to `Blue'
\labelTMs{\Romancount}              %  Label the TMs with roman numbers
\setfamily{legend}{sf}              %  Use sans serif font for legend texts
\setseries{legend}{md}              %  Use normal series for legend texts
\setshape {legend}{up}              %  Use upright shape for legend texts
\setsize  {legend}{normalsize}      %  Use normal font size for legends
\legendcolor{Black}                 %  Set legend text color to `Black'
\showlegend                         %  Show the legend
\hidegrid                           %  Do not show the grid

\labelstyle{CONFLICT}               %    Label style definitions for
 {diamond}{Black}{Blue}{White}      %
 {Conflicting reports in literatur} %       SwissProt data files

\labelstyle{VARIANT}                %                |
 {diamond}{Black}{Orange}{Black}    %                |
 {Sequence variants}                %                V

\labelstyle{VARSPLIC}               %
 {diamond}{Black}{Apricot}{Black}   %
 {Splice variants}                  %

\labelstyle{MUTAGEN}                %
 {diamond}{Black}{Red}{White}       %
 {Mutation sites}                   %

\labelstyle{SIGNAL}                 %
 {square}{Black}{Yellow}{Black}     %
 {Signal peptide}                   %

\labelstyle{TRANSIT}                %
 {square}{Black}{Green}{Black}      %
 {Transit peptide}                  %

\labelstyle{PROPEP}                 %
 {square}{Black}{Red}{White}        %
 {Propeptide}                       %

\labelstyle{CHAIN}                  %
 {circ}{Black}{Aquamarine}{Blue}    %
 {Polypeptide chain}                %

\labelstyle{PEPTIDE}                %
 {circ}{Black}{Peach}{Black}        %
 {Released peptide}                 %

\labelstyle{DOMAIN}                 %
 {circ}{Black}{Turquoise}{Black}    %
 {Domain}                           %

\labelstyle{CABIND}                 %
 {circ}{Black}{Gray50}{White}       %
 {Calcium binding domain}           %

\labelstyle{DNABIND}                %
 {circ}{Black}{YellowGreen}{Black}  %
 {DNA binding domain}               %

\labelstyle{NPBIND}                 %
 {circ}{Black}{Melon}{Black}        %
 {Nucleotide phosphate binding}     %

\labelstyle{ZNFING}                 %
 {circ}{Black}{Lavender}{Black}     %
 {Zinc finger}                      %

\labelstyle{SIMILAR}                %
 {circ}{Black}{SpringGreen}{Black}  %
 {Similar region}                   %

\labelstyle{REPEAT}                 %
 {circ}{Black}{Plum}{White}         %
 {Sequence repeat}                  %

\labelstyle{SITE}                   %
 {circ}{Black}{ForestGreen}{White}  %
 {Special site}                     %