diff --git a/profiles/base/.aliases b/profiles/base/.aliases index 8dc142f..6dadf85 100644 --- a/profiles/base/.aliases +++ b/profiles/base/.aliases @@ -4,7 +4,7 @@ if [ -f .cargo/bin/bat ]; then fi alias clip='xsel --clipboard' alias groclean='rm \#*' -alias sm='snakemake' +alias latexclean='for i in `*aux *bbl *blg *fdb_latexmk *fls *lof *log *lot *out *synctex.gz *toc`; do rm $i; done' alias ls='ls --color=auto -lh' alias workon='source activate' # enable anaconda environ alias cwl="cwl-runner" @@ -15,6 +15,18 @@ alias csum="ssh lcluster11 csum" alias csreport="ssh lcluster11 csreport" alias scancel="ssh lcluster11 scancel" +# snakemake use all cores by default +sm() { + if [[ "$*" == *"-j"* || "$*" == *"--jobs"* || "$*" == *"--cores"* ]]; then + snakemake $@ + else + snakemake -j all $@ + fi +} + +# extract whatever archive +alias extract="dtrx" + # faster sshfs #alias sshfs="sshfs -o Ciphers=arcfour,Compression=no,auto_cache" #alias sshfs="sshfs -o Compression=no,auto_cache" diff --git a/profiles/base/.environment b/profiles/base/.environment index 0a410cf..f262d59 100644 --- a/profiles/base/.environment +++ b/profiles/base/.environment @@ -1,5 +1,7 @@ #!/bin/bash +setxkbmap -option caps:escape + # system preferences export LANG=en_US.UTF-8 export SSH_KEY_PATH="~/.ssh/rsa_id" diff --git a/profiles/pymol/.pymolrc b/profiles/pymol/.pymolrc index f228fff..c75446d 100644 --- a/profiles/pymol/.pymolrc +++ b/profiles/pymol/.pymolrc @@ -5,6 +5,7 @@ set fetch_path, /tmp log_open /tmp/pymol_log.pml set retain_order +load ~/.pymol/chimera_colors.pml # interface set overlay, 1 @@ -47,6 +48,10 @@ set sphere_scale, 0.5 # custom colors set_color sodium, [0.0, 0.5, 1.0] +# bigger dashes +set dash_gap, .35 +set dash_length, .3 + # shortcuts set_key F1, toggle sticks, solvent set_key F2, toggle sticks, (r. POPC or r. POP) and not hydrogen @@ -61,8 +66,9 @@ set_key F12, ray 1600,1600 alias clean, hide everything, hydrogen or n. 1M* or n. 2M* or n. MC* -alias sf_as_sticks_HCN4, show sticks, residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483; show sticks, residue 475+468 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*) +alias sf_as_sticks_HCN4, show sticks, residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483; +# show sticks, residue 475+468 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*) alias sf_as_sticks_HCN1, show sticks, residue 357-362 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 358-361 - +alias ionwatch, hide everything; show cartoon; show spheres, n. NA or n. K; sf_as_sticks_HCN4; hide everything, ID 1-1899; hide everything, ID 3799-5695 alias dockfix, as sticks, bonded and not polymer diff --git a/profiles/shared/.config/i3/config b/profiles/shared/.config/i3/config index bd24af3..9bd7ec4 100644 --- a/profiles/shared/.config/i3/config +++ b/profiles/shared/.config/i3/config @@ -218,7 +218,7 @@ exec --no-startup-id thunderbird -exec feh --bg-scale ~/wallpaper.jpg +exec feh --bg-fill /home/bauer/artistic/artistici2.png #exec volumeicon exec thunar --daemon #exec --no-startup-id xautolock -time 5 -locker 'i3lock -i ~/.lockscreen/`ls /home/bauer/lockscreens | shuf -n 1` -t -f' diff --git a/profiles/shared/.config/sublime-text-3/Packages/User/Package Control.sublime-settings b/profiles/shared/.config/sublime-text-3/Packages/User/Package Control.sublime-settings index b1b8834..079240a 100644 --- a/profiles/shared/.config/sublime-text-3/Packages/User/Package Control.sublime-settings +++ b/profiles/shared/.config/sublime-text-3/Packages/User/Package Control.sublime-settings @@ -6,6 +6,7 @@ "installed_packages": [ "bioSyntax", + "Color Convert", "Color Highlight", "ColorPicker", "CWL Syntax Highlighting", @@ -19,7 +20,11 @@ "MarkdownLivePreview", "MarkdownPreview", "NeoVintageous", + "Ninja", "Package Control", + "PackageResourceViewer", + "Pymol Language", + "RemoteSubl", "RestructuredText Improved", "rsub", "Rust Enhanced", diff --git a/profiles/shared/.config/sublime-text-3/Packages/User/Preferences.sublime-settings b/profiles/shared/.config/sublime-text-3/Packages/User/Preferences.sublime-settings index 6dfbb5f..a667bd0 100644 --- a/profiles/shared/.config/sublime-text-3/Packages/User/Preferences.sublime-settings +++ b/profiles/shared/.config/sublime-text-3/Packages/User/Preferences.sublime-settings @@ -12,7 +12,7 @@ "detect_indentation": false, "dictionary": "Packages/Language - English/en_US.dic", "font_face": "Hack for Powerline Regular", - "font_size": 12, + "font_size": 15, "hot_exit": false, "ignored_packages": [ diff --git a/profiles/shared/.config/terminator/config b/profiles/shared/.config/terminator/config index b37ad2d..e70415e 100644 --- a/profiles/shared/.config/terminator/config +++ b/profiles/shared/.config/terminator/config @@ -2,6 +2,20 @@ enabled_plugins = InactivityWatch, ActivityWatch, TerminalShot, LaunchpadCodeURLHandler, APTURLHandler, LaunchpadBugURLHandler suppress_multiple_term_dialog = True [keybindings] + page_up = None + page_down = None +[profiles] + [[default]] + allow_bold = False + cursor_color = "#aaaaaa" + font = Hack 14 + show_titlebar = False + scrollback_lines = 5000 + scrollback_infinite = True + palette = "#282828:#cc241d:#98971a:#d79921:#458588:#b16286:#689d6a:#a89984:#928374:#fb4934:#b8bb26:#fabd2f:#83a598:#d3869b:#8ec07c:#ebdbb2" + use_system_font = False + copy_on_selection = True + rewrap_on_resize = False [layouts] [[default]] [[[child1]]] @@ -11,15 +25,3 @@ parent = "" type = Window [plugins] -[profiles] - [[default]] - allow_bold = False - copy_on_selection = True - cursor_color = "#aaaaaa" - font = Hack 14 - palette = "#282828:#cc241d:#98971a:#d79921:#458588:#b16286:#689d6a:#a89984:#928374:#fb4934:#b8bb26:#fabd2f:#83a598:#d3869b:#8ec07c:#ebdbb2" - rewrap_on_resize = False - scrollback_infinite = True - scrollback_lines = 5000 - show_titlebar = False - use_system_font = False