update

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"

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"

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

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'

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",

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":
 	[

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