update

README.md

@@ -0,0 +1,8 @@
+# dotfiles for linux/wsl
+
+clone to `.dotfiles`.
+
+Start by installing the base configuration via `./install.sh`.
+Then choose relevant configuration bundles with `./dotfiles.sh bundname`
+(i.e. `./dotfiles.sh gui`)
+

install.sh

@@ -14,16 +14,6 @@ else
 	echo "zgen already exists."
 fi
 
-# Powerlevel9k Theme
-if [ ! -d "$HOME/.zim/modules/prompt/external-themes/powerlevel9k" ]; then
-	echo "Installing Powerlevel9k theme"
-	git clone --depth=1 https://github.com/bhilburn/powerlevel9k.git \
-		~/.zim/modules/prompt/external-themes/powerlevel9k
-	ln -s ~/.zim/modules/prompt/external-themes/powerlevel9k/powerlevel9k.zsh-theme ~/.zim/modules/prompt/functions/prompt_powerlevel9k_setup
-else
-	echo "Powerlevel9k already exists."
-fi
-
 # Conda and pip
 if [ ! -d "$HOME/conda" ]; then
 	echo "Installing Conda"

profiles.md

@@ -1,5 +0,0 @@
-- base: base config files. includes zshrc, vim, fonts, etc
-- shared: configs shared between several computers 
-- workplace: configs related to workplace pc 
-- laptop: config related to laptop
-- pymol: Pymol plugins and config files

profiles/base/.condarc

@@ -1,3 +1,5 @@
 channels:
+  - conda-forge
   - salilab
   - defaults
+channel_priority: strict

profiles/base/.environment

@@ -1,7 +1,5 @@
 #!/bin/bash
 
-setxkbmap -option caps:escape
-
 # system preferences
 export LANG=en_US.UTF-8
 export SSH_KEY_PATH="~/.ssh/rsa_id"
@@ -18,4 +16,4 @@ export PATH="${PATH}:$HOME/.cargo/bin"
 export PATH="${PATH}:$HOME/bin" # binaries
 export PATH="${PATH}:$HOME/scripts" # scripts
 export PATH="${PATH}:$HOME/.local/bin" # python executeables
-export PATH="${PATH}:$HOME/bin/pushbullet-bash"
+export PATH="${PATH}:$HOME/bin/pushbullet-bash"

profiles/laptop/.Xresources

@@ -1,7 +0,0 @@
-Xft.dpi: 130
-Xft.autohint: 0
-Xft.lcdfilter:  lcddefault
-Xft.hintstyle:  hintfull
-Xft.hinting: 1
-Xft.antialias: 1
-Xft.rgba: rgb

profiles/laptop/.config/polybar/config

@@ -1,31 +0,0 @@
-
-include-file = ~/.config/polybar/config.d/colors
-include-file = ~/.config/polybar/config.d/settings
-include-file = ~/.config/polybar/config.d/modules
-include-file = ~/.config/polybar/config.d/base_bar
-
-[bar/laptop]
-inherit = bar/base
-monitor = ${env:MONITOR:}
-
-modules-left = i3 xwindow 
-modules-right = previous playpause next spotify pulseaudio cpu memory battery1 date notifyd
-
-tray-position = right
-tray-padding = 2
-
-
-[bar/laptop_standalone]
-inherit = bar/laptop
-monitor = ${env:MONITOR:}
-
-modules-right = previous playpause next spotify pulseaudio backlight-acpi cpu memory battery1 date notifyd
-
-[bar/laptop_secondary]
-inherit = bar/base
-monitor = ${env:MONITOR:}
-
-modules-left = i3 xwindow 
-modules-right = previous playpause next spotify pulseaudio cpu memory battery1 date
-
-tray-position = none

profiles/laptop/.config/polybar/polybar.sh

@@ -1,30 +0,0 @@
-#!/bin/bash
-
-killall -q polybar
-
-# Wait until the processes have been shut down
-while pgrep -u $UID -x polybar >/dev/null; do sleep 1; done
-
-if type "xrandr"; then
-    NUM_DEVICES=$(xrandr --query | grep " connected" | cut -d" " -f1 | wc -l);
-    if [[ $NUM_DEVICES -lt 2 ]]; then
-        for m in $(xrandr --query | grep " connected" | cut -d" " -f1); do
-            MONITOR=$m polybar --reload laptop &
-        done  
-    else
-        # primary screen
-        for m in $(xrandr --query | grep " connected" | grep "primary" | cut -d" " -f1); do
-            MONITOR=$m polybar --reload laptop &
-        done
-        # other screens
-        for m in $(xrandr --query | grep " connected" | grep -v "primary" | cut -d" " -f1); do
-            MONITOR=$m polybar --reload laptop_secondary &
-        done
-    fi
-else
-  polybar --reload laptop &
-fi
-# polybar -c ~/.config/polybar/config laptop &
-# polybar -c ~/.config/polybar/config laptop_extern &
-
-echo "Bars launched..."

profiles/pymol/.pymol/startup/color_h.py

@@ -1,128 +1,128 @@
-# color_h
-# -------
- 
-# PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
- 
-#
-# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
-# Amino acid scale: Normalized consensus hydrophobicity scale
-# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
-# Reference: J. Mol. Biol. 179:125-142 (1984)
-#
-# Amino acid scale values:
-#
-# Ala:  0.620
-# Arg: -2.530
-# Asn: -0.780
-# Asp: -0.900
-# Cys:  0.290
-# Gln: -0.850
-# Glu: -0.740
-# Gly:  0.480
-# His: -0.400
-# Ile:  1.380
-# Leu:  1.060
-# Lys: -1.500
-# Met:  0.640
-# Phe:  1.190
-# Pro:  0.120
-# Ser: -0.180
-# Thr: -0.050
-# Trp:  0.810
-# Tyr:  0.260
-# Val:  1.080
-#
-# Usage:
-# color_h (selection)
-#
-from pymol import cmd
- 
-def color_h(selection='all'):
-        s = str(selection)
-	print s
-        cmd.set_color('color_ile',[0.996,0.062,0.062])
-        cmd.set_color('color_phe',[0.996,0.109,0.109])
-        cmd.set_color('color_val',[0.992,0.156,0.156])
-        cmd.set_color('color_leu',[0.992,0.207,0.207])
-        cmd.set_color('color_trp',[0.992,0.254,0.254])
-        cmd.set_color('color_met',[0.988,0.301,0.301])
-        cmd.set_color('color_ala',[0.988,0.348,0.348])
-        cmd.set_color('color_gly',[0.984,0.394,0.394])
-        cmd.set_color('color_cys',[0.984,0.445,0.445])
-        cmd.set_color('color_tyr',[0.984,0.492,0.492])
-        cmd.set_color('color_pro',[0.980,0.539,0.539])
-        cmd.set_color('color_thr',[0.980,0.586,0.586])
-        cmd.set_color('color_ser',[0.980,0.637,0.637])
-        cmd.set_color('color_his',[0.977,0.684,0.684])
-        cmd.set_color('color_glu',[0.977,0.730,0.730])
-        cmd.set_color('color_asn',[0.973,0.777,0.777])
-        cmd.set_color('color_gln',[0.973,0.824,0.824])
-        cmd.set_color('color_asp',[0.973,0.875,0.875])
-        cmd.set_color('color_lys',[0.899,0.922,0.922])
-        cmd.set_color('color_arg',[0.899,0.969,0.969])
-        cmd.color("color_ile","("+s+" and resn ile)")
-        cmd.color("color_phe","("+s+" and resn phe)")
-        cmd.color("color_val","("+s+" and resn val)")
-        cmd.color("color_leu","("+s+" and resn leu)")
-        cmd.color("color_trp","("+s+" and resn trp)")
-        cmd.color("color_met","("+s+" and resn met)")
-        cmd.color("color_ala","("+s+" and resn ala)")
-        cmd.color("color_gly","("+s+" and resn gly)")
-        cmd.color("color_cys","("+s+" and resn cys)")
-        cmd.color("color_tyr","("+s+" and resn tyr)")
-        cmd.color("color_pro","("+s+" and resn pro)")
-        cmd.color("color_thr","("+s+" and resn thr)")
-        cmd.color("color_ser","("+s+" and resn ser)")
-        cmd.color("color_his","("+s+" and resn his)")
-        cmd.color("color_glu","("+s+" and resn glu)")
-        cmd.color("color_asn","("+s+" and resn asn)")
-        cmd.color("color_gln","("+s+" and resn gln)")
-        cmd.color("color_asp","("+s+" and resn asp)")
-        cmd.color("color_lys","("+s+" and resn lys)")
-        cmd.color("color_arg","("+s+" and resn arg)")
-cmd.extend('color_h',color_h)
- 
-def color_h2(selection='all'):
-        s = str(selection)
-	print s
-	cmd.set_color("color_ile2",[0.938,1,0.938])
-	cmd.set_color("color_phe2",[0.891,1,0.891])
-	cmd.set_color("color_val2",[0.844,1,0.844])
-	cmd.set_color("color_leu2",[0.793,1,0.793])
-	cmd.set_color("color_trp2",[0.746,1,0.746])
-	cmd.set_color("color_met2",[0.699,1,0.699])
-	cmd.set_color("color_ala2",[0.652,1,0.652])
-	cmd.set_color("color_gly2",[0.606,1,0.606])
-	cmd.set_color("color_cys2",[0.555,1,0.555])
-	cmd.set_color("color_tyr2",[0.508,1,0.508])
-	cmd.set_color("color_pro2",[0.461,1,0.461])
-	cmd.set_color("color_thr2",[0.414,1,0.414])
-	cmd.set_color("color_ser2",[0.363,1,0.363])
-	cmd.set_color("color_his2",[0.316,1,0.316])
-	cmd.set_color("color_glu2",[0.27,1,0.27])
-	cmd.set_color("color_asn2",[0.223,1,0.223])
-	cmd.set_color("color_gln2",[0.176,1,0.176])
-	cmd.set_color("color_asp2",[0.125,1,0.125])
-	cmd.set_color("color_lys2",[0.078,1,0.078])
-	cmd.set_color("color_arg2",[0.031,1,0.031])
-        cmd.color("color_ile2","("+s+" and resn ile)")
-        cmd.color("color_phe2","("+s+" and resn phe)")
-        cmd.color("color_val2","("+s+" and resn val)")
-        cmd.color("color_leu2","("+s+" and resn leu)")
-        cmd.color("color_trp2","("+s+" and resn trp)")
-        cmd.color("color_met2","("+s+" and resn met)")
-        cmd.color("color_ala2","("+s+" and resn ala)")
-        cmd.color("color_gly2","("+s+" and resn gly)")
-        cmd.color("color_cys2","("+s+" and resn cys)")
-        cmd.color("color_tyr2","("+s+" and resn tyr)")
-        cmd.color("color_pro2","("+s+" and resn pro)")
-        cmd.color("color_thr2","("+s+" and resn thr)")
-        cmd.color("color_ser2","("+s+" and resn ser)")
-        cmd.color("color_his2","("+s+" and resn his)")
-        cmd.color("color_glu2","("+s+" and resn glu)")
-        cmd.color("color_asn2","("+s+" and resn asn)")
-        cmd.color("color_gln2","("+s+" and resn gln)")
-        cmd.color("color_asp2","("+s+" and resn asp)")
-        cmd.color("color_lys2","("+s+" and resn lys)")
-        cmd.color("color_arg2","("+s+" and resn arg)")
+# color_h
+# -------
+ 
+# PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
+ 
+#
+# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
+# Amino acid scale: Normalized consensus hydrophobicity scale
+# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
+# Reference: J. Mol. Biol. 179:125-142 (1984)
+#
+# Amino acid scale values:
+#
+# Ala:  0.620
+# Arg: -2.530
+# Asn: -0.780
+# Asp: -0.900
+# Cys:  0.290
+# Gln: -0.850
+# Glu: -0.740
+# Gly:  0.480
+# His: -0.400
+# Ile:  1.380
+# Leu:  1.060
+# Lys: -1.500
+# Met:  0.640
+# Phe:  1.190
+# Pro:  0.120
+# Ser: -0.180
+# Thr: -0.050
+# Trp:  0.810
+# Tyr:  0.260
+# Val:  1.080
+#
+# Usage:
+# color_h (selection)
+#
+from pymol import cmd
+ 
+def color_h(selection='all'):
+        s = str(selection)
+	print s
+        cmd.set_color('color_ile',[0.996,0.062,0.062])
+        cmd.set_color('color_phe',[0.996,0.109,0.109])
+        cmd.set_color('color_val',[0.992,0.156,0.156])
+        cmd.set_color('color_leu',[0.992,0.207,0.207])
+        cmd.set_color('color_trp',[0.992,0.254,0.254])
+        cmd.set_color('color_met',[0.988,0.301,0.301])
+        cmd.set_color('color_ala',[0.988,0.348,0.348])
+        cmd.set_color('color_gly',[0.984,0.394,0.394])
+        cmd.set_color('color_cys',[0.984,0.445,0.445])
+        cmd.set_color('color_tyr',[0.984,0.492,0.492])
+        cmd.set_color('color_pro',[0.980,0.539,0.539])
+        cmd.set_color('color_thr',[0.980,0.586,0.586])
+        cmd.set_color('color_ser',[0.980,0.637,0.637])
+        cmd.set_color('color_his',[0.977,0.684,0.684])
+        cmd.set_color('color_glu',[0.977,0.730,0.730])
+        cmd.set_color('color_asn',[0.973,0.777,0.777])
+        cmd.set_color('color_gln',[0.973,0.824,0.824])
+        cmd.set_color('color_asp',[0.973,0.875,0.875])
+        cmd.set_color('color_lys',[0.899,0.922,0.922])
+        cmd.set_color('color_arg',[0.899,0.969,0.969])
+        cmd.color("color_ile","("+s+" and resn ile)")
+        cmd.color("color_phe","("+s+" and resn phe)")
+        cmd.color("color_val","("+s+" and resn val)")
+        cmd.color("color_leu","("+s+" and resn leu)")
+        cmd.color("color_trp","("+s+" and resn trp)")
+        cmd.color("color_met","("+s+" and resn met)")
+        cmd.color("color_ala","("+s+" and resn ala)")
+        cmd.color("color_gly","("+s+" and resn gly)")
+        cmd.color("color_cys","("+s+" and resn cys)")
+        cmd.color("color_tyr","("+s+" and resn tyr)")
+        cmd.color("color_pro","("+s+" and resn pro)")
+        cmd.color("color_thr","("+s+" and resn thr)")
+        cmd.color("color_ser","("+s+" and resn ser)")
+        cmd.color("color_his","("+s+" and resn his)")
+        cmd.color("color_glu","("+s+" and resn glu)")
+        cmd.color("color_asn","("+s+" and resn asn)")
+        cmd.color("color_gln","("+s+" and resn gln)")
+        cmd.color("color_asp","("+s+" and resn asp)")
+        cmd.color("color_lys","("+s+" and resn lys)")
+        cmd.color("color_arg","("+s+" and resn arg)")
+cmd.extend('color_h',color_h)
+ 
+def color_h2(selection='all'):
+        s = str(selection)
+	print s
+	cmd.set_color("color_ile2",[0.938,1,0.938])
+	cmd.set_color("color_phe2",[0.891,1,0.891])
+	cmd.set_color("color_val2",[0.844,1,0.844])
+	cmd.set_color("color_leu2",[0.793,1,0.793])
+	cmd.set_color("color_trp2",[0.746,1,0.746])
+	cmd.set_color("color_met2",[0.699,1,0.699])
+	cmd.set_color("color_ala2",[0.652,1,0.652])
+	cmd.set_color("color_gly2",[0.606,1,0.606])
+	cmd.set_color("color_cys2",[0.555,1,0.555])
+	cmd.set_color("color_tyr2",[0.508,1,0.508])
+	cmd.set_color("color_pro2",[0.461,1,0.461])
+	cmd.set_color("color_thr2",[0.414,1,0.414])
+	cmd.set_color("color_ser2",[0.363,1,0.363])
+	cmd.set_color("color_his2",[0.316,1,0.316])
+	cmd.set_color("color_glu2",[0.27,1,0.27])
+	cmd.set_color("color_asn2",[0.223,1,0.223])
+	cmd.set_color("color_gln2",[0.176,1,0.176])
+	cmd.set_color("color_asp2",[0.125,1,0.125])
+	cmd.set_color("color_lys2",[0.078,1,0.078])
+	cmd.set_color("color_arg2",[0.031,1,0.031])
+        cmd.color("color_ile2","("+s+" and resn ile)")
+        cmd.color("color_phe2","("+s+" and resn phe)")
+        cmd.color("color_val2","("+s+" and resn val)")
+        cmd.color("color_leu2","("+s+" and resn leu)")
+        cmd.color("color_trp2","("+s+" and resn trp)")
+        cmd.color("color_met2","("+s+" and resn met)")
+        cmd.color("color_ala2","("+s+" and resn ala)")
+        cmd.color("color_gly2","("+s+" and resn gly)")
+        cmd.color("color_cys2","("+s+" and resn cys)")
+        cmd.color("color_tyr2","("+s+" and resn tyr)")
+        cmd.color("color_pro2","("+s+" and resn pro)")
+        cmd.color("color_thr2","("+s+" and resn thr)")
+        cmd.color("color_ser2","("+s+" and resn ser)")
+        cmd.color("color_his2","("+s+" and resn his)")
+        cmd.color("color_glu2","("+s+" and resn glu)")
+        cmd.color("color_asn2","("+s+" and resn asn)")
+        cmd.color("color_gln2","("+s+" and resn gln)")
+        cmd.color("color_asp2","("+s+" and resn asp)")
+        cmd.color("color_lys2","("+s+" and resn lys)")
+        cmd.color("color_arg2","("+s+" and resn arg)")
 cmd.extend('color_h2',color_h2)

profiles/shared/.config/.xmodmaprc

@@ -1,5 +0,0 @@
-! Swap caps lock and escape
-remove Lock = Caps_Lock
-!keysym Escape = Caps_Lock
-keysym Caps_Lock = Escape
-add Lock = Caps_Lock

profiles/workplace/.config/polybar/config

@@ -1,20 +0,0 @@
-
-include-file = ~/.config/polybar/config.d/colors
-include-file = ~/.config/polybar/config.d/settings
-include-file = ~/.config/polybar/config.d/modules
-include-file = ~/.config/polybar/config.d/base_bar
-
-[bar/workstation]
-inherit = bar/base
-monitor = ${env:MONITOR:DP-4}
-modules-left = i3 xwindow
-modules-right = spotify previous playpause next mpd pulseaudio filesystem cpu gpu memory date xkeyboard 
-
-font-0 = "Noto Sans:size=12:style=Regular;1"
-font-1 = unifont:fontformat=truetype:size=12:antialias=false;0
-font-2 = FontAwesome:size=12;0
-
-[bar/workstation2]
-inherit = bar/workstation
-monitor = ${env:MONITOR:DP-2}
-tray-position = right

profiles/workplace/.config/polybar/polybar.sh

@@ -1,14 +0,0 @@
-#!/bin/bash
-
-killall -q polybar
-
-# Wait until the processes have been shut down
-while pgrep -u $UID -x polybar >/dev/null; do sleep 1; done
-
-# Launch bar1 and bar2
-polybar -c ~/.config/polybar/config workstation &
-polybar -c ~/.config/polybar/config workstation2 & 
-polybar -c ~/.config/polybar/config laptop &
-polybar -c ~/.config/polybar/config laptop_station &
-
-echo "Bars launched..."