migrate dotfiles to chezmoi

.chezmoiignore

@@ -0,0 +1 @@
+README.md

.gitignore

@@ -1 +0,0 @@
-./pymolrc/*pyc

README.md

@@ -1,8 +1,9 @@
-# dotfiles for linux/wsl
+# My dotfiles
 
-clone to `.dotfiles`.
+Set up on new machin:
 
-Start by installing the base configuration via `./install.sh`.
+```bash
-Then choose relevant configuration bundles with `./dotfiles.sh bundname`
+sh -c "$(curl -fsLS get.chezmoi.io)"
-(i.e. `./dotfiles.sh gui`)
+chezmoi init --apply dnlbauer
+```
 

auto-update.sh

@@ -1,59 +0,0 @@
-#!/bin/bash
-# adapted from: https://github.com/jez/dotfiles/blob/master/util/auto-update.sh	
-
-# Number of seconds to wait before printing a reminder
-UPDATE_THRESHOLD="604800" # 1 week
-
-check_for_updates() {
-  [ ! -e $HOME/.dotfiles_update ] && touch $HOME/.dotfiles_update
-  # Initialize for when we have no GNU date available
-  last_check=0
-  time_now=0
-
-  # Darwin uses BSD, check for gdate, else use date
-  if [[ $(uname) = "Darwin" && -n $(which gdate) ]]; then
-    last_login=$(gdate -r ~/.dotfiles_update +%s)
-    time_now=$(gdate +%s)
-  else
-    # Ensure this is GNU grep
-    if [ -n "$(date --version 2> /dev/null | grep GNU)" ]; then
-      last_login=$(date -r ~/.dotfiles_update +%s)
-      time_now=$(date +%s)
-    fi
-  fi
-
-  time_since_check=$((time_now - last_login))
-
-  if [ "$time_since_check" -ge "$UPDATE_THRESHOLD" ]; then
-    echo $time_since_check
-  else
-    echo 0
-  fi
-}
-
-update() {
-  # Record that we've update
-  touch $HOME/.dotfiles_update
-
-  # Update dotfiles repo
-  cd ~/.dotfiles/
-
-  echo "Checking for updates..."
-  git fetch --quiet origin
-  if [ "$(git rev-parse HEAD)" != "$(git rev-parse origin/master)" ]; then
-    echo "--> outdated."
-    git pull
-    ./install.sh
-  else
-    echo "--> nothing to do."
-  fi
-
-  cd - &> /dev/null
-}
-
-check=$(check_for_updates)
-if [[ $check -gt 0 ]]; then
-    echo "Dotfiles might be out of date."
-    update
-fi
-

dotfiles.sh

@@ -1,65 +0,0 @@
-#!/bin/bash
-
-
-PROFILE_BASE_DIR=$HOME/.dotfiles/profiles
-
-# Link files of a single profile
-link_profile() {
-    profile=$1
-    profile_dir=${PROFILE_BASE_DIR}/$profile
-    
-    
-    if [ ! -d $profile_dir ]; then
-    	echo "$profile does not exist"
-		exit 1
-	else
-		echo "Linking files from profile $profile"
-	fi
-
-	cd $profile_dir
-    OIFS="$IFS"
-    IFS=$'\n'
-	# Find all files to link
-    for file in `find . -type f | cut -c 3- | grep -v "^$"`; do
-   		dir=$(dirname "${file}")
-		src=`pwd`/$file
-		dst_dir=$HOME/$dir
-		dst=$HOME/$file
-		
-		# create folder if not exist
-		if [ ! -d "$dst_dir" ]; then
-			echo "Creating destination direcory $dst_dir"
-			mkdir -p $dst_dir
-		fi
-
-		# link file
-		echo "Linking $src to $dst"
-		if [ -f "${dst}" ] || [ -L "${dst}" ]; then
-			difference="$(diff -y $src $dst)"
-			if [ "$?" -ne 0 ]; then
-				echo "$difference"
-				echo "$(basename $dst) already exists (and differs). Override? [y/N]"
-				read response
-				if [ "$response" == 'y' ] || [ "$response" == 'Y' ] \
-					|| [ "$response" == 'yes' ] || [ "$response" == 'Yes' ]; then
-					ln -sf $src $dst
-				else
-					echo "Skipping $file"
-				fi
-			else
-				echo "Skipping $file (no diff)"
-			fi
-		else
-			ln -s $src $dst	
-		fi
-	done
-}
-
-# link profiles
-if [ "$1" == "link" ]; then
-	shift
-	while [ "$1" != "" ]; do
-		link_profile $1
-		shift
-	done
-fi 

install.sh

@@ -1,66 +0,0 @@
-# fzf
-if [ ! -d "$HOME/.fzf" ]; then
-    git clone --depth 1 https://github.com/junegunn/fzf.git $HOME/.fzf
-    if [ ! -f "$HOME/.fzf/bin" ]; then
-	$HOME/.fzf/install --completion --key-bindings --update-rc
-    fi
-fi
-
-# diff-so-fancy
-if [ ! -f "$HOME/.local/bin/diff-so-fancy" ]; then
-    if [ ! -d "$HOME/.local/lib/diff-so-fancy" ]; then
-        git clone --depth 1 https://github.com/so-fancy/diff-so-fancy.git $HOME/.local/lib/diff-so-fancy
-    fi
-    ln -s $HOME/.local/lib/diff-so-fancy/diff-so-fancy $HOME/.local/bin/diff-so-fancy
-fi
-
-# vimplug
-if [ ! -d "$HOME/.vim/autoload" ]; then
-    echo "setup vim plug"
-    curl -fLo $HOME/.vim/autoload/plug.vim --create-dirs \
-	    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
-fi
-
-# install rust
-if [ ! -d "$HOME/.cargo" ]; then
-    echo "setup cargo"
-    curl https://sh.rustup.rs -sSf | sh -s -- --no-modify-path -y --profile minimal -q
-fi
-
-# install some rust packages
-for package in ripgrep bat; do
-    echo "setup $package"
-    $HOME/.cargo/bin/cargo install -q $package
-done
-
-# linking dotfiles
-$HOME/.dotfiles/dotfiles.sh link base
-
-if ! type zsh > /dev/null; then
-    echo "Cannnot change default shell to zsh: not installed"
-else
-    # Make ZSH the default shell environment
-    if [ $(cat /etc/passwd | grep $USER | awk -F ':' '{print substr($7, length($7)-3)}') != "/zsh" ]; then
-        echo "Changing shell to zsh"
-        chsh -s $(which zsh)
-    fi
-
-    # Antidote Installation
-    if [ ! -d "$HOME/.antidote" ]; then
-        echo "Installing antidote"
-
-        # make sure git is installed
-        if ! type git > /dev/null; then
-            echo "Git not installed. Cannot install antidote"
-	else
-             git clone --depth=1 https://github.com/mattmc3/antidote.git $HOME/.antidote
-        fi
-
-    else
-	echo "antidote already exists."
-    fi
-    
-fi
-
-
-

profiles/base/.local/bin/github_http2ssh

@@ -1,33 +0,0 @@
-#/bin/bash
-#-- Script to automate https://help.github.com/articles/why-is-git-always-asking-for-my-password
-
-REPO_URL=`git remote -v | grep -m1 '^origin' | sed -Ene's#.*(https?://[^[:space:]]*).*#\1#p'`
-if [ -z "$REPO_URL" ]; then
-  echo "-- ERROR:  Could not identify Repo url."
-  echo "   It is possible this repo is already using SSH instead of HTTPS."
-  exit
-fi
-
-USER=`echo $REPO_URL | sed -Ene's#https?://github.com/([^/]*)/(.*)[\.git]?#\1#p'`
-if [ -z "$USER" ]; then
-  echo "-- ERROR:  Could not identify User."
-  exit
-fi
-
-REPO=`echo $REPO_URL | sed -Ene's#https?://github.com/([^/]*)/(.*)[\.git]?#\2#p'`
-if [ -z "$REPO" ]; then
-  echo "-- ERROR:  Could not identify Repo."
-  exit
-fi
-
-NEW_URL="git@github.com:$USER/$REPO.git"
-echo "Changing repo url from "
-echo "  '$REPO_URL'"
-echo "      to "
-echo "  '$NEW_URL'"
-echo ""
-
-CHANGE_CMD="git remote set-url origin $NEW_URL"
-`$CHANGE_CMD`
-
-echo "Success"

profiles/i3/.config/i3/config

@@ -1,258 +0,0 @@
-# This file has been auto-generated by i3-config-wizard(1).
-# It will not be overwritten, so edit it as you like.
-#
-# Should you change your keyboard layout somewhen, delete
-# this file and re-run i3-config-wizard(1).
-#
-
-# i3 config file (v4)
-#
-# Please see http://i3wm.org/docs/userguide.html for a complete reference!
-# exec xrandr --auto --output DP-4 --right-of HDMI-0 --primary --dpi 150
-exec --no-startup-id ~/.config/i3/xrandr.sh
-
-
-set $mod Mod4
-
-# Font for window titles. Will also be used by the bar unless a different font
-# is used in the bar {} block below. ISO 10646 = Unicode
-font -misc-fixed-medium-r-normal--13-120-75-75-C-70-iso10646-1
-# The font above is very space-efficient, that is, it looks good, sharp and
-# clear in small sizes. However, if you need a lot of unicode glyphs or
-# right-to-left text rendering, you should instead use pango for rendering and
-# chose a FreeType font, such as:
-font pango:Source Code Pro for Powerline, FontAwesome Regular, Icons 12.5
-
-new_window 1pixel
-
-# Use Mouse+$mod to drag floating windows to their wanted position
-floating_modifier $mod
-
-# start a terminal
-bindsym $mod+Return exec i3-sensible-terminal
-
-# kill focused window
-bindsym $mod+Shift+q kill
-
-# start dmenu (a program launcher)
-#bindsym $mod+d exec dmenu_run
-
-# rofi
-bindsym $mod+d exec "rofi -show combi"
-
-
-# There also is the (new) i3-dmenu-desktop which only displays applications
-# shipping a .desktop file. It is a wrapper around dmenu, so you need that
-# installed.
-# bindsym $mod+d exec --no-startup-id i3-dmenu-desktop
-
-# change focus
-bindsym $mod+j focus left
-bindsym $mod+k focus down
-bindsym $mod+l focus up
-bindsym $mod+semicolon focus right
-
-# alternatively, you can use the cursor keys:
-bindsym $mod+Left focus left
-bindsym $mod+Down focus down
-bindsym $mod+Up focus up
-bindsym $mod+Right focus right
-
-# move focused window
-bindsym $mod+Shift+j move left
-bindsym $mod+Shift+k move down
-bindsym $mod+Shift+l move up
-bindsym $mod+Shift+colon move right
-
-# alternatively, you can use the cursor keys:
-bindsym $mod+Shift+Left move left
-bindsym $mod+Shift+Down move down
-bindsym $mod+Shift+Up move up
-bindsym $mod+Shift+Right move right
-
-# move workspace left/right
-bindsym $mod+Shift+greater move workspace to output right
-bindsym $mod+Shift+less move workspace to output left
-
-# split in horizontal orientation
-bindsym $mod+h split h
-
-# split in vertical orientation
-bindsym $mod+v split v
-
-# enter fullscreen mode for the focused container
-bindsym $mod+f fullscreen
-
-# change container layout (stacked, tabbed, toggle split)
-#bindsym $mod+s layout stacking
-#bindsym $mod+w layout tabbed
-bindsym $mod+e layout toggle split
-
-# toggle tiling / floating
-bindsym $mod+Shift+space floating toggle
-
-# change focus between tiling / floating windows
-bindsym $mod+space focus mode_toggle
-
-# focus the parent container
-bindsym $mod+a focus parent
-
-# focus the child container
-#bindsym $mod+d focus child
-
-set $workspace1 1
-set $workspace2 2
-set $workspace3 3
-set $workspace4 4
-set $workspace5 5
-set $workspace6 6
-set $workspace7 7
- #
-set $workspace8 8
-#
-set $workspace9 9
-#
-
-# switch to workspace
-bindsym $mod+1 workspace $workspace1
-bindsym $mod+2 workspace $workspace2
-bindsym $mod+3 workspace $workspace3
-bindsym $mod+4 workspace $workspace4
-bindsym $mod+5 workspace $workspace5
-bindsym $mod+6 workspace $workspace6
-bindsym $mod+7 workspace $workspace7
-bindsym $mod+8 workspace $workspace8
-bindsym $mod+9 workspace $workspace9
-bindsym $mod+0 workspace $workspace10
-
-# move focused container to workspace
-bindsym $mod+Shift+1 move container to workspace $workspace1
-bindsym $mod+Shift+2 move container to workspace $workspace2
-bindsym $mod+Shift+3 move container to workspace $workspace3
-bindsym $mod+Shift+4 move container to workspace $workspace4
-bindsym $mod+Shift+5 move container to workspace $workspace5
-bindsym $mod+Shift+6 move container to workspace $workspace6
-bindsym $mod+Shift+7 move container to workspace $workspace7
-bindsym $mod+Shift+8 move container to workspace $workspace8
-bindsym $mod+Shift+9 move container to workspace $workspace9
-bindsym $mod+Shift+0 move container to workspace $workspace10
-
-# Make the currently focused window a scratchpad
-bindsym $mod+Shift+minus move scratchpad
-
-# Show the first scratchpad window
-bindsym $mod+minus scratchpad show
-
-# reload the configuration file
-bindsym $mod+Shift+c reload
-# restart i3 inplace (preserves your layout/session, can be used to upgrade i3)
-bindsym $mod+Shift+r restart
-# exit i3 (logs you out of your X session)
-bindsym $mod+Shift+e exec "i3-nagbar -t warning -m 'You pressed the exit shortcut. Do you really want to exit i3? This will end your X session.' -b 'Yes, exit i3' 'i3-msg exit'"
-
-# resize window (you can also use the mouse for that)
-mode "resize" {
-        # These bindings trigger as soon as you enter the resize mode
-
-        # Pressing left will shrink the window’s width.
-        # Pressing right will grow the window’s width.
-        # Pressing up will shrink the window’s height.
-        # Pressing down will grow the window’s height.
-        bindsym j resize shrink width 10 px or 10 ppt
-        bindsym k resize grow height 10 px or 10 ppt
-        bindsym l resize shrink height 10 px or 10 ppt
-        bindsym semicolon resize grow width 10 px or 10 ppt
-
-        # same bindings, but for the arrow keys
-        bindsym Left resize shrink width 10 px or 10 ppt
-        bindsym Down resize grow height 10 px or 10 ppt
-        bindsym Up resize shrink height 10 px or 10 ppt
-        bindsym Right resize grow width 10 px or 10 ppt
-
-        # back to normal: Enter or Escape
-        bindsym Return mode "default"
-        bindsym Escape mode "default"
-}
-
-bindsym $mod+r mode "resize"
-
-# Start i3bar to display a workspace bar (plus the system information i3status
-# finds out, if available)
-#bar {
-	#position top
-    #   status_command  2> /tmp/i3blocks.err  i3blocks -c ~/.config/i3/i3blocks.conf | tee /tmp/i3blocks.out
-#}
-
-
-# hide window border
-new_window 1pixel
-
-exec_always --no-startup-id ~/.config/polybar/polybar.sh
-
-
-# "special" workspaces
-# workspace7 => zotero
-# worksapce8 => chat
-# workspace9 => emailing
-# workspace0 => music
-workspace $workspace7 output eDP-1 
-assign [class="Zotero"] → $workspace7
-assign [class="Mendeley"] → $workspace7
-
-workspace $workspace8 output eDP-1
-assign [class="Skype" title="Skype"] → $workspace8
-assign [class="Mattermost" instance="mattermost"] → $workspace8
-assign [class="Rambox" instance="rambox"] → $workspace8
-
-workspace $workspace9 output eDP-1 
-assign [class="thunderbird" window_role="3pane"] → $workspace9
-
-workspace $workspace10 output eDP-1 
-assign [class="Spotify"] → $workspace10
-
-for_window [window_role="pop-up"] floating enable
-for_window [class="Chromium" window_role="pop-up"] floating disable
-for_window [class="Tk"] floating enable
-for_window [title="PyMOL Viewer"] floating enable
-for_window [class="Toplevel"] floating enable
-for_window [title="Figure*" instance="matplotlib"] floating enable
-for_window [window_role="conversation" class="Pidgin"] floating enable
-for_window [class="Com.github.alainm23.planner"] floating enable
-
-# use tiling mode only for main/chat Skype window and floating of all dialogs
-# Skype main window title looks like this - "alexey.diyan - Skype™"
-for_window [instance="skype" title="^.*?(?<!Skype™)$"] floating enable
-for_window [instance="skype" title="Skype|Skype™|Call with|File Transfers"] floating disable
-
-# Pulse Audio controls
-bindsym --release XF86AudioLowerVolume exec --no-startup-id amixer  sset Master 5%- #decrease sound volume
-bindsym --release XF86AudioRaiseVolume exec --no-startup-id amixer  sset Master 5%+ #increase sound volume
-bindsym --release XF86AudioMute exec --no-startup-id amixer sset Master toggle # mute sound
-
-# Sreen brightness controls
-bindsym XF86MonBrightnessUp exec xbacklight -inc 20 # increase screen brightness
-bindsym XF86MonBrightnessDown exec xbacklight -dec 20 # decrease screen brightness
-
-# Touchpad controls
-bindsym XF86TouchpadToggle exec /some/path/toggletouchpad.sh # toggle touchpad
-
-# Media player controls
-bindsym XF86AudioPlay exec playerctl play-pause
-bindsym XF86AudioNext exec playerctl next
-bindsym XF86AudioPrev exec playerctl previous
-bindsym XF86HomePage exec "i3lock -i ~/lockscreens/`ls ~/lockscreens | shuf -n 1` -t -f"
-
-# change ouput
-bindsym $mod+Shift+s exec --no-startup-id ~/.config/i3/scripts/change_monitor.sh	
-
-# reload workspace layouts
-#exec --no-startup-id "i3-msg 'workspace 9; append_layout /home/bauer/.i3/workspace-9.json'"
-#exec feh --bg-fill /home/bauer/artistic/artistici2.png
-#exec --no-startup-id xautolock -time 5 -locker 'i3lock -i ~/.lockscreen/`ls /home/bauer/lockscreens | shuf -n 1` -t -f'
-#exec --no-startup-id thunderbird
-#exec --no-startup-id skype
-#exec --no-startup-id mattermost-desktop
-#exec --no-startup-id nextcloud 
-#exec --no-startup-id nm-applet
-#exec --no-startup-id xfsettingsd --sm-client-disable &
-#exec --no-startup-id /usr/bin/blueman-applet

profiles/i3/.config/i3/scripts/change_monitor.sh

@@ -1,20 +0,0 @@
-#!/bin/bash
-EXTERNAL_OUTPUT="HDMI2"
-INTERNAL_OUTPUT="eDP1"
-
-# if we don't have a file, start at zero
-if [ ! -f "/tmp/monitor_mode.dat" ] ; then
-  monitor_mode="CLONES"
-# otherwise read the value from the file
-else
-  monitor_mode=`cat /tmp/monitor_mode.dat`
-fi
-
-if [ $monitor_mode = "CLONES" ]; then
-        monitor_mode="EXTERNAL"
-        $HOME/.screenlayout/external.sh
-elif [ $monitor_mode = "EXTERNAL" ]; then
-        monitor_mode="CLONES"
-        $HOME/.screenlayout/clone.sh
-fi
-echo "${monitor_mode}" > /tmp/monitor_mode.dat

profiles/i3/.config/i3/scripts/cpu_usage

@@ -1,60 +0,0 @@
-#!/usr/bin/perl
-#
-# Copyright 2014 Pierre Mavro <deimos@deimos.fr>
-# Copyright 2014 Vivien Didelot <vivien@didelot.org>
-# Copyright 2014 Andreas Guldstrand <andreas.guldstrand@gmail.com>
-#
-# Licensed under the terms of the GNU GPL v3, or any later version.
-
-use strict;
-use warnings;
-use utf8;
-use Getopt::Long;
-
-# default values
-my $t_warn = 50;
-my $t_crit = 80;
-my $cpu_usage = -1;
-my $decimals = 0;
-
-sub help {
-    print "Usage: cpu_usage [-w <warning>] [-c <critical>] [-d <decimals>]\n";
-    print "-w <percent>: warning threshold to become yellow\n";
-    print "-c <percent>: critical threshold to become red\n";
-    print "-d <decimals>:  Use <decimals> decimals for percentage (default is $decimals) \n"; 
-    exit 0;
-}
-
-GetOptions("help|h" => \&help,
-"w=i"    => \$t_warn,
-"c=i"    => \$t_crit,
-"d=i"    => \$decimals,
-);
-
-# Get CPU usage
-$ENV{LC_ALL}="en_US"; # if mpstat is not run under en_US locale, things may break, so make sure it is
-open (MPSTAT, 'mpstat 1 1 |') or die;
-while (<MPSTAT>) {
-if (/^.*\s+(\d+\.\d+)\s+$/) {
-$cpu_usage = 100 - $1; # 100% - %idle
-last;
-}
-}
-close(MPSTAT);
-
-$cpu_usage eq -1 and die 'Can\'t find CPU information';
-
-# Print short_text, full_text
-printf "%.${decimals}f%%\n", $cpu_usage;
-printf "%.${decimals}f%%\n", $cpu_usage;
-
-# Print color, if needed
-if ($cpu_usage >= $t_crit) {
-print "#fb4934\n";
-exit 33;
-} elsif ($cpu_usage >= $t_warn) {
-print "#fabd2f\n";
-}
-
-exit 0;
-

profiles/i3/.config/i3/scripts/current_track

@@ -1,4 +0,0 @@
-#!/bin/bash
-
-eval $($(dirname $0)/sp eval)
-echo ${SPOTIFY_ARTIST} - ${SPOTIFY_TITLE}

profiles/i3/.config/i3/scripts/disk

@@ -1,42 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2014 Julien Bonjean <julien@bonjean.info>
-
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-DIR="/scratch"
-ALERT_LOW="${1:-10}" # color will turn red under this value (default: 10%)
-
-df -h -P "$DIR" | awk -v alert_low=$ALERT_LOW '
-/\/.*/ {
-# full text
-print $4" ("$5")"
-
-# short text
-print $4
-
-use=$5
-
-# no need to continue parsing
-exit 0
-}
-
-END {
-gsub(/%$/,"",use)
-if (100 - use < alert_low) {
-    # color
-    print "#FF0000"
-}
-}
-'
-

profiles/i3/.config/i3/scripts/exit_menu

@@ -1,12 +0,0 @@
-#!/bin/bash
-while [ "$select" != "NO" -a "$select" != "YES" ]; do
-    select=$(echo -e 'NO\nYES' | dmenu  -nb '#2f343f' 
-                                        -nf '#f3f4f5' 
-                                        -sb '#9575cd' 
-                                        -sf '#f3f4f5' 
-                                        -fn '-*-*-medium-r-normal-*-*-*-*-*-*-100-*-*' -
-                                        i -p "Are you sure you want to logout?")
-    [ -z "$select" ] && exit 0
-done
-[ "$select" = "NO" ] && exit 0
-i3-msg exit

profiles/i3/.config/i3/scripts/gpu

@@ -1,21 +0,0 @@
-#!/bin/bash
-
-t_warn=50
-t_crit=70
-
-GPU=$(nvidia-smi -q | grep Gpu | awk '{print $3}')
-
-if [ $GPU -gt $t_crit ]
-then
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-    printf "\n#fb4934\n"
-elif [ $GPU -gt $t_warn ]
-then
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-    printf "\n#fabd2f\n"
-else
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-fi

profiles/i3/.config/i3/scripts/keyboard_layout

@@ -1 +0,0 @@
-xkb-switch

profiles/i3/.config/i3/scripts/load_average

@@ -1,35 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2014 Julien Bonjean <julien@bonjean.info>
-
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-load="$(cut -d ' ' -f1 /proc/loadavg)"
-cpus="$(nproc)"
-
-# full text
-echo "$load"
-
-# short text
-echo "$load"
-
-# color if load is too high
-awk -v cpus=$cpus -v cpuload=$load '
-    BEGIN {
-        if (cpus <= cpuload) {
-            print "#FF0000";
-            exit 33;
-        }
-    }
-'
-

profiles/i3/.config/i3/scripts/memory

@@ -1,67 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2014 Julien Bonjean <julien@bonjean.info>
-
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-TYPE="${BLOCK_INSTANCE:-mem}"
-
-awk -v type=$TYPE '
-/^MemTotal:/ {
-        mem_total=$2
-}
-/^MemFree:/ {
-        mem_free=$2
-}
-/^Buffers:/ {
-        mem_free+=$2
-}
-/^Cached:/ {
-        mem_free+=$2
-}
-/^SwapTotal:/ {
-        swap_total=$2
-}
-/^SwapFree:/ {
-        swap_free=$2
-}
-END {
-if (type == "swap") {
-    free=swap_free/1024/102
-    used=(swap_total-swap_free)/1024/1024 
-    total=swap_total/1024/1024
-} else {
-free=mem_free/1024/1024
-used=(mem_total-mem_free)/1024/1024
-total=mem_total/1024/1024
-}
-pct=used/total*100
-
-# full text
-printf("%.1fG / %.1fG ( %.f%% )\n", used, total, pct)
-
-# short text
-printf("%.f%%\n", pct)
-
-# color
-if (pct > 90) {
-    print("#E53935\n")
-
-} else if (pct > 80) {
-print("#FFAE00\n")
-} else if (pct > 70) {
-print("#FFF600\n")
-}
-}
-' /proc/meminfo
-

profiles/i3/.config/i3/scripts/openvpn

@@ -1,151 +0,0 @@
-#!/usr/bin/perl
-# Made by Pierre Mavro/Deimosfr <deimos@deimos.fr>
-# Minor contribution by Thor K. H. <thor@roht.no>
-# Licensed under the terms of the GNU GPL v3, or any later version.
-# Version: 0.3
-
-# Usage:
-# 1. The configuration name of OpenVPN should be familiar for you (home,work...)
-# 2. The device name in your configuration file should be fully named (tun0,tap1...not only tun or tap)
-# 3. When you launch one or multiple OpenVPN connexion, be sure the PID file is written in the correct folder (ex: --writepid /run/openvpn/home.pid)
-
-use strict;
-use warnings;
-use utf8;
-use Getopt::Long;
-
-my $openvpn_enabled='/dev/shm/openvpn_i3blocks_enabled';
-my $openvpn_disabled='/dev/shm/openvpn_i3blocks_disabled';
-
-# Print output
-sub print_output {
-    my $ref_pid_files = shift;
-    my @pid_files = @$ref_pid_files;
-    my $change=0;
-
-    # Total pid files
-    my $total_pid = @pid_files;
-    if ($total_pid == 0) {
-        print "down\n"x2;
-        # Delete OpenVPN i3blocks temp files
-        if (-f $openvpn_enabled) {
-            unlink $openvpn_enabled or die "Can't delete $openvpn_enabled\n";
-            # Colorize if VPN has just went down
-            print '#FF0000\n';
-        }
-        unless (-f $openvpn_disabled) {
-            open(my $shm, '>', $openvpn_disabled) or die "Can't write $openvpn_disabled\n";
-        }
-        exit(0);
-    }
-
-    # Check if interface device is present
-    my $vpn_found=0;
-    my $pid;
-    my $cmd_line;
-    my @config_name;
-    my @config_path;
-    my $interface;
-    my $current_config_path;
-    my $current_config_name;
-    foreach (@pid_files) {
-        # Get current PID
-        $pid=0;
-        open(PID, '<', $_);
-        while(<PID>) {
-            chomp $_;
-            $pid = $_;
-        }
-        close(PID);
-        # Check if PID has been found
-        if ($pid ==0) {
-            print "Can't get PID $_: $!\n";
-        }
-
-        # Check if PID is still alive
-        $cmd_line='/proc/'.$pid.'/cmdline';
-        if (-f $cmd_line) {
-            # Get config name
-            open(CMD_LINE, '<', $cmd_line);
-            while(<CMD_LINE>) {
-                chomp $_;
-                if ($_ =~ /--config\s*(.*\.conf)/) {
-                    # Get interface from config file
-                    $current_config_path = $1;
-                    # Remove unwanted escape chars
-                    $current_config_path =~ s/\x{00}//g;
-                    $interface = 'null';
-                    # Get configuration name
-                    if ($current_config_path =~ /(\w+).conf/) {
-                        $current_config_name=$1;
-                    } else {
-                        $current_config_name='unknow';
-                    }
-                    # Get OpenVPN interface device name
-                    open(CONFIG, '<', $current_config_path) or die "Can't read config file '$current_config_path': $!\n";
-                    while(<CONFIG>) {
-                        chomp $_;
-                        if ($_ =~ /dev\s+(\w+)/) {
-                            $interface=$1;
-                            last;
-                        }
-                    }
-                    close(CONFIG);
-                    # check if interface exist
-                    unless ($interface eq 'null') {
-                        if (-d "/sys/class/net/$interface") {
-                            push @config_name, $current_config_name;
-                            $vpn_found=1;
-                            # Write enabled file
-                            unless (-f $openvpn_enabled) {
-                                open(my $shm, '>', $openvpn_enabled) or die "Can't write $openvpn_enabled\n";
-                                $change=1;
-                            }
-                        }
-                    }
-                }
-            }
-            close(CMD_LINE);
-        }
-    }
-
-    # Check if PID found
-    my $names;
-    my $short_status;
-    if ($vpn_found == 1) {
-        $names = join('/', @config_name);
-        $short_status='up';
-    } else {
-        $short_status='down';
-        $names = $short_status;
-    }
-
-    print "$names\n";
-    print "$short_status\n";
-
-    # Print color if there were changes
-    print "#00FF00\n" if ($change == 1);
-
-    exit(0);
-}
-
-sub check_opts {
-    # Vars
-    my @pid_file=glob '/run/openvpn/*.pid';
-
-    # Set options
-    GetOptions( "help|h" => \&help,
-        "p=s"    => \@pid_file);
-
-    print_output(\@pid_file);
-}
-
-sub help {
-    print "Usage: openvpn [-d pid folder files]\n";
-    print "-d : pid folder files (default /run/openvpn/*.pid)\n";
-    print "Note: devices in configuration file should be named with their number (ex: tun0, tap1)\n";
-    exit(1);
-}
-
-&check_opts;
-

profiles/i3/.config/i3/scripts/shutdown_menu

@@ -1,186 +0,0 @@
-#!/usr/bin/env bash
-#
-# Use rofi/zenity to change system runstate thanks to systemd.
-#
-# Note: this currently relies on associative array support in the shell.
-#
-# Inspired from i3pystatus wiki:
-# https://github.com/enkore/i3pystatus/wiki/Shutdown-Menu
-#
-# Copyright 2015 Benjamin Chrétien <chretien at lirmm dot fr>
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-#######################################################################
-#                            BEGIN CONFIG                             #
-#######################################################################
-
-# Use a custom lock script
-#LOCKSCRIPT="i3lock-extra -m pixelize"
-
-# Colors: FG (foreground), BG (background), HL (highlighted)
-FG_COLOR="#bbbbbb"
-BG_COLOR="#111111"
-HLFG_COLOR="#111111"
-HLBG_COLOR="#bbbbbb"
-BORDER_COLOR="#222222"
-
-# Options not related to colors
-ROFI_TEXT="Menu:"
-ROFI_OPTIONS="-width -11 -location 3 -hide-scrollbar -bw 2"
-
-# Zenity options
-ZENITY_TITLE="Menu"
-ZENITY_TEXT="Action:"
-ZENITY_OPTIONS="--column= --hide-header"
-
-#######################################################################
-#                             END CONFIG                              #
-#######################################################################
-
-# Whether to ask for user's confirmation
-enable_confirmation=false
-
-# Preferred launcher if both are available
-preferred_launcher="rofi"
-
-usage="$(basename "$0") [-h] [-c] [-p name] -- display a menu for shutdown, reboot, lock etc.
-
-where:
--h  show this help text
--c  ask for user confirmation
--p  preferred launcher (rofi or zenity)
-
-This script depends on:
-- systemd,
-- i3,
-- rofi or zenity."
-
-# Check whether the user-defined launcher is valid
-launcher_list=(rofi zenity)
-function check_launcher() {
-    if [[ ! "${launcher_list[@]}" =~ (^|[[:space:]])"$1"($|[[:space:]]) ]]; then
-        echo "Supported launchers: ${launcher_list[*]}"
-        exit 1
-    else
-        # Get array with unique elements and preferred launcher first
-        # Note: uniq expects a sorted list, so we cannot use it
-        i=1
-        launcher_list=($(for l in "$1" "${launcher_list[@]}"; do printf "%i %s\n" "$i" "$l"; let i+=1; done \
-            | sort -uk2 | sort -nk1 | cut -d' ' -f2- | tr '\n' ' '))
-    fi
-}
-
-# Parse CLI arguments
-while getopts "hcp:" option; do
-    case "${option}" in
-        h) echo "${usage}"
-            exit 0
-            ;;
-        c) enable_confirmation=true
-            ;;
-        p) preferred_launcher="${OPTARG}"
-            check_launcher "${preferred_launcher}"
-            ;;
-        *) exit 1
-            ;;
-    esac
-done
-
-# Check whether a command exists
-function command_exists() {
-    command -v "$1" &> /dev/null 2>&1
-}
-
-# systemctl required
-if ! command_exists systemctl ; then
-    exit 1
-fi
-
-# menu defined as an associative array
-typeset -A menu
-
-# Menu with keys/commands
-menu=(
-[Shutdown]="systemctl poweroff"
-[Reboot]="systemctl reboot"
-[Hibernate]="systemctl hibernate"
-[Suspend]="systemctl suspend"
-[Halt]="systemctl halt"
-[Lock]="${LOCKSCRIPT:-i3lock --color=${BG_COLOR#"#"}}"
-[Logout]="i3-msg exit"
-[Cancel]=""
-)
-menu_nrows=${#menu[@]}
-
-# Menu entries that may trigger a confirmation message
-menu_confirm="Shutdown Reboot Hibernate Suspend Halt Logout"
-
-launcher_exe=""
-launcher_options=""
-rofi_colors=""
-
-function prepare_launcher() {
-    if [[ "$1" == "rofi" ]]; then
-        rofi_colors="-bc ${BORDER_COLOR} -bg ${BG_COLOR} -fg ${FG_COLOR} \
-            -hlfg ${HLFG_COLOR} -hlbg ${HLBG_COLOR}"
-        launcher_exe="rofi"
-        launcher_options="-dmenu -i -lines ${menu_nrows} -p ${ROFI_TEXT} \
-            ${rofi_colors} ${ROFI_OPTIONS}"
-    elif [[ "$1" == "zenity" ]]; then
-        launcher_exe="zenity"
-        launcher_options="--list --title=${ZENITY_TITLE} --text=${ZENITY_TEXT} \
-            ${ZENITY_OPTIONS}"
-    fi
-}
-
-for l in "${launcher_list[@]}"; do
-    if command_exists "${l}" ; then
-        prepare_launcher "${l}"
-        break
-    fi
-done
-
-# No launcher available
-if [[ -z "${launcher_exe}" ]]; then
-    exit 1
-fi
-
-launcher="${launcher_exe} ${launcher_options}"
-selection="$(printf '%s\n' "${!menu[@]}" | sort | ${launcher})"
-
-function ask_confirmation() {
-    if [ "${launcher_exe}" == "rofi" ]; then
-        confirmed=$(echo -e "Yes\nNo" | rofi -dmenu -i -lines 2 -p "${selection}?" \
-            ${rofi_colors} ${ROFI_OPTIONS})
-        [ "${confirmed}" == "Yes" ] && confirmed=0
-    elif [ "${launcher_exe}" == "zenity" ]; then
-        zenity --question --text "Are you sure you want to ${selection,,}?"
-        confirmed=$?
-    fi
-
-    if [ "${confirmed}" == 0 ]; then
-        i3-msg -q "exec ${menu[${selection}]}"
-    fi
-}
-
-if [[ $? -eq 0 && ! -z ${selection} ]]; then
-    if [[ "${enable_confirmation}" = true && \
-        ${menu_confirm} =~ (^|[[:space:]])"${selection}"($|[[:space:]]) ]]; then
-    ask_confirmation
-else
-    i3-msg -q "exec ${menu[${selection}]}"
-fi
-                                        fi
-

profiles/i3/.config/i3/scripts/song.awk

@@ -1,22 +0,0 @@
-/string  *"xesam:artist/{
-    while (1) {
-        getline line
-        if (line ~ /string "/) {
-            sub(/.*string "/, "artist:", line)
-            sub(/".*$/, "", line)
-            print line
-            break
-        }
-    }
-}
-/string  *"xesam:title/{
-    while(1) {
-        getline line
-        if (line ~ /string "/) {
-            sub(/.*string "/, "title:", line)
-            sub(/".*$/, "", line)
-            print line
-            break
-        }
-    }
-}

profiles/i3/.config/i3/scripts/spotify.py

@@ -1,12 +0,0 @@
-#!/usr/bin/python
-
-import dbus
-try:
-    bus = dbus.SessionBus()
-    spotify = bus.get_object("org.mpris.MediaPlayer2.spotify", "/org/mpris/MediaPlayer2")
-    spotify_iface = dbus.Interface(spotify, 'org.freedesktop.DBus.Properties')
-    props = spotify_iface.Get('org.mpris.MediaPlayer2.Player', 'Metadata')
-    print(str(props['xesam:artist'][0]) + " - " + str(props['xesam:title']))
-    exit
-except dbus.exceptions.DBusException:
-    exit

profiles/i3/.config/i3/scripts/spotify_control

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-if [ $# -lt 1 ]
-then
-    echo "No command?"
-    exit
-fi
-
-if [ "$(pidof spotify)" = "" ] 
-then
-    echo "Spotify is not running"
-    exit
-fi
-
-case $1 in
-    "play")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.PlayPause
-        ;;
-    "next")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Next
-        ;;
-    "prev")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Previous
-        ;;
-    "getTitle")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 1 "title"|egrep -v "title"|cut -b 44-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getArtist")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 2 "artist"|egrep -v "artist"|egrep -v "array"|cut -b 27-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getAlbum")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 2 "album"|egrep -v "album"|egrep -v "array"|cut -b 44-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getStatus")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'PlaybackStatus'|grep 'string "[^"]*"'|sed 's/.*"\(.*\)"[^"]*$/\1/'
-        ;;
-    *)
-        echo "Unknown command: " $1
-        ;;
-esac

profiles/i3/.config/i3/scripts/spotify_control.bck

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-if [ $# -lt 1 ]
-then
-    echo "No command?"
-    exit
-fi
-
-if [ "$(pidof spotify)" = "" ] 
-then
-    echo "Spotify is not running"
-    exit
-fi
-
-case $1 in
-    "play")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.PlayPause
-        ;;
-    "next")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Next
-        ;;
-    "prev")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Previous
-        ;;
-    "getTitle")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 1 "title"|egrep -v "title"|cut -b 44-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getArtist")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 2 "artist"|egrep -v "artist"|egrep -v "array"|cut -b 27-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getAlbum")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'Metadata'|egrep -A 2 "album"|egrep -v "album"|egrep -v "array"|cut -b 44-|cut -d '"' -f 1|egrep -v ^$
-        ;;
-    "getStatus")
-        dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.freedesktop.DBus.Properties.Get string:'org.mpris.MediaPlayer2.Player' string:'PlaybackStatus'|grep 'string "[^"]*"'|sed 's/.*"\(.*\)"[^"]*$/\1/'
-        ;;
-    *)
-        echo "Unknown command: " $1
-        ;;
-esac

profiles/i3/.config/i3/scripts/ssd

@@ -1,41 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2014 Julien Bonjean <julien@bonjean.info>
-
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-DIR="/"
-ALERT_LOW="${1:-10}" # color will turn red under this value (default: 10%)
-
-df -h -P "$DIR" | awk -v alert_low=$ALERT_LOW '
-/\/.*/ {
-	# full text
-	print $4" ("$5")"
-
-	# short text
-	print $4
-	use=$5
-
-	# no need to continue parsing
-	exit 0
-}
-
-END {
-	gsub(/%$/,"",use)
-	if (100 - use < alert_low) {
-		# color
-		print "#FF0000"
-	}
-}
-'
-

profiles/i3/.config/i3/scripts/tmux

@@ -1,4 +0,0 @@
-#!/bin/bash
-
-tmux list-sessions | wc -l
-

profiles/i3/.config/i3/scripts/volume

@@ -1,46 +0,0 @@
-#!/usr/bin/env perl 
-
-## The sink we are interested in should be given as the 
-## 1st argument to the script.
-my $sink=$ARGV[0] || die("Need a sink number as the first argument\n");
-
-## If the script has been run with a second argument,
-## that argument will be the volume threshold we are checking
-my $volume_limit=$ARGV[1]||undef;
-
-## Run the pactl command and save the output in 
-## ther filehandle $fh
-open(my $fh, '-|', 'pactl list sinks');
-
-## Set the record separator to consecutive newlines (same as -000)
-## this means we read the info for each sink as a single "line".
-$/="\n\n";
-
-## Go through the pactl output
-while (<$fh>) {
-    ## If this is the sink we are interested in
-    if (/#$sink/) {
-        ## Extract the current colume of this sink
-        /Volume:.*?(\d+)%/;
-        my $volume=$1;
-        ## If the script has been run with a second argument,
-        ## check whether the volume is above or below that
-        if ($volume_limit) {
-            ## If the volume os greater than or equal to the
-            ## value passed, print "y"
-            if ($volume >= $volume_limit) {
-               print "y\n";
-                exit 0;
-            }
-            else {
-                print "n\n";
-                exit 1;
-            }
-        }   
-        ## Else, if the script has been run with just one argument,
-        ## print the current volume.
-        else {
-            print "$volume%\n";
-        }
-    }#
-}

profiles/i3/.config/i3/scripts/volume-pulseaudio

@@ -1,162 +0,0 @@
-#!/bin/bash
-# Displays the default device, volume, and mute status for i3blocks
-
-AUDIO_HIGH_SYMBOL='  '
-
-AUDIO_MED_THRESH=50
-AUDIO_MED_SYMBOL='  '
-
-AUDIO_LOW_THRESH=0
-AUDIO_LOW_SYMBOL='  '
-
-AUDIO_MUTED_SYMBOL='  '
-
-AUDIO_INTERVAL=5
-
-DEFAULT_COLOR="#ffffff"
-MUTED_COLOR="#a0a0a0"
-
-LONG_FORMAT=0
-SHORT_FORMAT=2
-USE_PERCENT=1
-USE_ALSA_NAME=0
-USE_DESCRIPTION=0
-
-SUBSCRIBE=0
-
-while getopts F:Sf:padH:M:L:X:T:t:C:c:i:h opt; do
-    case "$opt" in
-        S) SUBSCRIBE=1 ;;
-        F) LONG_FORMAT="$OPTARG" ;;
-        f) SHORT_FORMAT="$OPTARG" ;;
-        p) USE_PERCENT=0 ;;
-        a) USE_ALSA_NAME=1 ;;
-        d) USE_DESCRIPTION=1 ;;
-        H) AUDIO_HIGH_SYMBOL="$OPTARG" ;;
-        M) AUDIO_MED_SYMBOL="$OPTARG" ;;
-        L) AUDIO_LOW_SYMBOL="$OPTARG" ;;
-        X) AUDIO_MUTED_SYMBOL="$OPTARG" ;;
-        T) AUDIO_MED_THRESH="$OPTARG" ;;
-        t) AUDIO_LOW_THRESH="$OPTARG" ;;
-        C) DEFAULT_COLOR="$OPTARG" ;;
-        c) MUTED_COLOR="$OPTARG" ;;
-        i) AUDIO_INTERVAL="$OPTARG" ;;
-        h) printf \
-"Usage: volume-pulseaudio [-S] [-F format] [-f format] [-p] [-a|-d] [-H symb] [-M symb]
-        [-L symb] [-X symb] [-T thresh] [-t thresh] [-C color] [-c color] [-i inter] [-h]
-Options:
--F, -f\tOutput format (-F long format, -f short format) to use, amonst:
-\t0\t symb vol [index:name]\t (default long)
-\t1\t symb vol [name]
-\t2\t symb vol [index]\t (default short)
-\t3\t symb vol
--S\tSubscribe to volume events (requires persistent block, always uses long format)
--p\tOmit the percent sign (%%) in volume
--a\tUse ALSA name if possible
--d\tUse device description instead of name if possible
--H\tSymbol to use when audio level is high. Default: '$AUDIO_HIGH_SYMBOL'
--M\tSymbol to use when audio level is medium. Default: '$AUDIO_MED_SYMBOL'
--L\tSymbol to use when audio level is low. Default: '$AUDIO_LOW_SYMBOL'
--X\tSymbol to use when audio is muted. Default: '$AUDIO_MUTED_SYMBOL'
--T\tThreshold for medium audio level. Default: $AUDIO_MED_THRESH
--t\tThreshold for low audio level. Default: $AUDIO_LOW_THRESH
--C\tColor for non-muted audio. Default: $DEFAULT_COLOR
--c\tColor for muted audio. Default: $MUTED_COLOR
--i\tInterval size of volume increase/decrease. Default: $AUDIO_INTERVAL
--h\tShow this help text
-" && exit 0;;
-    esac
-done
-
-function move_sinks_to_new_default {
-    DEFAULT_SINK=$1
-    pacmd list-sink-inputs | grep index: | grep -o '[0-9]\+' | while read SINK
-    do
-        pacmd move-sink-input $SINK $DEFAULT_SINK
-    done
-}
-
-function set_default_playback_device_next {
-    inc=${1:-1}
-    num_devices=$(pacmd list-sinks | grep -c index:)
-    sink_arr=($(pacmd list-sinks | grep index: | grep -o '[0-9]\+'))
-    default_sink_index=$(( $(pacmd list-sinks | grep index: | grep -no '*' | grep -o '^[0-9]\+') - 1 ))
-    default_sink_index=$(( ($default_sink_index + $num_devices + $inc) % $num_devices ))
-    default_sink=${sink_arr[$default_sink_index]}
-    pacmd set-default-sink $default_sink
-    move_sinks_to_new_default $default_sink
-}
-
-case "$BLOCK_BUTTON" in
-    1) set_default_playback_device_next ;;
-    2) amixer -q -D pulse sset Master toggle ;;
-    3) set_default_playback_device_next -1 ;;
-    4) amixer -q -D pulse sset Master $AUDIO_INTERVAL%+ ;;
-    5) amixer -q -D pulse sset Master $AUDIO_INTERVAL%- ;;
-esac
-
-function print_format {
-    PERCENT="%"
-    [[ $USE_PERCENT == 0 ]] && PERCENT=""
-    case "$1" in
-        1) echo "$SYMBOL$VOL$PERCENT [$NAME]" ;;
-        2) echo "$SYMBOL$VOL$PERCENT [$INDEX]";;
-        3) echo "$SYMBOL$VOL$PERCENT" ;;
-        *) echo "$SYMBOL$VOL$PERCENT [$INDEX:$NAME]" ;;
-    esac
-}
-
-function print_block {
-    for name in INDEX NAME VOL MUTED; do
-        read $name
-    done < <(pacmd list-sinks | grep "index:\|name:\|volume: front\|muted:" | grep -A3 '*')
-    INDEX=$(echo "$INDEX" | grep -o '[0-9]\+')
-    VOL=$(echo "$VOL" | grep -o "[0-9]*%" | head -1 )
-    VOL="${VOL%?}"
-
-    NAME=$(echo "$NAME" | sed \
-'s/.*<.*\.\(.*\)>.*/\1/; t;'\
-'s/.*<\(.*\)>.*/\1/; t;'\
-'s/.*/unknown/')
-
-    if [[ $USE_ALSA_NAME == 1 ]] ; then
-        ALSA_NAME=$(pacmd list-sinks |\
-awk '/^\s*\*/{f=1}/^\s*index:/{f=0}f' |\
-grep "alsa.name\|alsa.mixer_name" |\
-head -n1 |\
-sed 's/.*= "\(.*\)".*/\1/')
-        NAME=${ALSA_NAME:-$NAME}
-    elif [[ $USE_DESCRIPTION == 1 ]] ; then
-        DESCRIPTION=$(pacmd list-sinks |\
-awk '/^\s*\*/{f=1}/^\s*index:/{f=0}f' |\
-grep "device.description" |\
-head -n1 |\
-sed 's/.*= "\(.*\)".*/\1/')
-        NAME=${DESCRIPTION:-$NAME}
-    fi
-
-    if [[ $MUTED =~ "no" ]] ; then
-        SYMBOL=$AUDIO_HIGH_SYMBOL
-        [[ $VOL -le $AUDIO_MED_THRESH ]] && SYMBOL=$AUDIO_MED_SYMBOL
-        [[ $VOL -le $AUDIO_LOW_THRESH ]] && SYMBOL=$AUDIO_LOW_SYMBOL
-        COLOR=$DEFAULT_COLOR
-    else
-        SYMBOL=$AUDIO_MUTED_SYMBOL
-        COLOR=$MUTED_COLOR
-    fi
-
-    if [[ $SUBSCRIBE == 1 ]] ; then
-        print_format "$LONG_FORMAT"
-    else
-        print_format "$LONG_FORMAT"
-        print_format "$SHORT_FORMAT"
-        echo "$COLOR"
-    fi
-}
-
-print_block
-if [[ $SUBSCRIBE == 1 ]] ; then
-    while read -r EVENT; do
-        print_block
-    done < <(pactl subscribe | stdbuf -oL grep change)
-fi

profiles/i3/.config/i3/scripts/volume_1

@@ -1,71 +0,0 @@
-#!/bin/bash
-# Copyright (C) 2014 Julien Bonjean <julien@bonjean.info>
-# Copyright (C) 2014 Alexander Keller <github@nycroth.com>
-
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-#------------------------------------------------------------------------
-
-# The second parameter overrides the mixer selection
-# For PulseAudio users, use "pulse"
-# For Jack/Jack2 users, use "jackplug"
-# For ALSA users, you may use "default" for your primary card
-# or you may use hw:# where # is the number of the card desired
-MIXER="default"
-[ -n "$(lsmod | grep pulse)" ] && MIXER="pulse"
-[ -n "$(lsmod | grep jack)" ] && MIXER="jackplug"
-MIXER="${2:-$MIXER}"
-
-# The instance option sets the control to report and configure
-# This defaults to the first control of your selected mixer
-# For a list of the available, use `amixer -D $Your_Mixer scontrols`
-SCONTROL="${BLOCK_INSTANCE:-$(amixer -D $MIXER scontrols |
-sed -n "s/Simple mixer control '\([A-Za-z ]*\)',0/\1/p" |
-head -n1
-)}"
-
-# The first parameter sets the step to change the volume by (and units to display)
-# This may be in in % or dB (eg. 5% or 3dB)
-STEP="${1:-5%}"
-
-#------------------------------------------------------------------------
-
-capability() { # Return "Capture" if the device is a capture device
-    amixer -D $MIXER get $SCONTROL |
-    sed -n "s/  Capabilities:.*cvolume.*/Capture/p"
-}
-
-volume() {
-    amixer -D $MIXER get $SCONTROL $(capability)
-}
-
-format() {
-    perl_filter='if (/.*\[(\d+%)\] (\[(-?\d+.\d+dB)\] )?\[(on|off)\]/)'
-    perl_filter+='{CORE::say $4 eq "off" ? "0%" : "'
-    # If dB was selected, print that instead
-    perl_filter+=$([[ $STEP = *dB ]] && echo '$3' || echo '$1')
-    perl_filter+='"; exit}'
-    perl -ne "$perl_filter"
-}
-
-#------------------------------------------------------------------------
-
-case $BLOCK_BUTTON in
-    3) amixer -q -D $MIXER sset $SCONTROL $(capability) toggle ;;  # right click, mute/unmute
-    4) amixer -q -D $MIXER sset $SCONTROL $(capability) ${STEP}+ unmute ;; # scroll up, increase
-    5) amixer -q -D $MIXER sset $SCONTROL $(capability) ${STEP}- unmute ;; # scroll down, decrease
-esac
-
-volume | format
-

profiles/i3/.config/polybar/config.d/base_bar

@@ -1,19 +0,0 @@
-[bar/base]
-width=900 ;100%
-height=35
-radius=6.0
-fixed-center=false
-background=${colors.background}
-foreground=${colors.foreground}
-line-size=3
-line-color=#f00
-border-size=0
-border-color=#00000000
-padding-left=0
-padding-right=2
-module-margin-left=1
-module-margin-right=3
-
-font-0 = "Noto Sans:size=14:style=Regular;1"
-font-1 = unifont:fontformat=truetype:size=14:antialias=false;0
-font-2 = FontAwesome:size=14;0

profiles/i3/.config/polybar/config.d/colors

@@ -1,11 +0,0 @@
-[colors]
-background=#222
-background-alt=#444
-foreground=#dfdfdf
-foreground-alt=#555
-primary=#ffb52a
-secondary=#e60053
-alert=#bd2c40
-green=#689d6a
-yellow=#fabc2f
-red=#cc241d

profiles/i3/.config/polybar/config.d/modules

@@ -1,416 +0,0 @@
-[module/xwindow]
-type=internal/xwindow
-label="> %title:0:75:...%"
-
-
-[module/xkeyboard]
-type=internal/xkeyboard
-blacklist-0=num lock
-
-format-prefix=" "
-format-prefix-foreground=${colors.foreground-alt}
-format-prefix-underline=${colors.secondary}
-
-label-layout=%layout%
-label-layout-underline=${colors.secondary}
-
-label-indicator-padding=2
-label-indicator-margin=1
-label-indicator-background=${colors.secondary}
-label-indicator-underline=${colors.secondary}
-
-[module/filesystem]
-type=internal/fs
-interval=25
-
-mount-0=/
-mount-1=/data
-mount-2=/backup
-
-label-mounted=%{F#0a81f5}%mountpoint%%{F-}: %percentage_used%%
-label-unmounted=%mountpoint% not mounted
-label-unmounted-foreground=${colors.foreground-alt}
-
-[module/bspwm]
-type=internal/bspwm
-
-label-focused=%index%
-label-focused-background=${colors.background-alt}
-label-focused-underline=${colors.primary}
-label-focused-padding=2
-
-label-occupied=%index%
-label-occupied-padding=2
-
-label-urgent=%index%!
-label-urgent-background=${colors.alert}
-label-urgent-padding=2
-
-label-empty=%index%
-label-empty-foreground=${colors.foreground-alt}
-label-empty-padding=2
-
-[module/i3]
-type=internal/i3
-format=<label-state> <label-mode>
-index-sort=true
-wrapping-scroll=false
-strip-wsnumbers=true
-pin-workspaces=true
-
-label-mode-padding=2
-label-mode-foreground=#000
-label-mode-background=${colors.primary}
-
-label-focused=%icon%
-label-focused-background=${colors.green}
-label-focused-underline=${colors.green}
-label-focused-padding=${module/bspwm.label-focused-padding}
-
-label-unfocused=%icon%
-label-unfocused-padding=${module/bspwm.label-occupied-padding}
-
-label-urgent=%icon%
-label-urgent-background=${colors.red}
-label-urgent-underline=${colors.red}
-label-urgent-padding=${module/bspwm.label-urgent-padding}
-
-label-visible=%icon%
-label-visible-background=${self.label-focused-background}
-label-visible-underline=${self.label-focused-underline}
-label-visible-padding=${self.label-focused-padding}
-ws-icon-0=1;1
-ws-icon-1=2;2
-ws-icon-2=3;3
-ws-icon-3=4;4
-ws-icon-4=5;5
-ws-icon-5=6;6
-ws-icon-6=7;7 
-ws-icon-7=8;8 
-ws-icon-8=9;9 
-ws-icon-9=10;0 
-
-[module/mpd]
-type=internal/mpd
-format-online=<label-song>  <icon-prev> <icon-stop> <toggle> <icon-next>
-
-icon-prev=
-icon-stop=
-icon-play=
-icon-pause=
-icon-next=
-
-label-song-maxlen=25
-label-song-ellipsis=true
-
-[module/xbacklight]
-type=internal/xbacklight
-
-format=<label> <bar>
-label=BL
-
-bar-width=10
-bar-indicator=|
-bar-indicator-foreground=#ff
-bar-indicator-font=2
-bar-fill=─
-bar-fill-font=2
-bar-fill-foreground=#9f78e1
-bar-empty=─
-bar-empty-font=2
-bar-empty-foreground=${colors.foreground-alt}
-
-[module/backlight-acpi]
-inherit=module/xbacklight
-type=internal/backlight
-card=intel_backlight
-
-[module/cpu]
-type=internal/cpu
-interval=0.5
-format=<label> <ramp-coreload>
-label=CPU
-ramp-font=2
-ramp-coreload-0=▁
-ramp-coreload-font=3
-ramp-coreload-0-foreground=${colors.green}
-ramp-coreload-1=▂
-ramp-coreload-1-font=2
-ramp-coreload-1-foreground=${colors.green}
-ramp-coreload-2=▃
-ramp-coreload-2-font=2
-ramp-coreload-2-foreground=${colors.green}
-ramp-coreload-3=▄
-ramp-coreload-3-font=2
-ramp-coreload-3-foreground=${colors.green}
-ramp-coreload-4=▅
-ramp-coreload-4-font=2
-ramp-coreload-4-foreground=${colors.yellow}
-ramp-coreload-5=▆
-ramp-coreload-5-font=2
-ramp-coreload-5-foreground=${colors.yellow}
-ramp-coreload-6=▇
-ramp-coreload-6-font=2
-ramp-coreload-6-foreground=${colors.red}
-ramp-coreload-7=█
-ramp-coreload-7-font=2
-ramp-coreload-7-foreground=${colors.red}
-
-
-
-[module/memory]
-type=internal/memory
-format=<label> <bar-used>
-label=MEM
-
-bar-used-indicator=
-bar-used-width=20
-bar-used-foreground-0=${colors.green}
-bar-used-foreground-1=${colors.yellow}
-bar-used-foreground-2=${colors.red}
-bar-used-fill=▐
-bar-used-empty=▐
-bar-used-empty-foreground=#444444
-
-[module/wlan]
-type=internal/network
-interface=
-interval=3.0
-
-format-connected=<ramp-signal> <label-connected>
-format-connected-underline=#9f78e1
-label-connected=%essid%
-
-format-disconnected=
-;format-disconnected=<label-disconnected>
-;format-disconnected-underline=${self.format-connected-underline}
-;label-disconnected=%ifname% disconnected
-;label-disconnected-foreground=${colors.foreground-alt}
-
-ramp-signal-0=
-ramp-signal-1=
-ramp-signal-2=
-ramp-signal-3=
-ramp-signal-4=
-ramp-signal-foreground=${colors.foreground-alt}
-
-[module/eth]
-type=internal/network
-interface=
-interval=3.0
-
-format-connected-underline=#55aa55
-format-connected-prefix=" "
-format-connected-prefix-foreground=${colors.foreground-alt}
-label-connected=%local_ip%
-
-format-disconnected=
-;format-disconnected=<label-disconnected>
-;format-disconnected-underline=${self.format-connected-underline}
-;label-disconnected=%ifname% disconnected
-;label-disconnected-foreground=${colors.foreground-alt}
-
-[module/date]
-type=internal/date
-interval=1
-
-date=%a %d %b %Y%%{F-}
-date-alt=%a %d %b %Y%%{F-}
-
-time=%H:%M
-time-alt=%H:%M:%S
-
-format-prefix-foreground=${colors.foreground-alt}
-
-label=%time% %date%
-format=<label>
-
-[module/pulseaudio]
-type=internal/pulseaudio
-format-volume=<label-volume> <bar-volume>
-label-volume=
-label-volume-foreground=${root.foreground}
-
-format-muted-foreground=${colors.foreground-alt}
-label-muted=sound muted
-
-bar-volume-width=20
-bar-volume-foreground-0=#55aa55
-bar-volume-foreground-1=#55aa55
-bar-volume-foreground-2=#55aa55
-bar-volume-foreground-3=#55aa55
-bar-volume-foreground-4=#55aa55
-bar-volume-foreground-5=#f5a70a
-bar-volume-foreground-6=#ff5555
-bar-volume-gradient=false
-bar-volume-indicator=▐
-bar-volume-indicator-font=2
-bar-volume-fill=─
-bar-volume-fill-font=2
-bar-volume-empty=─
-bar-volume-empty-font=2
-bar-volume-empty-foreground=${colors.foreground-alt}
-
-
-[module/volume]
-type=internal/alsa
-format-volume=<label-volume> <bar-volume>
-label-volume=
-label-volume-foreground=${root.foreground}
-
-format-muted-foreground=${colors.foreground-alt}
-label-muted=sound muted
-
-bar-volume-width=20
-bar-volume-foreground-0=#55aa55
-bar-volume-foreground-1=#55aa55
-bar-volume-foreground-2=#55aa55
-bar-volume-foreground-3=#55aa55
-bar-volume-foreground-4=#55aa55
-bar-volume-foreground-5=#f5a70a
-bar-volume-foreground-6=#ff5555
-bar-volume-gradient=false
-bar-volume-indicator=▐
-bar-volume-indicator-font=2
-bar-volume-fill=─
-bar-volume-fill-font=2
-bar-volume-empty=─
-bar-volume-empty-font=2
-bar-volume-empty-foreground=${colors.foreground-alt}
-
-
-[module/temperature]
-type=internal/temperature
-thermal-zone=0
-warn-temperature=60
-
-format=<ramp> <label>
-format-underline=#f50a4d
-format-warn=<ramp> <label-warn>
-format-warn-underline=${self.format-underline}
-
-label=%temperature%
-label-warn=%temperature%
-label-warn-foreground=${colors.secondary}
-
-ramp-0=
-ramp-1=
-ramp-2=
-ramp-foreground=${colors.foreground-alt}
-
-[module/powermenu]
-type=custom/menu
-
-format-spacing=1
-
-label-open=
-label-open-foreground=${colors.secondary}
-label-close= cancel
-label-close-foreground=${colors.secondary}
-label-separator=|
-label-separator-foreground=${colors.foreground-alt}
-
-menu-0-0=reboot
-menu-0-0-exec=menu-open-1
-menu-0-1=power off
-menu-0-1-exec=menu-open-2
-
-menu-1-0=cancel
-menu-1-0-exec=menu-open-0
-menu-1-1=reboot
-menu-1-1-exec=sudo reboot
-
-menu-2-0=power off
-menu-2-0-exec=sudo poweroff
-menu-2-1=cancel
-menu-2-1-exec=menu-open-0
-
-[module/gpu]
-type=custom/script
-exec=/bin/bash ~/.config/polybar/gpu.sh
-interval=1
-tail=false
-format=GPU <label>
-
-[module/spotify]
-type=custom/script
-exec=python3 ~/.config/polybar/spotify.py "{artist} - {title}" 
-interval=1
-tail=false
-format= <label>
-; vim:ft=dosini
-
-[module/battery1]
-type=internal/battery
-full-at=95
-battery=BAT0
-adapter=ADP1
-time-format=%Hh:%Mm
-
-label-charging=%time% full
-format-charging=<label-charging>
-
-label-full=Fully charged
-format_full=<label-full>
-
-label-discharging=%percentage%% %time% left
-format-discharging=<ramp-capacity> <label-discharging>  
-
-ramp-capacity-0=
-ramp-capacity-0-foreground=${colors.red}
-ramp-capacity-1=
-ramp-capacity-1-foreground=${colors.yellow}
-ramp-capacity-2=
-ramp-capacity-2-foreground=${colors.green}
-ramp-capacity-3=
-ramp-capacity-3-foreground=${colors.green}
-ramp-capacity-4=
-ramp-capacity-4-foreground=${colors.green}
-
-animation-discharging-0=
-
-[module/previous]
-type=custom/script
-interval=86400
-format="%{T3}<label>"
-format-padding=1
-exec=echo ""
-exec-if="pgrep spotify"
-line-size=1
-click-left="dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Previous"
-
-[module/playpause]
-type=custom/script
-interval=86400
-format="%{T3}<label>"
-format-padding=1
-exec=echo "/"
-exec-if="pgrep spotify"
-line-size=1
-click-left="dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.PlayPause"
-
-
-[module/next]
-type=custom/script
-interval=86400
-format="%{T3}<label>"
-format-padding=1
-exec=echo ""
-exec-if="pgrep spotify"
-line-size=1
-click-left="dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Next"
-
-[module/unread_mail]
-type = custom/script
-exec = "/home/bauer/conda/bin/python3 /home/bauer/.config/polybar/UnseenMail/UnseenMail.py"
-interval = 100
-format = <label>
-click-left = thunderbird &;
-
-[module/notifyd]
-type = custom/ipc
-initial = 1
-format-foreground = ${colors.yellow}
-
-hook-0 = echo "%{xfconf-query -c xfce4-notifyd -p /do-not-disturb -s true}%{A}" &
-hook-1 = echo "%{xfconf-query -c xfce4-notifyd -p /do-not-disturb -s false}%{A}" &

profiles/i3/.config/polybar/config.d/settings

@@ -1,7 +0,0 @@
-wm-restack=i3
-scroll-up=i3wm-wsnext
-scroll-down=i3wm-wsprev
-
-[global/wm]
-margin-top=5
-margin-bottom=5

profiles/i3/.config/polybar/gpu.sh

@@ -1,21 +0,0 @@
-#!/bin/bash
-
-t_warn=50
-t_crit=70
-
-GPU=$(nvidia-smi -q | grep Gpu | awk '{print $3}')
-
-if [ $GPU -gt $t_crit ]
-then
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-    printf "\n#fb4934\n"
-elif [ $GPU -gt $t_warn ]
-then
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-    printf "\n#fabd2f\n"
-else
-    printf " %d%%" "$GPU"
-    printf "\n %d%%" "$GPU"
-fi

profiles/i3/.config/polybar/spotify.py

@@ -1,29 +0,0 @@
-#!/usr/bin/python2
-
-import dbus
-from sys import argv
-
-if len(argv) > 1:
-    fmt = argv[1]
-else:
-    fmt = None
-
-def format_output(artist, title, fmt=None):
-    if fmt is None:
-        fmt =  "{artist} - {title}"
-    return fmt.format(artist=artist, title=title)
-        
-
-try:
-    bus = dbus.SessionBus()
-    spotify = bus.get_object("org.mpris.MediaPlayer2.spotify", "/org/mpris/MediaPlayer2")
-    spotify_iface = dbus.Interface(spotify, 'org.freedesktop.DBus.Properties')
-    props = spotify_iface.Get('org.mpris.MediaPlayer2.Player', 'Metadata')
-    try: 
-        out = format_output((props['xesam:artist'][0]), str(props['xesam:title']), fmt)
-    except IndexError:
-        out = ''
-    print(out)
-    exit
-except dbus.exceptions.DBusException:
-    exit

profiles/i3/.config/polybar/spotify/launchlistener.sh

@@ -1,3 +0,0 @@
-#!/usr/bin/env sh
-
-/usr/bin/env python3 ~/scripts/spotify/py_spotify_listener.py

profiles/i3/.config/polybar/spotify/py_spotify_listener.py

@@ -1,125 +0,0 @@
-#!/usr/bin/env python3
-# Unwrap function: (C)2011-2015 Dennis Kaarsemaker
-# License: GPL3+
-"""Receiver related functionality."""
-import dbus.service
-import dbus.glib
-from gi.repository import GObject
-import dbus
-
-
-class Test(dbus.service.Object):
-    """Reciever test class."""
-
-    loop = None
-
-    def __init__(self, bus_name, object_path, loop):
-        """Initialize the DBUS service object."""
-        dbus.service.Object.__init__(self, bus_name, object_path)
-        self.loop = loop
-
-    @dbus.service.method('tld.domain.sub.TestInterface')
-    def foo(self):
-        """Return a string."""
-        return 'Foo'
-
-    # Stop the main loop
-    @dbus.service.method('tld.domain.sub.TestInterface')
-    def stop(self):
-        """Stop the receiver."""
-        self.loop.quit()
-        return 'Quit loop'
-
-    # Pass an exception through dbus
-    @dbus.service.method('tld.domain.sub.TestInterface')
-    def fail(self):
-        """Trigger an exception."""
-        raise Exception('FAIL!')
-
-
-def catchall_handler(*args, **kwargs):
-    """Catch all handler.
-    Catch and print information about all singals.
-    """
-    print('---- Caught signal ----')
-    print('%s:%s\n' % (kwargs['dbus_interface'], kwargs['member']))
-
-    print("\n")
-
-def quit_handler():
-    """Signal handler for quitting the receiver."""
-    print('Quitting....')
-    loop.quit()
-
-def event_handler(*args, **kwargs):
-    """event handler for the receiver."""
-    """arg[1] contains metadata"""
-    """arg[1][1] contains PlaybackStatus"""
-    data = unwrap(args)
-    if data[1]['PlaybackStatus'] == "Playing":
-        print("Music is playing")
-        """ Send IPC hook 2 to the bottom bar pid for module playpause """
-        with open("/tmp/ipc-bottom", "w") as text_file:
-            print("hook:module/playpause2", file=text_file)
-    if data[1]['PlaybackStatus'] == "Paused":
-        print("Music is paused.")
-        """ Send IPC hook 3 to the bottom bar pid for module playpause """
-        with open("/tmp/ipc-bottom", "w") as text_file:
-            print("hook:module/playpause3", file=text_file)
-    """ Send IPC hook 2 to the bottom bar pid for module spotify """
-    with open("/tmp/ipc-bottom", "w") as text_file:
-        print("hook:module/spotify2", file=text_file)
-
-def unwrap(val):
-    if isinstance(val, dbus.ByteArray):
-        return "".join([str(x) for x in val])
-    if isinstance(val, (dbus.Array, list, tuple)):
-        return [unwrap(x) for x in val]
-    if isinstance(val, (dbus.Dictionary, dict)):
-        return dict([(unwrap(x), unwrap(y)) for x, y in val.items()])
-    if isinstance(val, (dbus.Signature, dbus.String)):
-        return str(val)
-    if isinstance(val, dbus.Boolean):
-        return bool(val)
-    if isinstance(val, (dbus.Int16, dbus.UInt16, dbus.Int32, dbus.UInt32, dbus.Int64, dbus.UInt64)):
-        return int(val)
-    if isinstance(val, dbus.Byte):
-        return bytes([int(val)])
-    return val 
-
-loop = GObject.MainLoop()
-
-"""
-First we get the bus to attach to. This may be either the session bus, of the
-system bus. For system bus root permission is required.
-We claim a bus name on the chosen bus. The name should be in form of a
-domain name.
-"""
-bus = dbus.SessionBus()
-# bus = dbus.SystemBus()
-bus_name = dbus.service.BusName('sub.domain.tld', bus=bus)
-
-"""
-We initialize our service object with our name and object path. Object
-path should be in form of a reverse domain dame, delimited by / instead of .
-and the Class name as last part.
-The object path we set here is of importance for our invoker, since it will to
-call it exactly as defined here.
-"""
-obj = Test(bus_name, '/tld/domain/sub/Test', loop)
-
-
-"""
-Attach signal handler.
-Signal handlers may be attached in different ways, either by interface keyword
-or DBUS interface and a signal name or member keyword.
-You can easily gather all information by running the DBUS monitor.
-"""
-bus.add_signal_receiver(quit_handler,
-                        dbus_interface='tld.domain.sub.event',
-                        signal_name='quit_signal')
-bus.add_signal_receiver(event_handler,
-                        dbus_interface='org.freedesktop.DBus.Properties',
-                        member_keyword='PropertiesChanged')
-
-loop.run()

profiles/i3/.config/polybar/spotify/spotify_status.py

@@ -1,67 +0,0 @@
-#!/usr/bin/env python3
-
-import sys
-import dbus
-import argparse
-
-
-parser = argparse.ArgumentParser()
-parser.add_argument(
-    '-t',
-    '--trunclen',
-    type=int,
-    metavar='trunclen'
-)
-parser.add_argument(
-    '-f',
-    '--format',
-    type=str,
-    metavar='custom format',
-    dest='custom_format'
-)
-args = parser.parse_args()
-
-# Default parameters
-output = '{artist}: {song}'
-trunclen = 25
-
-# parameters can be overwritten by args
-if args.trunclen is not None:
-    trunclen = args.trunclen
-if args.custom_format is not None:
-    output = args.custom_format
-
-try:
-    session_bus = dbus.SessionBus()
-    spotify_bus = session_bus.get_object(
-        'org.mpris.MediaPlayer2.spotify',
-        '/org/mpris/MediaPlayer2'
-    )
-
-    spotify_properties = dbus.Interface(
-        spotify_bus,
-        'org.freedesktop.DBus.Properties'
-    )
-
-    metadata = spotify_properties.Get('org.mpris.MediaPlayer2.Player', 'Metadata')
-
-    artist = metadata['xesam:artist'][0]
-    song = metadata['xesam:title']
-
-    if len(song) > trunclen:
-        song = song[0:trunclen]
-        song += '...' 
-        if ('(' in song) and (')' not in song):
-            song += ')'
-    
-    # Python3 uses UTF-8 by default. 
-    if sys.version_info.major == 3:
-        print(output.format(artist=artist, song=song))
-    else:
-        print(output.format(artist=artist, song=song).encode('UTF-8'))
-except Exception as e:
-    if isinstance(e, dbus.exceptions.DBusException):
-        print('')
-    else:
-        print(e)
-

profiles/i3/.config/rofi/config.rasi

@@ -1,7 +0,0 @@
-configuration {
- modi: "window,drun,ssh,combi";
- theme: "slate";
- font: "hack 10";
- show-icons: true;
- combi-modi: "window,drun,ssh";
- }

profiles/i3/.config/rofi/slate.rasi

@@ -1,43 +0,0 @@
-* {
-  background-color: #222;
-  border-color: #2e343f;
-  text-color: #8ca0aa;
-  spacing: 3;
-}
-
-inputbar {
-  border: 0 0 1px 0;
-  children: [prompt,entry];
-}
-
-prompt {
-  padding: 16px;
-  border: 0 1px 0 0;
-}
-
-textbox {
-  background-color: #2e343f;
-  border: 0 0 1px 0;
-  border-color: #282C33;
-  padding: 8px 16px;
-}
-
-entry {
-  padding: 16px;
-}
-
-listview {
-  cycle: false;
-  margin: 0 0 -1px 0;
-  scrollbar: false;
-}
-
-element {
-  border: 0 0 1px 0;
-  padding: 16px;
-}
-
-element selected {
-  background-color: #689d6a;
-  text-color: #222;
-}

profiles/pymol/.pymol/.pymol

@@ -1 +0,0 @@
-/home/bauer/dotfiles/.pymol

profiles/pymol/.pymol/pymol-edu-license.lic

@@ -1,8 +0,0 @@
-INCREMENT PYMOL_MAIN SCHROD 999 01-may-2019 uncounted HOSTID=ANY \
-	ISSUED=01-Sep-2018 NOTICE="PyMOL for educational use only" \
-	START=01-Oct-2018 TS_OK SIGN="12F2 36C7 3B45 39DF 18BE 27F4 \
-	3043 09ED F843 D2B0 442F 4433 0630 2AF5 F31B 07D5 2E50 A361 \
-	156E BE21 288B A8F9 F975 1C1A 92E5 441F 9521 F8EF 140B 1997" \
-	SIGN2="0E48 A34C FD12 8A53 0CA8 EABC 2671 1CA5 A621 EBB8 C6B6 \
-	AC3C BB33 EA41 97FC 1445 B6EC 20BF 1EE1 7B08 68F8 9DB9 187A \
-	6F06 9124 4BAD BF40 86C1 9E29 F44E"

profiles/pymol/.pymol/startup/Draw_Protein_Dimensions.py

@@ -1,362 +0,0 @@
-
-'''
-Calculate and display the dimensions of a protein.
-
-
-This is a first version, please use at your own risk!
-
-REQUIREMENTS
-
-numpy (http://numpy.scipy.org) that should be built into the newers versions of Pymol
-
-(c) Pablo Guardado Calvo
-
-Based on "inertia_tensor.py" (c) 2010 by Mateusz Maciejewski
-
-License: MIT
-
-'''
-
-from __future__ import print_function
-
-__author__  = 'Pablo Guardado Calvo'
-__version__ = '0.1'
-__email__   = 'pablo.guardado (at) gmail.com'
-__date__    = '13/08/2015'
-
-###########################################################################################################################################################
-# USAGE
-#
-# The idea behing this script is to calculate an aproximate minimal bounding box to extract the cell dimensions of a protein. To calculate the minimal bounding
-# is not trivial and usually the Axis Aligned Bounding Box (AABB) does not show up the real dimensions of the protein. This script calculates the inertia tensor
-# of the object, extract the eigenvalues and use them to rotate the molecule (using as rotation matrix the transpose of the eigenvalues matrix). The result is that
-# the molecule is oriented with the inertia axis aligned with the cartesian axis. A new Bounding Box is calculated that is called Inertia Axis Aligned Bounding Box
-#(IABB), whose volume is always lower than AABB volume, and in many cases will correspond with the lowest volume. Of course, maybe it exists another Bounding Box
-# with a lower volume (the minimal Bounding Box).
-#
-# As always with these type of things, you have to use at your own risk. I did not try all the possible combinations, but if you find a bug, do
-# not hesitate to contact me (pablo.guardado (at) gmail.com) or try to modify the code for yourself to correct it.
-#
-# To load the script just type:
-#
-# run path-to-the-script/Draw_Protein_Dimensions.py
-#
-# or if you want something more permanent add the previous line to your .pymolrc file
-#
-# The script works just typing:
-#
-# draw_Protein_Dimensions selection
-#
-# This will draw the cell dimensions of your selection based on a IABB. It also generates the IABB box and the inertia axis, you just need to do "show cgo" to display them.
-#
-# You could also try:
-#
-# draw_BB selection
-#
-# This will draw the AABB and IABB boxes with their cell dimensions and show in the command line their volumes, you can compare both of them.
-############################################################################################################################################################
-
-from pymol import cmd, cgo
-from pymol.cgo import *
-import numpy
-from random import randint
-
-def matriz_inercia(selection):
-	'''
-	DESCRIPTION
-
-	The method calculates the mass center, the inertia tensor and the eigenvalues and eigenvectors
-	for a given selection. Mostly taken from inertia_tensor.py
-	'''
-
-	model = cmd.get_model(selection)
-	totmass = 0.0
-	x,y,z = 0,0,0
-	for a in model.atom:
-		m = a.get_mass()
-		x += a.coord[0]*m
-		y += a.coord[1]*m
-		z += a.coord[2]*m
-		totmass += m
-	global cM
-	cM = numpy.array([x/totmass, y/totmass, z/totmass])
-
-
-	I = []
-	for index in range(9):
-		I.append(0)
-
-	for a in model.atom:
-		temp_x, temp_y, temp_z = a.coord[0], a.coord[1], a.coord[2]
-		temp_x -= x
-		temp_y -= y
-		temp_z -= z
-
-		I[0] += a.get_mass() * (temp_y**2 + temp_z**2)
-		I[1] -= a.get_mass() * temp_x * temp_y
-		I[2] -= a.get_mass() * temp_x * temp_z
-		I[3] -= a.get_mass() * temp_x * temp_y
-		I[4] += a.get_mass() * (temp_x**2 + temp_z**2)
-		I[5] -= a.get_mass() * temp_y * temp_z
-		I[6] -= a.get_mass() * temp_x * temp_z
-		I[7] -= a.get_mass() * temp_y * temp_z
-		I[8] += a.get_mass() * (temp_x**2 + temp_y**2)
-
-	global tensor
-	tensor = numpy.array([(I[0:3]), (I[3:6]), (I[6:9])])
-
-	global autoval, autovect, ord_autoval, ord_autovect
-	autoval, autovect = numpy.linalg.eig(tensor)
-	auto_ord = numpy.argsort(autoval)
-	ord_autoval = autoval[auto_ord]
-	ord_autovect_complete = autovect[:, auto_ord].T
-	ord_autovect = numpy.around(ord_autovect_complete, 3)
-
-	return ord_autoval
-
-
-def draw_inertia_axis(selection):
-	'''
-	DESCRIPTION
-
-	This method draw the inertia axis calculated with the method matriz_inercia.
-	'''
-
-	matriz_inercia(selection)
-	axis1 = ord_autovect[0]
-	x1, y1, z1 = cM[0], cM[1], cM[2]
-	x2, y2, z2 = cM[0]+50*axis1[0], cM[1]+50*axis1[1], cM[2]+50*axis1[2]
-	eje1 = [cgo.CYLINDER, x1, y1, z1, x2, y2, z2, 0.6, 1, 0, 0, 1, 0, 0, 0.0]
-	cmd.load_cgo(eje1, 'Inertia_Axis1')
-	axis2 = ord_autovect[1]
-	x3, y3, z3 = cM[0]+40*axis2[0], cM[1]+40*axis2[1], cM[2]+40*axis2[2]
-	eje1 = [cgo.CYLINDER, x1, y1, z1, x3, y3, z3, 0.6, 1, 0.5, 0, 1, 0.5, 0, 0.0]
-	cmd.load_cgo(eje1, 'Inertia_Axis2')
-	axis4 = ord_autovect[2]
-	x4, y4, z4 = cM[0]+30*axis4[0], cM[1]+30*axis4[1], cM[2]+30*axis4[2]
-	eje1 = [cgo.CYLINDER, x1, y1, z1, x4, y4, z4, 0.6, 1, 1, 0, 1, 1, 0, 0.0]
-	cmd.load_cgo(eje1, 'Inertia_Axis3')
-
-def translacion_cM(selection):
-	'''
-	DESCRIPTION
-
-	Translate the center of mass of the molecule to the origin.
-	'''
-	model = cmd.get_model(selection)
-	totmass = 0.0
-	x,y,z = 0,0,0
-	for a in model.atom:
-		m = a.get_mass()
-		x += a.coord[0]*m
-		y += a.coord[1]*m
-		z += a.coord[2]*m
-		totmass += m
-	cM = numpy.array([x/totmass, y/totmass, z/totmass])
-	trans_array = ([1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, -cM[0], -cM[1], -cM[2], 1])
-	model_trans = cmd.transform_selection(selection, trans_array)
-
-
-def rotacion_orig(selection):
-	'''
-	DESCRIPTION
-
-	Find the proper rotation matrix, i.e. the transpose of the matrix formed by the eigenvectors of the inertia tensor
-	'''
-
-	translacion_cM(selection)
-	matriz_inercia(selection)
-	global transf, transf_array, ord_autovect_array, transf_array_print
-	ord_autovect_array = numpy.array([[ord_autovect[0][0], ord_autovect[0][1], ord_autovect[0][2]],
-	                                  [ord_autovect[1][0], ord_autovect[1][1], ord_autovect[1][2]],
-					  [ord_autovect[2][0], ord_autovect[2][1], ord_autovect[2][2]]])
-	if numpy.linalg.det(ord_autovect_array) == -1:
-		ord_autovect_array = numpy.array([[ord_autovect[2][0], ord_autovect[2][1], ord_autovect[2][2]],
-	                                  	  [ord_autovect[1][0], ord_autovect[1][1], ord_autovect[1][2]],
-	 				  	  [ord_autovect[0][0], ord_autovect[0][1], ord_autovect[0][2]]])
-	transf = numpy.transpose(ord_autovect_array)
-	transf_array = numpy.array([transf[0][0], transf[0][1], transf[0][2], 0,
-	                            transf[1][0], transf[1][1], transf[1][2], 0,
-				    transf[2][0], transf[2][1], transf[2][2], 0,
-				    0, 0, 0, 1])
-
-
-def transformar(selection):
-	'''
-	DESCRIPTION
-
-	Rotate the molecule and draw the inertia axis.
-	'''
-
-	rotacion_orig(selection)
-	model_rot = cmd.transform_selection(selection, transf_array, homogenous=0, transpose=1);
-	draw_inertia_axis(selection)
-
-
-
-def draw_AABB(selection):
-        """
-        DESCRIPTION
-        For a given selection, draw the Axes Aligned bounding box around it without padding. Code taken and modified from DrawBoundingBox.py.
-
-        """
-
- 	AA_original = selection + "_original"
-	model_orig = cmd.create(AA_original, selection)
-
-        ([min_X, min_Y, min_Z],[max_X, max_Y, max_Z]) = cmd.get_extent(AA_original)
-
-	print("The Axis Aligned Bounding Box (AABB) dimensions are (%.2f, %.2f, %.2f)" % (max_X-min_X, max_Y-min_Y, max_Z-min_Z))
-	print("The Axis Aligned Bounding Box (AABB) volume is %.2f A3" % ((max_X-min_X)*(max_Y-min_Y)*(max_Z-min_Z)))
-
-
-        min_X = min_X
-        min_Y = min_Y
-        min_Z = min_Z
-        max_X = max_X
-        max_Y = max_Y
-        max_Z = max_Z
-
-        boundingBox = [
-                LINEWIDTH, float(2),
-
-                BEGIN, LINES,
-                COLOR, float(1), float(1), float(0),
-
-                VERTEX, min_X, min_Y, min_Z,
-                VERTEX, min_X, min_Y, max_Z,
-                VERTEX, min_X, max_Y, min_Z,
-                VERTEX, min_X, max_Y, max_Z,
-                VERTEX, max_X, min_Y, min_Z,
-                VERTEX, max_X, min_Y, max_Z,
-                VERTEX, max_X, max_Y, min_Z,
-                VERTEX, max_X, max_Y, max_Z,
-                VERTEX, min_X, min_Y, min_Z,
-                VERTEX, max_X, min_Y, min_Z,
-                VERTEX, min_X, max_Y, min_Z,
-                VERTEX, max_X, max_Y, min_Z,
-                VERTEX, min_X, max_Y, max_Z,
-                VERTEX, max_X, max_Y, max_Z,
-                VERTEX, min_X, min_Y, max_Z,
-                VERTEX, max_X, min_Y, max_Z,
-                VERTEX, min_X, min_Y, min_Z,
-                VERTEX, min_X, max_Y, min_Z,
-                VERTEX, max_X, min_Y, min_Z,
-                VERTEX, max_X, max_Y, min_Z,
-                VERTEX, min_X, min_Y, max_Z,
-                VERTEX, min_X, max_Y, max_Z,
-                VERTEX, max_X, min_Y, max_Z,
-                VERTEX, max_X, max_Y, max_Z,
-
-		END
-	]
-
-	p0 = '_0'  + str(randint(0, 100))
-	p1 = '_1' + str(randint(0, 100))
-	p2 = '_2' + str(randint(0, 100))
-	p3 = '_3' + str(randint(0, 100))
-	cmd.pseudoatom (pos=[min_X, min_Y, min_Z], object=p0)
-	cmd.pseudoatom (pos=[min_X, min_Y, max_Z], object=p1)
-	cmd.pseudoatom (pos=[min_X, max_Y, min_Z], object=p2)
-	cmd.pseudoatom (pos=[max_X, min_Y, min_Z], object=p3)
-	cmd.distance(None, p0, p3)
-	cmd.distance(None, p0, p2)
-	cmd.distance(None, p0, p1)
-	cmd.hide("nonbonded")
-
-	boxName = "box_AABB_"  + str(randint(0, 100))
-        cmd.load_cgo(boundingBox,boxName)
-        return boxName
-
-
-def draw_IABB(selection):
-        """
-        DESCRIPTION
-        For a given selection, draw the Inertia Axes Aligned bounding box around it without padding. Code taken and modified from DrawBoundingBox.py.
-
-        """
-
-	transformar(selection)
-
-        ([minX, minY, minZ],[maxX, maxY, maxZ]) = cmd.get_extent(selection)
-
-	print("The Inertia Axis Aligned Bounding Box (IABB) dimensions are (%.2f, %.2f, %.2f)" % (maxX-minX, maxY-minY, maxZ-minZ))
-	print("The Inertia Axis Aligned Bounding Box (IABB) volume is %.2f A3" % ((maxX-minX)*(maxY-minY)*(maxZ-minZ)))
-
-
-        minX = minX
-        minY = minY
-        minZ = minZ
-        maxX = maxX
-        maxY = maxY
-        maxZ = maxZ
-
-        boundingBox = [
-                LINEWIDTH, float(2),
-
-                BEGIN, LINES,
-                COLOR, float(1), float(0), float(0),
-
-                VERTEX, minX, minY, minZ,
-                VERTEX, minX, minY, maxZ,
-                VERTEX, minX, maxY, minZ,
-                VERTEX, minX, maxY, maxZ,
-                VERTEX, maxX, minY, minZ,
-                VERTEX, maxX, minY, maxZ,
-                VERTEX, maxX, maxY, minZ,
-                VERTEX, maxX, maxY, maxZ,
-                VERTEX, minX, minY, minZ,
-                VERTEX, maxX, minY, minZ,
-                VERTEX, minX, maxY, minZ,
-                VERTEX, maxX, maxY, minZ,
-                VERTEX, minX, maxY, maxZ,
-                VERTEX, maxX, maxY, maxZ,
-                VERTEX, minX, minY, maxZ,
-                VERTEX, maxX, minY, maxZ,
-                VERTEX, minX, minY, minZ,
-                VERTEX, minX, maxY, minZ,
-                VERTEX, maxX, minY, minZ,
-                VERTEX, maxX, maxY, minZ,
-                VERTEX, minX, minY, maxZ,
-                VERTEX, minX, maxY, maxZ,
-                VERTEX, maxX, minY, maxZ,
-                VERTEX, maxX, maxY, maxZ,
-
-                END
-        ]
-
- 	p4 = '_4' + str(randint(0, 100))
-	p5 = '_5' + str(randint(0, 100))
-	p6 = '_6' + str(randint(0, 100))
-	p7 = '_7' + str(randint(0, 100))
-	cmd.pseudoatom (pos=[minX, minY, minZ], object=p4)
-	cmd.pseudoatom (pos=[minX, minY, maxZ], object=p5)
-	cmd.pseudoatom (pos=[minX, maxY, minZ], object=p6)
-	cmd.pseudoatom (pos=[maxX, minY, minZ], object=p7)
-	cmd.distance(None, p4, p7)
-	cmd.distance(None, p4, p6)
-	cmd.distance(None, p4, p5)
-	cmd.hide("nonbonded")
-
-	boxName = "box_IABB_" + str(randint(0, 100))
-        cmd.load_cgo(boundingBox,boxName)
-        return boxName
-
-
-def draw_BB(selection):
-	draw_AABB(selection)
-	draw_IABB(selection)
-
-def draw_Protein_Dimensions(selection):
-	draw_IABB(selection)
-	cmd.hide("cgo")
-
-cmd.extend ("draw_Protein_Dimensions", draw_Protein_Dimensions)
-cmd.extend ("draw_BB", draw_BB)
-
-
-
-
-
-
-

profiles/pymol/.pymol/startup/anglebetweenhelices.py

@@ -1,316 +0,0 @@
-'''
-(c) 2010 Thomas Holder
-'''
-
-from pymol import cmd, stored, CmdException
-from chempy import cpv
-import math
-
-if cmd.get_version()[1] < 1.2:
-    def get_unused_name(name):
-        import random
-        return name + '%04d' % random.randint(0, 1000)
-    STATE = 1
-else:
-    from pymol.cmd import get_unused_name
-    STATE = -1
-
-
-def _vec_sum(vec_list):
-    # this is the same as
-    # return numpy.array(vec_list).sum(0).tolist()
-    vec = cpv.get_null()
-    for x in vec_list:
-        vec = cpv.add(vec, x)
-    return vec
-
-
-def _mean_and_std(x):
-    # this is the same as
-    # return (numpy.mean(x), numpy.std(x, ddof=1))
-    N = len(x)
-    if N < 2:
-        return (x[0], 0.0)
-    mu = sum(x) / float(N)
-    var = sum([(i - mu) ** 2 for i in x]) / float(N - 1)
-    return (mu, var ** 0.5)
-
-
-def _common_orientation(selection, vec, visualize=1, quiet=0):
-    '''
-    Common part of different helix orientation functions. Does calculate
-    the center of mass and does the visual feedback.
-    '''
-    stored.x = []
-    cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
-                      'stored.x.append([x,y,z])')
-    if len(stored.x) < 2:
-        print('warning: count(CA) < 2')
-        raise CmdException
-    center = cpv.scale(_vec_sum(stored.x), 1. / len(stored.x))
-    if visualize:
-        scale = cpv.distance(stored.x[0], stored.x[-1])
-        visualize_orientation(vec, center, scale, True)
-        cmd.zoom(selection, buffer=2)
-    if not quiet:
-        print('Center: (%.2f, %.2f, %.2f) Direction: (%.2f, %.2f, %.2f)' % tuple(center + vec))
-    return center, vec
-
-
-def visualize_orientation(direction, center=[0, 0, 0], scale=1.0, symmetric=False, color='green', color2='red'):
-    '''
-    Draw an arrow. Helper function for "helix_orientation" etc.
-    '''
-    from pymol import cgo
-    color_list = cmd.get_color_tuple(color)
-    color2_list = cmd.get_color_tuple(color2)
-    if symmetric:
-        scale *= 0.5
-    end = cpv.add(center, cpv.scale(direction, scale))
-    radius = 0.3
-    obj = [cgo.SAUSAGE]
-    obj.extend(center)
-    obj.extend(end)
-    obj.extend([
-        radius,
-        0.8, 0.8, 0.8,
-    ])
-    obj.extend(color_list)
-    if symmetric:
-        start = cpv.sub(center, cpv.scale(direction, scale))
-        obj.append(cgo.SAUSAGE)
-        obj.extend(center)
-        obj.extend(start)
-        obj.extend([
-            radius,
-            0.8, 0.8, 0.8,
-        ])
-        obj.extend(color2_list)
-    coneend = cpv.add(end, cpv.scale(direction, 4.0 * radius))
-    if cmd.get_version()[1] >= 1.2:
-        obj.append(cgo.CONE)
-        obj.extend(end)
-        obj.extend(coneend)
-        obj.extend([
-            radius * 1.75,
-            0.0,
-        ])
-        obj.extend(color_list * 2)
-        obj.extend([
-            1.0, 1.0,  # Caps
-        ])
-    cmd.load_cgo(obj, get_unused_name('oriVec'), zoom=0)
-
-
-def cafit_orientation(selection, visualize=1, quiet=0):
-    '''
-DESCRIPTION
-
-    Get the center and direction of a peptide by least squares
-    linear fit on CA atoms.
-
-USAGE
-
-    cafit_orientation selection [, visualize]
-
-NOTES
-
-    Requires python module "numpy".
-
-SEE ALSO
-
-    helix_orientation
-    '''
-    visualize, quiet = int(visualize), int(quiet)
-    import numpy
-    stored.x = list()
-    cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
-                      'stored.x.append([x,y,z])')
-    x = numpy.array(stored.x)
-    U, s, Vh = numpy.linalg.svd(x - x.mean(0))
-    vec = cpv.normalize(Vh[0])
-    if cpv.dot_product(vec, x[-1] - x[0]) < 0:
-        vec = cpv.negate(vec)
-    return _common_orientation(selection, vec, visualize, quiet)
-
-
-def loop_orientation(selection, visualize=1, quiet=0):
-    '''
-DESCRIPTION
-
-    Get the center and approximate direction of a peptide. Works for any
-    secondary structure.
-    Averages direction of N(i)->C(i) pseudo bonds.
-
-USAGE
-
-    loop_orientation selection [, visualize]
-
-SEE ALSO
-
-    helix_orientation
-    '''
-    visualize, quiet = int(visualize), int(quiet)
-    stored.x = dict()
-    cmd.iterate_state(STATE, '(%s) and name N+C' % (selection),
-                      'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
-    vec = cpv.get_null()
-    count = 0
-    for x in stored.x.values():
-        if 'C' in x and 'N' in x:
-            vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
-            count += 1
-    if count == 0:
-        print('warning: count == 0')
-        raise CmdException
-    vec = cpv.normalize(vec)
-    return _common_orientation(selection, vec, visualize, quiet)
-
-
-def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
-    '''
-DESCRIPTION
-
-    Get the center and direction of a helix as vectors. Will only work
-    for helices and gives slightly different results than loop_orientation.
-    Averages direction of C(i)->O(i) bonds.
-
-USAGE
-
-    helix_orientation selection [, visualize [, sigma_cutoff]]
-
-ARGUMENTS
-
-    selection = string: atom selection of helix
-
-    visualize = 0 or 1: show fitted vector as arrow {default: 1}
-
-    sigma_cutoff = float: drop outliers outside
-    (standard_deviation * sigma_cutoff) {default: 1.5}
-
-SEE ALSO
-
-    angle_between_helices, helix_orientation_hbond, loop_orientation, cafit_orientation
-    '''
-    visualize, quiet, sigma_cutoff = int(visualize), int(quiet), float(sigma_cutoff)
-    stored.x = dict()
-    cmd.iterate_state(STATE, '(%s) and name C+O' % (selection),
-                      'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
-    vec_list = []
-    count = 0
-    for x in stored.x.values():
-        if 'C' in x and 'O' in x:
-            vec_list.append(cpv.sub(x['O'], x['C']))
-            count += 1
-    if count == 0:
-        print('warning: count == 0')
-        raise CmdException
-    vec = _vec_sum(vec_list)
-    if count > 2 and sigma_cutoff > 0:
-        angle_list = [cpv.get_angle(vec, x) for x in vec_list]
-        angle_mu, angle_sigma = _mean_and_std(angle_list)
-        vec_list = [vec_list[i] for i in range(len(vec_list))
-                    if abs(angle_list[i] - angle_mu) < angle_sigma * sigma_cutoff]
-        if not quiet:
-            print('Dropping %d outlier(s)' % (len(angle_list) - len(vec_list)))
-        vec = _vec_sum(vec_list)
-    vec = cpv.normalize(vec)
-    return _common_orientation(selection, vec, visualize, quiet)
-
-
-def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
-    '''
-DESCRIPTION
-
-    Get the center and direction of a helix as vectors. Will only work
-    for alpha helices and gives slightly different results than
-    helix_orientation. Averages direction of O(i)->N(i+4) hydrogen bonds.
-
-USAGE
-
-    helix_orientation selection [, visualize [, cutoff]]
-
-ARGUMENTS
-
-    cutoff = float: maximal hydrogen bond distance {default: 3.5}
-
-SEE ALSO
-
-    helix_orientation
-    '''
-    visualize, quiet, cutoff = int(visualize), int(quiet), float(cutoff)
-    stored.x = dict()
-    cmd.iterate_state(STATE, '(%s) and name N+O' % (selection),
-                      'stored.x.setdefault(resv, dict())[name] = x,y,z')
-    vec_list = []
-    for resi in stored.x:
-        resi_other = resi + 4
-        if 'O' in stored.x[resi] and resi_other in stored.x:
-            if 'N' in stored.x[resi_other]:
-                vec = cpv.sub(stored.x[resi_other]['N'], stored.x[resi]['O'])
-                if cpv.length(vec) < cutoff:
-                    vec_list.append(vec)
-    if len(vec_list) == 0:
-        print('warning: count == 0')
-        raise CmdException
-    vec = _vec_sum(vec_list)
-    vec = cpv.normalize(vec)
-    return _common_orientation(selection, vec, visualize, quiet)
-
-
-def angle_between_helices(selection1, selection2, method='helix_orientation', visualize=1, quiet=0):
-    '''
-DESCRIPTION
-
-    Calculates the angle between two helices
-
-USAGE
-
-    angle_between_helices selection1, selection2 [, method [, visualize]]
-
-ARGUMENTS
-
-    selection1 = string: atom selection of first helix
-
-    selection2 = string: atom selection of second helix
-
-    method = string: function to calculate orientation {default: helix_orientation}
-             or int: 0: helix_orientation, 1: helix_orientation_hbond,
-                     2: loop_orientation, 3: cafit_orientation
-
-    visualize = 0 or 1: show fitted vector as arrow {default: 1}
-
-SEE ALSO
-
-    helix_orientation, helix_orientation_hbond, loop_orientation, cafit_orientation
-    '''
-    visualize, quiet = int(visualize), int(quiet)
-    methods = {
-        '0': helix_orientation,
-        '1': helix_orientation_hbond,
-        '2': loop_orientation,
-        '3': cafit_orientation,
-    }
-    methods.update([(x.__name__, x) for x in list(methods.values())])
-    try:
-        orientation = methods[str(method)]
-    except KeyError:
-        print('no such method: ' + str(method))
-        raise CmdException
-    if not quiet:
-        print('Using method: ' + orientation.__name__)
-    cen1, dir1 = orientation(selection1, visualize, quiet=1)
-    cen2, dir2 = orientation(selection2, visualize, quiet=1)
-    angle = cpv.get_angle(dir1, dir2)
-    angle_deg = math.degrees(angle)
-    if not quiet:
-        print('Angle: %.2f deg' % (angle_deg))
-    if visualize:
-        cmd.zoom('(%s) or (%s)' % (selection1, selection2), buffer=2)
-    return angle_deg
-
-cmd.extend('helix_orientation', helix_orientation)
-cmd.extend('helix_orientation_hbond', helix_orientation_hbond)
-cmd.extend('loop_orientation', loop_orientation)
-cmd.extend('cafit_orientation', cafit_orientation)
-cmd.extend('angle_between_helices', angle_between_helices)

profiles/pymol/.pymol/startup/axes.py

@@ -1,68 +0,0 @@
-from pymol import cmd
-from chempy import cpv
-
-class PutCenterCallback(object):
-    prev_v = None
-
-    def __init__(self, name, corner=0):
-        self.name = name
-        self.corner = corner
-        self.cb_name = cmd.get_unused_name('_cb')
-
-    def load(self):
-        cmd.load_callback(self, self.cb_name)
-
-    def __call__(self):
-        if self.name not in cmd.get_names('objects'):
-            import threading
-            threading.Thread(None, cmd.delete, args=(self.cb_name,)).start()
-            return
-
-        v = cmd.get_view()
-        if v == self.prev_v:
-            return
-        self.prev_v = v
-
-        t = v[12:15]
-
-        if self.corner:
-            vp = cmd.get_viewport()
-            R_mc = [v[0:3], v[3:6], v[6:9]]
-            off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
-            if self.corner in [2,3]:
-                off_c[0] *= -1
-            if self.corner in [3,4]:
-                off_c[1] *= -1
-            off_m = cpv.transform(R_mc, off_c)
-            t = cpv.add(t, off_m)
-
-        z = -v[11] / 30.0
-        m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
-        cmd.set_object_ttt(self.name, m)
-
-def axes(name='axes'):
-    '''
-DESCRIPTION
-
-    Puts coordinate axes to the lower left corner of the viewport.
-    '''
-    from pymol import cgo
-
-    cmd.set('auto_zoom', 0)
-
-    w = 0.06 # cylinder width
-    l = 0.75 # cylinder length
-    h = 0.25 # cone hight
-    d = w * 1.618 # cone base diameter
-
-    obj = [cgo.CYLINDER, 0.0, 0.0, 0.0,   l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
-           cgo.CYLINDER, 0.0, 0.0, 0.0, 0.0,   l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
-           cgo.CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0,   l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
-           cgo.CONE,   l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0,
-           cgo.CONE, 0.0,   l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0,
-           cgo.CONE, 0.0, 0.0,   l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]
-
-    PutCenterCallback(name, 1).load()
-    cmd.load_cgo(obj, name)
-
-cmd.extend('axes', axes)

profiles/pymol/.pymol/startup/center_of_mass.py

@@ -1,86 +0,0 @@
-'''
-See more here: http://www.pymolwiki.org/index.php/center_of_mass
-
-DESCRIPTION
-
-   Places a pseudoatom at the center of mass
-
-   Author: Sean Law
-   Michigan State University
-   slaw (at) msu . edu
-
-SEE ALSO
-
-   pseudoatom, get_com
-'''
-
-from __future__ import print_function
-from pymol import cmd
-
-
-def com(selection, state=None, mass=None, object=None, quiet=1, **kwargs):
-    quiet = int(quiet)
-    if (object == None):
-        try:
-            object = cmd.get_legal_name(selection)
-            object = cmd.get_unused_name(object + "_COM", 0)
-        except AttributeError:
-            object = 'COM'
-    cmd.delete(object)
-
-    if (state != None):
-        x, y, z = get_com(selection, mass=mass, quiet=quiet)
-        if not quiet:
-            print("%f %f %f" % (x, y, z))
-        cmd.pseudoatom(object, pos=[x, y, z], **kwargs)
-        cmd.show("spheres", object)
-    else:
-        for i in range(cmd.count_states()):
-            x, y, z = get_com(selection, mass=mass, state=i + 1, quiet=quiet)
-            if not quiet:
-                print("State %d:%f %f %f" % (i + 1, x, y, z))
-            cmd.pseudoatom(object, pos=[x, y, z], state=i + 1, **kwargs)
-            cmd.show("spheres", 'last ' + object)
-
-cmd.extend("com", com)
-
-
-def get_com(selection, state=1, mass=None, quiet=1):
-    """
- DESCRIPTION
-
-    Calculates the center of mass
-
-    Author: Sean Law
-    Michigan State University
-    slaw (at) msu . edu
-    """
-    quiet = int(quiet)
-
-    totmass = 0.0
-    if mass != None and not quiet:
-        print("Calculating mass-weighted COM")
-
-    state = int(state)
-    model = cmd.get_model(selection, state)
-    x, y, z = 0, 0, 0
-    for a in model.atom:
-        if (mass != None):
-            m = a.get_mass()
-            x += a.coord[0] * m
-            y += a.coord[1] * m
-            z += a.coord[2] * m
-            totmass += m
-        else:
-            x += a.coord[0]
-            y += a.coord[1]
-            z += a.coord[2]
-
-    if (mass != None):
-        return x / totmass, y / totmass, z / totmass
-    else:
-        return x / len(model.atom), y / len(model.atom), z / len(model.atom)
-
-cmd.extend("get_com", get_com)
-
-# vi:expandtab:sw=3

profiles/pymol/.pymol/startup/centroid.py

@@ -1,66 +0,0 @@
-'''
-See more here: http://www.pymolwiki.org/index.php/centroid
-
-DESCRIPTION
-        get the centroid (geometric center) of a selection or move selection to the origin.
-
-ARGUMENTS
-        selection = string: a valid PyMOL selection {default: all}
-        center = 0 or 1: if center=1 center the selection {default: 0}
-        returns: centroid: [ x, y, z ]
-
-SEE ALSO
-        get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
-
-# @AUTHOR: Jason Vertrees
-# Copyright (c) 2008, Jason Vertrees
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following
-# conditions are met:
-#
-#     * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
-#     * disclaimer.
-#     * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
-#     * disclaimer in the documentation and/or other materials provided with the distribution.
-#     * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to endorse or promote products derived
-#     * from this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
-# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
-# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
-# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# DATE  : 2008-09-26
-# REV   : 1
-
-'''
-from __future__ import print_function
-from pymol import cmd
-from pymol import stored
-from chempy import cpv
-
-
-def centroid(selection='all', center=0, quiet=1):
-
-    model = cmd.get_model(selection)
-    nAtom = len(model.atom)
-
-    centroid = cpv.get_null()
-
-    for a in model.atom:
-        centroid = cpv.add(centroid, a.coord)
-    centroid = cpv.scale(centroid, 1. / nAtom)
-
-    if not int(quiet):
-        print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
-
-    if int(center):
-        cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
-                        space={'centroid': centroid, 'sub': cpv.sub})
-
-    return centroid
-
-cmd.extend("centroid", centroid)

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

@@ -1,128 +0,0 @@
-# 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/pymol/.pymol/startup/dssp_stride.py

@@ -1,981 +0,0 @@
-""" 2011_04_11: Hongbo Zhu
-      PyMOL plugin for running DSSP and display SS using different colors.
-      The DSSP codes for secondary structure are: 
-   
-      H  -  Alpha helix (4-12) 
-      G  -  3-10 helix 
-      I  -  pi helix 
-      E  -  Strand 
-      B  -  Isolated beta-bridge residue 
-      T  -  Turn 
-      S  -  Bend 
-      -  -  None
-      2011_04_24: add stride
-      STRIDE code (taken from stride.doc) is nearly the same as DSSP
-      H         Alpha helix
-      G         3-10 helix
-      I         PI-helix
-      E         Extended conformation
-      B or b    Isolated bridge
-      T         Turn
-      C         Coil (none of the above)
-"""
-
-# Copyright Notice
-# ================
-# 
-# The PyMOL Plugin source code in this file is copyrighted, but you can
-# freely use and copy it as long as you don't change or remove any of
-# the copyright notices.
-# 
-# ----------------------------------------------------------------------
-#               This PyMOL Plugin is Copyright (C) 2011 by 
-#            Hongbo Zhu <hongbo.zhu.cn at googlemail dot com>
-# 
-#                        All Rights Reserved
-# 
-# Permission to use, copy, modify, distribute, and distribute modified
-# versions of this software and its documentation for any purpose and
-# without fee is hereby granted, provided that the above copyright
-# notice appear in all copies and that both the copyright notice and
-# this permission notice appear in supporting documentation, and that
-# the name(s) of the author(s) not be used in advertising or publicity
-# pertaining to distribution of the software without specific, written
-# prior permission.
-# 
-# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
-# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
-# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
-# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
-# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
-# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
-# PERFORMANCE OF THIS SOFTWARE.
-# ----------------------------------------------------------------------
-
-# python lib
-import os
-import sys 
-import platform
-if sys.version_info >= (2,4):
-    import subprocess # subprocess is introduced in python 2.4
-import math
-import random
-import tempfile
-import tkSimpleDialog
-import tkMessageBox
-import tkFileDialog
-import tkColorChooser
-
-import Tkinter
-
-# pymol lib
-try: 
-    from pymol import cmd
-    from pymol.cgo import *
-except ImportError:
-    print 'Warning: pymol library cmd not found.'
-    sys.exit(1)
-    
-# external lib    
-try:
-    import Pmw
-except ImportError:
-    print 'Warning: failed to import Pmw. Exit ...'
-    sys.exit(1)
-    
-VERBOSE = True
-
-#################
-## here we go
-#################
-def __init__(self):
-    """ DSSP and Stride plugin for PyMol
-    """
-    self.menuBar.addmenuitem('Plugin', 'command',
-                             'DSSP & Stride', label = 'DSSP & Stride',
-                             command = lambda s=self : DSSPPlugin(s))
-    
-
-#################
-## GUI related
-#################
-class DSSPPlugin:
-  
-    def __init__(self, app):
-        
-        self.parent = app.root
-        self.dialog = Pmw.Dialog(self.parent,
-                                 buttons = ('Run DSSP',
-                                            'Run Stride',
-                                            'Update Color',
-                                            'Update ss',
-                                            'Exit'),
-                                 title = 'DSSP and Stride Plugin for PyMOL',
-                                 command = self.execute)
-        Pmw.setbusycursorattributes(self.dialog.component('hull'))
-
-        # parameters used by DSSP
-        self.pymol_sel     = Tkinter.StringVar()
-        self.dssp_bin      = Tkinter.StringVar()
-        self.stride_bin    = Tkinter.StringVar()
-        self.dssp_rlt_dict = {}
-        self.stride_rlt_dict = {}
-        self.ss_asgn_prog  = None # which program is used to assign ss
-        
-        self.sel_obj_list = [] # there may be more than one seletion or object
-                               # defined by self.pymol_sel
-                               # treat each selection and object separately
-        if 'DSSP_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
-            if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
-                initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","i86Linux2","dssp-2")
-                os.environ['DSSP_BIN'] = initialdir_dssp
-            elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
-                initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","ia64Linux2","dssp-2")
-                os.environ['DSSP_BIN'] = initialdir_dssp
-            elif sys.platform.startswith('win'):
-                initialdir_dssp = os.path.join(os.environ['PYMOL_GIT_MOD'],"DSSP","win32","dssp.exe")
-                os.environ['DSSP_BIN'] = initialdir_dssp
-            else:
-                pass
-        if 'DSSP_BIN' in os.environ:
-            if VERBOSE: print 'Found DSSP_BIN in environmental variables', os.environ['DSSP_BIN']
-            self.dssp_bin.set(os.environ['DSSP_BIN'])
-        else:
-            if VERBOSE: print 'DSSP_BIN not found in environmental variables.'
-            self.dssp_bin.set('')
-        if 'STRIDE_BIN' not in os.environ and 'PYMOL_GIT_MOD' in os.environ:
-            if sys.platform.startswith('linux') and platform.machine() == 'x86_32':
-                initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","i86Linux2","stride")
-                os.environ['STRIDE_BIN'] = initialdir_stride
-            elif sys.platform.startswith('linux') and platform.machine() == 'x86_64':
-                initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","ia64Linux2","stride")
-                os.environ['STRIDE_BIN'] = initialdir_stride
-            elif sys.platform.startswith('win'):
-                initialdir_stride = os.path.join(os.environ['PYMOL_GIT_MOD'],"Stride","win32","stride.exe")
-                os.environ['STRIDE_BIN'] = initialdir_stride
-            else:
-                pass
-        if 'STRIDE_BIN' in os.environ:
-            if VERBOSE: print 'Found STRIDE_BIN in environmental variables', os.environ['STRIDE_BIN']
-            self.stride_bin.set(os.environ['STRIDE_BIN'])
-        else:
-            if VERBOSE: print 'STRIDE_BIN not found in environmental variables.'
-            self.stride_bin.set('')
-        
-        # DSSP visualization color
-        # - H        Alpha helix (4-12) 
-        # - G        3-10 helix 
-        # - I        pi helix
-        #
-        # - E        Extended strand 
-        # - B        Isolated beta-bridge residue 
-        #
-        # - T        Turn 
-        # - S        Bend 
-        # - -        None
-        # STRIDE does not have S and None, but it has two more
-        # codes: 'b' same as 'B' and 'C' for coil
-        self.DSSP_SSE_list =   ['H','G','I', 'E','B','T','S','-'] # for the record of the order
-        self.STRIDE_SSE_list = ['H','G','I', 'E','B','b','T','C'] # for the record of the order
-        self.SSE_map = {'H':'H',
-                        'G':'H',
-                        'I':'H',
-                        'E':'S',
-                        'B':'S',
-                        'T':'L',
-                        'S':'L',
-                        '-':'L',
-
-                        'b':'S',
-                        'C':'L'
-                        }
-        self.SSE_name = {
-            'H'  :  'Alpha helix', 
-            'G'  :  '3-10 helix', 
-            'I'  :  'Pi helix', 
-                     
-            'E'  :  'Extended strand',
-            'B'  :  'Isolated beta-bridge',
-                     
-            'T'  :  'Turn', 
-            'S'  :  'Bend', 
-            '-'  :  'None',
-
-            'b'  :  'Isolated beta-bridge',
-            'C'  :  'Coil'
-            }
-
-        self.SSE_col_RGB = {
-            'H':(255,  0,  0),
-            'G':(255,  0,128),
-            'I':(255,170,170),
-
-            'E':(255,255,  0),
-            'B':(153,119, 85),
-            
-            'T':(  0,255,255),
-            'S':(153,255,119),
-            '-':(179,179,179),
-
-            'b':(153,119, 85), # same as 'B'
-            'C':(  0,  0,255)
-            }
-        self.SSE_col = {}
-        for sse in self.SSE_col_RGB.keys():
-            self.SSE_col[sse] = '#%s%s%s' % (hex(self.SSE_col_RGB[sse][0])[2:].zfill(2),
-                                             hex(self.SSE_col_RGB[sse][1])[2:].zfill(2),
-                                             hex(self.SSE_col_RGB[sse][2])[2:].zfill(2))
-
-        self.SSE_res_dict = {}
-        self.SSE_sel_dict = {}
-        
-        w = Tkinter.Label(self.dialog.interior(),
-#                          text = '\nDSSP Plugin for PyMOL\nHongbo Zhu, 2011.\n\nColor proteins according to the secondary structure determined by DSSP.',
-                          text = '\nDSSP and Stride Plugin for PyMOL\nby Hongbo Zhu, 2011\n',
-                          background = 'black', foreground = 'green'
-                          )
-        w.pack(expand = 1, fill = 'both', padx = 10, pady = 5)
-
-        # make a few tabs within the dialog
-        self.notebook = Pmw.NoteBook(self.dialog.interior())
-        self.notebook.pack(fill = 'both', expand=1, padx=10, pady=10)
-
-
-        ######################
-        # Tab : Structure Tab
-        ######################
-        page = self.notebook.add('Structure')       
-        self.notebook.tab('Structure').focus_set()
-        group_struc = Tkinter.LabelFrame(page, text = 'Structure')
-        group_struc.pack(fill='both', expand=True, padx=10, pady=5)
-
-        pymol_sel_ent = Pmw.EntryField(group_struc,
-                                       label_text='PyMOL selection/object:',
-                                       labelpos='wn',
-                                       entry_textvariable=self.pymol_sel
-                                       )
-
-        dssp_bin_ent = Pmw.EntryField(group_struc,
-                                      label_text='DSSP binary:', labelpos='wn',
-                                      entry_textvariable=self.dssp_bin,
-                                      entry_width=20)
-        dssp_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
-                                      command = self.getDSSPBin)
-        
-        stride_bin_ent = Pmw.EntryField(group_struc,
-                                      label_text='Stride binary:', labelpos='wn',
-                                      entry_textvariable=self.stride_bin,
-                                      entry_width=20)
-        stride_bin_but = Tkinter.Button(group_struc, text = 'Browse...',
-                                      command = self.getStrideBin)
-
-        # arrange widgets using grid
-        pymol_sel_ent.grid(sticky='we', row=0, column=0,
-                           columnspan=2, padx=5, pady=5)
-        dssp_bin_ent.grid(sticky='we', row=1, column=0, padx=5, pady=1)
-        dssp_bin_but.grid(sticky='we', row=1, column=1, padx=5, pady=1)
-        stride_bin_ent.grid(sticky='we', row=2, column=0, padx=5, pady=1)
-        stride_bin_but.grid(sticky='we', row=2, column=1, padx=5, pady=1)
-        group_struc.columnconfigure(0, weight=9)
-        group_struc.columnconfigure(1, weight=1)
-
-
-        ######################
-        # Tab : Color Tab
-        ######################
-        # H = alpha helix
-        # G = 3-helix (3/10 helix)
-        # I = 5 helix (pi helix)
-
-        # E = extended strand, participates in beta ladder
-        # B = residue in isolated beta-bridge
-
-        # T = hydrogen bonded turn
-        # S = bend
-        # 
-        #  H        Alpha helix (4-12) 
-        #  G        3-10 helix 
-        #  I        pi helix 
-        #  E        Strand 
-        #  B        Isolated beta-bridge residue 
-        #  T        Turn 
-        #  S        Bend 
-        #  -        None 
-        
-        page = self.notebook.add('Color')
-        
-        group_sse_color = Tkinter.LabelFrame(page, text = 'Secondary Structure Element Color')
-        group_sse_color.grid(sticky='eswn', row=0, column=0, padx=10, pady=5)
-
-        # colors for DSSP surface
-        H_col_lab = Tkinter.Label(group_sse_color, text='Alpha helix (H):')
-        self.H_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['H'],
-                                        activebackground=self.SSE_col['H'],
-                                        command = self.custermizeHColor)
-        G_col_lab = Tkinter.Label(group_sse_color, text='3-10 helix (G):')
-        self.G_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['G'],
-                                        activebackground=self.SSE_col['G'],
-                                        command = self.custermizeGColor)
-        I_col_lab = Tkinter.Label(group_sse_color, text='PI helix (I):')
-        self.I_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['I'],
-                                        activebackground=self.SSE_col['G'],
-                                        command = self.custermizeIColor)
-
-
-        E_col_lab = Tkinter.Label(group_sse_color, text='Extended strand (E):')
-        self.E_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['E'],
-                                        activebackground=self.SSE_col['E'],
-                                        command = self.custermizeEColor)
-        B_col_lab = Tkinter.Label(group_sse_color, text='Isolated beta-bridge (B):')
-        self.B_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['B'],
-                                        activebackground=self.SSE_col['B'],
-                                        command = self.custermizeBColor)
-
-        T_col_lab = Tkinter.Label(group_sse_color, text='Turn (T):')
-        self.T_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['T'],
-                                        activebackground=self.SSE_col['T'],
-                                        command = self.custermizeTColor)
-        S_col_lab = Tkinter.Label(group_sse_color, text='Bend (DSSP S):')
-        self.S_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['S'],
-                                        activebackground=self.SSE_col['S'],
-                                        command = self.custermizeSColor)
-        N_col_lab = Tkinter.Label(group_sse_color, text='None (DSSP NA):')
-        self.N_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['-'],
-                                        activebackground=self.SSE_col['-'],
-                                        command = self.custermizeNColor)
-         
-
-        b_col_lab = Tkinter.Label(group_sse_color, text='Isolated beta-bridge (Stride b):')
-        self.b_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['b'],
-                                        activebackground=self.SSE_col['b'],
-                                        command = self.custermizebColor)
-
-        C_col_lab = Tkinter.Label(group_sse_color, text='Coil (Stride C):')
-        self.C_col_but = Tkinter.Button(group_sse_color,
-                                        bg=self.SSE_col['C'],
-                                        activebackground=self.SSE_col['C'],
-                                        command = self.custermizeCColor)
-
-
-
-        H_col_lab.grid(sticky='e', row=0, column=0, padx=5, pady=3)
-        self.H_col_but.grid(sticky='we', row=0, column=1, padx=5, pady=3)
-        G_col_lab.grid(sticky='e', row=1, column=0, padx=5, pady=3)
-        self.G_col_but.grid(sticky='we', row=1, column=1, padx=5, pady=3)
-        I_col_lab.grid(sticky='e', row=2, column=0, padx=5, pady=3)
-        self.I_col_but.grid(sticky='we', row=2, column=1, padx=5, pady=3)
-
-        E_col_lab.grid(sticky='e', row=0, column=2, padx=5, pady=3)
-        self.E_col_but.grid(sticky='we', row=0, column=3, padx=5, pady=3)
-        B_col_lab.grid(sticky='e', row=1, column=2, padx=5, pady=3)
-        self.B_col_but.grid(sticky='we', row=1, column=3, padx=5, pady=3)
-
-        T_col_lab.grid(sticky='e', row=0, column=4, padx=5, pady=3)
-        self.T_col_but.grid(sticky='we', row=0, column=5, padx=5, pady=3)
-        S_col_lab.grid(sticky='e', row=1, column=4, padx=5, pady=3)
-        self.S_col_but.grid(sticky='we', row=1, column=5, padx=5, pady=3)
-        N_col_lab.grid(sticky='e', row=2, column=4, padx=5, pady=3)
-        self.N_col_but.grid(sticky='we', row=2, column=5, padx=5, pady=3)
-
-        b_col_lab.grid(sticky='e', row=2, column=2, padx=5, pady=3)
-        self.b_col_but.grid(sticky='we', row=2, column=3, padx=5, pady=3)
-
-        C_col_lab.grid(sticky='e', row=3, column=4, padx=5, pady=3)
-        self.C_col_but.grid(sticky='we', row=3, column=5, padx=5, pady=3)
-        ######################
-        # Tab : About Tab
-        ######################
-        page = self.notebook.add('About')
-        group_about = Tkinter.LabelFrame(page, text = 'About DSSP and Stride Plugin for PyMOL')
-        group_about.grid(sticky='we', row=0,column=0,padx=5,pady=3)
-        about_plugin = """ Assign and color secondary structures using DSSP or Stride.
-by Hongbo Zhu <hongbo.zhu.cn .at. googlemail.com>
-Please cite this plugin if you use it in a publication.
-Hongbo Zhu. DSSP and Stride plugin for PyMOL, 2011, BIOTEC, TU Dresden.
-"""
-        
-        label_about = Tkinter.Label(group_about,text=about_plugin)
-        label_about.grid(sticky='we', row=0, column=0, padx=5, pady=10)
-        
-        self.notebook.setnaturalsize()    
-
-        return
-
-
-    def getDSSPBin(self):
-        dssp_bin_fname = tkFileDialog.askopenfilename(
-            title='DSSP Binary', initialdir='',
-            filetypes=[('all','*')], parent=self.parent)
-        if dssp_bin_fname: # if nonempty
-            self.dssp_bin.set(dssp_bin_fname)
-        return
-    
-    def getStrideBin(self):
-        stride_bin_fname = tkFileDialog.askopenfilename(
-            title='Stride Binary', initialdir='',
-            filetypes=[('all','*')], parent=self.parent)
-        if stride_bin_fname: # if nonempty
-            self.stride_bin.set(stride_bin_fname)
-        return
-
-    def runDSSPOneObj(self, one_obj_sel):
-        """ Run DSSP on only one object.
-        
-            @param one_obj_sel: the selection/object involving only one object
-            @param type: string
-        """
-        SSE_res = {
-            'H':{}, 'G':{}, 'I':{},
-            'E':{}, 'B':{},
-            'T':{}, 'S':{}, '-':{}
-            }
-        SSE_sel = {
-            'H':None, 'G':None, 'I':None,
-            'E':None, 'B':None,
-            'T':None, 'S':None, '-':None
-            }
-        
-        pdb_fn = None
-        pdb_os_fh, pdb_fn = tempfile.mkstemp(suffix='.pdb') # file os handle, file name
-        os.close(pdb_os_fh)
-        # DSSP 2.0.4 ignores all residues after 1st TER in the same chain
-        v = cmd.get(name='pdb_use_ter_records') 
-        if v: cmd.set(name='pdb_use_ter_records', value=0) # do not insert TER into the pdb 
-        cmd.save(filename=pdb_fn, selection=one_obj_sel)
-        if v: cmd.set(name='pdb_use_ter_records', value=v) # restore old value
-
-        if VERBOSE:
-            print 'Selection %s saved to %s.' % (one_obj_sel, pdb_fn)
-
-        if pdb_fn is None:
-            print 'WARNING: DSSP has no pdb file to work on!'
-            return None
-
-        print 'Running DSSP for %s ...' % (one_obj_sel,)
-        dssp_sse_dict = {}
-        if sys.version_info >= (2,4):
-            dssp_proc = subprocess.Popen([self.dssp_bin.get(), pdb_fn],
-                                         stdout=subprocess.PIPE,
-                                         stderr=subprocess.STDOUT)
-            dssp_stdout, dssp_stderr = dssp_proc.communicate()
-        else: # use os.system + tempfile
-            dssp_tmpout_os_fh, dssp_tmpout_fn = tempfile.mkstemp(suffix='.dssp')
-            os.close(dssp_tmpout_os_fh)
-            dssp_cmd = '%s %s > %s' % (self.dssp_bin.get(), pdb_fn, dssp_tmpout_fn)
-            os.system(dssp_cmd)
-            fh = open(dssp_tmpout_fn)
-            dssp_stdout = ''.join(fh.readlines())
-            fh.close()           
-
-        sse_started = False
-        for line in dssp_stdout.splitlines():
-            if line.startswith('  #  RESIDUE'):
-                sse_started = True
-                continue
-            elif line.startswith(' !!!'):
-                sse_started = False
-                continue
-            elif sse_started:
-                if len(line) < 10 or line[9] == ' ': continue
-                ch,resname = line[11],line[13]
-                residen,sscode = line[5:11].strip(),line[16] # residen = resnum+icode, col 10 is for icode
-                if sscode == ' ': sscode = '-'
-                k = (ch,resname,residen)
-                dssp_sse_dict[k] = sscode
-
-        self.dssp_rlt_dict[one_obj_sel] = dssp_sse_dict
-        print 'Got SSE for %d residues.' % (len(self.dssp_rlt_dict[one_obj_sel]),)
-
-        # group residues according to their SSE, and chain name
-        for k in self.dssp_rlt_dict[one_obj_sel].keys():
-            #res = '/%s//%s/%d%s/' % (sel,k[0],k[1][1], k[1][2].strip()) # sel name, chain ID, res serial num, icode
-            sse = self.dssp_rlt_dict[one_obj_sel][k]
-            chn = k[0]
-            res = k[2]
-            if VERBOSE: print '(%s) and \"%s\"/%s/  sse=%s' % (str(one_obj_sel),
-                                                               chn.strip(), res, sse)
-            SSE_res[sse].setdefault(chn,[]).append(res)
-            
-        self.SSE_res_dict[one_obj_sel] = SSE_res
-
-        for sse in self.DSSP_SSE_list:
-            sse_sel_name = self.selectSSE(one_obj_sel, sse)
-            SSE_sel[sse] = sse_sel_name
-
-        self.SSE_sel_dict[one_obj_sel] = SSE_sel
-
-        print '\nNumber of residues with SSE element:'
-        for sse in self.DSSP_SSE_list:
-            num = sum([len(SSE_res[sse][chn]) for chn in SSE_res[sse]])
-            print '%20s (%s) : %5d' % (self.SSE_name[sse], sse, num)
-        print
-
-        # clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
-        if os.path.isfile(pdb_fn):
-            os.remove(pdb_fn)
-        if sys.version_info < (2,4) and os.path.isfile(dssp_tmpout_fn):
-            os.remove(dssp_tmpout_fn)
-
-        return
-
-
-    def runDSSP(self):
-        """
-            @return: whether DSSP has been executed successfully
-            @rtype: boolean
-        """
-        # delete old results
-        self.sel_obj_list  = [] 
-        self.dssp_rlt_dict = {}
-        self.SSE_res_dict  = {}
-        self.SSE_sel_dict  = {}
-        
-        pdb_fn = None
-        sel_name= None
-        sel = self.pymol_sel.get()
-        
-        if len(sel) > 0: # if any pymol selection/object is specified
-            # save the pymol selection/object in the tmp dir
-            all_sel_names = cmd.get_names('all') # get names of all selections            
-            if sel in all_sel_names:
-                if cmd.count_atoms(sel) == 0:
-                    err_msg = 'ERROR: The selection %s is empty.' % (sel,)
-                    print 'ERROR: %s' % (err_msg,)
-                    tkMessageBox.showinfo(title='ERROR', message=err_msg)
-                    return False
-                else:
-                    sel_name = sel
-            # no selection/object with the input name is found
-            # we assume either a single-word selector or
-            # some other selection-expression is used
-            # NOTE: if more than one selection is selected, they should be 
-            #       saved separately and SSE should be calculated for each 
-            #       of the selections.
-            else:
-                print 'The selection/object you specified is not found.'
-                print 'Your input will be interpreted as a selection-expression.'
-                # check whether the selection is empty
-                tmpsel = self.randomSeleName(prefix='your_sele_')
-                cmd.select(tmpsel,sel)
-                if cmd.count_atoms(tmpsel) == 0:
-                    cmd.delete(tmpsel)
-                    err_msg = 'ERROR: The selection %s is empty.' % (sel,)
-                    print 'ERROR: %s' % (err_msg,)
-                    tkMessageBox.showinfo(title='ERROR', message=err_msg)
-                    return False
-                else:
-                    sel_name = tmpsel
-        else:   # what structure do you want DSSP to work on?
-            err_msg = 'No PyMOL selection/object specified!'
-            print 'ERROR: %s' % (err_msg,)
-            tkMessageBox.showinfo(title='ERROR', message=err_msg)
-            return False
-
-        # each object in the selection is treated as an independent struc
-        objlist = cmd.get_object_list(sel_name)
-        self.ss_asgn_prog = 'DSSP'
-        print 'Starting %s ...' % (self.ss_asgn_prog, )
-
-        for objname in objlist:
-            self.sel_obj_list.append('%s and %s' % (sel_name, objname))
-            self.runDSSPOneObj(self.sel_obj_list[-1])
-
-##        cmd.delete(tmpsel)
-
-        return True
-
-
-    def runStrideOneObj(self, one_obj_sel):
-        """ Run Stride on only one object.
-        
-            @param one_obj_sel: the selection/object involving only one object
-            @param type: string
-        """
-        SSE_res = {
-            'H':{}, 'G':{}, 'I':{},
-            'E':{}, 'B':{}, 'b':{},
-            'T':{}, 'C':{}
-            }
-        SSE_sel = {
-            'H':None, 'G':None, 'I':None,
-            'E':None, 'B':None, 'b':None,
-            'T':None, 'C':None
-            }
-        
-        pdb_fn = None
-        pdb_os_fh, pdb_fn = tempfile.mkstemp(suffix='.pdb') # file os handle, file name
-        os.close(pdb_os_fh)
-        cmd.save(filename=pdb_fn, selection=one_obj_sel)
-        if VERBOSE:
-            print 'Selection %s saved to %s.' % (one_obj_sel, pdb_fn)
-
-        if pdb_fn is None:
-            print 'WARNING: Stride has no pdb file to work on!'
-            return None
-        
-        print 'Running Stride for %s ...' % (one_obj_sel,)        
-        stride_sse_dict = {}
-        if sys.version_info >= (2,4):
-            stride_proc = subprocess.Popen([self.stride_bin.get(), pdb_fn],
-                                           stdout=subprocess.PIPE,
-                                           stderr=subprocess.STDOUT
-                                           )
-            stride_stdout, stride_stderr = stride_proc.communicate()
-        else: # use os.system + tempfile
-            stride_tmpout_os_fh, stride_tmpout_fn = tempfile.mkstemp(suffix='.stride')
-            os.close(stride_tmpout_os_fh)
-            stride_cmd = '%s %s > %s' % (self.stride_bin.get(), pdb_fn, stride_tmpout_fn)
-            os.system(stride_cmd)
-            fh = open(stride_tmpout_fn)
-            stride_stdout = ''.join(fh.readlines())
-            fh.close()
-
-        for line in stride_stdout.splitlines():
-            if line.startswith('ASG'):
-                resname,ch=line[5:8], line[9]
-                # according to stride doc, col 12-15 are used for residue number
-                # actually, resnum+icode is used in 12-15.
-                # In addition, if residue number is 4-digit or longer,
-                # the field 12-16 or more are used. 
-
-                if line[15] == ' ': # col 16 is not occupied
-                    residen, sscode = line[11:15].strip(),line[24] # residen = resnum+icode
-                else:
-                    shift = line[15:].find(' ') # find where residen stops
-                    residen, sscode = line[11:15+shift].strip(),line[24+shift]
-
-                k = (ch,resname,residen)
-                stride_sse_dict[k] = sscode
-
-        self.stride_rlt_dict[one_obj_sel] = stride_sse_dict
-        print 'Got SSE for %d residues.' % (len(self.stride_rlt_dict[one_obj_sel]),)
-
-        # group residues according to their SSE, and chain name
-        for k in self.stride_rlt_dict[one_obj_sel].keys():
-            sse=self.stride_rlt_dict[one_obj_sel][k]
-            chn = k[0] # this can be a space!
-            res = k[2]
-            if VERBOSE: print '(%s) and \"%s\"/%s/  sse=%s' % (str(one_obj_sel),
-                                                               chn.strip(), res, sse)
-            SSE_res[sse].setdefault(chn,[]).append(res)
-
-        self.SSE_res_dict[one_obj_sel] = SSE_res
-
-        for sse in self.STRIDE_SSE_list:
-            sse_sel_name = self.selectSSE(one_obj_sel, sse)
-            SSE_sel[sse] = sse_sel_name
-        self.SSE_sel_dict[one_obj_sel] = SSE_sel
-        
-        print '\nNumber of residues with SSE element:'
-        for sse in self.STRIDE_SSE_list:
-            num = sum([len(SSE_res[sse][chn]) for chn in SSE_res[sse]])
-            print '%20s (%s) : %5d' % (self.SSE_name[sse], sse, num)
-        print
-        
-        # clean up pdb_fn and dssp_tmpout_fn created by tempfile.mkstemp()
-        if os.path.isfile(pdb_fn):
-            os.remove(pdb_fn)
-        if sys.version_info < (2,4) and os.path.isfile(stride_tmpout_fn):
-            os.remove(stride_tmpout_fn)        
-        
-        return True
-    
-
-    def runStride(self):
-        """
-        """
-        # delete old results
-        self.sel_obj_list = [] 
-        self.stride_rlt_dict = {}
-        self.SSE_res_dict = {}
-        self.SSE_sel_dict = {}
-
-        pdb_fn = None
-        sel_name= None
-        sel = self.pymol_sel.get()
-        
-        if len(sel) > 0: # if any pymol selection/object is specified
-            all_sel_names = cmd.get_names('all') # get names of all selections            
-            if sel in all_sel_names:
-                if cmd.count_atoms(sel) == 0:
-                    err_msg = 'ERROR: The selection %s is empty.' % (sel,)
-                    print 'ERROR: %s' % (err_msg,)
-                    tkMessageBox.showinfo(title='ERROR', message=err_msg)
-                    return False
-                else:
-                    sel_name = sel
-            # no selection/object with the input name is found
-            # we assume either a single-word selector or
-            # some other selection-expression is uesd
-            else:
-                print 'The selection/object you specified is not found.'
-                print 'Your input will be interpreted as a selection-expression.'
-                tmpsel = self.randomSeleName(prefix='your_sele_')
-                cmd.select(tmpsel,sel)
-                if cmd.count_atoms(tmpsel) == 0:
-                    cmd.delete(tmpsel)
-                    err_msg = 'ERROR: The selection %s is empty.' % (sel,)
-                    print 'ERROR: %s' % (err_msg,)
-                    tkMessageBox.showinfo(title='ERROR', message=err_msg)
-                    return False
-                else:
-                    sel_name = tmpsel
-                
-        else:   # what structure do you want Stride to work on?
-            err_msg = 'No PyMOL selection/object specified!'
-            print 'ERROR: %s' % (err_msg,)
-            tkMessageBox.showinfo(title='ERROR', message=err_msg)
-            return False
-        
-        # each object in the selection is treated as an independent struc
-        objlist = cmd.get_object_list(sel_name)
-        self.ss_asgn_prog = 'Stride'
-        print 'Starting %s ...' % (self.ss_asgn_prog, )
-
-        for objname in objlist:
-            self.sel_obj_list.append('%s and %s' % (sel_name, objname))
-            self.runStrideOneObj(self.sel_obj_list[-1])
-
-        return True
-
-
-    def randomSeleName(self, prefix='sele',suffix=''):
-        """ generate a random selection name.
-        """
-        sel_list = cmd.get_names('all')
-        sel_dict = dict(zip(sel_list, range(len(sel_list))))
-        sel_name = '%s%d%s' % (prefix, random.randint(1000,9999), suffix)
-        while(sel_name in sel_dict):
-            sel_name = '%s%d%s' % (prefix, random.randint(1000,9999), suffix)
-            
-        return sel_name
-        
-
-    def selectSSE(self, sel, sse):
-        """ generate selector for selecting all residues having the given sse.
-            return the selection name.
-        """
-        #sel = self.pymol_sel.get()
-        sel_list_chn = []
-
-        if VERBOSE: print '\nSelecting SSE %s ... \n' % (sse)
-        
-        for chn in self.SSE_res_dict[sel][sse]: # color one chain at a time
-            if chn == ' ': chn_str = '-'
-            else: chn_str = chn
-            if VERBOSE: print 'Selecting SSE %s on chain %s ... \n' % (sse, chn)
-            limit=150  # color every 150 residues
-            sel_name_chn = self.randomSeleName(prefix='%s_%s_%s_' % ('_'.join(sel.split()),chn_str,sse))
-                
-            if len(self.SSE_res_dict[sel][sse][chn]) < limit:
-                #sel_expr = '/%s//%s/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res[sse][chn]))
-                # always quote chain name in case it is empty (otherwise sel misinterpreted)
-                sel_expr = '(%s) and \"%s\"/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res_dict[sel][sse][chn]))
-                cmd.select(sel_name_chn, sel_expr)
-                if VERBOSE: print 'select %s, %s' % (sel_name_chn, sel_expr)
-                sel_list_chn.append(sel_name_chn)
-            else:
-                rn = len(self.SSE_res_dict[sel][sse][chn])
-                print 'total number of res with %s = %d' % (sse,rn)
-                sz = int(math.ceil(rn/float(limit)))
-                sel_list_seg = []
-                for i in xrange(sz):
-                    s,e = i*limit, min((i+1)*limit, rn)
-                    print s,e
-                    #sel_expr = '/%s//%s/%s/' % (sel,chn.strip(), '+'.join(self.SSE_res[sse][chn][s:e]))
-                    # always quote chain name in case it is empty (otherwise sel misinterpreted)
-                    sel_expr = '(%s) and \"%s\"/%s/' % (sel, chn.strip(),
-                                                        '+'.join(self.SSE_res_dict[sel][sse][chn][s:e]))
-                    sel_name_seg =  self.randomSeleName(prefix='%s_%s_%s_tmp_' % ('_'.join(sel.split()),chn_str,sse))
-                    cmd.select(sel_name_seg, sel_expr)
-                    if VERBOSE: print 'select %s, %s' % (sel_name_seg, sel_expr)
-                    sel_list_seg.append(sel_name_seg)
-                    
-                sel_expr = ' or '.join(sel_list_seg)
-                cmd.select(sel_name_chn, sel_expr)
-                if VERBOSE: print 'select %s, %s' % (sel_name_chn, sel_expr)
-                [cmd.delete(asel) for asel in sel_list_seg]
-                sel_list_chn.append(sel_name_chn)
-
-        if len(sel_list_chn) > 0:
-            sel_name = self.randomSeleName(prefix='%s_%s_%s_' % ('_'.join(sel.split()), sse, self.ss_asgn_prog))
-            sel_expr = ' or '.join(sel_list_chn)
-            cmd.select(sel_name,sel_expr)
-            [cmd.delete(asel) for asel in sel_list_chn]
-        else:
-            print 'INFO: No residues are assigned to SSE \'%s\'.' % (sse,)
-            sel_name = None
-        
-        return sel_name
-
-
-    def updateColor(self):
-        if self.ss_asgn_prog is None:
-            err_msg = 'Run DSSP or Stride to assign secondary structures first!'
-            print 'ERROR: %s' % (err_msg,)
-            tkMessageBox.showinfo(title='ERROR', message=err_msg)
-        else:
-            print 'Update color for %s' % (self.pymol_sel.get()),
-            print 'using secondary structure assignment by %s' % (self.ss_asgn_prog,)
-
-            if self.ss_asgn_prog == 'DSSP':     SSE_list = self.DSSP_SSE_list
-            elif self.ss_asgn_prog == 'Stride': SSE_list = self.STRIDE_SSE_list
-
-            for sse in SSE_list: # give color names
-                cmd.set_color('%s_color'%(sse,), self.SSE_col_RGB[sse])
-            for sse in SSE_list: # color each SSE
-                for sel_obj in self.sel_obj_list:
-                    if self.SSE_sel_dict[sel_obj][sse] is not None:
-                        cmd.color('%s_color'%(sse,), self.SSE_sel_dict[sel_obj][sse])
-                        print 'color',self.SSE_sel_dict[sel_obj][sse],',',self.SSE_col_RGB[sse]
-                    else:
-                        print 'No residues with SSE \'%s\' to color.' % (sse,)
-
-        return
-    
-    def updateSS(self):
-        if self.ss_asgn_prog is None:
-            err_msg = 'Run DSSP or Stride to assign secondary structures first!'
-            print 'ERROR: %s' % (err_msg,)
-            tkMessageBox.showinfo(title='ERROR', message=err_msg)
-        else:
-            print 'Update secondary structures for %s' % (self.pymol_sel.get()),
-            print 'using secondary structure assignment by %s' % (self.ss_asgn_prog,)
-            print 'SSE mapping: (H,G,I) ==> H; (E,B,b) ==> S; (T,S,-,C) ==> L'
-
-            if self.ss_asgn_prog == 'DSSP':     SSE_list = self.DSSP_SSE_list
-            elif self.ss_asgn_prog == 'Stride': SSE_list = self.STRIDE_SSE_list
-
-            for sse in SSE_list:
-                for sel_obj in self.sel_obj_list:
-                    if self.SSE_sel_dict[sel_obj][sse] is not None:
-                        cmd.alter(self.SSE_sel_dict[sel_obj][sse], 'ss=\'%s\''% (self.SSE_map[sse],))
-                        print 'alter %s, ss=%s' % (self.SSE_sel_dict[sel_obj][sse], self.SSE_map[sse])
-                    else:
-                        print 'No residue with SSE %s to update ss.' % (sse,)
-
-            # show cartoon for the input selection, and rebuild
-            cmd.show('cartoon',self.pymol_sel.get())
-            cmd.rebuild(self.pymol_sel.get()) 
-            return
-    
-
-    def custermizeHColor(self):
-        self.custermizeSSEColor('H')
-    def custermizeGColor(self):
-        self.custermizeSSEColor('G')
-    def custermizeIColor(self):
-        self.custermizeSSEColor('I')
-
-    def custermizeEColor(self):
-        self.custermizeSSEColor('E')
-    def custermizeBColor(self):
-        self.custermizeSSEColor('B')
-
-    def custermizeTColor(self):
-        self.custermizeSSEColor('T')
-    def custermizeSColor(self):
-        self.custermizeSSEColor('S')
-    def custermizeNColor(self):
-        self.custermizeSSEColor('-')
-
-    def custermizebColor(self):
-        self.custermizeSSEColor('b')
-    def custermizeCColor(self):
-        self.custermizeSSEColor('C')
-
-    def custermizeSSEColor(self,sse):
-        SSE_col_but = {
-            'H':self.H_col_but,
-            'G':self.G_col_but,
-            'I':self.I_col_but,
-
-            'E':self.E_col_but,
-            'B':self.B_col_but,
-            
-            'T':self.T_col_but,
-            'S':self.S_col_but,
-            '-':self.N_col_but,
-            
-            'b':self.b_col_but,
-            'C':self.C_col_but,
-            }
-        try:
-            color_tuple, color = tkColorChooser.askcolor(color=self.SSE_col[sse])
-            if color_tuple is not None and color is not None:
-                self.SSE_col_RGB[sse] = color_tuple
-                self.SSE_col[sse] = color
-                
-                SSE_col_but[sse]['bg']=self.SSE_col[sse]
-                SSE_col_but[sse]['activebackground']=self.SSE_col[sse]
-                SSE_col_but[sse].update()
-        except Tkinter._tkinter.TclError:
-            print 'Old color (%s) will be used.' % (self.mesh_col)
-            
-        
-    def execute(self, butcmd):
-        """ Run the cmd represented by the botton clicked by user.
-        """        
-        if butcmd == 'OK':
-            print 'is everything OK?'
-            
-        elif butcmd == 'Run DSSP':
-            rtn = self.runDSSP()
-            if rtn and VERBOSE: print 'Done with DSSP!'
-            
-        elif butcmd == 'Run Stride':
-            rtn = self.runStride()
-            if rtn and VERBOSE:     print 'Done with Stride!'
-
-        elif butcmd == 'Update Color':
-            self.updateColor()
-            
-        elif butcmd == 'Update ss':
-            self.updateSS()
-
-        elif butcmd == 'Exit':
-            print 'Exiting DSSP and Stride Plugin ...'
-            if __name__ == '__main__':
-                self.parent.destroy()
-            else:
-                self.dialog.withdraw()
-            print 'Done.'
-        else:
-            print 'Exiting DSSP and Stride Plugin because of unknown button click ...'
-            self.dialog.withdraw()
-            print 'Done.'
-            
-    
-    def quit(self):
-        self.dialog.destroy() 
-
-
-#############################################
-#
-#
-# Create demo in root window for testing.
-#
-#
-##############################################
-if __name__ == '__main__':
-    
-    class App:
-        def my_show(self,*args,**kwargs):
-            pass
-
-    app = App()
-    app.root = Tkinter.Tk()
-    Pmw.initialise(app.root)   
-    app.root.title('It seems to work!')
-
-    widget = DSSPPlugin(app)
-    app.root.mainloop()

profiles/pymol/.pymol/startup/propka.py

@@ -1,887 +0,0 @@
-'''
-Described at PyMOL wiki:
-http://www.pymolwiki.org/index.php/propka
-
-#-------------------------------------------------------------------------------
-# Name:		propka for pymol
-# Purpose:	To fetch and display the pka values for protein of intetest
-#
-# Author:	Troels E. Linnet
-#
-# Created:	14/08/2011
-# Copyright:	(c) Troels E. Linnet 2011
-# Contact:	tlinnet snabela gmail dot com
-# Licence:	Free for all
-#
-#
-#-------------------------------------------------------------------------------
-
-	    The PROPKA method is developed by the
-		  Jensen Research Group
-		 Department of Chemistry
-		University of Copenhagen
-
-	Please cite these references in publications:
-Hui Li, Andrew D. Robertson, and Jan H. Jensen
-"Very Fast Empirical Prediction and Interpretation of Protein pKa Values"
-Proteins, 2005, 61, 704-721.
-
-Delphine C. Bas, David M. Rogers, and Jan H. Jensen
-"Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes"
-Proteins, 2008, 73, 765-783.
-
-Mats H.M. Olsson, Chresten R. Soendergard, Michal Rostkowski, and Jan H. Jensen
-"PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions"
-Journal of Chemical Theory and Computation, 2011 7 (2), 525-537
-
-Chresten R. Soendergaard, Mats H.M. Olsson, Michaz Rostkowski, and Jan H. Jensen
-"Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values"
-Journal of Chemical Theory and Computation, 2011 in press
-"""
-#-------------------------------------------------------------------------------
-# The script needs mechanize to run.
-# On windows, it is not easy to make additional modules available for pymol. So put in into your working folder.
-#1)The easy manual way:
-#a)Go to: http://wwwsearch.sourceforge.net/mechanize/download.html
-#b)Download mechanize-0.2.5.zip. http://pypi.python.org/packages/source/m/mechanize/mechanize-0.2.5.zip
-#c)Extract to .\mechanize-0.2.5 then move the in-side folder "mechanize" to your folder with propka.py. The rest of .\mechanize-0.2.5 you don't need.
-#You can also see other places where you could put the "mechanize" folder. Write this in pymol to see the paths where pymol is searching for "mechanize"
-# import sys; print(sys.path)
-
-#-------------------------------------------------------------------------------
-"""
-Example for pymol script to start the functions. For example: trypropka.pml
-Execute with pymol or start pymol and: File->Run->trypropka.pml
-##############################################################################################################################################################################################################################
-
-### Point to your directory with your pdb file and where to save the results
-#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/propka
-cd C:/Users/tlinnet/Documents/My Dropbox/Speciale/5NT-project/Mutant-construct/predict_reactivity/propka
-
-### The fastest method is just to write propka. Then the last pymol molecule is assumed and send to server. verbose=yes makes the script gossip mode.
-import propka
-
-fetch 4ins, async=0
-propka
-#fetch 1hp1, async=0
-#propka logtime=_, resi=5-10.20-30, resn=CYS.ATP.TRP, verbose=yes
-
-### Fetch 4ins from web. async make sure, we dont execute script before molecule is loaded. The resi and resn prints the interesting results right to command line.
-#fetch 4ins, async=0
-#propka chain=*, resi=5-10.20-30, resn=ASP.CYS, logtime=_
-
-### If there is no web connection, one can process a local .pka file. Either from a previous run or from a downloaded propka webpage result.
-### Then run and point to .pka file with: pkafile=./Results_propka/pkafile.pka Remember the dot "." in the start, to make it start in the current directory.
-#load 4ins.pdb
-#propka pkafile=./Results_propka/4ins_.pka, resi=18.25-30, resn=cys,
-
-### Some more examples. This molecule has 550 residues, so takes a longer time. We select to run the last molecule, by writing: molecule=1hp1
-#fetch 4ins, async=0
-#fetch 1hp1, async=0
-#propka molecule=1hp1, chain=A, resi=300-308.513, resn=CYS.ATP.TRP, logtime=_, verbose=no, showresult=no
-#propka molecule=1hp1, pkafile=./Results_propka/1hp1_.pka, verbose=yes
-
-### One can also just make a lookup for a protein. Use function: getpropka
-### Note. This does only print the result to the pymol command line
-#getpropka source=ID, PDBID=4ake, logtime=_, showresult=yes
-#getpropka source=ID, PDBID=4ins, logtime=_, server_wait=10.0, verbose=yes, showresult=no
-############################################Input parameters: propka############################################
-############# The order of input and changable things:
-############# propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL")
-# method : method=upload is default. This sends .pdb file and request result from propka server.
-## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
-## If one points to an local .pka file, then method is auto-changed to method=file. This is handsome in off-line environment, ex. teaching or seminar.
-# pkafile: Write the path to .pka file. Ex: pkafile=./Results_propka/4ins_.pka
-# molecule : name of the molecule. Ending of file is assumed to be .pdb
-# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
-# resi : Select by residue number, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
-## Separate with "." or make ranges with "-". Ex: resi=35.40-50
-# resn : Select by residue name, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
-## Separate with "." Ex: resn=cys.tyr
-# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
-## Normal it usefull to set it empty. Ex: logtime=_
-# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
-# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
-# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds.
-# version=v3.1 is default. This is what version of propka which would be used.
-## Possible: 'v3.1','v3.0','v2.0'. If a newer version is available than the current v3.1, a error message is raised to make user update the script.
-############################################Input parameters: getpropka############################################
-############# The order of input and changable things:
-############# getpropka(PDB="NIL",chain="*",resi="0",resn="NIL",source="upload",PDBID="",logtime=time.strftime("%Y%m%d%H%M%S",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no")
-# PDB: points the path to a .pdb file. This is auto-set from propka function.
-# source : source=upload is default and is set at the propka webpage.
-# source=ID, PDBID=4ake , one can print to the command line, the pka value for any official pdb ID. No files are displayed in pymol.
-# PDBID: is used as the 4 number/letter pdb code, when invoking source=ID.
-
-##############################################################################################################################################################################################################################
-'''
-
-from __future__ import print_function
-
-try:
-    from pymol import cmd
-    runningpymol = 'yes'
-except:
-    runningpymol = 'no'
-    pass
-import time
-import platform
-import os
-import sys
-
-
-def propka(molecule="NIL", chain="*", resi="0", resn="NIL", method="upload", logtime=time.strftime("%m%d", time.localtime()), server_wait=3.0, version="v3.1", verbose="no", showresult="no", pkafile="NIL", makebonds="yes"):
-    Script_Version = "20110823"
-    # First we have to be sure, we give reasonable arguments
-    if pkafile != "NIL":
-        method = 'file'
-    assert method in ['upload', 'file'], "'method' has to be either: method=upload or method=file"
-    # If molecule="all", then try to get the last molecule
-    ##assert molecule not in ['NIL'], "You always have to provide molecule name. Example: molecule=4ins"
-    if molecule == "NIL":
-        assert len(cmd.get_names()) != 0, "Did you forget to load a molecule? There are no objects in pymol."
-        molecule = cmd.get_names()[-1]
-    # To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
-    if resi != "0":
-        resi_range = ResiRange(resi)
-    else:
-        resi_range = []
-    # Also works for residue names. They are all converted to bigger letters. Example: resn="cys.Tyr"
-    if resn != "NIL":
-        resn_range = ResnRange(resn)
-    else:
-        resn_range = resn
-    # Make chain range, and upper case.
-    chain = ChainRange(chain)
-    # Make result directory. We also the absolut path to the new directory.
-    Newdir = createdirs()
-    if method == "upload":
-        # We try to load mechanize. If this fail, one can always get the .pka file manual and the run: method=file
-        try:
-            from modules import mechanize
-            importedmechanize = 'yes'
-        except ImportError:
-            print("Import error. Is a module missing?")
-            print(sys.exc_info())
-            print("Look if missing module is in your python path\n%s" % sys.path)
-            importedmechanize = 'no'
-            import modules.mechanize as mechanize
-        # The name for the new molecule
-        newmolecule = "%s%s" % (molecule, logtime)
-        # Create the new molecule from original loaded and for the specified chains. Save it, and disable the old molecule.
-        cmd.create("%s" % newmolecule, "%s and chain %s" % (molecule, chain))
-        cmd.save("%s%s.pdb" % (Newdir, newmolecule), "%s" % newmolecule)
-        cmd.disable("%s" % molecule)
-        if molecule == "all":
-            cmd.enable("%s" % molecule)
-            cmd.show("cartoon", "%s" % molecule)
-        # Let the new molecule be shown in cartoon.
-        cmd.hide("everything", "%s" % newmolecule)
-        cmd.show("cartoon", "%s" % newmolecule)
-        # Make the absolut path to the newly created .pdb file.
-        PDB = "%s%s.pdb" % (Newdir, newmolecule)
-        source = "upload"
-        PDBID = ""
-        # Request server, and get the absolut path to the result file.
-        pkafile = getpropka(PDB, chain, resi, resn, source, PDBID, logtime, server_wait, version, verbose, showresult)
-        # Open the result file and put in into a handy list.
-        list_results, ligands_results = importpropkaresult(pkafile)
-    if method == "file":
-        assert pkafile not in ['NIL'], "You have to provide path to file. Example: pkafile=./Results_propka/4ins_2011.pka"
-        assert ".pka" in pkafile, 'The propka result file should end with ".pka" \nExample: pkafile=./Results_propka/4ins_2011.pka \npkafile=%s' % (pkafile)
-        # The name for the molecule we pass to the writing script of pymol commands
-        newmolecule = "%s" % molecule
-        cmd.hide("everything", "%s" % newmolecule)
-        cmd.show("cartoon", "%s" % newmolecule)
-        # We open the result file we have got in the manual way and put in into a handy list.
-        list_results, ligands_results = importpropkaresult(pkafile)
-        # Then we print the interesting residues to the screen.
-        printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult, ligands_results)
-    # Now create the pymol command file. This should label the protein. We get back the absolut path to the file, so we can execute it.
-    result_pka_pymol_name = writepymolcmd(newmolecule, pkafile, verbose, makebonds)
-    # Now run our command file. But only if we are running pymol.
-    if runningpymol == 'yes':
-        cmd.do("run %s" % result_pka_pymol_name)
-    ##if runningpymol=='yes': cmd.do("@%s"%result_pka_pymol_name)
-    return(list_results)
-if runningpymol != 'no':
-    cmd.extend("propka", propka)
-
-
-def getpropka(PDB="NIL", chain="*", resi="0", resn="NIL", source="upload", PDBID="", logtime=time.strftime("%Y%m%d%H%M%S", time.localtime()), server_wait=3.0, version="v3.1", verbose="no", showresult="no"):
-    try:
-        import modules.mechanize as mechanize
-        importedmechanize = 'yes'
-    except ImportError:
-        print("Import error. Is a module missing?")
-        print(sys.exc_info())
-        print("Look if missing module is in your python path \n %s" % sys.path)
-        importedmechanize = 'no'
-    propka_v_201108 = 3.1
-    url = "http://propka.ki.ku.dk/"
-    assert version in ['v2.0', 'v3.0', 'v3.1'], "'version' has to be either: 'v2.0', 'v3.0', 'v3.1'"
-    assert source in ['ID', 'upload', 'addr', 'input_file'], "'source' has to be either: 'ID', 'upload', 'addr', 'input_file'"
-    if source == "upload":
-        assert PDB not in ['NIL'], "You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
-    if source == "ID":
-        assert len(PDBID) == 4, "PDBID has to be 4 characters"
-    # To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
-    if resi != "0":
-        resi_range = ResiRange(resi)
-    else:
-        resi_range = []
-    # Also works for residue names. They are all converted to bigger letters. Example: resn="cys.Tyr"
-    if resn != "NIL":
-        resn_range = ResnRange(resn)
-    else:
-        resn_range = resn
-    # Start the browser
-    br = mechanize.Browser()
-    # We pass to the server, that we are not a browser, but this python script. Can be used for statistics at the propka server.
-    br.addheaders = [('User-agent', 'pythonMechanizeClient')]
-    # To turn on debugging messages
-    # br.set_debug_http(True)
-    # To open the start page.
-    page_start = br.open(url)
-    read_start = page_start.read()
-    if verbose == 'yes':
-        print(br.title())
-        print(br.geturl())
-    # To get available forms
-    page_forms = [f.name for f in br.forms()]
-    if verbose == 'yes':
-        print(page_forms)
-    # Select first form
-    br.select_form(name=page_forms[0])
-    # Print the current selected form, so we see that we values we start with.
-    if verbose == 'yes':
-        print(br.form)
-    # Print the parameters of the 'version' RadioControl button and current value
-    if verbose == 'yes':
-        print(br.find_control(name='version'), br.find_control(name='version').value)
-    # This is to check, that the current script is "up-to-date".
-    propka_v_present = float(br.find_control(name='version').value[0].replace('v', ''))
-    if propka_v_present > propka_v_201108:
-        raise UserWarning('\nNew version of propka exist.\nCheck/Update your script.\nPresent:v%s > Script:v%s' % (propka_v_present, propka_v_201108))
-    # Change the parameters of the 'version' radio button and then reprint the new value. Input has to be in a list [input].
-    br.form['version'] = [version]
-    if verbose == 'yes':
-        print(br.find_control(name='version').value)
-    # Print the parameters of the 'source' RadioControl button and current value
-    if verbose == 'yes':
-        print(br.find_control(name='source'), br.find_control(name='source').value)
-    # Change the parameters of the 'source' radio button and then reprint the new value. Input has to be in a list [input].
-    br.form['source'] = [source]
-    if verbose == 'yes':
-        print(br.find_control(name='source').value)
-    # This step was the must strange and took a long time. For finding the information and the double negative way.
-    # One have to enable the pdb button. Read more here: http://wwwsearch.sourceforge.net/old/ClientForm/ ("# All Controls may be disabled.....)
-    PDBID_control = br.find_control("PDBID")
-    PDB_control = br.find_control("PDB")
-    if verbose == 'yes':
-        print(PDBID_control.disabled, PDB_control.disabled)
-    if source == "ID":
-        PDBID_control.disabled = False
-        PDB_control.disabled = True
-    if source == "upload":
-        PDBID_control.disabled = True
-        PDB_control.disabled = False
-    if verbose == 'yes':
-        print(PDBID_control.disabled, PDB_control.disabled)
-    # We create the result dir, and take with us the 'path' to the result dir.
-    Newdir = createdirs()
-    # Open all the files, and assign them.
-    if source == "upload":
-        filename = PDB
-    if source == "ID":
-        filename = PDBID
-    files = openfiles(Newdir, filename, logtime, source)
-    result_pka_file = files[0]
-    result_input_pka_file = files[1]
-    result_log = files[2]
-    filepath = files[3]
-    result_pka_pkafile = files[4]
-    result_pka_file_stripped = files[5]
-    result_pka_file_bonds = files[6]
-    # Print the parameters of the 'PDBID' TextControl button and current value
-    if source == "ID" and verbose == 'yes':
-        print(br.find_control(name='PDBID'))
-        print(br.find_control(name='PDBID').value)
-    # Change the parameters of the 'PDBID' TextControl and then reprint the new value. Input has just to be a string.
-    if source == "ID":
-        br.form["PDBID"] = PDBID
-    if source == "ID" and verbose == 'yes':
-        print(br.find_control(name='PDBID').value)
-    # Print the parameters of the 'PDB' TextControl button and current value
-    if source == "upload" and verbose == 'yes':
-        print(br.find_control(name='PDB'))
-        print(br.find_control(name='PDB').value)
-    # Change the parameters of the 'PDB' FileControl and then reprint the new value. Input has just to be a string.
-    if source == "upload":
-        PDBfilename = PDB
-        PDBfilenamepath = PDB
-    if source == "upload":
-        br.form.add_file(open(PDBfilename), 'text/plain', PDBfilenamepath, name='PDB')
-    if source == "upload" and verbose == 'yes':
-        print(br.find_control(name='PDB'))
-        print(br.find_control(name='PDB').value)
-    # Now reprint the current selected form, so we see that we have the right values.
-    if verbose == 'yes':
-        print(br.form)
-    # Make "how" we would like the next request. We would like to "Click the submit button", but we have not opened the request yet.
-    req = br.click(type="submit", nr=0)
-    # Have to pass by a mechanize exception. Thats the reason for the why True
-    # The error was due to: br.open(req)
-    # mechanize._response.httperror_seek_wrapper: HTTP Error refresh: The HTTP server returned a redirect error that would lead to an infinite loop.
-    # The last 30x error message was:
-    # OK
-    # I haven't been able to find the refresh problem or extend the time. So we make a pass on the raised exception.
-    try:
-        print("Now sending request to server")
-        br.open(req)
-    # If there is raised an exception, we jump through to the result page after some sleep.
-    except mechanize.HTTPError:
-        # We can extract the jobid from the current browser url.
-        jobid = br.geturl()[32:-5]
-        # We notice how the script at the server presents the final result page.
-        url_result = url + "pka/" + jobid + ".html"
-        # Now we continue to try to find the result page, until we have succes. If page doesn't exist, we wait a little.
-        while True:
-            print("Result still not there. Waiting %s seconds more" % server_wait)
-            time.sleep(float(server_wait))
-            # To pass the "break" after the exception, we make a hack, wait and then go to the result page, which is the jobid.
-            try:
-                page_result = br.open(url_result)
-                read_result = page_result.read()
-                # If we don't receive a error in getting the result page, we break out of the while loop.
-                break
-            # If the page doesn't exist yet. We go back in the while loop.
-            except mechanize.HTTPError:
-                # Wait another round
-                pass
-            # If we get a timeout, we also wait.
-            except mechanize.URLError:
-                # Wait another round
-                pass
-    htmlresult = "The detailed result is now available at: %s" % br.geturl()
-    print(htmlresult)
-    read_result = br.response().read()
-    # Now save the available links from the current page. But only links that satisfy the expression.
-    links_result = []
-    for l in br.links(url_regex='http://propka.ki.ku.dk/pka'):
-        links_result.append(l)
-    # We also extract the information for neighbour bons. This is given in the url links.
-    bonds = []
-    for l in br.links(url_regex='http://propka.ki.ku.dk/view/new_view.cgi'):
-        l_split = str(l).split()
-        lresn = l_split[2]
-        lresi = l_split[3]
-        lchain = l_split[4]
-        lurl = l_split[1]
-        lurl_split = lurl.split("&")
-        lresn2 = lurl_split[1]
-        lchain2 = lurl_split[2]
-        lpka = lurl_split[3]
-        ldesolvation = lurl_split[4]
-        lneighbours = lurl_split[5:]
-        for i in range(len(lneighbours)):
-            bonds.append([lresn, lresi, lchain, lresn2, lchain2, lpka, ldesolvation, lneighbours[i]])
-    # Now follow the link to the .propka_input resultpage
-    if len(links_result) > 1:
-        br.follow_link(links_result[1])
-    # Now get the page text for the current link
-    if len(links_result) > 1:
-        read_result1 = br.response().read()
-    # Save the result
-    if len(links_result) > 1:
-        result_input_pka_file.write(read_result1)
-    # Now follow the link to the .pka resultpage
-    if len(links_result) > 1:
-        br.back()
-    result_input_pka_file.close()
-    # Now follow first link. "Should be" available for all versions of propka.
-    br.follow_link(links_result[0])
-    # Now get the page for the current link
-    read_result0 = br.response().read()
-    # Save the result and close file.
-    result_pka_file.write(read_result0)
-    result_pka_file.close()
-    # Now get the result in a list, which is sorted
-    list_results, ligands_results = importpropkaresult(result_pka_pkafile)
-    # Print to log file
-    result_log.write("# executed: %s \n# logtime: %s \n# source=%s \n# PDB=%s \n# chain=%s \n# PDBID=%s \n# server_wait=%s version=%s verbose=%s showresult=%s \n# resi=%s resn=%s\n# %s \n" % (time.strftime("%Y%m%d%H%M%S", time.localtime()), logtime, source, PDB, chain, PDBID, server_wait, version, verbose, showresult, resi, resn, htmlresult))
-    # Print to screen
-    printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult, ligands_results)
-    # Now write to log and the stripped file
-    for l in list_results:
-        if resi != "0" and int(l[1]) in resi_range:
-            result_log.write("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]) + '\n')
-        if resn != "NIL" and l[0] in resn_range and int(l[1]) not in resi_range:
-            result_log.write("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]) + '\n')
-        result_pka_file_stripped.write("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]) + '\n')
-    for l in ligands_results:
-        if resn != "NIL" and l[0] in resn_range:
-            result_log.write("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]) + '\n')
-        result_pka_file_stripped.write("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]) + '\n')
-    result_pka_file_stripped.close()
-    result_log.close()
-    # Now handle the bonds. We have to delete dublicates first.
-    bonds.sort()
-    last = bonds[-1]
-    for i in range(len(bonds) - 2, -1, -1):
-        if last == bonds[i]:
-            del bonds[i]
-        else:
-            last = bonds[i]
-    # Now make a selection for known residue
-    bonds_selected = []
-    bonds_ligands = []
-    for l in bonds:
-        if l[0][6:] in ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR', 'C-', 'N+']:
-            bonds_selected.append(l)
-        else:
-            bonds_ligands.append(l)
-    # And now sort it.
-    bonds_selected.sort(key=lambda residue: int(residue[1]))
-    # Now write it to file
-    bonddic = {'=': ' ', ':': ' ', ',': ' ', "'": " "}
-    for l in bonds_selected:
-        nb = replace_all(l[7], bonddic)
-        result_pka_file_bonds.write("%3s %3s %s %7s %7s %9s %17s %s" % (l[0][6:], l[1], l[2][:1], l[3][8:], l[4], l[5], l[6], nb) + '\n')
-    for l in bonds_ligands:
-        nb = replace_all(l[7], bonddic)
-        result_pka_file_bonds.write("%3s %3s %s %7s %7s %9s %17s %s" % (l[0][6:], l[1], l[2][:1], l[3][8:], l[4], l[5], l[6], nb) + '\n')
-    result_pka_file_bonds.close()
-    return(result_pka_pkafile)
-if runningpymol != 'no':
-    cmd.extend("getpropka", getpropka)
-
-
-def openpymolfiles(pkafile):
-    result_pka_pymol_name = pkafile.replace(".pka", ".pml")
-    result_pka_pymol = open(result_pka_pymol_name, "w")
-    return(result_pka_pymol, result_pka_pymol_name)
-
-
-def printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult, ligands_results):
-    for l in list_results:
-        if resi != "0" and int(l[1]) in resi_range:
-            if showresult != 'yes':
-                print("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]))
-        if resn != "NIL" and l[0] in resn_range and int(l[1]) not in resi_range:
-            if showresult != 'yes':
-                print("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]))
-        if showresult == 'yes':
-            print("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]))
-    for l in ligands_results:
-        if resn != "NIL" and l[0] in resn_range:
-            if showresult != 'yes':
-                print("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]))
-        if showresult == 'yes':
-            print("%3s %3s %s %6s %3s %5s %3s %4s %s" % (l[0], l[1], l[2], l[3], l[4], l[5], l[6], l[7], l[8]))
-
-
-def importpropkaresult(result_pka_pkafile):
-    result_pka_file = open(result_pka_pkafile, "r")
-    list_results = []
-    ligands_results = []
-    ##bonding_partners = []
-    for l in result_pka_file:
-        if not l.strip():
-            continue
-        else:
-            # To search for the right lines
-            if l.strip().split()[0] in ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR', 'C-', 'N+'] and len(l.strip().split()) > 20:
-                list_results.append([l.strip().split()[0], l.strip().split()[1], l.strip().split()[2], l.strip().split()[3], l.strip().split()[4], l.strip().split()[6], l.strip().split()[7], l.strip().split()[8], l.strip().split()[9]])
-                # bonding_partners.append(l.strip().split()[11]);bonding_partners.append(l.strip().split()[15]);bonding_partners.append(l.strip().split()[19])
-            if l.strip().split()[0] not in ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR', 'C-', 'N+'] and len(l.strip().split()) > 20:
-                ligands_results.append([l.strip().split()[0], l.strip().split()[1], l.strip().split()[2], l.strip().split()[3], l.strip().split()[4], l.strip().split()[6], l.strip().split()[7], l.strip().split()[8], l.strip().split()[9]])
-                # bonding_partners.append(l.strip().split()[11]);bonding_partners.append(l.strip().split()[15]);bonding_partners.append(l.strip().split()[19])
-    # Sort the result after the residue number and then chain.
-    list_results.sort(key=lambda residue: int(residue[1]))
-    list_results.sort(key=lambda chain: chain[2])
-    # bonding_partners=uniqifi(bonding_partners)
-    ##bonding_partners[:] = [x for x in bonding_partners if x != "XXX"]
-    result_pka_file.close()
-    return(list_results, ligands_results)
-
-
-def importpropkabonds(result_pka_pkafile):
-    bonds = []
-    result_pka_file_bonds = open(result_pka_pkafile[:-4] + ".bonds", "r")
-    for l in result_pka_file_bonds:
-        bonds.append(l.split())
-    result_pka_file_bonds.close()
-    return(bonds)
-
-
-def createdirs():
-    if platform.system() == 'Windows':
-        Newdir = os.getcwd() + "\Results_propka\\"
-    if platform.system() == 'Linux':
-        Newdir = os.getcwd() + "/Results_propka/"
-    if not os.path.exists(Newdir):
-        os.makedirs(Newdir)
-    return(Newdir)
-
-
-def openfiles(Newdir, filename, logtime, source):
-    if source == "upload":
-        result_pka_pkafile = filename.replace(".pdb", ".pka")
-        result_pka_input_pkafile = filename.replace(".pdb", ".propka_input")
-        result_log_name = "%s_Results.log" % (Newdir)
-        result_pka_file_stripped_name = filename.replace(".pdb", ".stripped")
-        result_pka_file_bonds_name = filename.replace(".pdb", ".bonds")
-    if source == "ID":
-        result_pka_pkafile = "%s%s%s.pka" % (Newdir, filename, logtime)
-        result_pka_input_pkafile = "%s%s%s.propka_input" % (Newdir, filename, logtime)
-        result_log_name = "%s_Results.log" % (Newdir)
-        result_pka_file_stripped_name = "%s%s%s.stripped" % (Newdir, filename, logtime)
-        result_pka_file_bonds_name = "%s%s%s.bonds" % (Newdir, filename, logtime)
-    if platform.system() == 'Windows':
-        filepath = "\\"
-    if platform.system() == 'Linux':
-        filepath = "/"
-    # Open the files
-    result_pka_file = open(result_pka_pkafile, "w")
-    result_input_pka_file = open(result_pka_input_pkafile, "w")
-    result_log = open(result_log_name, "a")
-    result_pka_file_stripped = open(result_pka_file_stripped_name, "w")
-    result_pka_file_bonds = open(result_pka_file_bonds_name, "w")
-    return(result_pka_file, result_input_pka_file, result_log, filepath, result_pka_pkafile, result_pka_file_stripped, result_pka_file_bonds)
-
-
-def ResiRange(resi):
-    resi = resi.split('.')
-    resiList = []
-    for i in resi:
-        if '-' in i:
-            tmp = i.split('-')
-            resiList.extend(list(range(int(tmp[0]), int(tmp[-1]) + 1)))
-        if '-' not in i:
-            resiList.append(int(i))
-    return(resiList)
-
-
-def ResnRange(resn):
-    resn_split = resn.split('.')
-    resn_range = [resnr.upper() for resnr in resn_split]
-    return(resn_range)
-
-
-def ChainRange(chain):
-    chainstring = chain.replace(".", "+").upper()
-    return(chainstring)
-
-
-def writepymolcmd(newmolecule, pkafile, verbose, makebonds):
-    list_results, ligands_results = importpropkaresult(pkafile)
-    # Now find the available bonding partners that pymol knows of
-    bonding_partners = []
-    bonding_partners_str = cmd.get_pdbstr("%s and resn * and not resn ASP+GLU+ARG+LYS+HIS+CYS+TYR+GLN+ASN+SER+THR+GLY+PHE+LEU+ALA+ILE+TRP+MET+PRO+VAL+HOH" % (newmolecule))
-    for i in range(len(bonding_partners_str.splitlines()) - 1):
-        bonding_partners_split = bonding_partners_str.splitlines()[i].split()
-        if bonding_partners_split[0] == "HETATM" or bonding_partners_split[0] == "ATOM":
-            bonding_partners_single = bonding_partners_split[3]
-            bonding_partners.append(bonding_partners_single)
-    bonding_partners = uniqifi(bonding_partners)
-    if verbose == 'yes':
-        print("And other possible bonding partners is: %s" % bonding_partners)
-    # Read in the bond file, if it exists
-    writebonds = "no"
-    if os.path.isfile(pkafile[:-4] + ".bonds") and makebonds == "yes":
-        bonds = importpropkabonds(pkafile)
-        writebonds = "yes"
-    # Open the pymol command file for writing
-    files_pka_pymol = openpymolfiles(pkafile)
-    result_pka_pymol = files_pka_pymol[0]
-    result_pka_pymol_name = files_pka_pymol[1]
-    # Make some dictionary for propka->pymol name conversion
-    dictio = {'ASP': 'CG', 'GLU': 'CD', 'ARG': 'CZ', 'LYS': 'NZ', 'HIS': 'CG', 'CYS': 'SG', 'TYR': 'OH', 'C-': 'C', 'N+': 'N', 'NTR': 'N', 'CTR': 'C', 'GLN': 'CD', 'ASN': 'CG', 'SER': 'OG', 'THR': 'OG1', 'GLY': 'CA', 'PHE': 'CZ', 'LEU': 'CG', 'ALA': 'CB', 'ILE': 'CD1', 'TRP': 'NE1', 'MET': 'SD', 'PRO': 'CG', 'VAL': 'CB'}
-    dictio2 = {'ASP': 'D', 'GLU': 'E', 'ARG': 'R', 'LYS': 'K', 'HIS': 'H', 'CYS': 'C', 'TYR': 'Y', 'C-': 'C-', 'N+': 'N+'}
-    # This list is from: http://en.wikipedia.org/wiki/Protein_pKa_calculations
-    pkaaminoacid = ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR']
-    pkadictio = {'ASP': 3.9, 'GLU': 4.3, 'ARG': 12.0, 'LYS': 10.5, 'HIS': 6.0, 'CYS': 8.3, 'TYR': 10.1}
-    # Now start write to the file.
-    # Try to make silent
-    # result_pka_pymol.write("cmd.feedback('disable','all','actions')\n")
-    # result_pka_pymol.write("cmd.feedback('disable','all','results')\n")
-    # Change the GUI width, to make the long names possible.
-    result_pka_pymol.write("cmd.set('internal_gui_width','360')\n")
-    # Set fonts
-    result_pka_pymol.write("cmd.set('label_font_id','12')\n")
-    result_pka_pymol.write("cmd.set('label_size','-0.5')\n")
-    result_pka_pymol.write("cmd.set('label_color','grey')\n")
-    # No auto zoom the new objects
-    result_pka_pymol.write("cmd.set('auto_zoom','off')\n")
-    # The name for the molecules are defined here
-    pkamolecule = "%spKa" % (newmolecule)
-    pkalabelmolecule = "%sLab" % (newmolecule)
-    # Create the groups now, so they come in order. They will be empty
-    result_pka_pymol.write("cmd.group('%sResi','Res*')\n" % (newmolecule))
-    result_pka_pymol.write("cmd.group('%sLigands','Lig*')\n" % (newmolecule))
-    if writebonds == "yes":
-        result_pka_pymol.write("cmd.group('%sBonds','%sBond*')\n" % (newmolecule, newmolecule))
-    # Create new empty pymol pka molecules. For pka atoms and its label. This is a "bucket" we where we will put in the atoms together.
-    result_pka_pymol.write("cmd.create('%s','None')\n" % (pkamolecule))
-    result_pka_pymol.write("cmd.create('%s','None')\n" % (pkalabelmolecule))
-    # Now make the pka atoms and alter, color and such
-    for l in list_results:
-        name = dictio[l[0]]
-        resn = dictio2[l[0]]
-        resi = l[1]
-        chain = l[2]
-        pka = l[3]
-        buried = l[4]
-        if "*" in pka:
-            pka = pka.replace("*", "")
-            comment = "*Coupled residue"
-        else:
-            comment = ""
-        if l[0] in pkaaminoacid:
-            pkadiff = (float(pka) - pkadictio[l[0]])
-            pkadiff = "(%s)" % pkadiff
-            if pka == "99.99":
-                pkadiff = ""
-        else:
-            pkadiff = ""
-        # Make the selection for which atom to copy
-        newselection = ("/%s//%s/%s/%s" % (newmolecule, chain, resi, name))
-        protselect = ("%sRes_%s%s%s" % (newmolecule, chain, resn, resi))
-        result_pka_pymol.write("cmd.select('%s','byres %s')\n" % (protselect, newselection))
-        result_pka_pymol.write("cmd.show('sticks','byres %s')\n" % (protselect))
-        # The temporary name
-        tempname = ("%s%s%s%s" % (pkamolecule, chain, resi, name))
-        tempnamelabel = ("%s%s%s%s" % (pkalabelmolecule, chain, resi, name))
-        tempselect = ("/%s//%s/%s" % (tempname, chain, resi))
-        tempselectlabel = ("/%s//%s/%s" % (tempnamelabel, chain, resi))
-        # Copy the atom, call it by the residue name
-        result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n" % (tempname, newselection))
-        # Alter the name and the b value of the newly created atom
-        result_pka_pymol.write("cmd.alter('%s','b=%s')\n" % (tempselect, pka))
-        result_pka_pymol.write("cmd.alter('%s','vdw=0.5')\n" % (tempselect))
-        result_pka_pymol.write("cmd.alter('%s','name=%s%s%s')\n" % (tempselect, '"', pka, '"'))
-        # Now create a fake label atom, and translate it
-        result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n" % (tempnamelabel, tempname))
-        movelabelxyz = (1.5, 0, 0)
-        result_pka_pymol.write("cmd.translate('[%s,%s,%s]','%s',camera=0)\n" % (movelabelxyz[0], movelabelxyz[1], movelabelxyz[2], tempnamelabel))
-        # Labelling alternate positions are not allowed, so we delete that attribute for the label atoms.
-        result_pka_pymol.write("cmd.alter('%s','alt=%s%s')\n" % (tempselectlabel, '"', '"'))
-        result_pka_pymol.write("cmd.label('%s','text_type=%spka=%s%s Bu:%s%s%s%s')\n" % (tempselectlabel, '"', pka, pkadiff, buried, '%', comment, '"'))
-        # Now put the atoms into a bucket of atoms
-        result_pka_pymol.write("cmd.create('%s','%s or (%s)',quiet=1)\n" % (pkamolecule, pkamolecule, tempselect))
-        result_pka_pymol.write("cmd.create('%s','%s or (%s)',quiet=1)\n" % (pkalabelmolecule, pkalabelmolecule, tempselectlabel))
-        # Remove the temporary atoms
-        result_pka_pymol.write("cmd.remove('%s')\n" % (tempname))
-        result_pka_pymol.write("cmd.remove('%s')\n" % (tempnamelabel))
-        # Delete the temporary molecule/selection
-        result_pka_pymol.write("cmd.delete('%s')\n" % (tempname))
-        result_pka_pymol.write("cmd.delete('%s')\n" % (tempnamelabel))
-    # Group the resi together
-    result_pka_pymol.write("cmd.group('%sResi','%sRes*')\n" % (newmolecule, newmolecule))
-    for l in ligands_results:
-        resn = l[0]
-        atom = l[1]
-        chain = l[2]
-        pka = l[3]
-        buried = l[4]
-        if verbose == 'yes':
-            print("Ligand. resn:%s atom:%s chain:%s pka:%s buried:%s" % (resn, atom, chain, pka, buried))
-        if Check_bonding_partners(bonding_partners, resn)[0]:
-            if "*" in pka:
-                pka = pka.replace("*", "")
-                comment = "*Coupled residue"
-            else:
-                comment = ""
-            # Make the selection for which atom to copy
-            ligselection = ("/%s and chain %s and resn %s and name %s" % (newmolecule, chain, resn, atom))
-            ligselect = ("%sLig_%s%s%s" % (newmolecule, chain, resn, atom))
-            result_pka_pymol.write("cmd.select('%s','%s')\n" % (ligselect, ligselection))
-            result_pka_pymol.write("cmd.show('sticks','byres %s')\n" % (ligselect))
-            result_pka_pymol.write("cmd.util.cbap('byres %s')\n" % (ligselect))
-            # The temporary name
-            tempname = ("%s%s%s%s" % (pkamolecule, chain, resn, atom))
-            tempnamelabel = ("%s%s%s%s" % (pkalabelmolecule, chain, resn, atom))
-            tempselect = ("/%s and chain %s and resn %s" % (tempname, chain, resn))
-            tempselectlabel = ("/%s and chain %s and resn %s" % (tempnamelabel, chain, resn))
-            # Copy the atom, call it by the residue name
-            result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n" % (tempname, ligselection))
-            # Alter the name and the b value of the newly created atom
-            result_pka_pymol.write("cmd.alter('%s','b=%s')\n" % (tempselect, pka))
-            result_pka_pymol.write("cmd.alter('%s','vdw=0.5')\n" % (tempselect))
-            result_pka_pymol.write("cmd.alter('%s','name=%s%s%s')\n" % (tempselect, '"', pka, '"'))
-            # Now create a fake label atom, and translate it
-            result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n" % (tempnamelabel, tempname))
-            movelabelxyz = (1.5, 0, 0)
-            result_pka_pymol.write("cmd.translate('[%s,%s,%s]','%s',camera=0)\n" % (movelabelxyz[0], movelabelxyz[1], movelabelxyz[2], tempnamelabel))
-            # Labelling alternate positions are not allowed, so we delete that attribute for the label atoms.
-            result_pka_pymol.write("cmd.alter('%s','alt=%s%s')\n" % (tempselectlabel, '"', '"'))
-            result_pka_pymol.write("cmd.label('%s','text_type=%spka=%s Bu:%s%s%s%s')\n" % (tempselectlabel, '"', pka, buried, '%', comment, '"'))
-            # Now put the atoms into a bucket of atoms
-            result_pka_pymol.write("cmd.create('%s','%s or (%s)',quiet=1)\n" % (pkamolecule, pkamolecule, tempselect))
-            result_pka_pymol.write("cmd.create('%s','%s or (%s)',quiet=1)\n" % (pkalabelmolecule, pkalabelmolecule, tempselectlabel))
-            # Remove the temporary atoms
-            result_pka_pymol.write("cmd.remove('%s')\n" % (tempname))
-            result_pka_pymol.write("cmd.remove('%s')\n" % (tempnamelabel))
-            # Delete the temporary molecule/selection
-            result_pka_pymol.write("cmd.delete('%s')\n" % (tempname))
-            result_pka_pymol.write("cmd.delete('%s')\n" % (tempnamelabel))
-    # Group the resi together
-    result_pka_pymol.write("cmd.group('%sLigands','%sLig*')\n" % (newmolecule, newmolecule))
-    # Finish the pka atoms, and show spheres
-    result_pka_pymol.write("cmd.show('spheres','%s')\n" % (pkamolecule))
-    result_pka_pymol.write("cmd.spectrum('b','red_white_blue',selection='%s',minimum='0',maximum='14')\n" % (pkamolecule))
-    result_pka_pymol.write("cmd.alter('%s and name 99.9','vdw=0.8')\n" % (pkamolecule))
-    result_pka_pymol.write("cmd.show('spheres','%s and name 99.9')\n" % (pkamolecule))
-    result_pka_pymol.write("cmd.color('sulfur','%s and name 99.9')\n" % (pkamolecule))
-    # Now we make the bonds
-    if writebonds == "yes":
-        Bondgroups = []
-        naturalaminoacids = ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR', 'NTR', 'N+', 'CTR', 'C-', 'GLN', 'ASN', 'SER', 'THR', 'GLY', 'PHE', 'LEU', 'ALA', 'ILE', 'TRP', 'MET', 'PRO', 'VAL']
-        for l in bonds:
-            if l[0] in naturalaminoacids:
-                name = dictio[l[0]]
-                resi = l[1]
-                chain = l[2]
-                desolvation = l[6][12:]
-                pkachange = l[11]
-                NBresi = l[8][3:]
-                NBchain = l[9]
-                NBbond = l[-1][:2]
-                if l[8][:3] in naturalaminoacids:
-                    NBname, cutoff = BondTypeName(dictio[l[8][:3]], NBbond)
-                    fromselection = ("/%s//%s/%s/%s" % (newmolecule, chain, resi, name))
-                    toselection = ("/%s//%s/%s/%s" % (newmolecule, NBchain, NBresi, NBname))
-                    if l[8][:3] == 'NTR':
-                        extind = cmd.identify("chain %s and name N" % (NBchain))[0]
-                        toselection = ("/%s and id %s and name N" % (newmolecule, extind))
-                        NBresi = "N+"
-                    if l[8][:3] == 'CTR':
-                        extind = cmd.identify("chain %s and name C" % (NBchain))[-1]
-                        toselection = ("/%s and id %s and name C" % (newmolecule, extind))
-                        NBresi = "C-"
-                    distname = ("%s_%s%s%s%s_%s_%s" % (newmolecule, chain, resi, NBchain, NBresi, NBbond, pkachange))
-                    result_pka_pymol.write("cmd.distance('%s','%s','%s'%s)\n" % (distname, fromselection, toselection, cutoff))
-                    result_pka_pymol.write("cmd.color('%s','%s')\n" % (SetDashColor(NBbond), distname))
-                    # result_pka_pymol.write("cmd.disable('%s')\n"%(distname))
-                    Bondgroups.append("%s%s" % (chain, resi))
-                if l[8][:3] not in naturalaminoacids and Check_bonding_partners(bonding_partners, l[8])[0]:
-                    cutoff = ""
-                    NBresn = Check_bonding_partners(bonding_partners, l[8])[1]
-                    NBname = l[8][len(NBresn):] + "*"
-                    fromselection = ("/%s//%s/%s/%s" % (newmolecule, chain, resi, name))
-                    toselection = ("/%s and chain %s and resn %s and name %s" % (newmolecule, NBchain, NBresn, NBname))
-                    if verbose == 'yes':
-                        print("Res->Ligand: (%s) -> (%s)" % (fromselection, toselection))
-                    result_pka_pymol.write("cmd.show('sticks','%s')\n" % (toselection))
-                    distname = ("%s_%s%s%s_%s_%s" % (newmolecule, chain, resi, NBresn, NBbond, pkachange))
-                    result_pka_pymol.write("cmd.distance('%s','%s','%s'%s)\n" % (distname, fromselection, toselection, cutoff))
-                    result_pka_pymol.write("cmd.color('%s','%s')\n" % (SetDashColor(NBbond), distname))
-                    # result_pka_pymol.write("cmd.disable('%s')\n"%(distname))
-                    Bondgroups.append("%s%s" % (chain, resi))
-            if l[0] in bonding_partners:
-                resn = l[0]
-                atom = l[1]
-                chain = l[2]
-                desolvation = l[6][12:]
-                pkachange = l[11]
-                NBresi = l[8][3:]
-                NBchain = l[9]
-                NBbond = l[-1][:2]
-                if not Check_bonding_partners(bonding_partners, l[8])[0]:
-                    NBname, cutoff = BondTypeName(dictio[l[8][:3]], NBbond)
-                    fromselection = ("/%s and chain %s and resn %s and name %s" % (newmolecule, chain, resn, atom))
-                    toselection = ("/%s//%s/%s/%s" % (newmolecule, NBchain, NBresi, NBname))
-                    if l[8][:3] == 'NTR':
-                        extind = cmd.identify("chain %s and name N" % (NBchain))[0]
-                        toselection = ("/%s and id %s and name N" % (newmolecule, extind))
-                        NBresi = "N+"
-                    if l[8][:3] == 'CTR':
-                        extind = cmd.identify("chain %s and name C" % (NBchain))[-1]
-                        toselection = ("/%s and id %s and name C" % (newmolecule, extind))
-                        NBresi = "C-"
-                    distname = ("%s_%s%s%s%s%s_%s_%s" % (newmolecule, chain, resn, atom, NBchain, NBresi, NBbond, pkachange))
-                    result_pka_pymol.write("cmd.distance('%s','%s','%s'%s)\n" % (distname, fromselection, toselection, cutoff))
-                    result_pka_pymol.write("cmd.color('%s','%s')\n" % (SetDashColor(NBbond), distname))
-                    Bondgroups.append("%s%s%s" % (chain, resn, atom))
-                    # result_pka_pymol.write("cmd.disable('%s')\n"%(distname))
-                if Check_bonding_partners(bonding_partners, l[8])[0]:
-                    cutoff = ""
-                    NBresn = Check_bonding_partners(bonding_partners, l[8])[1]
-                    NBname = l[8][len(NBresn):] + "*"
-                    fromselection = ("/%s and chain %s and resn %s and name %s" % (newmolecule, chain, resn, atom))
-                    toselection = ("/%s and chain %s and resn %s and name %s" % (newmolecule, NBchain, NBresn, NBname))
-                    if verbose == 'yes':
-                        print("Ligand->Ligand: (%s) -> (%s)" % (fromselection, toselection))
-                    result_pka_pymol.write("cmd.show('sticks','%s')\n" % (toselection))
-                    distname = ("%s_%s%s%s%s_%s_%s" % (newmolecule, chain, resn, atom, NBresn, NBbond, pkachange))
-                    result_pka_pymol.write("cmd.distance('%s','%s','%s'%s)\n" % (distname, fromselection, toselection, cutoff))
-                    result_pka_pymol.write("cmd.color('%s','%s')\n" % (SetDashColor(NBbond), distname))
-                    # result_pka_pymol.write("cmd.disable('%s')\n"%(distname))
-                    Bondgroups.append("%s%s%s" % (chain, resn, atom))
-        Bondgroups = uniqifi(Bondgroups)
-        for l in Bondgroups:
-            result_pka_pymol.write("cmd.group('%sBonds_%s','%s_%s*')\n" % (newmolecule, l, newmolecule, l))
-            result_pka_pymol.write("cmd.disable('%sBonds_%s')\n" % (newmolecule, l))
-        result_pka_pymol.write("cmd.group('%sBonds','%sBonds_*')\n" % (newmolecule, newmolecule))
-    result_pka_pymol.write("cmd.set('auto_zoom','on')\n")
-    # result_pka_pymol.write("cmd.feedback('enable','all','actions')\n")
-    # result_pka_pymol.write("cmd.feedback('enable','all','results')\n")
-    result_pka_pymol.close()
-    return(result_pka_pymol_name)
-
-
-def replace_all(text, dic):
-    for i, j in dic.items():
-        text = text.replace(i, j)
-    return(text)
-
-
-def uniqifi(seq, idfun=None):
-    # Order preserving
-    if idfun is None:
-        def idfun(x):
-            return x
-    seen = {}
-    result = []
-    for item in seq:
-        marker = idfun(item)
-        if marker in seen:
-            continue
-        seen[marker] = 1
-        result.append(item)
-    return(result)
-
-
-def BondTypeName(NBname, NBbond):
-    if NBbond == "SH":
-        cutoff = ""
-        return(NBname, cutoff)
-    if NBbond == "BH":
-        cutoff = ""
-        return("N", cutoff)
-    else:
-        cutoff = ""
-        return(NBname, cutoff)
-
-
-def Check_bonding_partners(bonding_partners, NBname):
-    answer = False
-    for l in bonding_partners:
-        if l in NBname:
-            answer = True
-            NBname = l
-            break
-        else:
-            answer = False
-    return(answer, NBname)
-
-
-def SetDashColor(NBbond):
-    if NBbond == "SH":
-        color = "brightorange"
-    if NBbond == "BH":
-        color = "lightorange"
-    if NBbond == "CC":
-        color = "red"
-    return(color)

profiles/pymol/.pymol/startup/show_contact_map.py

@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-
-import tkFileDialog
-import tkSimpleDialog
-from pymol import cmd
-import math
-from distutils.util import strtobool
-
-def __init__(self):
-	self.menuBar.addmenuitem('Plugin', 'command', 'Contact map', label='Show contact map', command=lambda s=self: load_map(s))
-
-def load_map(app):
-	contacts_file = tkFileDialog.askopenfile(initialdir=".", title="Load contact map")
-	if contacts_file is None:
-		return
-	show_contact_map(file=contacts_file)
-
-def show_contact_map(selection="all", file=None, as_bonds=1, quiet=0):
-	""" Visualize contact map
-	"""
-	as_bonds = bool(as_bonds)
-	quiet = bool(quiet)
-	contacts = read_contacts(file)
-
-	for contact in contacts:	
-		name = "contact{}-{}".format(contact[0], contact[1])
-		seleA = "id %s and %s" % (contact[0], selection)
-		seleB = "id %s and %s" % (contact[1], selection)
-		
-		# skip non-exsistant
-		if cmd.select("seleA", seleA) == "0" or cmd.select("seleB", seleB) == "0":
-			print("%s to %s not found!" % (seleA, seleB))
-
-		if not quiet:
-			print("New bond: residue %s to %s" % (contact[0], contact[1]))
-
-		if as_bonds:
-			cmd.bond(seleA, seleB)
-		else:
-			cmd.distance(name, seleA, seleB)
-
-	cmd.delete('seleA')
-	cmd.delete('seleB')
-
-
-def read_contacts(contacts_file, separator=' '):
-	contacts = []
-	if not isinstance(contacts_file, file):
-		contacts_file = open(contacts_file, 'r')
-	for line in contacts_file.readlines():
-		split = line.split(",")
-		resA = int(split[0])
-		resB = int(split[1])
-		contacts.append([resA, resB])
-	contacts_file.close()
-	return contacts
-	
-cmd.extend("contact_map", show_contact_map)

profiles/pymol/.pymol/startup/spectrum_states.py

@@ -1,92 +0,0 @@
-'''
-http://pymolwiki.org/index.php/spectrum_states
-
-(c) 2011 Takanori Nakane and Thomas Holder
-
-License: BSD-2-Clause
-'''
-
-from __future__ import print_function
-
-from pymol import cmd, CmdException
-
-
-def spectrum_states(selection='all', representations='cartoon ribbon',
-                    color_list='blue cyan green yellow orange red',
-                    first=1, last=0, quiet=1):
-    '''
-DESCRIPTION
-
-    Color each state in a multi-state object different.
-
-USAGE
-
-    spectrum_states [ selection [, representations [, color_list [, first [, last ]]]]]
-
-ARGUMENTS
-
-    selection = string: object names (works with complete objects only)
-    {default: all}
-
-    representations = string: space separated list of representations
-    {default: cartoon ribbon}
-
-    color_list = string: space separated list of colors {default: blue cyan
-    green yellow orange red}
-
-SEE ALSO
-
-    spectrum, spectrumany
-    '''
-    from math import floor, ceil
-
-    first, last, quiet = int(first), int(last), int(quiet)
-    colors = color_list.split()
-    if len(colors) < 2:
-        print(' Error: please provide at least 2 colors')
-        raise CmdException
-
-    colvec = [cmd.get_color_tuple(i) for i in colors]
-
-    # filter for valid <repr>_color settings
-    settings = []
-    for r in representations.split():
-        if r[-1] == 's':
-            r = r[:-1]
-        s = r + '_color'
-        if s in cmd.setting.name_list:
-            settings.append(s)
-        elif not quiet:
-            print(' Warning: no such setting:', s)
-
-    # object names only
-    selection = ' '.join(cmd.get_object_list('(' + selection + ')'))
-    if cmd.count_atoms(selection) == 0:
-        print(' Error: empty selection')
-        raise CmdException
-
-    if last < 1:
-        last = cmd.count_states(selection)
-
-    val_range = int(last - first + 1)
-    if val_range < 2:
-        print(' Error: no spectrum possible, need more than 1 state')
-        raise CmdException
-
-    for i in range(val_range):
-        p = float(i) / (val_range - 1) * (len(colvec) - 1)
-        p0, p1 = int(floor(p)), int(ceil(p))
-        ii = (p - p0)
-        col_list = [colvec[p1][j] * ii + colvec[p0][j] * (1.0 - ii) for j in range(3)]
-        col_name = '0x%02x%02x%02x' % (col_list[0] * 255, col_list[1] * 255, col_list[2] * 255)
-        for s in settings:
-            cmd.set(s, col_name, selection, state=i + first)
-
-cmd.extend('spectrum_states', spectrum_states)
-
-# tab-completion of arguments
-cmd.auto_arg[0]['spectrum_states'] = cmd.auto_arg[0]['disable']
-cmd.auto_arg[1]['spectrum_states'] = [cmd.auto_arg[0]['show'][0], 'representation', ' ']
-cmd.auto_arg[2]['spectrum_states'] = [cmd.auto_arg[0]['color'][0], 'color', ' ']
-
-# vi:expandtab:smarttab

profiles/pymol/.pymol/startup/visualize_dca_scores.py

@@ -1,87 +0,0 @@
-#!/usr/bin/env python
-
-import tkFileDialog
-import tkSimpleDialog
-from pymol import cmd
-import math
-
-DEFAULT_CUTOFF = 10
-DEFAULT_FLOOR = 0.6
-DEFAULT_MAX_CONTACTS = -1
-
-def __init__(self):
-    self.menuBar.addmenuitem('Plugin', 'command', 'MSA Scores', label='MSA Scores', command=lambda s=self: load_scores_dialog(s))
-
-def load_scores_dialog(app):
-    scores_file = tkFileDialog.askopenfile(initialdir=".", title="Load scores")
-    if scores_file is None:
-        return
-    cutoff = tkSimpleDialog.askinteger("Cutoff", "Backbone cutoff", initialvalue=DEFAULT_CUTOFF, minvalue=1)
-    if cutoff is None:
-        return
-    floor = tkSimpleDialog.askfloat("Minimal Score", "Minimal Score", initialvalue=DEFAULT_FLOOR)
-    if floor is None:
-        return
-    max_contacts = tkSimpleDialog.askfloat("Limit contacts", "Maximal contacts to show", initialvalue=DEFAULT_MAX_CONTACTS)
-    if max_contacts is None:
-        return
-    show_scores(scores=scores_file, cutoff=cutoff, floor=floor, max_contacts=max_contacts)
-
-def show_scores(selection='all', scores="scores.csv", floor=DEFAULT_FLOOR, cutoff=DEFAULT_CUTOFF, max_contacts=None):
-    """ Visualize score csv 
-        selection: Selection for visualization
-        floor: minimal score for visualization
-        cutoff: minimal distance between amino acids
-        scores: scores file for visualization
-    """
-    cutoff = int(cutoff)
-    floor = float(floor)
-    scores = read_scores(scores)
-    
-    max_contacts = int(max_contacts)
-    if max_contacts is None or max_contacts == -1:
-        max_contacts = len(scores)
-
-    # filter for cutoff
-    scores = list(filter(lambda x: x[1] - x[0] >= cutoff, scores))
-
-    # filter for score floor
-    scores = list(filter(lambda x: x[2] >= floor, scores))
-
-    # show distances
-    counter = 0
-    for score in scores:    
-        if counter > max_contacts:
-            print("max contacts reached! (%s contacts not shown)" % (len(scores)-int(max_contacts)))
-            break
-        print("new msa contact between %s and %s" % (score[0], score[1]))
-        name = "msa{}-{}_{:.3f}".format(score[0], score[1], score[2])
-        seleA = "resid %s and n. CA and %s" % (score[0], selection)
-        seleB = "resid %s and n. CA and %s" % (score[1], selection)
-        if cmd.select("seleA", seleA) == "0" or cmd.select("seleB", seleB) == "0":
-            continue
-        cmd.distance(name, seleA, seleB)
-        counter += 1
-        
-    cmd.delete('seleA')
-    cmd.delete('seleB')
-
-
-def read_scores(scores_file):
-    scores = []
-    if not isinstance(scores_file, file):
-        scores_file = open(scores_file, 'r')
-    for line in scores_file.readlines():
-        split = line.split(",")
-        resA = int(split[0])
-        resB = int(split[1])
-        score = float(split[2])
-        dist = abs(resB - resA)
-        scores.append([resA, resB, score, dist])
-    scores_file.close()
-    return scores
-
-def remove_scores():
-    cmd.delete("msa*")
-cmd.extend("remove_scores", remove_scores)    
-cmd.extend("show_scores", show_scores)

profiles/pymol/.pymolrc

@@ -1,76 +0,0 @@
-# general environment
-bg_color white
-#space cmyk
-set fetch_path, /tmp
-log_open /tmp/pymol_log.pml
-set retain_order
-
-load ~/.pymol/chimera_colors.pml
-
-# interface
-set overlay, 1
-
-# performance
-set async_builds, on
-set max_threads, 8
-set cache_mode
-set defer_builds_mode, 3
-set hash_max, 500
-
-# raytrace
-set depth_cue, 0
-set ray_opaque_background, false
-set orthoscopic, 0
-#set ray_shadow, false 
-set spec_reflect, 0.25
-set antialias, 1
-set surface_quality, 1
-set ray_trace_mode, 0
-
-# hide nonbonded and nbsphreres
-set nonbonded_transparency, 1
-set nb_spheres_size, 0
-
-# stick settings
-set valence, 0
-
-# cartoon
-set cartoon_gap_cutoff, 1
-set cartoon_side_chain_helper, 1
-set cartoon_discrete_colors, on
-#set cartoon_highlight_color, gray
-set cartoon_oval_length, 0.8
-
-
-# spheres
-set sphere_scale, 0.5
-
-# custom colors
-set_color sodium, [1.0, 0.87, 0.37]
-set_color potassium, [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
-set_key F3, toggle spheres, inorganic and (n. NA or n. K)
-set_key F4, toggle spheres, n. CL
-
-set_key F9, set depth_cue
-set_key F10, set depth_cue, off
-set_key F11, ray 800,800
-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;
-alias sf_as_sticks_HCN4_sele, show sticks, sele and 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;
-alias sideview_HCN4, hide sticks; hide everything, polymer and chain B+D; select polymer and chain A+C; sf_as_sticks_HCN4_sele; deselect;
-
-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

run_onchange_before_0_install-packages.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -e
+
+echo "Installing packages"
+sudo apt update -qq
+
+for package in git neovim git ripgrep; do
+    if dpkg -s "$package" >/dev/null 2>&1; then
+        echo $package is already installed.
+    else
+        echo Installing $package
+        sudo apt install -y $package
+    fi
+done

run_onchange_before_1_zsh.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+if ! type zsh > /dev/null; then
+    echo "Cannnot change default shell to zsh: not installed"
+else
+    # Make ZSH the default shell environment
+    if [ $(cat /etc/passwd | grep $USER | awk -F ':' '{print substr($7, length($7)-3)}') != "/zsh" ]; then
+        echo "Changing shell to zsh."
+        chsh -s $(which zsh)
+    else
+        echo "Shell is already zsh."
+    fi
+
+    # Antidote Installation
+    if [ ! -d "$HOME/.antidote" ]; then
+        echo "Installing Antidote"
+
+        # make sure git is installed
+        if ! type git > /dev/null; then
+            echo "Git not installed. Cannot install antidote"
+	else
+             git clone --depth=1 https://github.com/mattmc3/antidote.git $HOME/.antidote
+        fi
+
+    else
+	echo "Antidote already exists."
+    fi
+    
+fi

run_onchange_before_20_fzf.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env sh
+
+if [ ! -d "$HOME/.fzf" ]; then
+    echo "Installing fzf into ~/.fzf"
+    git clone --depth 1 https://github.com/junegunn/fzf.git $HOME/.fzf
+    if [ ! -f "$HOME/.fzf/bin" ]; then
+	$HOME/.fzf/install --completion --key-bindings --update-rc
+    fi
+fi
+

run_onchange_before_21_diff-so-fancy.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+if [ ! -f "$HOME/.local/bin/diff-so-fancy" ]; then
+    echo "Installing diff-so-fance into .local/bin"
+    if [ ! -d "$HOME/.local/lib/diff-so-fancy" ]; then
+        git clone --depth 1 https://github.com/so-fancy/diff-so-fancy.git $HOME/.local/lib/diff-so-fancy
+    fi
+    ln -s $HOME/.local/lib/diff-so-fancy/diff-so-fancy $HOME/.local/bin/diff-so-fancy
+fi

run_onchange_before_22_vimplug.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env sh
+
+if [ ! -d "$HOME/.vim/autoload" ]; then
+    echo "setup vim plug"
+    curl -fLo $HOME/.vim/autoload/plug.vim --create-dirs \
+	    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
+fi