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/usr/share/massxpert/chem_pad.conf is in massxpert-data 3.6.0-1.

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The actual contents of the file can be viewed below.

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# This is the layout for the chempad of the molecular calculator 'extremecalc'
# in the massXpert software program.
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009 Filippo Rusconi. 
# GNU General Public License.

# The format of this file allows the definition of colors
# according to the following syntax:
#
# color%OneColor%xxx,yyy,zzz 
#
# with xxx, yyy and zzz numerical values in range [0,255] for the red,
# green and blue component of the color respectively.
#
# Available colors are: white, black, red, darkRed, green, darkGreen,
#  blue, darkBlue, cyan, darkCyan, magenta, darkMagenta, yellow,
#  darkYellow, gray, darkGray, lightGray, please, see
#  http://www.w3.org/TR/SVG/types.html#ColorKeywords for a list of
#  commonly used colors associated to their rgb value.
#
# A separator might be used between sections of buttons. Its syntax is:
#
# chempadsep%Hexoses & Fucose%[midnightblue]
#
# The color specification (%[midnightblue]) is not compulsory

# General button syntax is like the example below:
#
# chempadkey%hydrate%+H2O1%adds a water molecule%[red,blue]
# 
# Each line is divided into 4 compulsory elements:
# 'chempadkey' starts the line
# 'hydrate' is the label of the button
# '+H2O1' is the formula that is applied when the button gets clicked
# 'adds a water molecule' is the text to display in the tooltip
# '[red,blue]' are the background and foreground colors, respectively
#
# The colors specification (last %[color,color]) is not compulsory
#
# The geometry is specified by the number of columns of buttons:
# chempad_columns%3 would specify that all the buttons in the 
# chemical pad should be laid out using three columns and as
# many rows as necessary to display them all.

chempad_columns%3


chempadgroup%Generic

chempadkey%protonate%+H1%adds a proton
chempadkey%hydrate%+H2O1%adds a water molecule
chempadkey%0H-ylate%+O1H1%adds an hydroxyl group
chempadkey%acetylate%-H1+C2H3O1%adds an acetyl group
chempadkey%phosphorylate%-H+H2PO3%add a phosphate group
chempadkey%sulfide bond%-H2%oxydizes with loss of hydrogen