# &app; manual

# &app; Manual V&manrevision;

2006-2010
Jean Bréfort

&legal;

GNOME Documentation Project
Jean
Bréfort

     jean.brefort@normalesup.org

&app; Manual V&manrevision;
&date;

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

&app; Manual V0.2
September 2008

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

&app; Manual V0.1
February 2006

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

This manual describes version &appversion; of &app;.

## Feedback

To report a bug or make a suggestion regarding the &app; application or this manual, go to the&app; &app; home page.

&app; allows you to evaluate some molecular properties.

## Introduction

The &app; application is a simple calculator for chemistry. It parses chemical formula to calculate raw formula, molecular weights, mass composition and isotopic patterns.

## Getting started

### To Start &app;

You can start &app; in the following ways:

Applications menu

  Choose Education Chemical calculator .

Command line

  Type `gchemcalc` [formula], then press Return. [Formula] stands for an optional chemical formula.

### When You Start &app;

When you start &app;, the following window is displayed:

#### &app; window

Screenshot of the &app;window.

The &app; window contains the following elements:

Menubar

  The menus on the menubar contain all of the commands you need to work with &app;.

Formula entry

  This is where you can type a formula.

Results

  The next three lines give the entered formula as parsed by &app;, the raw formula and the molecular weight.

Notebook

  The first page of the notebook gives the analysis as mass percent of the elements of the current formula. The second page displays the isotopic pattern. This page is hidden when the formula is empty.

## Usage

### Entering a formula

Formulas can be entered from the command line, from GChemPaint, or directly in the formula entry.

When using the formula entry, just type a valid formula as in the following example:

#### Entering a formula

Entering a formula.

After validating, if the formula has been succesfully parsed, you get:

#### Results

Result after parsing a formula.

The isotopic pattern is displayed on the second page of the notebook:

#### Isotopic pattern

Result after parsing a formula.

If an error occurs while parsing the formula, a message box will pop up and the cursor will be moved in the entry to the error position.

### Features

&app; supports parenthesis and brackets to any level provided each one is matched as in the following example:

#### Using parenthesis and brackets

Using parenthesis and brackets.

Abbreviations such as "Ph" for a phenyl substituant are supported.

This is also true for abbreviations such as Pr which might represent either a praseodymium atom or a propyl group. Three options are available in the Mode menu:

Guess

  &app; try to guess if the symbol represents an atom or a group, PrCl is analyzed as propyl chloride, while PrCl3 is praseodymium chloride; however, this method might fail in some cases such as PrPr3 which will not be recognized as trypropylpraseodymium, at least with this version of &app;.

Atom

  Ambiguous symbols are interpreted as atoms.

Nickname

  Ambiguous symbols are interpreted as groups.

Custom nicknames can be defined using the GChemPaint application.

### To Print the Isotopic Pattern Graph

To print a isotopic pattern graph, choose File Print... .

File Preview opens a window with a preview of the printed output.

To tune the printed output, choose File Page setup... as explained below.

#### The page setup dialog.

the first tab of the dialog concerns the paper and margins setup. Headers and footers are not supported in the version of &app;

##### The Page Setup tab.

Screenshot of page setup dialog.

The second tab allows you tio choose the scale of the output. With no scaling or scaling at 100%, the output will have the same size in points as the size in pixels on the screen. If you choose automatic scaling, you can make the output fill the available space either horizontally, vertically, or both (none of the options is equivalent to no scaling).

Printing to more than one page is not supported in this version of &app;

##### The Print Scale tab.

Screenshot of the printing scale page.

### Export the Isotopic Pattern as an Image.

To export the displayed isotopic pattern to an image, use File Save As Image .

Available formats are SVG, EPS, PS, PDF, and the formats with write support in GdkPixbuf.

To choose a format, you can use an appropriate extension in the file name, or explicitly select a format in the combo box. With the first method, if &app; does not recognize an extension, the exported file will be a SVG file. &app; will add an extension to the file name if needed.

You might change the default width and height of the exported image using the appropriate entries.

Postscript and PDF files can also be produced using the File Print... command.

### Copying the Isotopic Pattern Graph.

To copy the isotopic pattern graph, choose Edit Copy and paste in the target application. Graphs will be copied as native graphs to Abiword and as svg or png data to other applications which support such formats.

## Support.

### To Ask a Question

If you choose Help Ask a question, your mail agent should pop up with a new message to the Gnome Chemistry Utils mailing list.

Another way to get some help is to connect on the #gchemutils channel at irc.gimp.net and ask your question there (if you are not alone on the channel).

### To Find the Gnome Chemistry Utils on the Web.

If you choose Help Gnome Chemistry Utils on the web, the default web browser should pop up and display the main page for the Gnome Chemsitry Utils.

The main page is http://gchemutils.nongnu.org and the project page at savannah http://savannah.nongnu.org/projects/gchemutils.

### To Report a Bug

To report a bug, you must use the bug page for the Gnome Chemistry Utils at Savannah. You can access it by choosing Help Report Bugs (hopefully you'll have only one at once to report).

You can also type the bug report page address directly in the browser. The bug repository is at https://savannah.nongnu.org/bugs/?group=gchemutils

## License

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.

A copy of the GNU General Public License is included as an appendix to the GNOME Users Guide. You may also obtain a copy of the GNU General Public License from the Free Software Foundation by visiting their Web site or by writing to

        Free Software Foundation, Inc.
        51 Franklin St - Fifth Floor
        Boston, MA 02111-1307
        USA