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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
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<title>Introduction to Brailchem</title>
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<h1>Introduction to Brailchem</h1>
<ul>
<li><a href="#what-is-brailchem">What is Brailchem</a></li>
<li><a href="#usage">Usage</a></li>
<li><a href="#molecule-browser">Molecule Browser Application</a></li>
<li><a href="#periodic-table">Periodic Table Application</a></li>
<li><a href="#keys">Overview of Keyboard Commands</a></li>
</ul>
<a name="what-is-brailchem">
<h2>What is Brailchem</h2>
</a>
<p>
<a href="http://ict.brailcom.org/brailchem">Brailchem</a> is a tool to
help blind and visually impaired students to study chemistry. Visually
impaired students have to deal with special difficulties during their
study such as understanding information commonly presented visually
(e.g. structures of organic molecules) or learning structurally
complicated relations without using its visual presentation
(e.g. periodic table of elements). The purpose of Brailchem is to
present chemical information using computers in a way accessible to
blind and visually impaired students.
</p>
<p>
Brailchem is developed as a part of
the <a href="http://ict.brailcom.org">ICT project</a>.
</p>
<a name="usage">
<h2>Usage</h2>
</a>
<p>Brailchem contains two subapplications: molecule browser and periodic
table of elements. The subapplications can be started from corresponding
menu items in the <em>Application</em> menu. If you want, you can run
each of the applications in one or more separate windows, created from
the <em>File / New Window</em> menu.
</p>
<p>Brailchem is an Internet oriented application. It consists of two
parts: a client and a server. The server, basically invisible to the
user, provides all chemical data to the client. The client is dumb and
does not know anything about chemical elements or molecule structures, it
is just a presentation tool of data retrieved from the server. So in
order to work the client must be connected to Internet and have access to
a Brailchem server. One such server is already preset in the application
and it is used by default; if you would like to use another one, you can
set it in the client preferences dialog. Please use only trusted
servers, otherwise you risk privacy problems.</p>
<p>To start using Brailchem, look into its menus, read available help and
try to use the available subapplications. All important information
about current state of the program and performed actions is printed in
the application window status bar.</p>
<p>For now there is just a single special global command key in
Brailchem:</p>
<table>
<tr><td><code>Control+Q</code></td><td>Close Brailchem window</td></tr>
</table>
<p>Of course, you can additionally use menu access keys. Other command
keys are specific to particular Brailchem subapplications.
</p>
<p>The following sections describe the Brailchem subapplications.</p>
<a name="molecule-browser">
<h2>Molecule Browser Application</h2>
</a>
<p>Molecule browser is capable of inspecting molecule structures and
chemical reactions written in one of supported chemical notations or
specified by their names. The molecule or reaction is written into the
input box in the application. Alternatively you can write a URL of a
location containing the molecule or reaction descripition into the input
box. <code>file</code> and <code>http</code> URLs are supported.</p>
<p>Then specify the input format in the following combo box and press the
submit button. If the molecule input is recognized, the given molecule
or a chemical reaction consisting of several molecules is inserted in a
browsable expanded form to the application window.</p>
<p>The application works by connecting to the server part of Brailchem and
asking it for information represented by the given notation. The server
tries to identify molecule names and to expand molecules into sequences
of atoms and <em>fragments</em> connected by bonds. Fragments are well
known groups of atoms identified by the server (e.g. carboxyl group)
which can be represented by a single item rather than an unnecessarily
complex list of single atoms.</p>
<p>When a molecule is inspected (for instance <em>acetic acid</em> is
written as <code>CC(=O)O</code> in SMILES notation), its name, list of
basic properties (such as summary formula or molecular weight) and
sequence of atoms and fragments are displayed. Each atom or fragment
displays all items connected to it through bonds. These items can be of
two kinds: <em>attached elements</em> which connect just to this atom and
nothing else (so there is no need to jump to them from here to explore
the molecule structure) and <em>neighbors</em> which can be connected to
multiple atoms.</p>
<p>There are special marks for some atom and bonds properties:</p>
<ul>
<li>If an atom is part of some rings, this is indicated after the atom
symbol by the <code>R</code> characters, one <code>R</code> character
for each ring.</li>
<li>If atom multiplicity is other than 1, this is indicated after the
atom symbol by the symbol <code>xNUMBER</code>
where <code>NUMBER</code> is the atom multiplicity.
</li>
<li>Aromatic bonds are indicated by the letter <code>A</code> at the ends
of their descriptions.</li>
</ul>
<p>You can navigate through the items by using the
standard <code>TAB</code> and <code>Shift+TAB</code> Firefox navigational
keys or by using one of the special application keys:</p>
<table>
<tr><td><code>Control+A</code></td><td>jump to molecule atoms; using
this key you can jump from the molecule name directly to the list of
atoms and fragments without walking through the molecule
properties</td></tr>
<tr><td><code>Control+N</code></td><td>go to the next atom</td></tr>
<tr><td><code>Control+P</code></td><td>go to the previous atom</td></tr>
<tr><td><code>Alt+M</code></td><td>jump to the molecule input box</td></tr>
<tr><td><code>Alt+G</code></td><td>toggle displaying of atom groups (if applicable)</td></tr>
</table>
<p>Additionally when pressing <code>Enter</code> on any of the attached
elements or neighbor names, the focus jumps to the referenced
element.</p>
<p>If a displayed molecule contains any fragments, a check box is added at
the end. This check box can switch between atom groups view, displaying
fragments instead of certain groups of atoms, and simple atom view,
displaying just all atoms and no fragments.</p>
<p>When inspecting a whole chemical reaction rather than a single molecule
(for instance <code>CC(=O)O.CCO>[H+]>CC(=O)OCC.O</code> in SMILES
notation), the view is a bit more complex. First in the page a summary
of reactants, reagents and products is displayed. You can
press <code>Enter</code> on any of the reaction component names to jump
to the corresponding molecule view. Then molecules are displayed in the
same way as when inspecting a single molecule.</p>
<p>The same command keys are available as in single molecule browsing. The
atom movement keys restrict movement just to a current molecule.
Additional keys are defined to move across the molecules:</p>
<table>
<tr><td><code>Control+Arrow Down</code></td><td>go to the next displayed molecule</td></tr>
<tr><td><code>Control+Arrow Up</code></td><td>go to the previous displayed molecule</td></tr>
<tr><td><code>Control+T</code></td><td>jump back to reaction summary</td></tr>
</table>
<a name="periodic-table">
<h2>Periodic Table Application</h2>
</a>
<p>Periodic table provides information about elements, their properties and
relations. You can navigate through it using arrow keys while pressing
the Shift modifier. Pressing an element button using the Enter key shows
complete information about the given element. </p>
<p>For the purpose of easier orientation the periodic table is split
according to the traditional presentation style in two parts: The main
periodic table and the table of lanthanoids and actinoids. You can jump
into the main table by pressing <code>Control+T</code> and into the table
of lanthanoids and actinoids by pressing <code>Control+Shift+T</code>.
<p>Summary of basic periodic table command keys:</p>
<table>
<tr><td><code>Shift+arrow keys</code></td><td>navigate through elements of the periodic table</td></tr>
<tr><td><code>Control+T</code></td><td>jump to the main periodic table</td></tr>
<tr><td><code>Control+Shift+T</code></td><td>jump to the table of lanthanoids and actinoids</td></tr>
<tr><td><code>Control+E</code></td><td>jump to given element</td></tr>
</table>
<p>You can limit the periodic table view by using filters. Filters can
reduce the set of browsable periodic table elements to only those
elements which satisfy given criteria based on some of element properties
(such as group or oxidation number). You enable filters by specifying
them in the <em>Filters</em> box below the periodic table. If you
specify more than one filter, only those elements which satisfy all the
given conditions are present in the resulting filtered set. Defined
filters can be disabled or enabled using the check box in the filters
box.</p>
<p>You can use the following keyboard shortcuts to work with filters:</p>
<table>
<tr><td><code>Control+F dot</code></td><td>go to filters</td></tr>
<tr><td><code>Control+F E</code></td><td>go to electronegativity filtering</td></tr>
<tr><td><code>Control+F G</code></td><td>go to group filtering</td></tr>
<tr><td><code>Control+F O</code></td><td>go to oxidation number filtering</td></tr>
<tr><td><code>Control+F S</code></td><td>go to set of elements filtering</td></tr>
<tr><td><code>Control+F ?</code></td><td>show currently filtered elements</td></tr>
</table>
<p>These shortcuts are composed of sequences of several keys. First press
the <code>Control+F</code> key and then the second key.</p>
<p>A special filter is the <em>Set of elements</em> filter. You activate
it by pressing the <samp>Change</samp> button in the <em>Set of
elements</em> filter. Then you are directed to the periodic table where
you can insert or remove elements into or from the custom element set by
pressing their buttons with the Enter key. The following additional
command keys are available during element set selection:</p>
<table>
<tr><td><code>Control+S dot</code></td><td>finish element selection and activate it</td></tr>
<tr><td><code>Control+S A</code></td><td>select all currently active elements</td></tr>
<tr><td><code>Control+S N</code></td><td>unselect all elements</td></tr>
</table>
<a name="keys">
<h2>Overview of Keyboard Commands</h2>
</a>
<h3>Global</h3>
<table>
<tr><td><code>Control+Q</code></td><td>Close Brailchem window</td></tr>
</table>
<h3>Molecule Browser</h3>
<table>
<tr><td><code>Enter</code></td><td>follow reference</td></tr>
<tr><td><code>Control+A</code></td><td>jump to molecule atoms</td></tr>
<tr><td><code>Control+N</code></td><td>go to the next atom within a molecule</td></tr>
<tr><td><code>Control+P</code></td><td>go to the previous atom within a molecule</td></tr>
<tr><td><code>Control+Arrow Down</code></td><td>go to the next displayed molecule</td></tr>
<tr><td><code>Control+Arrow Up</code></td><td>go to the previous displayed molecule</td></tr>
<tr><td><code>Control+T</code></td><td>jump back to reaction summary</td></tr>
<tr><td><code>Alt+M</code></td><td>jump to the molecule input box</td></tr>
<tr><td><code>Alt+G</code></td><td>toggle displaying of atom groups</td></tr>
</table>
<h3>Periodic Table</h3>
<table>
<tr><td><code>Shift+arrow keys</code></td><td>navigate through elements of the periodic table</td></tr>
<tr><td><code>Control+T</code></td><td>jump to the main periodic table</td></tr>
<tr><td><code>Control+Shift+T</code></td><td>jump to the table of lanthanoids and actinoids</td></tr>
<tr><td><code>Control+E</code></td><td>jump to given element</td></tr>
<tr><td><code>Control+F dot</code></td><td>go to filters</td></tr>
<tr><td><code>Control+F E</code></td><td>go to electronegativity filtering</td></tr>
<tr><td><code>Control+F G</code></td><td>go to group filtering</td></tr>
<tr><td><code>Control+F O</code></td><td>go to oxidation number filtering</td></tr>
<tr><td><code>Control+F S</code></td><td>go to set of elements filtering</td></tr>
<tr><td><code>Control+F ?</code></td><td>show currently filtered elements</td></tr>
<tr><td><code>Control+S dot</code></td><td>finish element selection and activate it</td></tr>
<tr><td><code>Control+S A</code></td><td>select all currently active elements</td></tr>
<tr><td><code>Control+S N</code></td><td>unselect all elements</td></tr>
</table>
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