Introduction to Brailchem

What is Brailchem

Brailchem 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.

Brailchem is developed as a part of the ICT project.

Usage

Brailchem contains two subapplications: molecule browser and periodic table of elements. The subapplications can be started from corresponding menu items in the Application menu. If you want, you can run each of the applications in one or more separate windows, created from the File / New Window menu.

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.

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.

For now there is just a single special global command key in Brailchem:

Control+QClose Brailchem window

Of course, you can additionally use menu access keys. Other command keys are specific to particular Brailchem subapplications.

The following sections describe the Brailchem subapplications.

Molecule Browser Application

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. file and http URLs are supported.

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.

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 fragments 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.

When a molecule is inspected (for instance acetic acid is written as CC(=O)O 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: attached elements 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 neighbors which can be connected to multiple atoms.

There are special marks for some atom and bonds properties:

You can navigate through the items by using the standard TAB and Shift+TAB Firefox navigational keys or by using one of the special application keys:

Control+Ajump 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
Control+Ngo to the next atom
Control+Pgo to the previous atom
Alt+Mjump to the molecule input box
Alt+Gtoggle displaying of atom groups (if applicable)

Additionally when pressing Enter on any of the attached elements or neighbor names, the focus jumps to the referenced element.

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.

When inspecting a whole chemical reaction rather than a single molecule (for instance CC(=O)O.CCO>[H+]>CC(=O)OCC.O 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 Enter 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.

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:

Control+Arrow Downgo to the next displayed molecule
Control+Arrow Upgo to the previous displayed molecule
Control+Tjump back to reaction summary

Periodic Table Application

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.

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 Control+T and into the table of lanthanoids and actinoids by pressing Control+Shift+T.

Summary of basic periodic table command keys:

Shift+arrow keysnavigate through elements of the periodic table
Control+Tjump to the main periodic table
Control+Shift+Tjump to the table of lanthanoids and actinoids
Control+Ejump to given element

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 Filters 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.

You can use the following keyboard shortcuts to work with filters:

Control+F dotgo to filters
Control+F Ego to electronegativity filtering
Control+F Ggo to group filtering
Control+F Ogo to oxidation number filtering
Control+F Sgo to set of elements filtering
Control+F ?show currently filtered elements

These shortcuts are composed of sequences of several keys. First press the Control+F key and then the second key.

A special filter is the Set of elements filter. You activate it by pressing the Change button in the Set of elements 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:

Control+S dotfinish element selection and activate it
Control+S Aselect all currently active elements
Control+S Nunselect all elements

Overview of Keyboard Commands

Global

Control+QClose Brailchem window

Molecule Browser

Enterfollow reference
Control+Ajump to molecule atoms
Control+Ngo to the next atom within a molecule
Control+Pgo to the previous atom within a molecule
Control+Arrow Downgo to the next displayed molecule
Control+Arrow Upgo to the previous displayed molecule
Control+Tjump back to reaction summary
Alt+Mjump to the molecule input box
Alt+Gtoggle displaying of atom groups

Periodic Table

Shift+arrow keysnavigate through elements of the periodic table
Control+Tjump to the main periodic table
Control+Shift+Tjump to the table of lanthanoids and actinoids
Control+Ejump to given element
Control+F dotgo to filters
Control+F Ego to electronegativity filtering
Control+F Ggo to group filtering
Control+F Ogo to oxidation number filtering
Control+F Sgo to set of elements filtering
Control+F ?show currently filtered elements
Control+S dotfinish element selection and activate it
Control+S Aselect all currently active elements
Control+S Nunselect all elements