The user manual can be downloaded here.
Contents
1. list of rings it is implied that at least some if not all of the smaller rings with six or less atoms are fused together by one or more bonds 3 8 Functional group search The identification of the main functional groups in a molecule is one of the main tasks if not the first when first studying a new molecule Navmol uses SMARTS in order to carry out this task which is not a simple one The details on the SMARTS go beyond the scope of this manual and can be found in many places on the Internet e g at http www daylight com dayhtml doc theory theory smarts html Navmol reads the functional groups SMARTS from the file functional_groups smarts in the conf directory located in the navmol root installation directory This is a simple text file that the user can easily edit in order to add modify or customize the list of functional groups he she wants to detect and it is already configured to detect the most common functional groups In the file each line configures a functional group to be searched for except for sets of functional groups This is to allow the possibility of turning on or off entire families of functional groups to be searched for The format of a line to define a functional group is as follows e Columns are separated by spaces e The first column is a number 0 or 1 that sets the functional group to be off 0 or on 1 e The second column is a word specifying the name of the functional group Any space2. general information on the molecule This information is already reported at the beginning of the navmol session when the molecule is first loaded Navmol will then report the following properties 1 The chemical symbol and number I D 2 Number of bonded neighbours followed by list of all neighbours and respective clock coordinates and type of bonds for each bonded neighbour 3 Formal charge of this atom if it is charged 7 10 3 10 Open file with new molecule To load a new molecule the user can press the ALT O keys A file selection dialogue will appear for that effect After selecting a file the current loaded molecule will be lost and a new molecule will be loaded from the file Currently only SMILES and MDL MOL formats are supported 4 Single molecule edit mode All the features implemented for the browsing mode are also available for the edit mode To enter the edit mode the user must press the key E when in browser mode Pressing the E key again will bring the user to browsing mode 4 1 Add atom Pressing A in edit mode will bring up a dialog for choosing an atom to be added to the molecule The atom will be bonded to the current atom The user can choose de element the direction and the stereochemical information up down 4 2 Add bond Pressing B will bring up a dialog for adding a bond to the current atom The user will be given a list of atoms to which it can be bonded to The list will be ordered in descending ord
3. User manual for Navmol by Rui Fartaria Florbela Pereira Jodo Aires de Sousa October 2012 Navmol is a software built for enhanced browsing and editing of molecular structures by visually impaired users This document presents a short set of instructions for using the software and the description of the main features implemented in the current version Table of Contents 1 Basic desciiptiom arene cacincaalcan secs ace a aa usa ud EAE DASANE EO ESETERE 2 2 Software requirements sesseeeeessessesseesserseessessesseessesseeseessrsseesoessessoesserseesorsseeseessessensoessrsseessseessses 2 3 Single molecule browsing mode seeseesseeseeseessreseeseeeseeserssressessrsseesesseeseeseeessstessseeesseeesseresseees 3 3 1 Basi Mavis alles cosescs aserleiausnieeiatenionreedaanladusianiieuasnnviaseianiiednianhnenlinielon cease peranieonemnaaaeicnvalys 3 32 At m nformat ON mesei Genesys eea E Ea cosas EE Eia Eer LETE a needa eine 4 Bid Bo kmarks isei eriin e E EuR AE AE aT E A EEE AK re 4 3 4 J mp t at me iSi airn a e T a E aaia aa ahead Eee i O a a setie 5 3 5 Navigation NiStOrY csi ipe ireo a a a E Te E 5 3 6 Navigation by numerical order eseeeessesseeseeseesseeseessreseessessreseeseesseesessesseesstessseesssresssseessee 5 3 7 EASE EIN GS oeei EOE ea ASE RAEE OE S Ea EREE EE ASE catia twee 5 3 8 Functional group search eseseeeesseseessressessesseessessessessesseesseseeeseestesseeseeseessreseeserssresesses
4. ard coded in the program Therefore adding a new messages_ lt locale gt properties will not automatically add a new entry to the language list This will be changed soon 10 10
5. drants corresponding to having an oblique cross superimposed on a circle e The TOP quadrant is related to the UP direction UP ARROWKEY and corresponds to the 11 12 and 1 o clock coordinates e The RIGHT quadrant is related to the RIGHT direction RIGHT ARROWKEY and corresponds to the 2 3 and 4 o clock coordinates e The BOTTOM quadrant is related to the DOWN direction DOWN ARROWKEY and corresponds to the 5 6 and 7 o clock coordinates e The LEFT quadrant is related to the LEFT direction LEFT ARROWKEY and corresponds to the 8 9 and 10 o clock coordinates 3 2 Atom information Atoms in Navmol are referenced by their chemical symbol followed by their number I D in the molecule When the user is at an atom information can be requested for the current atom where the cursor is positioned by pressing the SPACE key Navmol will then report the following properties 1 The chemical symbol and number I D 2 Number of bonded neighbours followed by list of all neighbours and respective clock coordinates and type of bonds for each bonded neighbour 3 Formal charge of this atom if it is charged 3 3 Bookmarks Navmol allows for the user to set up a number of bookmarks at different locations on the molecule This way the user can mark locations e g functional groups on the molecule and then jump between them Bookmarks are set by pressing the keys CTRL plus 1 to 0 which means the user can set up ten different bo
6. ename Currently only MDL MOL formats are supported for saving 5 Reaction browsing mode Reaction mode is activated when a reaction file is loaded In this mode the user can navigate the individual molecules with all features implemented for the browsing mode and move to the next or previous molecule of reactants or products pressing TAB key or SHIFT TAB Keys respectively The user can as well swap from reactants to products using the mapping key M that allows the moving between corresponding atoms in the reactant and product molecules according to the reaction mapping 6 Summary of keyboard instructions This is the list of keys and key combinations used to browse a molecule in navmol It is also accessible on the program by pressing the H key List of keys e UPARROW KEY go to a bonded atom at 11 12 or 1 o clock RIGHT ARROW KEY go to a bonded atom at 2 3 or 4 o clock DOWN ARROW KEY go to a bonded atom at 5 6 or 7 o clock e LEFT ARROW KEY go to a bonded atom at 8 9 or 10 o clock e CTRL KEY UP OR DOWN KEYS go to atom next or previous following number label e CTRL KEY LEFT OR RIGHT KEYS follow browsing history on forward or backward directions respectively J KEY jump to atom labelled by given number SPACE KEY give information about current atom e CTRL SPACE KEY give information about the molecule e FKEY give list of functional groups found on the molecule e CTRL KEY 0 TO 9 KEYS set a boo
7. er of geometrical distances to the current atom 4 3 Remove atom The option of directly removing an atom does not exist Instead the user can press CTRL A and a dialog will come up to transform the current atom and its respective bonds to dummy objects The dummy atoms and bonds do not exist in the chemical compound and are only used to connected sets of atoms After pressing the keys CTRL A the user will be prompted to confirm with Y or N that he she wants to transform the current atom and all connected bonds to dummy objects 4 4 Remove bond The option to directly remove a bond does not exist Instead the user can press CTRL B and a dialog will come up to transform a bond into a dummy object The user will be given a list of the bonds connecting to the current atom 4 5 Clear dummy objects The user must go to a real atom i e a non dummy atom and then press CTRL C to effectively remove all the dummy objects The user will be asked to confirm this operation Navmol will identify any loose fragments and reconnect them with dummy bonds 4 6 Change atom charge Pressing C will bring up a dialog for changing the formal charge of the current atom from 8 to 8 8 10 4 7 Save file with a new molecule To save a file with the current molecule the user can press the ALT S keys A file save dialogue will appear for that effect After saving the new file the Navmol will inform the user that the file extension mol will be added to the fil
8. kmark e 0TO9 KEYS go to bookmark e R KEY give short list of rings SHIFT KEY R KEY give long list of rings ALT KEY O KEY open file with new molecule or reaction ALT KEY S KEY save file with a new molecule 9 10 E KEY enter the single molecule edit mode e AKEY add an atom in edit mode e CTRL KEY A KEY transform the current atom and all connected bonds to dummy objects in edit mode e CTRL KEY B KEY transform a bond into a dummy object in edit mode e CTRL KEY C KEY clear dummy objects in edit mode e C KEY change atom charge in edit mode TAB KEY move to the next molecule in the reaction SHIFT KEY TAB KEY SHIFT KEY TAB KEY move to the previous molecule in the reaction e M KEY move to the same atom in different molecule according to reaction mapping 7 Integration with JAWS and other screen readers Navmol by default uses the FreeTTS speech synthesizer to communicate with the user but it also integrates with JAWS and NVDA and possibly other screen readers that support the java access bridge and that listen to accessible description change events from Java applications The user can interchange between using the synthesizer or other supported speech synthesizer by pressing the CTRL S keys 8 Language selection The Navmol interface is internationalized The user can select between available languages by pressing CTRL L Currently the language list is h
9. oals in mind The first is to make a sketch available to people that are not completely blind and the second is to enhance the interaction between sighted and blind people when using the software together e g in a classroom Using the keyboard the user can browse the molecule and get extra information on atoms set up bookmarks browse the history list functional groups add remove atoms and bonds change atom charge browse a chemical reaction and perform a wide variety of operations 2 Software requirements Navmol is a Java based application therefore a basic requirement is the installation of a Java virtual machine Navmol has been developed and tested with the Java SE Runtime Environment build 1 6 0_22 b04 or just JRE 1 6 0 22 distributed by Sun The download link for this software is http www java com getjava The other software needed is e The Java access bridge Download at http www oracle com technetwork java javase tech index jsp 136191 html for Windows and at http ftp gnome org pub gnome sources java access bridge 1 26 java access bridge 1 26 2 tar bz2 for Linux to be used with the Gnome desktop environment e The FreeTTS speech synthesizer downloadable at http freetts sourceforge net docs index php e The eSpeak software downloadable at http sourceforge net projects espeak files espeak espeak 1 46 espeakedit 1 46 02 win zip download e The CDK libraries downloadable at htt
10. okmarks In order to jump to an atom referenced by a bookmark the user presses one of the 1 to 0 keys For example a user could set up the bookmark number 1 by pressing CTRL 1 at atom 3 of lets say hexane and then move along to other atoms If the user wanted to 4 10 go immediately to atom number 3 again it would have just to press 1 in order to do so 3 4 Jump to atom By pressing the key J the user will be prompted to insert the number I D of the atom he she wants to navigate to finish by pressing RETURN KEY This of course implies that the user already has some knowledge of the ordering of the atoms on the molecule When jumping from one atom to another Navmol will describe the move that was made with the following information 1 The atom s chemical symbol and number I D where the cursor is jumping to 2 The clock coordinates for the direction of the jump 3 The number of bonds involved in the jumping 4 If this is the first time the atom is visited 3 5 Navigation history Navmol registers all the navigation actions taken by the user In order to navigate according to history the user has to press the CTRL LEFT ARRWOWKEY and CTRL RIGHT ARROWKEY to go back and forward in history respectively This way the user can remake all steps he ger has done until that point If the user goes back to a certain point in history and performs any navigation action from that point on a new history is started The previous histo
11. ow will move the cursor to that atom Furthermore navmol uses the clock coordinate system to more accurately report on the direction of the neighbour bonded atoms The current atom where the cursor is positioned is located at the centre of the clock and the bonds work as if they were the clock pointers When the cursor is moved to another atom that atom becomes the centre of the clock Lets say we have the molecule Cl and in the sketch this molecule is drawn horizontally Lets say the user starts with the cursor on the atom at the left side This atom will have only one neighbour the one at the right side at 3 o clock of the current atom If the user presses the RIGHT ARROW key the cursor will be moved to the atom on the right Now there is only on neighbour for this atom positioned at 9 o clock which is the opposite direction to 3 o clock When a move is made Navmol will give the following information to the user 1 The atom where the cursor is moving to 2 The clock coordinates for the direction of the move 3 The type of bond through which the move is being performed 4 If this is the first time the atom is visited 3 10 For example in the case of Cl in the first move to the right Navmol would say Moved to atom C12 at 3 o clock through a SINGLE bond First time visited The correspondence between the clock coordinate system and the arrow keys is made as follows e The clock circle is divided in four qua
12. p sourceforge net apps mediawiki cdk e The JchemPaint libraries downloadable at http sourceforge net apps mediawiki cdk 2 10 FreeTTS CDK and JchemPaint are usually distributed with Navmol so that the the user only needs to have the Java virtual machine and the Java access bridge properly installed The users must install the eSpeak program which supports several different languages to use their native language i e other than English However in the current version only English and Portuguese languages are available but any user can easily convert Navmol to their native language by translating the existent language file 3 Single molecule browsing mode Here we present the main navigation features of Navmol The items in this section are thought to be presented in a way that allows the user to start by reading about the most frequently used features Therefore we start by describing the features related to navigation and we will leave the ones related to structure and function analysis more to the end 3 1 Basic navigation At start the user will be located in an atom of the molecule In order to navigate on the molecule the user has to press the arrow keys UP DOWN LEFT and RIGH The directions pointed by these keys are loosely related to the real direction at which the neighbour atoms will be For example if the current atom is bonded to another atom that on the sketch is above the current atom then pressing the UP arr
13. ry is kept but all the steps that were forward to that point are lost 3 6 Navigation by numerical order If the user wants to explore the molecule by moving from atom to atom following the numerical ordering of the atoms in the molecule he she can do so by using the keys CTRL UP ARRWOWKEY or CTRL DOWN ARRWOWKEY in order to go to higher or lower numbered atoms respectively 3 7 List rings Navmol can analyse the molecule and report a list of rings in case they exist found on the molecule By pressing the R key the user will get a list of all rings that have six or less atoms Navmol will also inform if a ring is aromatic or not By pressing the SHIFT R keys the user will 5 10 get a list of all rings in the molecule The rings reported this way are not the conventional rings sighted users are used to perceive from molecule sketches which are usually the rings given on the short list of rings reported by pressing R With SHIFT R Navmol reports all rings Lets try to envision a simple case two aromatic rings sharing one bond as in the case of naphthalene for example Navmol will report the existence of three aromatic rings Two correspond to the benzene rings with 6 atoms and the remaining one concerns the ring formed by the outer parts of the benzene rings By outer we mean the bonds belonging to the two benzene rings that are not shared Therefore if the long list of rings enlists more rings than the short
14. s on the name of the functional group must be substituted by underscore _ characters The third column is the SMARTS string sequence of characters specifying the functional group The format of a line to start a set of functional groups is 6 10 e Columns are separated by spaces e The first column is a number 0 or 1 that sets the set to be off 0 or on 1 The second column is the word BEGIN capital letters e The third column is the name of the set Any spaces on the name of the set must be substituted by underscore _ characters The format of a line to end a set of functional groups is e Columns are separated by spaces e The first column is a number 0 or 1 No meaning here The second column is the word END capital letters The third column is the name of the set Any spaces on the name of the set must be substituted by underscore _ characters By pressing the F key the user will get a list of the functional groups in the molecule including the atoms where those groups are found For example on ethanol C C O H navmol would report ALCOHOL at atoms 2 and 3 in the following way Functional group ALCOHOL Times found 1 Atom list 2 3 1 The name of the functional group 2 The number of times that the functional group is found in the molecule 3 List of atoms by number I D that defined the functional group 3 9 Molecule information The user can press CTRL SPACE to get
15. sseresse 6 3 9 Mo lec le information sisne airian i n n a ania a e e i e aE 7 3 10 Open file with new molecule s nsnesneseeeseessessessoessesseesoessesseessesseesoessersessoessessosssesseessseesssereseo 8 AS Singlemolecde edit Moderisano EE E E a EOE EE ERTE Eisd 8 AD a Ca IEE LOT i T E E 8 AD Add BONdaiponsiie e nee a ieee a E aaa ea a a ee 8 4 32 Remoye atosi scare cece aree EE E E E E E E EEE E EE EREE 8 44 Remove bond eren eisene ea i e eaaa a es i ag hee aa dada a gute ae daa eed pop Ea 8 4 5 Clear d mmy DC Cts sneri e a A EE E AiR EEE Ria 9 4 6 Change atom Charge voice ccesscasysceysseyasessesadniveds EE E E O RAE E S ER 9 4 7 Save file with a new Molecules eee eccccccccccecececececececececeeeceseseseceeeseessesesesssessceseuunnceseseaees 9 5 Reaction browsi g TOUS 2225 ccicicnsdecdhscadapisataesedias acetal ansyovaddcnlugaaapsasenteascesahahaensdanuisasasccauateaeaueiacewae 9 6 Summary of keyboard MSU CONS cc sce Besancon lessen sapcuicyas tence sdeseeseandeeuss tardedposs ee vbenaudsdbyedeseance 9 7 Integration with JAWS and other screen readeTS csccesccssseceseceseeceeeeseeceaeceseeceaeeeseeseeeeneeeeaeees 10 8 Lang age selection eresie Spends AR E p lds paven A E E N EA 10 1 Basic description The main window of Navmol is composed of a large visualization area and a small text area placed bellow it The purpose of the visualization area is to show a large sketch of the molecules loaded in Navmol with two g
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