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NavMol 1.0


The NavMol program works via the MS-DOS command-line or the Linux shell. If you are not familiar with the use of the command line of the MS-DOS, the following advices can simplify the use of the NavMol.



You must first go to the directory of the NavMol program and the file (MDL.mol) that you want to read. For example, if you placed the navmol4h.exe and the file A_1.mol in directory C:/example1, to open this file with NavMol, you have to take the following steps:


Open an MS-DOS window and go to the directory example1 by typing

“C:\” and Press [Enter];

“cd c:\example1” and Press [Enter];


And now you start to navigate the molecular structure of the A_1.mol file.


Navigating molecules:


1. Start the program and load a MDL .mol file with the command

            navmol filename


2. You are starting at the atom with id=1.


3. To get information about the neighbors (up to 6 neighbors) type q, w, e, r, t, or y. It displays the atomic symbol, the id, the charge, and the bond order. J indicates this is the atom visited immediately before. X indicates the atom has already been visited.


4. To jump to a new atom, type the id of the atom.


5. To get information about the current atom, type a.


6. To clean the memory about atoms previously visited, type 0.


7. To list the total number of atoms and bonds, type v.


8. To get a list of available commands, type h.


9. To end, type x.



Editing molecules:


1. Add a new atom connected to the current atom by typing

+ A B C

where A is the bond order (1, 2, or 3), B is the atomic symbol of the new atom, and C is the charge of the new atom.


2. Add a bond between two existing atoms (useful to close rings) by typing

b A B C

where A and C are the id of the atoms to be connected, and B is the bond order.


3. Add a benzene ring to the current atom by typing ‘z’.


4. Delete the atom with the highest number by typing '.' (the bonds involving this atom are also deleted).


5. Delete the bond between two atoms by typing

            - A B

            where A and B are the two atoms of the bond.

6. Change the charge of an atom by typing

           c A B

            where A is the id of the atom and B is the new charge

7. Save the molecular structure in MDL .mol format by typing

            s filename



The new edited chemical structures that were built and saved with NavMol in an electronic format can be visualized by non-blind people using a common molecular visualizer with a GUI. However first you must generate a drawing (the 2D coordinates) with molconvert:


“molconvert -2:2 mol aspirin.mol -o aspirin_2D.mol”


More details on the use of molconverter are available.





With the current version, to build molecules, one has to start with one existing file. You can always start with a file with only a bond between two atoms.


When a molecule is saved, all information available in the loaded file regarding stereochemistry, radicals, or isotopes is discarded.


If aromaticity is specified in the MDL Molfile, the bond order of aromatic bonds are displayed as 4. However, addition of bonds with bond order >3 is not allowed with the current version of NavMol.




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Webmaster: Vasco Bonifácio

last update: 01.06.2010