Molecule Viewer

mimv - Molinspiration Molecule Viewer

Molinspiration Molecule Viewer mimv allows visualization of MDL SDfiles or molecules encoded as Daylight SMILES. Viewer is written in Java, therefore is platform independent and may by used on any computer where the Java runtime is installed.
The Viewer is started by a command

java -jar mimv.jar -f datafile

Where the data file is a SDfile or Molfile (should have extension .sd .sdf or .mol) or a file containing molecules in SMILES format, where SMILES is a first item in a line, tab-separated from other data items (molecule name, etc.).

For navigation buttons on the bottom command panel may be used. Several keyboard shortcuts are also supported:

PgUp / PgDn - show next / previous page
Home / End - go to begin / end of the data (in a single batch 2'000 molecules may be displayed, Viewer allows to step through batches to display molecules also in larger files)
d(ata) - show molecule data (other items on a molecule line after smiles)
l(arge) m(edium) s(mall) t(iny) - change size of the molecules
r(m) - removes bottom menu panel (useful when taking screenshots of the Viewer, on Windows systems by Alt PrtScr)
p(ack) - pack molecules after resizing
q - save image with molecules to file mimv.png
Esc - close the Viewer

Viewer allows selection of molecules from the whole set by a Ctrl click and supports various operations on selected molecules (for example revert selection). Selected molecules may be saved into a file mimv.smi (use option save in the Selection menu). Substructure search of molecules in the Viewer is also possible (option substructure in the Selection menu).


The Viewer window may be resized to accommodate proper number of molecules in grid (you may use then a p keyword to pack the molecules).
By double-clicking the molecule a new window with all data for this molecule including smiles is shown (see image on the left).

It may be useful to create a script to launch the Smiles Viewer. On LINUX systems this may have a form

#!/usr/bin/bash
java -jar c:/molinspiration/mimv.jar $*

When this script (you may name it mimv) is saved in the /usr/local/bin the visualizer is simply started by a command
mimv file

On Windows systems you may also wish to create a bat file which launches the Molecule Viewer



The "Options" menu allows selection of rendering mode and various molecule rendering options, including a choice whether the original coordinates read-in from SDfile should be used, or new coordinates created by automatic Molinspiration depiction.

Displayed molecules may be easily saved as a png image (the q keyboard shortcut), which may be used in publications, presentations, or when building web sites.

Click with a right mouse button on a molecule launches a pop-up menu, allowing to copy either molecule SMILES or molecule image to the clipbourd.


Please contact info[at]molinspiration.com concerning a test installation of Molinspiration Molecule Viewer, as well as for price and license conditions (special discount is applicable to academia).