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MOLinsight

 

 

A web portal for the processing of molecular structures by blind students

 

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last update: 14.08.2014

 

The MOLinsight web portal is a gateway to open-source software as well as software freely accessible to students that can be integrated in strategies for blind users to process chemical structures. Here you can find documentation for available programs  and a guide to decide about the tools for specific tasks.

 

Software

 

How to do common tasks?

  1. Guidelines to interpret a molecular structure

  2. Guidelines to build a molecular structure

  3. Verify if two chemical structures in different file formats are the same

  4. Get information about general properties of a molecule (e.g. molecular weight, exact mass, number of atoms, estimated logP)

  5. Interpret the stereochemical features of a molecule

 

 

NavMol

 

NavMol 1.0

 

NavMol was developed as a part of the ICT Project and is a prototype of a molecular editor for visually impaired users. The program supports MDL .mol files. The NavMol program is a very simple standalone application written in the C programming language, which provides an MS-DOS or Linux shell command-line interface. Users can interact with the program via the keyboard and text-to-speech software, or Braille hardware. The NavMol program enables the user to navigate the molecule atom-by-atom, providing information about neighbors of each atom and bond types. It also allows structures to be changed by adding or deleting atoms and bonds.

 

WINDOWS:

Download the navmol 1.0 file to your desktop. To know how the NavMol 1.0 works please read the NavMol 1.0 notes.

 

LINUX:

Download the navmol 1.0 file to your desktop. To know how the NavMol 1.0 works please read the NavMol 1.0 notes.

 

 

NavMol 2.0

 

 

The latest version version of NavMol (NavMol 2.0) has been completely rewritten and has a lot more features. NavMol was developed in Java using the FreeTTS speech synthesizer and is also possible to use it with a screen reader software by installing the Java Access Bridge. This feature was tested on Windows 7 and Vista with JAWS.

 

Instalation of NavMol step by step:

 

1. You will need to install the latest JavaTM from SUN in your computer. Download JavaTM here.

 

 

2. Instalation for WINDOWS users:

  • Download the navmol 2.0.zip file to your desktop.

  • Unzip navmol.zip to C:\ and perform the following actions:

          Open the file manager,

          Right click on the navmol.zip file and choose "Extract all",

          Specify the location to extract the files, for example C:\

  • Using the file manager navigate to C:\navmol\bin.

  • Double left click on the navmol.jar file to run NavMol.

 

 

3.  Instalation for LINUX users:

  • Download the navmol 2.0.zip file to your home folder.

  • Open a console (terminal).

  • Unzip the navmol.zip file to your home folder:

          $ unzip navmol.zip

  • Run NavMol using the command line: java -jar ~/navmol/bin/navmol.jar

 

 

List of features currently implemented on NavMol 2.0 (written by Dr. Rui Fartaria):

  • Geometry-based browsing of the molecule using the arrow keys.

  • Bookmarks - allow the user to mark important points on the molecule.

  • Jump to any atom by giving the number.

  • Current atom information:
          a) bonded neighbours, with type of bonds and directions (using the clock coordinates).
          b) implicit hydrogens.
          c) charge.
          d) aromaticity.

  • Molecule information:
          a) Number of atoms (excluding implicit hydrogens).
          b) Formula.
          c) Number and location of rings.
          d) List, with location, of functional groups (alcohol, ketone, aldehyde, amide, ester, and many others).

 

We hope you enjoy the new software. Your feedback will be very welcome.

For more information please contact Dr. Rui Fartaria (rui.fartaria@gmail.com) or Prof. João Aires de Sousa (jas@fct.unl.pt).

 

The NavMol development team: Rui Fartaria, Florbela Pereira and João Aires de Sousa.

 

Tips:

For examples of molecular structures of organic compounds in MDL .mol file download the zipped file formulae.

You need to start with an existing mol file to build a molecule. You can always start with a file with at least a bond between two atoms, for example a simple organic compound such as methane (CH4), methane.mol.

 

Outreach:

The NavMol software was highlighted in the portuguese science TV show "Com Ciência" (RTP 2) in 02.05.2012. In the interview Dr. Florbela Pereira explains the main features of NavMol and a demonstration of the software is also made by a visually impared  student.

 

 

Publications:

 

 

BrailChem

 

BrailChem was developed as a part of the ICT Project and is a software for visually impaired users. The program supports a wide range of file types, namely: IUPAC name, SMILES, CDXML, CDX, CML, InChI, MOL and PDB.
BrailChem contains two subapplications: a molecular browser and the periodic table of elements.
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 molecular structures, it is just a presentation tool of data retrieved from the server. So in order to work the client must be connected to the Internet and have access to a BrailChem server.
 

 

The BrailChem server is available in the web and it can navigate a molecular structure, read molecular properties, identify functional groups, and read chemical reactions. It can also convert a name into a structure if it is available in a very large dictionary based on the PubChem database. Furthermore it can navigate the periodic table of the elements.
 

To know how the BrailChem works please go to the introduction to Brailchem webpage.

 

Download BrailChem:

BrailChem client is available as a Firefox extension. You can download and install it directly from Firefox by clicking on this link pointing to the extension module. Continue according to the instructions of the browser. After the installation and final restart of Mozilla Firefox, BrailChem can be opened from the tools tab.
 

The BrailChem software was written by Bedřich Košata (responsible for the server part) and  Milan Zamazal (responsible for the client part).

 

 

 

Marvin Sketch/View

 

Marvin Sketch/View is a proprietary software from ChemAxon, both in commercial and academic versions. This program supports a wide range of file formats, namely: MOL, MOL2, SDF, RXN, RDF (V2000/V3000), SMILES, SMARTS/SMIRKS (recursive), MRV, InChI, CML, PDB, and IUPAC name.
 

To download the Marvin Sketch/View please go to the ChemAxon's free academic package, visit the download page, select  Marvin software and register. If you have any questions about how to apply for, maintain or access software provided under the Academic Package conditions please visit the ChemAxon academic package support forum or contact us.
 

Command-line applications:

MolConverter  is a command-line program in Marvin Beans that converts between the following file formats: smiles, name, or mol for SMILES, IUPAC name, and MDL Molfile.
 

To know how the MolConverter works please read the MolConverter notes.

 

 

 

OpenBabel

 

OpenBabel is a free software with a chemical expert system mainly used for converting chemical file formats, which also provides the calculation of molecular properties. It supports a huge variety of common chemical file formats, including SDF/MOL, Sybyl mol2, PDB, SMILES, XYZ, and CML.

 

Download OpenBabel:

Executable for Windows NT OpenBabel2.2.3b_Windows_Installer

Macintosh – OpenBabel-2.2.3.mac.zip.

 

For specific installation instructions of OpenBabel-2.2.3 for Mac please go to the OpenBabel install webpage. The OpenBabel package includes a variety of programs, including the babel conversion tools Obprop and Obchiral.

 

Babel is a command-line program in OpenBabel that converts between file formats. To know how the babel conversion tool works please go to the OpenBabel command-line program webpage or read the Babel conversion tool notes.

 

The Obprop program can print a set of standard molecular properties (e.g. molecular weight, exact mass, number of atoms, estimated logP) for all molecules in a file. Obprop works with a single command:

obprop filename

 

The Obchiral program can print chirality information for all molecules in a file.

 

To know how the obchiral tool works please go to the OpenBabel command-line program webpage or read the Obchiral tool notes. You can find examples of stereochemical structures of organic compounds in MDL .mol file in the directory formulae enantiomers.

 

With the Obchiral tool and the NavMol program you can interpret the configuration of chiral molecules. To know more about stereochemistry please read the stereochemistry notes.

 

 

 

Molecular Editors

 

A molecular editor is a computer program for creating and modifying representations of chemical structures. There are several types of molecular editors. Molecular drawing programs are used to generate two-dimensional (flat) representations of molecules and chemical reactions. In the following you can find a breef description of three available standalone programs:

 

1. Marvin Sketch/View (described above )

2. MolsKetch

3. BKchem

 

 

2. MolsKetch

MolsKetch is an open-source multiplatform editor based on Qt4. This program supports the formats of the Open Babel library. This includes popular formats like MOL, SMILES and CML.
 

Download MolsKetch:

Executable for Windows NT molsketch-0.1.1deuterium
 

To know how the MolsKetch works please go to the MolsKetch webpage and visit the page documentation of MolsKetch.

 

Keyboard Commands:

Control+O opens the  MOL format file.
Control+I import
s the  MOL format file.
Control+E use your molecule for other purposes, you can export it as an image (*jpeg, *png, *bmp
or *svg).
 

 

3.  BKchem

BKchem is an open-source software, GPL, Python, largely platform-independent.

This program supports a wide range of file types for import, namely: MOL, SMILES (stereochemistry is not supported) and InChI (stereochemistry is not supported).

This program supports a wide range of file types for exports, namely: SVG, OpenOffice Draw, PDF, EPS (Encapsulated Postcript), MOL, PNG, SMILES (stereochemistry is not supported) and InChI (stereochemistry is not supported).

 

Download BKchem:

Executable for Windows NT bkchem-0.13.0

Linux and other Unix systems – the source code distribution has to be used, the program uses the standard distutils package for deployment and the details are in the INSTALL zipped file in the main BKchem directory, bkchem-0.13.0_2.zip. For specific information related to the MAC OS please go to the page How do I install BKChem on Mac OS X?.

 

To know how the BKchem works please go to the BKchem webpage.

 

Keyboard Commands:

Control+X and Control+N for a new file

Control+X and Control+S to save a file

Control+Shift+A to select all

Control+O and Control+I for chemical information (name, id, molecular formula, weight and atomic composition)

Control+X and Control+C to close the BKchem window

 

 

 

Sonification of IR Spectra

 

Using an open source software (JDXview and CSV to MIDI converter) infrared spectra can be converted into sounds of varying tones. In the sonified infrared spectra (SIRS) the visual information is converted into non-speech sounds to convey information that is used in the interpretation of scientific results (see the example for Aspirin® in the figure).

 

Publications:

Sonified infrared spectra and their Interpretation by blind and visually impaired students, F. Pereira*, J.C. Ponte-e-Sousa, R.P.S. Fartaria, V.D.B. Bonifacio, P. Mata, J. Aires-de-Sousa, A.M. Lobo, J. Chem. Educ. 2013 (in press).

 

In the Press:

The sound of spectra, Chemical and Engineering News, 2013, 91, 30.

 

In the Web:

Sounds science: research results for the visually challenged, Pasco Phronesis Science Blog.

 

 

 

HOW TO DO COMMON TASKS?

 

 

1. Guidelines to interpret a molecular structure

 

Your approach to interpret a molecular structure depends on how it is represented, and your knowledge of different notations, nomenclature systems, and expertise with software. 

If you know the fundamentals of the IUPAC nomenclature you should be able to interpret a molecular structure from its IUPAC name, at least for simple structures. 

If you learn and get trained with the SMILES linear notation you should be able to interpret a molecule represented by a SMILES string (see the SMILES notes on the Molinsight portal). Some structures may be easier to interpret from SMILES than from their IUPAC names, others not. 

You may navigate a molecular structure represented in the MDL Molfile format with the program NavMol. It enables the user to jump from atom to atom getting information about the neighbors and bonds of each atom. With NavMol you can get explicit information about the atoms of the molecule and how they are bonded. You can get the program from the Molinsight portal, as well as its documentation. 

For more complex structures it may help to get structures represented simultaneously in the three formats (SMILES, IUPAC name, and MDL Molfile). The different formats are complementary for the quick recognition of specific aspects of the structure. 

There are several software tools enabling the interconversion of molecular formats. Recommended examples of available software are babel (OpenBabel) and molconvert (Marvin Beans). 

Examples are provided to convert molecules between SMILES, IUPAC name, and MDL Molfile with these programs:

 

Molconvert

To convert a molecular file into another format, use the command:

molconvert outformat inputfile

where outformat is the desired output format (smiles, name, or mol for SMILES, IUPAC name, and MDL Molfile respectively), and inputfile is the file to be converted. More details on the use of Molconverter are available.

 

Babel:

To convert a molecular file into another use the command:

babel –i informat inputfile –o outformat outputfile

where informat is the input format, inputfile is the file to be converted, outformat is the desired output format (e.g. smiles, mol, cdx for SMILES, MDL Molfile and  Chemdraw respectively), and outputfile is the new file to be saved. ChemDraw is a popular commercial molecular editor developed by CambridgeSoft. More details on the use of Babel are available.

 

 

2. Guidelines to build a molecular structure

 

Similarly to the interpretation of a molecular structure you may follow several approaches to build a structure depending on your expertise with different methods and tools. 

Learning the SMILES notation will empower you with a very easy way of building molecules. A SMILES representation of a molecule is a very logical sequence of ASCII characters. This string can be directly read by most molecular editors and can be converted to virtually any molecular format (e.g. with molconvert or babel as described in section 1) 

The IUPAC name can also be converted to another format with molconvert. You can also build a molecule with NavMol. See the NavMol documentation to learn it.

 

 

3. Verify if two chemical structures in different file formats are the same

 

An InChI (IUPAC International Chemical Identifier) is a string of characters capable of uniquely representing a chemical compound. It was designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web.

A good way of checking if two molecules are the same is to convert both into the InChI format, and compare the two strings. You can generate InChI files with molconvert or babel.

With molconvert you can generate the InChI for a molecule in file Y.mol with:

Molconvert inchi Y.mol

(then take the line starting with “InChI=”) 

Because the InChI representation of a molecule is unique and non-ambiguous, the two structures are the same if and only if their InChI representations match. You can compare the two strings for example with a spreadsheet, by pasting each string into a different cell and implementing a formula to compare the two cells. 

You can follow the same approach to find if a molecule is included in a list of molecules.

 

 

4. Get information about general properties of a molecule (e.g. molecular weight, exact mass, number of atoms, estimated logP)

 

The obprop program from the OpenBabel package can provide the main general properties of a molecule (in file filename) with a single command:

 

obprop filename 

 

If you want to save the result into a file result.txt you can enter the command

 

Obprop filename > result.txt

 

 

5. Interpret the stereochemical features of a molecule

 

One way to obtain the stereochemical features of a chemical structure is to generate the IUPAC name with the molconvert tool. If the molecule is stored in a chemical format with stereochemical information properly specified, then you can usually get the R/S label. If you know the fundamentals of the IUPAC nomenclature, and the CIP rules (Cahn-Ingold-Prelog rules, see the stereochemistry notes), you should be able to interpret the IUPAC name in terms of the geometrical configuration of the molecule, at least for simple structures. 

 

Molconvert command:

 

molconvert name name.mol

 

If you want to save the IUPAC name into a file name.name you can enter the command:

 

molconvert name name.mol –o name.name

 

Another approach to the stereochemical information of a chemical structure is via the SMILES string obtained e.g. with molconvert or babel.

The SMILES chirality label of a chiral tetrahedral carbon atom is based on the order in which neighbor atoms of the chiral center occur in the SMILES string. Looking at the chiral center from the first atom occurring in the SMILES (or the second atom if the first is the chiral atom), the symbol "@" indicates that the following neighbors are listed anticlockwise and "@@" indicates that the neighbors are listed clockwise. 

If you learn and get trained with the SMILES linear notation, and the CIP rules, you should be able to obtain the CIP R/S label from the SMILES stereochemical specification and vice-versa, and to perceive the geometrical arrangement of the ligands.

To know more about stereochemistry specification in SMILES, see the Daylight website.

 

A different approach to obtain stereochemical information of a chemical structure is with the obchiral tool (OpenBabel) together with NavMol. The obchiral program identifies chiral atoms and displays the ordered list of the neighbors (sorted by the atoms’ id) as well as the parity value (see the stereochemistry notes on the Molinsight portal).

With the NavMol program you can know what the four ligands of the chiral center are, and you can assign priorities according to the CIP rules. The idea is that the geometrical arrangement of the ligands can be perceived from the parity value, and this information combined with the assignment of the CIP priorities is enough to derive the R/S label. 

To assign the parity value, the four ligands are sorted by ascending atom id and the chiral center is observed with the fourth ligand pointing away from the observer. If the first three ligands in the sorted list are arranged clockwise, then the parity is 1. Otherwise it is 0. If one ligand is a hydrogen atom it is always the last ligand. If the list of ligands sorted according to the CIP rules coincides with the parity list, then the parity value 1 corresponds to R and the parity value 0 corresponds to S. The same is valid if even numbers of permutations are required to transform one list into the other. If odd numbers of permutations are required then the parity value 0 corresponds to R and the parity value 1 corresponds to S.

 

Obchiral command:

 

obchiral name.mol

 

If you want to save the obchiral results into a file results.txt you can enter the command:

 

Obchiral name.mol > result.txt

 

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