MOLinsight

Welcome

The MOLinsight web portal is a gateway to open-source and freely accessible software for blind and visually impaired students to process chemical structures. Here you will find documentation, guides, and recommended programs to empower learning and research.

NavMol

NavMol is a molecular editor for visually impaired users, with command-line and Java versions. Navigate molecules atom-by-atom, get bond and neighbor info, and edit structures using keyboard and assistive tech.

• Navigate molecule geometry with arrow keys
• Bookmarks to mark important points
• Jump to any atom by number
• View bonded neighbors, implicit hydrogens, charges, aromaticity
• Edit: add, change, delete atoms/bonds; specify stereocenters
• Spatialized sound (v2.1a+): binaural audio description

BrailChem

BrailChem is a client-server app for visually impaired users. It supports IUPAC, SMILES, CDXML, CDX, CML, InChI, MOL, and PDB. Browse molecules, read properties, identify functional groups, convert names to structures, and navigate the periodic table.

• Visit the BrailChem webpage for more.
• Firefox users: Install BrailChem extension.

Marvin Beans

Marvin is proprietary software from ChemAxon (free for academics). Supports many chemical formats (MOL, SDF, SMILES, InChI, etc). Its MolConverter command-line tool converts between formats.

• Get Marvin Beans (free academic package)

OpenBabel

OpenBabel is a free chemical expert system for converting file formats and calculating properties. Includes babel (conversion), obprop (properties), and obchiral (chirality).

• Download OpenBabel

Molecular Editors for Non-Blind Users

• Marvin Sketch (see above)
• MolsKetch: Open-source Qt4 editor, supports Open Babel formats. Download | Webpage
• BKchem: Open-source, Python-based, supports MOL, SMILES, InChI, SVG, PDF, etc. Download | Webpage

Sonification of IR Spectra

Using open source tools (JDXview, CSV2MIDI), IR spectra can be converted to sound, enabling blind students to interpret scientific results through audio.

• Tutorial for sonification of IR spectra
• Download tutorial files for SIRS of cholesterol

Interpretation varies by format: IUPAC names, SMILES, and MDL Molfile. Use software like NavMol for navigation, and tools like Babel and MolConverter for interconversion between formats.

• Molconvert: molconvert outformat inputfile
• Babel: babel -i informat inputfile -o outformat outputfile

Learn SMILES notation for intuitive molecular building; use IUPAC names and convert with molconvert. NavMol can also be used to build molecules interactively.

Convert both molecules to InChI (with molconvert or babel) and compare the strings. If they match, the structures are identical.

Use obprop filename (from OpenBabel) to get molecular weight, exact mass, atom count, logP, etc. Redirect output with > result.txt to save results.

Use molconvert name name.mol to obtain IUPAC names with R/S labels. For SMILES, chirality is specified with @ and @@. Use obchiral name.mol for parity analysis and combine with NavMol for detailed analysis.