BioGem Blog

JME/JSME is a free and open-source molecule editor developed by Peter Ertl and Bruno Bienfait. JSME (JavaScript Molecule Editor) is the successor of JME (Java Molecule Editor). JME is a Java applet application converted to JavaScript due to security and portability issues in Java. JSME is a popular lightweight molecule editor application developed so far. Jmol/JSmol is a free and open-source molecule visualization tool developed by Bob Hanson . JSmol (JavaScript Molecule Viewer) is the successor of Jmol (Java Molecule Viewer). Jmol is a JAR (Java ARchive) application converted to JavaScript due to security and portability issues in Java. Jmol is the most popular molecule visualization tool implemented in many bioinformatics or cheminformatics web applications. JSmol in collaboration with JSME, has implemented a 2D ( SMILES string) to 3D structure conversion method by integrating the API of the CACTUS server. The link to an interactive demo of JSME and JSmol is here . B...

OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images, as they appear in journal articles, patent documents, textbooks, trade magazines etc., to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. The CACTUS OSRA tool parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure. Note that any software designed for optical recognition is unlikely to b...

VEGA ZZ is a free (for non-profit academic uses) molecular modelling suite. It consists of many third-party packages, which act as an interface to the VEGA ZZ software. OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. VEGA ZZ consists of an OSRA plug-in that acts as an interface to it. Moreover, it supports imaging devices such as cameras and image scanners for acquiring documents through the TWAIN interface. The VEG...