Marvin sketch

Marvin Sketch is a stmcture-editing tool, a component of java-based Marvin Tools provided via an academic license from the ChemAxon company [30] (Fig. 1.4). 

Open-Source Tools, Techniques, and Data in Chemoinforniatics 

CD/ChemSketch is a freeware for drawing chemical structures including organics, organometallics, polymers, and Markush stmctures [31]. It has options for structure cleaning, viewing and naming, inch conversion, stereo descriptors etc. For freeware, no technical support is provided and the functionalities are less compared to the commercial version which has structure search capabilities (Fig. 1.5). 

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Graphical input and output is essential to any chemical Web application. One common method to provide this is using Marvin or another sketching tool. Rather than have each application generate the javascript needed to present the sketcher or viewer, consider storing this code in the database and selecting it when needed. The marvin sketch function returns javascript that will cause a marvin sketch applet to appear on a Web page. 

Create Or Replace Function marvin sketch() Returns Text As EOSQL ... 

The marvin sketch SQL function can be called from any client program using database access methods described in Chapter 5. The marvin sketch program can be modified to allow specification of the sketch applet size, loading an initial SMILES, or any other option provided by the Marvin sketch applet. 

Fig. 1.4 The GUI of Marvin Sketch with advance options to display explicit atomic coordinates and connection table. It has all the features of a basic drawing tool and also some additional features like structure to name generation, prediction of few properties, and conversion to 3D...

Fig. 1.13 GUI for copying a structure in SMILES format using Marvin Sketch...

Calculator plug-in in Marvin Beans from ChemAxon is used for ealeulating a number of descriptors and is available via an aeademie request [38], It ean be accessed from Marvin Sketch and Marvin view modules. For effieieney, it is advisable to run it using cxcalc command in batch mode from eommand prompt. A number of diverse descriptors can be eomputed in a short time. 

We can also compute 3D descriptors using the cxcalc option. Draw a structure of aspirin molecule (acetyl salicylic acid) in Marvin Sketch and save it as. smi in the Marvin Beans folder. In the command window, type cxcalc stereoisomers -v true aspirin.mol to generate the stereoisomer of the molecule. Similarly, the command cxcalc lowestenergyconformer -f mrv test aspuin.mol calculates the lowest energy conformer of aspirin (Fig. 2.5). 

JChem Marvin KNIME extensions are also available [22]. The modules allow researchers to handle chemical structure data using ChemAxon s software tools such as Marvin, JChem and Standardizer within the open-source KNIME workflow environment. The KNIME platform provides a modular environment to visually create data flows, analyse and build predictive models. The JChem Extensions contain some nodes that are free of charge for general use. These nodes are called Marvin Family Nodes which include a set of nodes for structure conversion, Marvin Sketch , Marvin View and Marvin Space which offer sophisticated rendering capabilities for chemical structures. 

Marvin Sketch is an advanced chemical editor used for drawing stmctures, queries and reactions [20], This tool can be integrated into the portlet by using javascript as follows ... 

Steps for using Marvin Sketch Portlet available at http //moltable.ncl.ies.in Step 1 Chck Draw Molecule to start MSketch Molecule Editor (Fig. 10.12) Step 2 If you are working behind a proxy server, use login details to load web appUcation (Fig. 10.13)... 

ChemAxon Marvin Sketch, http //www.chemaxon.com/marvin/help/index.html. Accessed 8 May 2013... 

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