Marvin View

It is beyond the scope of this book to present an entire Web application. The purpose of this discussion is to show how creating and using SQL functions can facilitate the creation of Web applications. The final example shows how SMILES stored in a database can be formatted for display using Marvin. The marvin view SQL function is defined as ... 

Create Or Replace Function marvin view(text, text) Returns Text As EOSQL ... 

PSQL -c "Select marvin view(isosmiles) from " 2 ".structure" else... 

Fig. 1.16 lUPAC name to structure conversion in Marvin View... 

File information M)541- Marvin ID(marvin view was used for visualisation) 06281309572D- 28-June-2013 09 57Ctime) 2-dimensional... 

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. 

Data processed in one program can be piped into another using the vertical line command. Let us compute the logP values for 100 molecules in Ames data set and then pipe the output data to Marvin view to view the table alongside. The command to do so is cxcalc -S -t myLOGP logP -a 0.15 -k 0.05 test ameslOO.smi mview— (Fig. 2.7). 

Fig. 2.7 LogP data for 100 molecules piped to Marvin View to visualize the tabulated results...

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. 

Regardie, Israel. An interview with Israel Regardie his final thoughts and views / edited by Christopher S. Hyatt introduction by J. Marvin Spiegelman. Edited by Christopher S. Hyatt and J. Marvin Spiegelman. Phoenix (AZ) Falcon P, 1985. x, 144 p. Includes Alchemy in the World Today (Which May or May Not Be Relevant)... 

Three nearest neighbors, indexed as 0, 6, and 11, are indicated. The axial slab shown represents 1% of the total length of the virion. From Marvin.31a (B) A 2.0 nm section through the virus coat with the helices shown as curved cylinders. The view is down the axis from the N-terminal ends of the rods. The rods extend upward and outward. The rods with indices 0 to -4 start at the same level, forming a five-start helical array. The rods with more negative indices start at lower levels and are therefore further out when they are cut in this section. (C) The same view but with "wire models" of the atomic structure of the rods. From Marvin et al 2... 

Figure 2.33. A fragment analysis application developed by AstraZeneca by integrating Fragmenter and Marvin in Spotfire. The application provides integrated views on hit frequencies of the fragments from a library in various targeted compound collection spaces. The structure and hit frequencies for the fragments are displayed in the lower-right corner while the user can interactively click one fragment dot or select a set of fragments. This screenshot is provided by Paul Xie of AstraZeneca...

Figure 2.35. Web-based chemistry search tool that combines multiple search criteria to query compound structures and related data. Uses Marvin for structure input and viewing and JChem Base for structural search, designed by Zhenbin Li of Neurogen Corporation...

All these structures can be viewed. More structures can be imported. The selected structures can be exported to any of the following viz. MOLFILE, SDFILE, SMILES, JTF, RDF, Marvin Document. The stractures can be modified as well. A query of 2D structure can also be placed to be searched within the database. For querying, MarvinSketch application from the JChem package is used. 

Liu K, Feng J, Young SS (2005) A software environment for moleeular viewing, descriptor generation, data analysis and hit evaluation. J Chem Inf Model 45(2) 515-522 http //www.ehemaxon.eom/marvin/help/calculations/calculator-plugins.html http //cheminformatics.org/datasets/... 

Marvin E. Tate, Psalms51-100 (wbc 20 Dallas Word, 1990), 241 n. i.c., suggests that ld)nesah lacks a durative force and sometimes is best translated by words such as totally or completely. He suggests that it may on occasion be ambiguous, moving back and forth between for ever and totally. It seems to me that, especially in the present psalm, and not least in view of v. 9 ( and no one knows how long this will be ), the durative sense is to he preferred. Tate, Psalms 50-100, 247, notes several references in this connection 1 Kgs 14 25-26 15 18 2 Kgs 14 14 i6 8 24 13. 

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