If the number of structures is large, this popup can be very slowĪnd the structures so small as to be unusable. The final way to display compound structures is asĪ small popup with just the selected structures displayed. Second way is to display the compound structure directly on the node. Includes not only a 2D representation of the compound, but also information about the node or edge associated with theĬompound or calculated chemical descriptors such as the molecular weight. Or edges or for nodes and edges with large numbers of compounds, the easiest way to view the compounds is with a table that Thisĭialog allows users to customize the settings used by chemViz2 for various cutoffs and settings Maximum number of compounds to show in 2D structure popup chemViz2 has three ways of displaying the 2D structures corresponding to SMILES or InCHI strings. Each of the settings is discussed briefly below.įigure 2. Similarity edges and restricting the number of compounds to show in a dialogĭialog can also be used to change the default cutoffs for creating These attributes may contain Cytoscape lists or comma-separated values.Įither of these settings can be overridden through the Settings. InCHI strings will be searched for in the attributes: InCHI, inchi, InChi, or InChI. By defaultĬhemViz2 will look for SMILES strings in the Cytoscape attributes: SMILES, Smiles, smiles, The first step in using chemViz2 is to adjust the settings to correspond to your network attributes. The settings dialog is discussed in more detail in the next section. Submenus since its only function is to bring up the settings dialog. The exception to the above discussion is the Settings. (grayed out) if no chemical information is detected on any of the selected nodes or edges as appropriate. Node and edge context menus only apply to nodes or edges, as appropriate, and most items will be disabled The all nodes and all edges menu items willĪlways appear, but will be disabled (grayed out) if chemical information is not detected on any or the Similarly, the selected edges menu will appear only if edgesĪre selected. The action should be performed on all nodes, all edges, Chemical information is appropriate onĮither edges or nodes, so the global submenu provides submenus that allow the user to indicate whether Provides a Cheminformatics Tools submenu. The chemViz2 source is available on github atĬhemViz2 functionality is available through a "global" menu under theĪpps and as either node or edge context menus. In either approach, select the app and press Install. Is tagged with them molecular structure tag, or you can just searchįor chemViz2.
Cytoscape citation install#
To install chemViz2 start Cytoscape 3.1 or better and either navigate directlyĬytoscape App Store using a web browser, orīring up the App Manager ( Apps→App Manager). You must be running Cytoscape 3.1 or newer.
Cytoscape citation download#
To download chemViz2 using the app manager, Version 3.0 of Cytoscape and is available from the Cytoscape appĬhemViz2 is available through the Cytoscape App store or In the network above, nodes areĬolored by the number of hydrogen bond acceptors and node borders areĬolored by the number of hydrogen bond donors. Mapped onto Cytsocape attributes where they can be used by the Weight, ALogP, molecular refractivity, number of Rule of Five Hydrogen bond donors, number of hydrogen bond acceptors, molecular
Cytoscape citation windows#
Independent windows or as part of a table also showing CytoscapeĪttributes and calculated compound descriptors, including number of The 2D diagrams can be presented as scalable Values to create chemical similarity networks. chemViz2Ĭan also calculate Tanimoto similarities of compounds and use the chemViz2 displays 2Dĭiagrams of compounds specified by InCHI or SMILES strings.
UCSF chemViz2 is a Cytoscape app that extends the capabilities ofĬytoscape into the domain of cheminformatics.
and the Results Panel shows one of the compounds that tested positive in the assay. Larger images of two of the structuresĢD structures for the compounds have been painted directly Generated for the selected nodes, and the number of hydrogen bond acceptors and donorsįor the compounds have been calculated and added to the table. Shows a portion of a network of compounds similar to a compound that was a "hit" in an assayįor activity against malaria.
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