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The GUI requires that Tkinter, a python binding to the Tk GUI toolkit, be installed. For example, the program includes a graphical user interface (GUI, Figure 2) for those not comfortable using the command line. WebChem Viewer’s enhanced features may require some additional installations. We recommend the free Anaconda python distribution provided by Continuum Analytics, Inc. Simple-to-use installers are available for Windows as well. Python comes installed by default on OS X and most Linux distributions. Strictly speaking, the program requires only a python interpreter. To aid those generating these output files, we also kept the required dependencies of WebChem Viewer itself to a minimum.
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Tutorials describing how to use WebChem Viewer and Simley2png can be found in the Supporting Information (Additional files 1 and 2).
The service can be accessed through the National Biomedical Computation Resource’s Web Services Opal Dashboard, which is directly linked to from the NBCR homepage at.
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We encourage the use of this remote service independent of WebChem Viewer, both directly through its web interface and programmatically as a component of other software packages. However, to simplify the user experience we also created an online web application (i.e., Opal service ) called “Smiley2png 1.0” that can generate these images remotely, thus eliminating the need for a local Open Babel installation. The program can be downloaded from and is released under the FreeBSD license.īy default, WebChem Viewer inserts images of molecular structures into user-provided data sets using the Open Babel software package. To this end, we have created a program called WebChem Viewer with unique capabilities currently lacking in similar software packages. There is a need for a simple, free, open-source program that can automatically generate data files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Sharing these data sets effectively is a common task that is greatly enhanced when images of the relevant molecular structures are incorporated into collaborative reports. īiological and chemical projects often generate large amounts of chemical data, ranging from percent yields to docking scores to in vivo drug activities.
The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at.
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The program is released under the FreeBSD license and can be downloaded from. With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. We encourage the direct use of this online application as well as its incorporation into other software packages. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings.
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We here present a program called WebChem Viewer that automatically generates these types of highly portable reports.
There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry.