Clicks

At the start of the development, it had been intended use an expert system shell to implement this tool, however, after careful consideration, it was concluded that this was not the optimum strategy. An examination procedure can be considered as consisting of two parts fixed documentary information and variable parameters. For the fixed documentary information, a hypertext-like browser can be incorporated to provide point-and-click navigation through the standard. For the variable parameters, such as probe scanning paths, the decisions involved are too complex to be easily specified in a set of rules. Therefore a software module was developed to perfonn calculations on 3D geometric models, created fi om templates scaled by the user. 

The 3D representation of the test object can be rotated by means of an ARCBALL interface. Clicking on the main client area will produce a circle which is actually the silhouette of a sphere. Dragging the mouse rotates the sphere, and the model moves aceordingly. An arc on the surface of the sphere is drawn for visual feedback of orientation additionally a set of coordinate axes in the bottom left comer provides further feedback. 

A section view at defect height permits a detailed analysis. Printouts of the front panels are made by clicking. 

The probes themselves could be fitted with a button, like a computer mouse, for clicking when over a grid point. This would allow one-hand operation and make sampling in... 

One or more interesting hits can be selected by clicking the small white box next to the structure. The resulting list of literature can be analyzed or refined (Figure 5-14). 

In order to allow any multiple chlorination of the biphenyl skeleton, the user may define an atom list (eonsisting of hydrogen and chlorine atoms) and substitute all H-atoms by this list. One may click on the drop-down selection box behind the element icons, select the options Generics. .set the user-defined atom to A1 and quit by the OK button. As a result this atom selection is active for the subsequent drawing steps. After this atom list is drawn ten times as the ten substituents, its composition has to be defined by clicking the A, icon on the left-hand side of the structure editor and by selecting H and Cl in the periodic table (Figure 5-16). 

Click the Select network parameter button and choose the Kohonen network pai ameters topology, width and height of the network, neuron dimension, the index of the class identifier, and the number of training cycles,... 

Analyze the Kohonen map. The content of the neurons is given when clicking on the map. 

The left-hand side gives the Kohonen network, which can be investigated by clicking on the neuron. The contents of the neuron, here the chemical structures, are shown in an additional window plotted on the right-hand side of the figure. 

The right-hand side of the form gives the network map in the upper part and to its right the simulated IR spectrum is plotted, which can be downloaded as a JCAMP File (cf. Section 2,4.5, Section 4,2,4.2). By clicking on tbe neurons in the map one obtains the RDF code and the spectrum of the corresponding structure in the lower part of the form and compared with those of the winning neuron,... 

The strategic bond is disconnected by just clicking with the mouse on it. A suitable synthesis precursor is then generated automatically by WODCA by adding appropriate atoms or groups to the open valences. 

Before startiu g a in olecular dyri am ics simulation, L-click on Averages in the Molecular Dynamics Option s dialog box. 

Choose D ETOTand Add to average this value. Repeat this process for ETOT. L-click OK. 

Along with the curve fitting process, TableCurve also calculates the area under the curve. According to the previous discussion, this is the entropy of the test substance, lead. To find the integral, click on the numeric at the left of the desktop and find 65.06 as the area under the curve over the range of x. The literature value depends slightly on the source one value (CRC Handbook of Chemistry and Physics) is 64.8 J K mol. ... 

Before posing the problem for this computer project, we shall introduce another vei y useful piece of microcomputer software by repeating the integration of Eq. (l-36a) with Mathcad (Appendix A). Like other software of this kind, there is a short learning process before mathcad can be used with ease. Once one has entered the equation of interest, mathcad solves it with a click on the = sign. In the present example, the constants of (Eq. l-36a) are entered followed by the desired integral... 

Up to this point, we have used a numerical input file to stress the fact that computers work on numbers, not diagrams, MM3 and TINKER work from numerical input files that are similar but not identical. Both can be adapted to wo rk u n de r th e c om m an d o f a g ra p h i c al w se r i n terface, G UI (p ro n o u n c ed g oo ey , Before going into more detail concerning MM, we shall solve a geometry optimization using the GUT of PCMODEL (Serena Sortware). The input is constructed by using a mouse to point and click on each atom of the connected atom list or skeleton of the molecule. This yields Fig. 4-6 (top). 

Compute (LVIMX. Search on bonds. Setup bonds, select all and hit OK. Enter Job Name 1-butene and Run (Jininx. Yon will see the model being kicked" repeatedly, l.eft click outside of the GMMX Hun box. You should see 3 minimized and 3 found. We already know that there are only three con formers, two of which are degenerate hetice, because E un nuirn we know all the... 

If you are running an updated version (V 8.0) of PC Model, click on force fields mm3. Omit this step for older versions. Click on Analyze (or compute depending on the version of PCMODEL) to obtain a menu of options. Select minimize. The geometry changes can be seen on the screen and a sequence of numbers appears in the right panel of the CRT screen, ending in Hf, the enthalpy of formation. This is the PCMODEL-MM3 calculated value of for cis-2-... 

The atomic symbol is one or two letters chosen to represent an element ("H" for "hydrogen," etc.). These symbols are used internationally. Typically, a symbol is the truncated name of the element or the truncated Latin name of the element. Click here for... 

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