| QSAR |
This chapter explains how to use the equation viewer:
To open the equation viewer at any time
Go to the QSAR card deck, then choose View Equations from the EQUATION VIEWER card. The Equation Viewer control panel appears.
For more information about controlling the display of study table information, see the Equation viewer section on page 219.
If your statistical method produces more than one equation (for example, Simple or GFA), you may need to select an equation from the group of equations displayed in the equation viewer. You need to select an individual equation when you want to:
Selecting equations
2. You may want to sort the equation set by some term. To do this, click the upper More... button (above the equation browser) in the equation viewer. This opens the QSAR equations sets control panel.
5. Repeat Steps 2 through 4 to select other equations in the equation set and display information about them.
You can use the equation viewer to delete both entire equation sets and individual equations within a set.
Deleting equations
To delete an entire equation set
2. Click Delete QSAR Equation Set in the QSAR Equation Sets control panel (opened by clicking the upper More... button in the equation viewer).
2. Select the equation you want to delete (for example, by clicking the equation). For more about selecting an equation, see Selecting equations on page 253.
3. Click Delete QSAR Equation Set in the QSAR Equation Sets control panel (opened by clicking the upper More... button in the equation viewer).
To display a graph of an equation
2. Select the equation that you want to plot (for example, by clicking the equation).
3. Click the Plot Equation button.
You can select a subset of points (that is, rows) in the study table and highlight them in the Cerius2 Graphs window in which the current equation is plotted. Select the rows in the study table that you want to highlight, then click the Equation button. This causes the selection made in the study table to be colored in the 2D Graph window.
Identifying study table observations from a graph
You can also select points in the 2D Graph window and identify them in the study table:
2. Click Show Selected Points.
The rows of the study table corresponding to the graph points become highlighted. Information about those points is shown in the text window.
For more about working with graphs in Cerius2, see the Cerius2 Modeling Environment.
Recall that QSAR+ enables you to save individual QSAR equations in the QSAR+ descriptor database. You can use these saved QSAR equations both to predict activity for new molecular structures and as descriptors in the generation of new QSAR equations. For detailed information about saving QSAR equations, see Saving QSAR equations on page 257.
Renaming equation sets
QSAR+ also enables you to rename an entire equation set. Whenever you request generation of a QSAR equation, QSAR+ creates an equation set containing one or more QSAR equations and, based on the statistical method you select, automatically assigns a name to that equation set. For example, if you choose Linear as your statistical method, QSAR+ automatically names the resulting equation set QSAR Simple Linear Regression. If you again choose Linear as your statistical method, QSAR+ again automatically names the resulting equation set QSAR Simple Linear Regression, and overwrites the original equation set. Thus, to retain the original equation set, you must first rename it.
2. Enter the equation set's new name in the New Name entry box.
To save a QSAR equation set, click on the Save Equations... button. The Save QSAR Equations control panel appears.
Saving QSAR equations
The Save QSAR Equations control panel contains a popup, Current Equation/Equations set, which lets you decide whether to save the entire set of equations or just the currently selected equation. The Name and Comments entry boxes allow you to give a name to and attach a comment to the saved item, and QSAR equations file allows you to name the file to which the data is saved. Browse... opens the Save QSAR Equation File control panel, which lets you select a name from a list of existing equation filenames. The extension .qsar is automatically appended to the name you supply.
Clicking the Open Equations... button opens the Open QSAR Equations control panel, which is used to load a previously saved set of QSAR equations or a single QSAR equation.
Opening QSAR equations
This control panel controls which equation file is read into QSAR+ and what is done with it. You may read in a single equation and create a new set with it or add it to an existing set. You may also read in a set of equations.
Adding an equation to an existing set
1. Choose Equation from the popup.
1. Change the popup to Equation.
2. Select the file you want to read in from the file list.
3. Enter the name of your new equation set in the New Equations
Set entry box.
1. Change the popup to Equations Set.
2. Select the file you want to read in from the file list.
3. Enter the name of your new equation set in the New Equations
Set entry box.
1. Select the equation that you want to delete from the equation browser then click the lower More... button in the Equation Viewer control panel. This opens the QSAR Equations control panel.
3. Click OK. The equation is deleted.
Two applications, MFA and Receptor, create columns in the study table that refer to a point in space near a molecular model or a (possibly aligned) group of models.
Labelling 3D QSAR equations
The controls to display these points are in the QSAR Equation control panel, which is accessed from the lower More... button in the Equation Viewer control panel.
The main control is the MFA/Receptor popup, which must be set to MFA if you want to label MFA 3D points and to Receptor if you want to label 3D points on a receptor surface model. The Label Current Equation pushbutton draws 3D points associated with terms in the current equation (highlighted in the equation viewer), and the Label Independent Variables pushbutton draws 3D points corresponding to columns in the study table marked Independent X. The Clear Labels pushbutton removes both kinds of labels from the Cerius2 Models window.
The bottom three checkboxes in the QSAR Equations control panel control how 3D points are displayed. If Show Column Name is checked, the 3D points are labelled with the column heading from the study table. If it is not checked, the 3D labels simply appear as crosses. If Show Loading Value is checked, the loading value is attached to the 3D label. The loading value is the coefficient of the term as it appears in the equation viewer multiplied by the standard deviation of the descriptor. Independent variables do not have a loading value, so this checkbox affects only the display of the current equation. The Scale Cross by Loading Value pushbutton applies only to labelling of the current equation and scales the size of the cross by the coefficient of the term that it represents.