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<h1 class=title><span class="glide">Glide &mdash; Edit Feature Dialog Box</span></h1>
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<ul>
<li><a href="#summary">Summary</a></li>
<li><a href="#opening">Opening the <span class="GUI">Edit Feature</span> Dialog
Box</a></li>
<li><a href="#using">Using the <span class="GUI">Edit Feature</span> Dialog
Box</a></li>
<li><a href="#features"><span class="GUI">Edit Feature</span> Dialog Box
Features</a></li>
<li><a href="#links">Related Topics</a></li>
</ul>

<a name="summary"></a>
<h2>Summary</h2>


<p>The <span class="GUI">Edit Features</span> dialog box allows you to
edit the features that the ligand must match. Features are defined in terms of
SMARTS patterns. You can add patterns, edit and delete custom patterns, and you can
exclude patterns in a feature definition.</p>

<a name="opening"></a>
<h2>Opening the Edit Feature Dialog Box</h2>

<p>To open the <span class="GUI">Edit Feature</span> dialog box</p>
<ul>
<li><p>Click <span class="GUI">Edit Feature</span> in the <span
class="GUI">Constraints</span> tab of the Glide 
<span class="GUI">Ligand Docking</span> panel.</p></li>
</ul>

<a name="using"></a>
<h2>Using the Edit Feature Dialog Box</h2>

<h3>Loading and Saving Feature Sets</h3>

<p>Built-in feature sets are stored with the distribution.

<p>You can import a feature set for the selected constraint from a file by
clicking <span class="GUI">Import</span>, and navigating to the
feature file. When you import a feature set, the definitions of all features
are replaced, not just the selected feature. The feature definitions are
replaced only for the selected constraint, but are replaced
for that constraint in all groups.

<p>Feature sets can be saved to a file by clicking <span class="GUI">Export</span>, and specifying the file
location in the file selector that is displayed. </p>

<p>The patterns that define a feature are displayed in the
<span class="GUI">Pattern list</span> table when you choose the feature
from the <span class="GUI">Feature</span> option menu.</p>

<h3>Adding, Editing, and Deleting Patterns</h3>

<p>If the patterns in a given feature definition do not cover all the functional groups
that you want to include in the feature, you can add extra patterns. To add a
new SMARTS pattern, click the table row above which you want the pattern to be
inserted, then click <span class="GUI">New</span>. In the
<a href="new_pattern.html"><span class="GUI">New Pattern</span>
dialog box</a>, you can enter a SMARTS pattern and enter the atom numbers
in the pattern that must satisfy the constraint.</p>
<p>To edit a pattern, select the table row for the pattern, then click
<span class="GUI">Edit</span>. In the
<a href="edit_pattern.html"><span class="GUI">Edit
Pattern</span> dialog box</a>, you can modify the SMARTS pattern and the atoms in the
pattern that must match.</p>
<p>To delete a pattern, select the table row for the pattern, then click <span class="GUI">Delete</span>.</p>

<h3>Setting the Status of Patterns</h3>

<p>Matching of patterns to ligand structures is done in the order specified in the
<span class="GUI">Pattern list</span> table. You cannot change the
order of the patterns once they are in the table, so you must add new patterns
in the appropriate place. If you want to move patterns, you must delete them then
add them back in the appropriate place. Excluded patterns are processed first,
regardless of their position in the table.</p>

<p>If you want to ensure that certain functional groups are not matched, you can select
the check box in the <span class="GUI">Exclude</span> column for the
pattern for that group. For example, you might want to exclude a carboxylic acid
group from being considered as a hydrogen bond donor, because it will be ionized
under physiological conditions.</p>


<h3>Visualizing Patterns</h3>

<p>If you want to see a pattern for a given ligand or group of ligands, you
can select the check box in the <span class="GUI">Mark</span> column
for the pattern. Any occurrences of the pattern are marked in the Workspace.</p>

<p>You can display markers for more than one pattern, but the markers do not
distinguish between patterns. If you want to see the atoms and bonds as well as
the markers, select <span class="GUI">Apply marker offset</span>.</p>

<a name="features"></a>
<h2>Edit Feature Dialog Box Features</h2>

<ul>
<li><a href="#feature1"><span class="GUI">Feature</span> controls</a></li>
<li><a href="#feature2"><span class="GUI">Pattern list</span> table</a></li>
<li><a href="#feature3">Pattern editing buttons</a></li>
</ul>

<a name="feature1"></a>
<h3>Feature Controls</h3>

<p>This section has three controls:</p>

<dl>
<dt><span class="GUI">Feature</span> option menu</dt>
<dd><p>Select a feature type. The selected feature type is assigned to the
constraint and appears in the <span class="GUI">Available constraints</span>
table of the <span class="GUI">Constraints</span> tab. The patterns
that define the selected feature type are listed in the 
<span class="GUI">Pattern list</span> table.
You must select a feature type to edit its definition.
</p></dd>

<dt><span class="GUI">Import</span> button</dt>
<dd><p>Opens a file selector in which you can browse for feature files.
</p></dd>

<dt><span class="GUI">Export</span> button</dt>
<dd><p>Opens a file selector in which you can browse to a location to write a feature file.
</p></dd>

</dl>

<a name="feature2"></a>
<h3>Pattern list table</h3>
<p>The <span class="GUI">Pattern list</span> table lists all the patterns
that are used to define the feature. You can only select one row
at a time in the table, and the text fields are not editable. The table columns
are described below.
</p>

<dl>

<a name="feature2.1"></a>
<dt><span class="GUI">Mark</span></dt>
<dd><p>Column of check boxes. Selecting a check box marks the pattern on any
structures that are displayed in the Workspace.
</p></dd>

<a name="feature2.2"></a>
<dt><span class="GUI">Pattern</span></dt>
<dd><p>Pattern definition. The definitions are SMARTS strings.
</p></dd>

<a name="feature2.5"></a>
<dt><span class="GUI">Atoms</span></dt>
<dd><p>The list of atoms that must satisfy the constraint, numbered
according to the SMARTS string.
</p></dd>

<a name="feature2.6"></a>
<dt><span class="GUI">Exclude</span></dt>
<dd><p>Column of check boxes. If a check box is selected, atoms in a ligand are matched
by other patterns only if they do not match this pattern. This is essentially a NOT
operator. Excluded patterns are processed before other patterns.
</p></dd>


</dl>

<a name="feature3"></a>
<h3>Pattern Editing Buttons</h3>

<dl>

<a name="feature3.1"></a>
<dt><span class="GUI">New</span> button</dt>
<dd><p>Opens the <a href="new_pattern.html"><span class="GUI">New
Pattern</span> dialog box</a>, in which you can enter a SMARTS pattern and
choose the atoms that are used to match the ligand feature.
</p></dd>

<a name="feature3.2"></a>
<dt><span class="GUI">Edit</span> button</dt>
<dd><p>Opens the <a href="edit_pattern.html"><span class="GUI">Edit
Pattern</span> dialog box</a>, in which you can edit the selected
pattern.
</p></dd>

<a name="feature3.3"></a>
<dt><span class="GUI">Delete</span> button</dt>
<dd><p>Deletes the selected pattern.
</p></dd>

</dl>

<a name="links"></a>
<h2>Related Topics</h2>

<ul>
<li><a href="dock_constraints.html">Glide Docking Constraints Tab</a></li>
<li><a href="new_pattern.html">Glide New Pattern Dialog Box</a></li>
<li><a href="edit_pattern.html">Glide Edit Pattern Dialog Box</a></li>
</ul>

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File: glide/edit_feature.html<br />
Last updated: 10 Jan 2012
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