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<title>GAMGI Interfaces: Bond Create </title>
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<h1>Bond Create</h1>
<div id="notebook">
<ul>
<li><a href="create_type.html">Type</a></li>
<li><span>Length</span></li>
<li><a href="create_property.html">Property</a></li>
<li><a href="create_view.html">View</a></li>
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Set here the length and element criteria used in <b>Length</b>
and <b>Delaunay</b> models to create new bonds.
<h3>Element, Element</h3>
When the <b>Element</b> entries are empty (the default), GAMGI attempts
to create bonds for all pairs of atoms. When the <b>Element</b> entries
are occupied with valid element names, only bonds between atoms of these
elements are considered.
<p/>
When both elements are recognized, minimum and maximum bond length
limits for this element pair - calculated according to the rules
described below - are automatically writen in the <b>Minimum</b>,
<b>Maximum</b> entries, otherwise these entries are left empty.
<p/>
When pressing <b>Ok</b>, the <b>Element</b> entries must be
both empty or valid, otherwise an error dialog is shown.
<h3>Minimum, Maximum</h3>
When the <b>Minimum</b>, <b>Maximum</b> entries are empty (the default),
GAMGI attempts to use its own data to set a valid range of bond lengths,
for each element pair.
<p/>
For each atom pair, GAMGI checks whether specific minimum and maximum
bond length limits have been configured. If the atoms distance is in
the configured interval, a new bond is created. To configure bond
length limits for specific element pairs, select <b>Bond->Config</b>.
<p/>
If no bond length interval has been configured for this element pair,
GAMGI attempts to calculate automatic minimum and maximum limits, summing
the two atom radius and multiplying by lower and upper factors (currently
0.80 and 1.10 by default). If the atoms distance is in the calculated
interval, a new bond is created. To configure these lower and upper
factors, valid for all element pairs, select <b>Bond->Config</b>.
<p/>
If no radius is defined for at least one of the elements, then no bond
is created. To configure the atom radius, for specific elements, select
<b>Atom->Config</b>.
<p/>
When the <b>Minimum</b>, <b>Maximum</b> entries are occupied with
valid length values, only bonds between these limits will be considered,
for all element pairs.
<p/>
When pressing <b>Ok</b>, the <b>Minimum</b>, <b>Maximum</b> entries must
be both empty or valid, otherwise an error is shown. The <b>Minimum</b>
cannot excede the <b>Maximum</b> length, otherwise an error is shown.
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