Changes in doc/userguide/userguide.xml [066442:f3db60]

File:

• doc/userguide/userguide.xml (modified) (4 diffs)

doc/userguide/userguide.xml

@@ -962 +962 @@
         </section>
 
+        <section xml:id='atoms.saturate-atom'>
+          <title xml:id='atoms.saturate-atom.title'>Saturating atoms</title>
+
+          <para>Newly instantiated atoms have no bonds to any other atom. If
+          you want to fill up their valence by a slew of hydrogen atoms 
+          residing on a sphere around this atom, use this action.</para>
+
+          <programlisting>
+                ... --saturate-atoms
+          </programlisting>
+
+          <para>A number of hydrogen atoms is added. The number corrresponding
+          to the valence of each selected atom. They are placed in the same
+          distance to this atom and approximately with same distance to their
+          nearest neighbors.</para>
+        </section>
+
         <section xml:id='atoms.translate-atom'>
           <title xml:id='atoms.translate-atom.title'>Translating atoms</title>
@@ -1133 +1150 @@
         </section>
 
-        <section xml:id='bond.add-bond'>
-          <title xml:id='bond.add-bond.title'>Adding a bond manually</title>
+        <section xml:id='bond.adds-bond'>
+          <title xml:id='bond.adds-bond.title'>Adding a bond manually</title>
 
           <para>When the automatically created adjacency or bond graph
           contains faulty bonds or lacks some, you can add them manually.
-          First, you must have selected two atoms.</para>
-
-          <programlisting>... --add-bond</programlisting>
-        </section>
-
-        <section xml:id='bond.remove-bond'>
-          <title xml:id='bond.remove-bond.title'>Removing a bond manually
+          </para>
+
+          <programlisting>... --add-bonds</programlisting>
+
+          <para>If two atoms are selected, the single bond in between, if not
+          present, is added. If more than two atoms are selected, than the
+          bond between any pair of these is added.</para>
+         <note><para>This is especially useful in conjunction with the
+          fragmentation scheme. If you want to know the contribution from
+          certain fragments whose subgraph is not connected you can simply
+          make the associated subset of atoms connected by selecting all
+          bonds and adding the bonds.</para>
+         </note>
+        </section>
+
+        <section xml:id='bond.remove-bonds'>
+          <title xml:id='bond.remove-bonds.title'>Removing a bond manually
           </title>
 
@@ -1150 +1177 @@
           bond.</para>
 
-          <programlisting>... --remove-bond</programlisting>
+          <programlisting>... --remove-bonds</programlisting>
+
+          <para>Similarly, if more than two atoms are selected, then all bonds
+          found between any pair of these is removed.</para>
         </section>
 
@@ -2511 +2541 @@
           <programlisting>... -v 4</programlisting>
         </section>
+        
+        <section xml:id='various.dry-run'>
+          <title xml:id='various.dry-run.title'>Dry runs</title>
+
+          <para>A "dry run" refers to a test run where commands are not 
+          actually executed. You may bracket a certain set of actions by
+          putting --dry-run before and --no-dry-run afterwards. Then, all
+          action in between will be looked at but not executed, i.e. they
+          make it to the history but nothing is changed in the World.</para>
+
+          <para>As an example, the following listing contains the adding of a
+          hydrogen atom at position (5,5,5) inside the aforementioned dry run
+          statements. Hence, no hydrogen atom is added but the add action is
+          stored in the history and will make it to a stored session.</para>
+
+          <programlisting>
+          ... --dry-run \
+          --add-atom 1 --domain-position "5,5,5"
+          --no-dry-run
+          </programlisting>
+
+        </section>
 
         <section xml:id='various.element-db'>