Changeset 5fa1e86 for doc/userguide/userguide.xml

Timestamp:

Apr 23, 2021, 8:51:24 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

e70818

Parents:

51d384a

git-author:

Frederik Heber <frederik.heber@…> (10/07/20 22:21:33)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:51:24)

Message:

Added BondifyAction.

• this allows to add non-hydrogen bonds and is complementary to saturate bonds where hydrogens are added.
• we generate all possible candidate sets taken from non-hydrogen atoms in vicinity with hydrogens and pick one at random.
• DOCU: added to userguide.
• TEST: added regression test case.

File:

• doc/userguide/userguide.xml (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1054 +1054 @@
           atoms) are taken into account and left intact.</para>
         </section>
+        <section xml:id="atoms.bondify-atom">
+          <title xml:id="atoms.bondify-atom.title">Bonding atoms</title>
+          <para>This action is to an extend the opposite of 
+        <link linkend='atoms.saturate-atom'>saturate-atom</link>. Instead of
+          adding hydrogens to saturate an atom with unoccupied valence orbitals
+          MoleCuilder looks for other non-hydrogen atoms in the vicinity that
+          have bonds with hydrogen atoms. If these non-hydrogen atoms are 
+          within suitable bonding distance, the hydrogen bond with the hydrogen
+          atom is removed and a bond between the two non-hydrogen atoms is
+          added. Hence, while saturate-atom adds more hydrogens, bondify-atom
+          will try to remove hydrogens and saturate atom valencies by 
+          additional bonds.</para>
+          <note>The typical bond distances between the two non-hydrogen atoms
+          is taken from bond table, loaded through
+        <link linkend='bond.create-adjacency'>bond-table</link>.</note>
+          <para>The action is called as follows:
+          <programlisting>
+  ... --bondify-atoms
+   </programlisting>
+          and will work on a single, currrently selected atom.
+          </para>
+        </section>
         <section xml:id="atoms.translate-atom">
           <title xml:id="atoms.translate-atom.title">Translating atoms</title>