Changeset 5fa1e86

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.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/AtomAction/BondifyAction.cpp (added)
• src/Actions/AtomAction/BondifyAction.def (added)
• src/Actions/AtomAction/BondifyAction.hpp (added)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• tests/regression/Bond/Bondify/post/test.data (added)
• tests/regression/Bond/Bondify/pre/test.data (added)
• tests/regression/Bond/Bondify/testsuite-bond-bondify.at (added)
• tests/regression/Bond/testsuite-bond.at (modified) (1 diff)
• tests/regression/Makefile.am (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>

src/Actions/GlobalListOfActions.hpp

@@ -31 +31 @@
   (AnalysisSurfaceCorrelation) \
   (AtomAdd) \
+  (AtomBondify) \
   (AtomChangeElement) \
   (AtomMirror) \

src/Actions/Makefile.am

@@ -150 +150 @@
 ATOMACTIONSOURCE = \
   Actions/AtomAction/AddAction.cpp \
+  Actions/AtomAction/BondifyAction.cpp \
   Actions/AtomAction/ChangeElementAction.cpp \
   Actions/AtomAction/MirrorAction.cpp \
@@ -161 +162 @@
 ATOMACTIONHEADER = \
   Actions/AtomAction/AddAction.hpp \
+  Actions/AtomAction/BondifyAction.hpp \
   Actions/AtomAction/ChangeElementAction.hpp \
   Actions/AtomAction/MirrorAction.hpp \
@@ -172 +174 @@
 ATOMACTIONDEFS = \
   Actions/AtomAction/AddAction.def \
+  Actions/AtomAction/BondifyAction.def \
   Actions/AtomAction/ChangeElementAction.def \
   Actions/AtomAction/MirrorAction.def \

tests/regression/Bond/testsuite-bond.at

@@ -33 +33 @@
 m4_include([Bond/SetDegree/testsuite-bond-set-degree_multiple.at])
 
+# bondify
+# m4_include(Bond/Bondify/testsuite-bond-bondify.at)

tests/regression/Makefile.am

@@ -81 +81 @@
         $(srcdir)/Bond/Add/testsuite-bond-add_multiple.at \
         $(srcdir)/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at \
+        $(srcdir)/Bond/Bondify/testsuite-bond-bondify.at \
         $(srcdir)/Bond/Remove/testsuite-bond-remove.at \
         $(srcdir)/Bond/Remove/testsuite-bond-remove_multiple.at \