Changeset f5ea10 for doc

Timestamp:

Jun 22, 2018, 7:26:09 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.6.1, ChemicalSpaceEvaluator

Children:

99c705

Parents:

8d56a6

git-author:

Frederik Heber <frederik.heber@…> (09/26/17 22:30:01)

git-committer:

Frederik Heber <frederik.heber@…> (06/22/18 07:26:09)

Message:

Added Graph6Reader, extended BoostGraphCreator, added ChemicalSpaceEvaluatorAction.

• added visible generateAllInducedSubgraphs to Extractors.
• TESTS: due to new option "graph6" containing a digit we needed to modify moltest_check.py to also scan for digits and not just letters.
• DOCU: Added evaluate-chemical-space to userguide.

File:

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

doc/userguide/userguide.xml

@@ -1268 +1268 @@
           to both other atoms serves as rotation joint).</para>
         </section>
+        <section xml:id="bond.evaluate-chemical-space">
+          <title xml:id="bond.evaluate-chemical-space.title">Evaluate the Chemical Space</title>
+          <para>Imagine that we are given a graph consisting of nodes and edges.
+          As we have been speaking extensively of the adjacency graph before, then
+          any graph where nodes are assigned a chemical element and edges are given
+          a degree, effectively represent a molecule of covalently bonded atoms.</para>
+          <para>This is the notion behind constructing parts of the chemical space that
+          encompasses all molecules that either already exist or could be devised,
+          i.e. that are stable.</para>
+          <para>One method of creating points in this chemical space, i.e. stable
+          molecules, is presented in the article by Hamaekers et al. 2017, where
+          they follow the well-known <emphasis>octet rule</emphasis>.</para>
+          <para>In this action essentially the same method is implemented. Given
+          an arbitrary graph, encoded as Graph6 string, such as produced by
+          the <link xlink:href="http://users.cecs.anu.edu.au/~bdm/nauty/">nauty</link> 
+          toolset (Brendan McKay and Adolfo Piperno), and a set of chemical
+          elements, the action creates every possible molecule using the graph
+          and the given elements for each of its nodes, changing bond degrees
+          as long as to fulfil the octet rule.</para>
+          <programlisting>--evaluate-chemical-space \
+  --graph6 "B`" --elements C C</programlisting>
+        <para>The graph6 string "B`" represents the simplest graph consisting
+        of just two nodes, connected by a single edge. Designating each node
+        to be a carbon atom, this action will then produce the carbonhydrates
+        C2H6, C2H4, and C2H2.</para>
+        <para>At the moment, the molecules are not created but their signatures
+        are used in looking up the fragments in the internal homology container,
+        see <link linkend="fragmentation">Fragmentation </link> and 
+        <link linkend="homology">Homologies</link>. Instead of creating atomic
+        coordinates, approximate energies are given that allow to estimate
+        whether the molecule candidate is stable or not. Note that this requires
+        that a suitable homology container file has been loaded first that contains
+        all necessary fragments.</para>
+        <note>The graph is automatically saturated with hydrogens in obeying
+        the octet rule, i.e. hydrogen should not be given in the list of elements.</note>
+        <para>Using nauty that produces all possible graphs with a fixed number
+        of nodes, these can be simply fed into <productname>MoleCuilder </productname>
+        to produce all associated molecules.</para>
+        </section>
       </section>
       <section xml:id="molecule">