Changeset 78ea3c for doc

Timestamp:

Jun 21, 2017, 10:02:50 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChangeBugEmailaddress, ChemicalSpaceEvaluator, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_Verbose_Codepatterns, ForceAnnealing_oldresults, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps

Children:

310445

Parents:

be848d (diff), 101d2d (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Docu_Python_wait' into Candidate_v1.6.1

Conflicts:

tests/Python/AllActions/options.dat

• two options introduced at same place, both get in.

File:

• doc/userguide/userguide.xml (modified) (2 diffs)

doc/userguide/userguide.xml

@@ -1177 +1177 @@
         <link linkend='geometry'>Geometry</link>.</para>
         </section>
+        <section xml:id="molecule.rotate-around-bond">
+          <title xml:id="molecule.rotate-around-bond.title">Rotate around bond </title>
+          <para>This rotates parts of a molecule around a given bond, i.e. the
+          bond vector becomes the rotation axis but only atoms on the side of
+          second atom get rotated. This naturally does not work for bonds in a
+          cycle.</para>
+          <programlisting>
+  ... --rotate-around-bond &quot;90&quot; \
+      --bond-side 0\
+   </programlisting>
+        </section>
         <section xml:id="molecule.rotate-around-self">
           <title xml:id="molecule.rotate-around-self.title">Rotate around self </title>
@@ -2658 +2669 @@
       under the command-line interface and look up the function name via
       help.</para>
+      <para>You can freely mix calls to the pymolecuilder module and other python commands.</para>
+      <note>However, be aware that all Actions are executed in another thread,
+      i.e. run in parallel. That means that a pymolecuilder command is not 
+      necessarily finished when python steps on to the next line!</note>
+      <para>In order to make python wait for the Actions to finish before
+      stepping, there is the special wait() command.</para>
+      <programlisting>
+         mol.MoleculeLoad("...")
+         mol.wait()
+      </programlisting>
+      <para>This will continue first after the molecule has been fully loaded.
+      </para>
+      <warning>These wait()s will have no effect if the python script is loaded
+      via the "load-session" command inside a User Interface (command-line,
+      GUI, ...) as this would cause the queue to wait indefinitely, namely till
+      the load-session itself would have finished.</warning>
+      <para>Therefore, more complex python scripts need to be called with
+      python and a set PYTHONPATH as described above.</para>
     </section>
   </chapter>