Ignore:
Timestamp:
Sep 17, 2014, 9:30:38 PM (10 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
054d47, 7a7b34, 7acbfc, 98d166, bbf6dc, c4c20a, f4b626a
Parents:
f73e06
git-author:
Frederik Heber <heber@…> (09/14/14 19:26:46)
git-committer:
Frederik Heber <heber@…> (09/17/14 21:30:38)
Message:

DOCU: Fixed all missing links in userguide.

  • each section now has a linkname.
File:
1 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    rf73e06 r9bce96  
    4444    </figure>
    4545
    46     <section>
    47       <title>What is MoleCuilder?</title>
     46    <section xml:id='whatis'>
     47      <title  xml:id='whatis.title'>What is MoleCuilder?</title>
    4848
    4949      <para>In Short,<command> MoleCuilder</command> is a concatenation of
    … …  
    6969      many, related molecular systems have to be created.</para>
    7070
    71       <section>
    72         <title>Installation requirements</title>
     71      <section xml:id='installation'>
     72        <title xml:id='installation.title'>Installation requirements</title>
    7373
    7474        <para>For installations requirements and instructions we refer to the
    … …  
    7777      </section>
    7878
    79       <section>
    80         <title>License</title>
     79      <section xml:id='license'>
     80        <title xml:id='license.title'>License</title>
    8181
    8282        <para>As long as no other license statement is given, MoleCuilder is
    … …  
    8585      </section>
    8686
    87       <section>
    88         <title>Disclaimer</title>
     87      <section xml:id='disclaimer'>
     88        <title xml:id='disclaimer.title'>Disclaimer</title>
    8989
    9090        <para>We quote section 11 from the GPLv2 license:</para>
    … …  
    101101      </section>
    102102
    103       <section>
    104         <title>Feedback</title>
     103      <section xml:id='feedback'>
     104        <title xml:id='feedback.title'>Feedback</title>
    105105
    106106        <para>If you encounter any bugs, errors, or would like to submit
    … …  
    112112      </section>
    113113
    114       <section>
    115         <title>Notation</title>
     114      <section xml:id='notation'>
     115        <title xml:id='notation.title'>Notation</title>
    116116
    117117        <para>We briefly explain a few specific wordings associated with the
    … …  
    139139      </section>
    140140
    141       <section>
    142         <title>Completeness</title>
     141      <section xml:id='completeness'>
     142        <title xml:id='completeness.title'>Completeness</title>
    143143
    144144        <para>This documentation takes quite some effort to write. Hence, the
    … …  
    162162    interface.</para>
    163163
    164     <section>
    165       <title>Concepts</title>
     164    <section xml:id='concepts'>
     165      <title xml:id='concepts.title'>Concepts</title>
    166166
    167167      <para>In general, we divide the molecular systems into three different
    … …  
    214214    </section>
    215215
    216     <section>
    217       <title>Interfaces</title>
     216    <section xml:id='interfaces'>
     217      <title xml:id='interfaces.title'>Interfaces</title>
    218218
    219219      <para>MoleCuilder has four different interfaces: Command-line, text
    … …  
    268268    </section>
    269269
    270     <section>
    271       <title>Known File formats</title>
     270    <section xml:id='fileformats'>
     271      <title xml:id='fileformats.title'>Known File formats</title>
    272272
    273273      <para>We briefly the file formats MoleCuilder can parse and
    … …  
    282282
    283283        <listitem>
    284           <para><productname>MPQC</productname>, <filename>.in</filename>
    285           (<link xlink:href="???">http://www.mpqc.org/</link>)</para>
     284          <para><link xlink:href="http://www.mpqc.org/"><productname>MPQC
     285          </productname></link>, <filename>.in</filename></para>
    286286        </listitem>
    287287
    288288        <listitem>
    289           <para>PDB, <filename>.pdb</filename> (<link
    290           xlink:href="???">http://www.pdb.org/</link>)</para>
     289          <para><link xlink:href="http://www.pdb.org/">PDB</link>, <filename>
     290          .pdb</filename></para>
    291291        </listitem>
    292292
    … …  
    298298
    299299        <listitem>
    300           <para><productname>PSI4</productname>, <filename>.psi</filename>
    301           (<link xlink:href="???">http://www.psicode.org/</link>)</para>
     300          <para><link xlink:href="http://www.psicode.org/"><productname>PSI4
     301          </productname></link>, <filename>.psi</filename></para>
    302302        </listitem>
    303303
    304304        <listitem>
    305           <para><productname>TREMOLO</productname>, <filename>.data</filename>
    306           (<link xlink:href="???">http://www.tremolo-x.org/</link>)</para>
     305          <para><link xlink:href="http://www.tremolo-x.org/"><productname>
     306          TREMOLO</productname></link>, <filename>.data</filename></para>
    307307        </listitem>
    308308
    309309        <listitem>
    310           <para>XML, <filename>.xml</filename> (XML as read by scafacos
    311           project, <link
    312           xlink:href="???">http://www.scafacos.org</link>/)</para>
     310          <para>XML, <filename>.xml</filename> (XML as read by
     311          <link xlink:href="http://www.scafacos.org/">ScaFaCoS</link>
     312          project)</para>
    313313        </listitem>
    314314      </itemizedlist>
    … …  
    346346    been done.</para>
    347347
    348     <section>
    349       <title>Command-line interface</title>
     348    <section xml:id='command-line-interface'>
     349      <title xml:id='command-line-interface.title'>Command-line interface</title>
    350350
    351351      <para>The command-line interface reads options and commands from the
    … …  
    392392      </note>
    393393
    394       <section>
    395         <title>Preliminaries</title>
     394      <section xml:id='preliminaries'>
     395        <title xml:id='preliminaries.title'>Preliminaries</title>
    396396
    397397        <para>Some preliminary remarks are in order which we have gathered
    … …  
    440440      </section>
    441441
    442       <section>
    443         <title>File parsers</title>
     442      <section xml:id='fileparsers'>
     443        <title xml:id='fileparsers.title'>File parsers</title>
    444444
    445445        <para>We have already given a list of all known file formats, see
    446         <link linkend="???">File formats</link>. Next, we explain how these
     446        <link linkend="fileformats">File formats</link>. Next, we explain how these
    447447        file formats are picked and manipulated.</para>
    448448
    449         <section>
    450           <title>Parsing files</title>
     449        <section xml:id='fileparsers.parsing'>
     450          <title xml:id='fileparsers.parsing.title'>Parsing files</title>
    451451
    452452          <para>We already discussed that the command-line interface works
    … …  
    473473        </section>
    474474
    475         <section>
    476           <title>Adding output file formats</title>
     475        <section xml:id='fileparsers.set-output'>
     476          <title xml:id='fileparsers.set-output.tile'>Adding output file
     477          formats</title>
    477478
    478479          <para>We already know that loading a file also picks a file format
    … …  
    487488        </section>
    488489
    489         <section>
    490           <title>Output the current molecular system</title>
     490        <section xml:id='fileparsers.output-as'>
     491          <title xml:id='fileparsers.output-as.title'>Output the current
     492          molecular system</title>
    491493
    492494          <para>This will store the current World, i.e. all its atoms, to a
    … …  
    497499        </section>
    498500
    499         <section>
    500           <title>Output the current molecular system</title>
     501        <section xml:id='fileparsers.save-selected-molecules'>
     502          <title xml:id='fileparsers.save-selected-molecules.title'>Output
     503          the current molecular system</title>
    501504
    502505          <para>This will store all atoms contained in the currently selected
    … …  
    509512        </section>
    510513
    511         <section>
    512           <title>Load extra bond information</title>
     514        <section xml:id='fileparsers.bond-file'>
     515          <title xml:id='fileparsers.bond-file.title'>Load extra bond
     516          information</title>
    513517
    514518          <para>For some parsers bond information is stored not with the atoms
    … …  
    520524      </section>
    521525
    522       <section>
    523         <title>Selections and unselections</title>
     526      <section xml:id='selections'>
     527        <title xml:id='selections.title'>Selections and unselections</title>
    524528
    525529        <para>In order to tell MoleCuilder on what subset of atoms a specific
    … …  
    752756      </section>
    753757
    754       <section>
    755         <title>Shapes</title>
     758      <section xml:id='shapes'>
     759        <title xml:id='shapes.title'>Shapes</title>
    756760
    757761        <para>Shapes are specific regions of the domain. There are just a few
    … …  
    763767        obtain a spherical surface of specific thickness.</para>
    764768
    765         <section>
    766           <title>Creating shapes</title>
     769        <section xml:id='shapes.create-shape'>
     770          <title xml:id='shapes.create-shape.title'>Creating shapes</title>
    767771
    768772          <para>Primitive shapes can be created as follows,</para>
    … …  
    791795        </section>
    792796
    793         <section>
    794           <title>Combining shapes</title>
     797        <section xml:id='shapes.combine-shapes'>
     798          <title xml:id='shapes.combine-shapes.title'>Combining shapes</title>
    795799
    796800          <para>Any two shapes can be combined by boolean operations as follows</para>
    … …  
    824828        </section>
    825829
    826         <section>
    827           <title>Removing shapes</title>
     830        <section xml:id='shapes.remove-shape'>
     831          <title xml:id='shapes.remove-shape.title'>Removing shapes</title>
    828832
    829833          <para>Removing a shape is as simple as removing an atom.</para>
    … …  
    834838        </section>
    835839
    836         <section>
    837           <title>Manipulating shapes</title>
     840        <section xml:id='shapes.manipulation'>
     841          <title xml:id='shapes.manipulation.title'>Manipulating shapes</title>
    838842
    839843          <para>Shapes can be stretched, scaled, rotated, and translated to
    … …  
    869873      </section>
    870874
    871       <section>
    872         <title>Randomization</title>
     875      <section xml:id='randomization'>
     876        <title xml:id='randomization.title'>Randomization</title>
    873877
    874878        <para>Some operations require randomness as input, e.g. when filling a
    … …  
    905909      </section>
    906910
    907       <section>
    908         <title>Manipulate atoms</title>
     911      <section xml:id='atoms'>
     912        <title xml:id='atoms.title'>Manipulate atoms</title>
    909913
    910914        <para>Here, we explain in detail how to add, remove atoms, change its
    … …  
    912916        angle.</para>
    913917
    914         <section>
    915           <title>Adding atoms</title>
     918        <section xml:id='atoms.add-atom'>
     919          <title xml:id='atoms.add-atom.title'>Adding atoms</title>
    916920
    917921          <para>Adding an atom to the domain requires the element of the atom
    … …  
    927931        </section>
    928932
    929         <section>
    930           <title>Removing atoms</title>
     933        <section xml:id='atoms.remove-atom'>
     934          <title xml:id='atoms.remove-atom.title'>Removing atoms</title>
    931935
    932936          <para>Removing atom(s) does not need any option and operates on the
    … …  
    936940        </section>
    937941
    938         <section>
    939           <title>Translating atoms</title>
     942        <section xml:id='atoms.translate-atom'>
     943          <title xml:id='atoms.translate-atom.title'>Translating atoms</title>
    940944
    941945          <para>In order to translate the current selected subset of atoms you
    … …  
    952956        </section>
    953957
    954         <section>
    955           <title>Changing an atoms element</title>
     958        <section xml:id='atoms.change-element'>
     959          <title xml:id='atoms.change-element.title'>Changing an atoms element
     960          </title>
    956961
    957962          <para>You can easily turn lead or silver into gold, by selecting the
    … …  
    962967      </section>
    963968
    964       <section>
    965         <title>Bond-related manipulation</title>
     969      <section xml:id='bond'>
     970        <title xml:id='bond.title'>Bond-related manipulation</title>
    966971
    967972        <para>Atoms can also be manipulated with respect to the bonds.
    … …  
    971976        and angles.</para>
    972977
    973         <section>
    974           <title>Creating a bond graph</title>
     978        <section xml:id='bond.create-adjacency'>
     979          <title xml:id='bond.create-adjacency.title'>Creating a bond graph
     980          </title>
    975981
    976982          <para>In case you have loaded a configuration file with no bond
    … …  
    10111017        </section>
    10121018
    1013         <section>
    1014           <title>Destroying the bond graph</title>
     1019        <section xml:id='bond.destroy-adjacency'>
     1020          <title xml:id='bond.destroy-adjacency.title'>Destroying the bond
     1021          graph</title>
    10151022
    10161023          <para>The bond graph can be removed completely (and all bonds along
    … …  
    10201027        </section>
    10211028
    1022         <section>
    1023           <title>Correcting bond degrees</title>
     1029        <section xml:id='bond.correct-bonddegree'>
     1030          <title xml:id='bond.correct-bonddegree.title'>Correcting bond
     1031          degrees</title>
    10241032
    10251033          <para>Typically, after loading an input file bond information, e.g.
    … …  
    10361044        </section>
    10371045
    1038         <section>
    1039           <title>Analysing a bond graph</title>
     1046        <section xml:id='bond.depth-first-search'>
     1047          <title xml:id='bond.depth-first-search.title'>Analysing a bond
     1048          graph</title>
    10401049
    10411050          <para>You can perform a depth-first search analysis that reveals
    … …  
    10451054        </section>
    10461055
    1047         <section>
    1048           <title>Dissecting the molecular system into molecules</title>
     1056        <section xml:id='bond.subgraph-dissection'>
     1057          <title xml:id='bond.subgraph-dissection.title'>Dissecting the
     1058          molecular system into molecules</title>
    10491059
    10501060          <para>The bond graph information can be used to recognize the
    … …  
    10631073        </section>
    10641074
    1065         <section>
    1066           <title>Updating molecule structure</title>
     1075        <section xml:id='bond.update-molecules'>
     1076          <title xml:id='bond.update-molecules.title'>Updating molecule
     1077          structure</title>
    10671078
    10681079          <para>When the bond information has changed, new molecules might
    … …  
    10741085        </section>
    10751086
    1076         <section>
    1077           <title>Adding a bond manually</title>
     1087        <section xml:id='bond.add-bond'>
     1088          <title xml:id='bond.add-bond.title'>Adding a bond manually</title>
    10781089
    10791090          <para>When the automatically created adjacency or bond graph
    … …  
    10841095        </section>
    10851096
    1086         <section>
    1087           <title>Removing a bond manually</title>
     1097        <section xml:id='bond.remove-bond'>
     1098          <title xml:id='bond.remove-bond.title'>Removing a bond manually
     1099          </title>
    10881100
    10891101          <para>In much the same way as adding a bond, you can also remove a
    … …  
    10931105        </section>
    10941106
    1095         <section>
    1096           <title>Saving bond information</title>
     1107        <section xml:id='bond.save-bonds'>
     1108          <title xml:id='bond.save-bonds.title'>Saving bond information
     1109          </title>
    10971110
    10981111          <para>Bond information can be saved to a file in <link
    1099           xlink:href="http://www.molecuilder.com/"><programname>TREMOLO
    1100           </programname></link>'s dbond style.</para>
     1112          xlink:href="http://www.molecuilder.com/"><productname>TREMOLO
     1113          </productname></link>'s dbond style.</para>
    11011114
    11021115          <programlisting>... --save-bonds system.dbonds</programlisting>
    … …  
    11111124        </section>
    11121125
    1113         <section>
    1114           <title>Stretching a bond</title>
     1126        <section xml:id='bond.stretch-bond'>
     1127          <title xml:id='bond.stretch-bond.title'>Stretching a bond</title>
    11151128
    11161129          <para>Stretching a bond actually refers to translation of the
    … …  
    11301143        </section>
    11311144
    1132         <section>
    1133           <title>Changing a bond angle</title>
     1145        <section xml:id='bond.change-bond-angle'>
     1146          <title xml:id='bond.change-bond-angle.title'>Changing a bond angle
     1147          </title>
    11341148
    11351149          <para>In the same way as stretching a bond, you can change the angle
    … …  
    11451159      </section>
    11461160
    1147       <section>
    1148         <title>Manipulate molecules</title>
     1161      <section xml:id='molecule'>
     1162        <title xml:id='molecule.title'>Manipulate molecules</title>
    11491163
    11501164        <para>Molecules are agglomerations of atoms that are bonded. Hence,
    … …  
    11591173          <para>Initially when you load a file via the input action all atoms
    11601174          are placed in a single molecule despite any present bond
    1161           information, see <link linkend="???">Dissecting the molecular system
    1162           into molecules</link></para>
     1175          information, see <link linkend="fragmentation">Dissecting the
     1176          molecular system into molecules</link></para>
    11631177        </note>
    11641178
    1165         <section>
    1166           <title>Copy molecules</title>
     1179        <section xml:id='molecule.copy'>
     1180          <title xml:id='molecule.copy.title'>Copy molecules</title>
    11671181
    11681182          <para>A basic operation is to duplicate a molecule. This works on a
    … …  
    11831197        </section>
    11841198
    1185         <section>
    1186           <title>Change a molecules name</title>
     1199        <section xml:id='molecule.change-molname'>
     1200          <title xml:id='molecule.change-molname.title'>Change a molecules
     1201          name</title>
    11871202
    11881203          <para>You can change the name of a molecule which is important for
    … …  
    12081223        </section>
    12091224
    1210         <section>
    1211           <title>Rotate around self</title>
     1225        <section xml:id='molecule.rotate-around-self'>
     1226          <title xml:id='molecule.rotate-around-self.title'>Rotate around self
     1227          </title>
    12121228
    12131229          <para>You can rotate a molecule around its own axis.</para>
    … …  
    12221238        </section>
    12231239
    1224         <section>
    1225           <title>Rotate around origin</title>
     1240        <section xml:id='molecule.rotate-around-origin'>
     1241          <title xml:id='molecule.rotate-around-origin.title'>Rotate around
     1242          origin</title>
    12261243
    12271244          <para>In the same manner the molecule can be rotated around an
    … …  
    12371254        </section>
    12381255
    1239         <section>
    1240           <title>Rotate to principal axis system</title>
     1256        <section xml:id='molecule.rotate-to-principal-axis-system'>
     1257          <title xml:id='molecule.rotate-to-principal-axis-system.title'>
     1258          Rotate to principal axis system</title>
    12411259
    12421260          <para>The principal axis system is given by an ellipsoid that mostly
    … …  
    12491267          do as follows.</para>
    12501268
    1251           <programlisting>... --rotate-to-principal-axis-system "0,0,1"</programlisting>
     1269          <programlisting>... --rotate-to-principal-axis-system "0,0,1"
     1270          </programlisting>
    12521271
    12531272          <para>This rotates the molecule in such a manner that the ellipsoids
    … …  
    12561275        </section>
    12571276
    1258         <section>
    1259           <title>Perform verlet integration</title>
     1277        <section xml:id='molecule.verlet-integration'>
     1278          <title xml:id='molecule.verlet-integration.title'>Perform verlet
     1279          integration</title>
    12601280
    12611281          <para>Atoms not only have a position, but each instance also stores
    … …  
    12781298        </section>
    12791299
    1280         <section>
    1281           <title>Anneal the atomic forces</title>
     1300        <section xml:id='molecule.force-annealing'>
     1301          <title xml:id='molecule.force-annealing.title'>Anneal the atomic
     1302          forces</title>
    12821303
    12831304          <para>This will shift the atoms in a such a way as to decrease (or
    … …  
    13001321        </section>
    13011322
    1302         <section>
    1303           <title>Linear interpolation between configurations</title>
     1323        <section xml:id='molecule.linear-interpolation-of-trajectories'>
     1324          <title xml:id='molecule.linear-interpolation-of-trajectories.title'>
     1325          Linear interpolation between configurations</title>
    13041326
    13051327          <para>This is similar to verlet-integration, only that it performs
    … …  
    13231345      </section>
    13241346
    1325       <section>
    1326         <title>Manipulate domain</title>
     1347      <section xml:id='domain'>
     1348        <title xml:id='domain.title'>Manipulate domain</title>
    13271349
    13281350        <para>Here, we elaborate on how to duplicate all the atoms inside the
    … …  
    13321354        domain.</para>
    13331355
    1334         <section>
    1335           <title>Changing the domain</title>
     1356        <section xml:id='domain.change-box'>
     1357          <title xml:id='domain.change-box.title'>Changing the domain</title>
    13361358
    13371359          <para>The domain is specified by a symmetric 3x3 matrix. The
    … …  
    13481370        </section>
    13491371
    1350         <section>
    1351           <title>Bound atoms inside box</title>
     1372        <section xml:id='domain.bound-in-box'>
     1373          <title xml:id='domain.bound-in-box.title'>Bound atoms inside box
     1374          </title>
    13521375
    13531376          <para>The following applies the current boundary conditions to the
    … …  
    13591382        </section>
    13601383
    1361         <section>
    1362           <title>Center atoms inside the domain</title>
     1384        <section xml:id='domain.center-in-box'>
     1385          <title xml:id='domain.center-in-box.title'>Center atoms inside the
     1386          domain</title>
    13631387
    13641388          <para>This is a combination of changing the box and bounding the
    … …  
    13681392        </section>
    13691393
    1370         <section>
    1371           <title>Center the atoms at an edge</title>
     1394        <section xml:id='domain.center-edge'>
     1395          <title xml:id='domain.center-edge.title'>Center the atoms at an
     1396          edge</title>
    13721397
    13731398          <para>MoleCuilder can calculate the minimum box (parallel to the
    … …  
    13791404        </section>
    13801405
    1381         <section>
    1382           <title>Extending the boundary by adding an empty boundary</title>
     1406        <section xml:id='domain.add-empty-boundary'>
     1407          <title xml:id='domain.add-empty-boundary.title'>Extending the
     1408          boundary by adding an empty boundary</title>
    13831409
    13841410          <para>In the same manner as above a minimum box is determined that
    … …  
    13931419        </section>
    13941420
    1395         <section>
    1396           <title>Scaling the box</title>
     1421        <section xml:id='domain.scale-box'>
     1422          <title xml:id='domain.scale-box.title'>Scaling the box</title>
    13971423
    13981424          <para>You can enlarge the domain by simple scaling factors.</para>
    … …  
    14041430        </section>
    14051431
    1406         <section>
    1407           <title>Repeating the box</title>
     1432        <section xml:id='domain.repeat-box'>
     1433          <title xml:id='domain.repeat-box.title'>Repeating the box</title>
    14081434
    14091435          <para>Under periodic boundary conditions often only the minimal
    … …  
    14211447        </section>
    14221448       
    1423         <section>
    1424           <title>Change the boundary conditions</title>
     1449        <section xml:id='domain.set-boundary-conditions'>
     1450          <title xml:id='domain.set-boundary-conditions.title'>Change the
     1451          boundary conditions</title>
    14251452
    14261453          <para>Various boundary conditions can be applied that affect how
    … …  
    14521479      </section>
    14531480
    1454       <section>
    1455         <title>Filling</title>
     1481      <section xml:id='filling'>
     1482        <title xml:id='filling.title'>Filling</title>
    14561483       
    14571484          <para>Filling a specific part of the domain with one type of
    … …  
    14831510          additionally excluded from the filling region.</para>
    14841511
    1485         <section>
    1486           <title>Fill the domain with molecules</title>
     1512        <section xml:id='filling.fill-regular-grid'>
     1513          <title xml:id='filling.fill-regular-grid.title'>Fill the domain with
     1514          molecules</title>
    14871515
    14881516          <para>The call to fill the volume of the selected shape with the
    … …  
    15071535          molecules' volume is obtained by tesselating their surface and
    15081536          excluding every fill-in point whose distance to this surface does
    1509           not exceed 1. We refer to our comments in <link linkend="???">1.4
    1510           Randomization </link>for details on changing the randomness.</para>
    1511         </section>
    1512 
    1513         <section>
    1514           <title>Fill a shape's volume with molecules</title>
     1537          not exceed 1. We refer to our comments in
     1538          <link linkend="randomization">Randomization</link>for details on
     1539          changing the randomness.</para>
     1540        </section>
     1541
     1542        <section xml:id='filling.fill-volume'>
     1543          <title xml:id='filling.fill-volume.title'>Fill a shape's volume
     1544          with molecules</title>
    15151545         
    15161546          <para>More specifically than filling the whole domain with molecules,
    … …  
    15301560        </section>
    15311561         
    1532         <section>
    1533           <title>Fill a shape's surface with molecules</title>
     1562        <section xml:id='filling.fill-surface'>
     1563          <title xml:id='filling.fill-surface.title'>Fill a shape's surface
     1564          with molecules</title>
    15341565
    15351566                  <para>Filling a surface is very similar to filling its volume.
    … …  
    15571588        </section>
    15581589
    1559         <section>
    1560           <title>Suspend in molecule</title>
     1590        <section xml:id='filling.suspend-in-molecule'>
     1591          <title xml:id='filling.suspend-in-molecule.title'>Suspend in molecule
     1592          </title>
    15611593
    15621594          <para>Add a given molecule in the simulation domain in such a way
    … …  
    15681600        </section>
    15691601
    1570         <section>
    1571           <title>Fill in molecule</title>
     1602        <section xml:id='filling.fill-molecule'>
     1603          <title xml:id='filling.fill-molecule.title'>Fill in molecule</title>
    15721604
    15731605          <para>This action will be soon be removed.</para>
    … …  
    15781610        </section>
    15791611
    1580         <section>
    1581           <title>Fill void with molecule</title>
     1612        <section xml:id='filling.fill-void'>
     1613          <title xml:id='filling.fill-void.title'>Fill void with molecule
     1614          </title>
    15821615
    15831616          <para>This action will be soon be removed.</para>
    … …  
    15891622      </section>
    15901623
    1591       <section>
    1592         <title>Analysis</title>
     1624      <section xml:id='analysis'>
     1625        <title xml:id='analysis.title'>Analysis</title>
    15931626
    15941627                <para></para>
    15951628
    1596         <section>
    1597           <title>Pair Correlation</title>
     1629        <section xml:id='analysis.pair-correlation'>
     1630          <title xml:id='analysis.pair-correlation.title'>Pair Correlation
     1631          </title>
    15981632         
    15991633          <para>Pair correlation checks for two given elements on the typical
    … …  
    16191653        </section>
    16201654
    1621         <section>
    1622           <title>Dipole Correlation</title>
     1655        <section xml:id='analysis.dipole-correlation'>
     1656          <title xml:id='analysis.dipole-correlation.title'>Dipole Correlation
     1657          </title>
    16231658         
    16241659          <para>The dipole correlation is similar to the pair correlation, only
    … …  
    16391674        </section>
    16401675
    1641         <section>
    1642           <title>Dipole Angular Correlation</title>
     1676        <section xml:id='analysis.dipole-angular-correlation'>
     1677          <title xml:id='analysis.dipole-angular-correlation.title'>Dipole
     1678          Angular Correlation</title>
    16431679         
    16441680          <para>The dipole angular correlation looks at the angles of a
    … …  
    16651701        </section>
    16661702
    1667         <section>
    1668           <title>Point Correlation</title>
     1703        <section xml:id='analysis.point-correlation'>
     1704          <title xml:id='analysis.point-correlation.title'>Point Correlation
     1705          </title>
    16691706         
    16701707          <para>Point correlation is very similar to pair correlation, only
    … …  
    16881725        </section>
    16891726
    1690         <section>
    1691           <title>Surface Correlation</title>
     1727        <section xml:id='analysis.surface-correlation'>
     1728          <title xml:id='analysis.surface-correlation.title'>Surface
     1729          Correlation</title>
    16921730         
    16931731          <para>The surface correlation calculates the distance of a set
    … …  
    17061744        </section>
    17071745
    1708         <section>
    1709           <title>Molecular Volume</title>
     1746        <section xml:id='analysis.molecullar-volume'>
     1747          <title xml:id='analysis.molecullar-volume.title'>Molecular Volume
     1748          </title>
    17101749         
    17111750          <para>This simply calculates the volume that a selected molecule
    … …  
    17201759      </section>
    17211760
    1722       <section>
    1723         <title>Fragmentation</title>
     1761      <section xml:id='fragmentation'>
     1762        <title xml:id='fragmentation.title'>Fragmentation</title>
    17241763
    17251764        <para>Fragmentation refers to a so-called linear-scaling method called
    … …  
    17711810        off).</para>
    17721811
    1773         <section>
    1774           <title>Fragmenting a molecular system</title>
     1812        <section xml:id='fragmentation.fragment-molecule'>
     1813          <title xml:id='fragmentation.fragment-molecule.title'>Fragmenting a
     1814          molecular system</title>
    17751815
    17761816          <para>For the current selection of atoms, all fragments consisting
    … …  
    18191859          XYZ (mainly for checking the configurations visually) and MPQC,
    18201860          which is a very robust Hartree-Fock solver. We refer to the
    1821           discussion of the <link linkend="???">Parsers</link> above on how to
    1822           change the parameters of the ab-initio calculation.</para>
     1861          discussion of the <link linkend="fileparsers">Parsers</link> above
     1862          on how to change the parameters of the ab-initio calculation.</para>
    18231863
    18241864          <para>After having written all fragment configuration files, you
    … …  
    18301870        </section>
    18311871
    1832         <section>
    1833           <title>Calculating fragment energies automatically</title>
     1872        <section xml:id='fragmentation.fragment-automation'>
     1873          <title xml:id='fragmentation.fragment-automation.title'>Calculating
     1874          fragment energies automatically</title>
    18341875
    18351876          <para>Another way of doing this is enabled if you have
    … …  
    18481889          <para>Stored fragment jobs can also be parsed again, i.e. reversing
    18491890          the effect of having output-types specified in <link
    1850           linkend="???">Fragmenting a molecule</link>.</para>
     1891          linkend="fragmentation.fragment-molecule">Fragmenting a molecule
     1892          </link>.</para>
    18511893
    18521894          <programlisting>
    … …  
    19141956        </section>
    19151957
    1916         <section>
    1917           <title>Analyse fragment results</title>
     1958        <section xml:id='fragmentation.analyse-fragment-results'>
     1959          <title xml:id='fragmentation.analyse-fragment-results.title'>
     1960          Analyse fragment results</title>
    19181961
    19191962          <para>After the energies and force vectors of each fragment have
    … …  
    19401983
    19411984          <para>Note that this action sets the force vector if these have been
    1942           calculated for the fragment. Hence, a <link linkend="???">verlet
    1943           integration</link> is possible afterwards.</para>
     1985          calculated for the fragment. Hence, a
     1986          <link linkend="molecule.verlet-integration">verlet integration</link>
     1987          is possible afterwards.</para>
    19441988        </section>
    19451989       
    1946         <section>
    1947           <title>Store a saturated fragment</title>
     1990        <section xml:id='fragmentation.store-saturated-fragment'>
     1991          <title xml:id='fragmentation.store-saturated-fragment.title'>Store
     1992          a saturated fragment</title>
    19481993
    19491994          <para>After the energies and force vectors of each fragment have
    … …  
    19662011      </section>
    19672012
    1968       <section>
    1969         <title>Homologies</title>
     2013      <section xml:id='homology'>
     2014        <title xml:id='homology.title'>Homologies</title>
    19702015
    19712016        <para>After a fragmentation procedure has been performed fully, what
    … …  
    20152060      </section>
    20162061
    2017       <section>
    2018         <title>Potentials</title>
     2062      <section xml:id='potentials'>
     2063        <title xml:id='potentials.title'>Potentials</title>
    20192064
    20202065        <para>In much the same manner, we would now ask what are homology
    … …  
    20242069        surface of the full system.</para>
    20252070
    2026         <section>
    2027           <title>Fitting empirical potentials</title>
     2071        <section xml:id='potentials.fit-potential'>
     2072          <title xml:id='potentials.fit-potential.title'>Fitting empirical
     2073          potentials</title>
    20282074
    20292075          <para>Let's take a look at an exemplary call to the fit potential
    … …  
    20972143        </section>
    20982144
    2099         <section>
    2100           <title>Fitting particle charges</title>
     2145        <section xml:id='potentials.fit-particle-charges'>
     2146          <title xml:id='potentials.fit-particle-charges.title'>Fitting
     2147          particle charges</title>
    21012148
    21022149          <para>The above empirical potential just model the short-range
    … …  
    21092156          <para>To allow least-squares regression of these partial charges we
    21102157          need the results of long-range calculations and the store-grids
    2111           option (see above under <link linkend="???">Fragmentation</link>)
    2112           must have been given. With these sampled charge density and Coulomb
    2113           potential stored in the homology containers, we call this action as
    2114           follows.</para>
     2158          option (see above under <link linkend="fragmentation">Fragmentation
     2159          </link>) must have been given. With these sampled charge density and
     2160          Coulomb potential stored in the homology containers, we call this
     2161          action as follows.</para>
    21152162
    21162163          <programlisting>
    … …  
    21322179      </section>
    21332180
    2134       <section>
    2135         <title>Dynamics</title>
     2181      <section xml:id='dynamics'>
     2182        <title xml:id='dynamics.title'>Dynamics</title>
    21362183
    21372184        <para>For fitting potentials or charges we need many homologuous but
    … …  
    21432190        energies but also forces if the chosen solver, such as
    21442191        <link xlink:href="http://www.mpqc.org/"><productname>MPQC
    2145         </productname></link>, supports it. Integrating these forces discretely over time
    2146         gives insight into vibrational features of a molecular system and
    2147         allows to generate those positions for fitting potentials that
    2148         describe these vibrations.</para>
    2149 
    2150         <section>
    2151           <title>Molecular dynamics</title>
     2192        </productname></link>, supports it. Integrating these forces
     2193        discretely over time  gives insight into vibrational features of a
     2194        molecular system and allows to generate those positions for fitting
     2195        potentials that describe these vibrations.</para>
     2196
     2197        <section xml:id='dynamics.molecular-dynamics'>
     2198          <title xml:id='dynamics.molecular-dynamics.title'>Molecular dynamics
     2199          </title>
    21522200
    21532201          <para>The molecular dynamics action is a so-called macro Action,
    … …  
    22042252        </section>
    22052253
    2206         <section>
    2207           <title>Structure optimization</title>
     2254        <section xml:id='dynamics.optimize-structure'>
     2255          <title xml:id='dynamics.optimize-structure.title'>Structure
     2256          optimization</title>
    22082257
    22092258                  <para>Structure optimization is also a macro Action, it basically
    … …  
    22352284        </section>
    22362285
    2237         <section>
    2238           <title>Set the world's time step</title>
     2286        <section xml:id='dynamics.set-world-time'>
     2287          <title xml:id='dynamics.set-world-time.title'>Set the world's time
     2288          step</title>
    22392289
    22402290                  <para>In order to inspect or manipulate atoms and molecules at a
    … …  
    22492299        </section>
    22502300
    2251         <section>
    2252           <title>Save the temperature information</title>
     2301        <section xml:id='dynamics.save-temperature'>
     2302          <title xml:id='dynamics.save-temperature.title'>Save the
     2303          temperature information</title>
    22532304
    22542305                  <para>For each time step the temperature (i.e. the average velocity
    … …  
    22612312      </section>
    22622313   
    2263       <section>
    2264         <title>Tesselations</title>
     2314      <section xml:id='dynamics.tesselation'>
     2315        <title xml:id='dynamics.tesselation.title'>Tesselations</title>
    22652316
    22662317        <para>Tesselations obtain molecular surfaces (and volumes) by rolling
    … …  
    22682319        surface of connected triangles is created.</para>
    22692320
    2270         <section>
    2271           <title>Non-convex envelope</title>
     2321        <section xml:id='dynamics.tesselation.nonconvex-envelope'>
     2322          <title xml:id='dynamics.tesselation.nonconvex-envelope.title'>
     2323          Non-convex envelope</title>
    22722324         
    22732325          <para>This will create a non-convex envelope for a molecule.</para>
    … …  
    22792331
    22802332          <para>This tesselation file can be conveniently viewed with
    2281           <programname>TecPlot</programname> or with one of the Tcl script
    2282           in the util folder with <programname>VMD</programname>.</para>
    2283         </section>
    2284 
    2285         <section>
    2286           <title>Convex envelope</title>
     2333          <productname>TecPlot</productname> or with one of the Tcl script
     2334          in the util folder with <productname>VMD</productname>.</para>
     2335        </section>
     2336
     2337        <section xml:id='dynamics.tesselation.convex-envelope'>
     2338          <title xml:id='dynamics.tesselation.convex-envelope.title'>Convex
     2339          envelope</title>
    22872340         
    22882341          <para>This will create a convex envelope for a molecule.</para>
    … …  
    22942347
    22952348          <para>This tesselation file can be conveniently viewed with
    2296           <programname>TecPlot</programname> or with one of the Tcl script
    2297           in the util folder with <programname>VMD</programname>.</para>
     2349          <productname>TecPlot</productname> or with one of the Tcl script
     2350          in the util folder with <productname>VMD</productname>.</para>
    22982351        </section>
    22992352      </section>
    23002353
    2301       <section>
    2302         <title>Various commands</title>
     2354      <section xml:id='various'>
     2355        <title xml:id='various.title'>Various commands</title>
    23032356
    23042357        <para>Here, we gather all commands that do not fit into one of above
    23052358        categories for completeness.</para>
    23062359
    2307         <section>
    2308           <title>Changing verbosity</title>
     2360        <section xml:id='various.verbose'>
     2361          <title xml:id='various.verbose.title'>Changing verbosity</title>
    23092362
    23102363          <para>The verbosity level is the amount of stuff printed to screen.
    … …  
    23222375        </section>
    23232376
    2324         <section>
    2325           <title>Loading an element database</title>
     2377        <section xml:id='various.element-db'>
     2378          <title xml:id='various.element-db.title'>Loading an element
     2379          database</title>
    23262380
    23272381          <para>Element databases contain information on valency, van der
    … …  
    23352389        </section>
    23362390
    2337         <section>
    2338           <title>Fast parsing</title>
     2391        <section xml:id='various.fastparsing'>
     2392          <title xml:id='various.fastparsing.title'>Fast parsing</title>
    23392393
    23402394          <para>Parsing all time steps from a given input file can take a
    … …  
    23452399        </section>
    23462400
    2347         <section>
    2348           <title>Giving the version of the program</title>
     2401        <section xml:id='various.version'>
     2402          <title xml:id='various.version.title'>Giving the version of the
     2403          program</title>
    23492404
    23502405          <para>This prints the version information of the code, especially
    … …  
    23552410        </section>
    23562411
    2357         <section>
    2358           <title>Giving warranty information</title>
     2412        <section xml:id='various.warranty'>
     2413          <title xml:id='various.warranty.title'>Giving warranty
     2414          information</title>
    23592415
    23602416          <para>As follows warranty information is given,</para>
    … …  
    23632419        </section>
    23642420
    2365         <section>
    2366           <title>Giving redistribution information</title>
     2421        <section xml:id='various.help-redistribute'>
     2422          <title xml:id='various.help-redistribute.title'>Giving
     2423          redistribution information</title>
    23672424
    23682425          <para>This gives information on the license and how to redistribute
    … …  
    23732430      </section>
    23742431
    2375       <section>
    2376         <title>Sessions</title>
     2432      <section xml:id='sessions'>
     2433        <title xml:id='sessions.title'>Sessions</title>
    23772434
    23782435        <para>A session refers to the queue of actions you have executed.
    … …  
    23842441        another.</para>
    23852442
    2386         <section>
    2387           <title>Storing a session</title>
     2443        <section xml:id='sessions.store-session'>
     2444          <title xml:id='sessions.store-session.title'>Storing a session
     2445          </title>
    23882446
    23892447          <para>Storing sessions is simple,</para>
    … …  
    24012459        </section>
    24022460
    2403         <section>
    2404           <title>Loading a session</title>
     2461        <section xml:id='sessions.load-session'>
     2462          <title xml:id='sessions.load-session.title'>Loading a session</title>
    24052463
    24062464          <para>Loading a session only works for python scripts. This actually
    … …  
    24172475      </section>
    24182476
    2419       <section>
    2420         <title>Various specific commands</title>
     2477      <section xml:id='various-specific'>
     2478        <title xml:id='various-specific.title'>Various specific commands
     2479        </title>
    24212480       
    24222481        <para>In this (final) section of the action description we list a number
    … …  
    24242483        </para>
    24252484       
    2426         <section>
    2427           <title>Saving exttypes of a set of atoms</title>
     2485        <section xml:id='various-specific.save-selected-atoms-as-exttypes'>
     2486          <title xml:id='various-specific.save-selected-atoms-as-exttypes.title'>
     2487          Saving exttypes of a set of atoms</title>
    24282488         
    24292489          <para>This saves the atomic ids of all currently selected atoms in a
    2430            <link xlink:href="http://www.tremolo-x.com/"><programname>TREMOLO
    2431            </programname></link> exttypes file with the given name.</para>
     2490           <link xlink:href="http://www.tremolo-x.com/"><productname>TREMOLO
     2491           </productname></link> exttypes file with the given name.</para>
    24322492
    24332493          <programlisting>
    … …  
    24362496        </section>
    24372497       
    2438         <section>
    2439           <title>Setting parser specific parameters</title>
     2498        <section xml:id='various-specific.set-parser-parameters'>
     2499          <title xml:id='various-specific.set-parser-parameters.title'>Setting
     2500          parser specific parameters</title>
    24402501
    24412502          <para>You can also tweak the parameters stored in this file easily.
    … …  
    24582519        </section>
    24592520
    2460         <section>
    2461           <title>Tremolo specific options and potential files</title>
     2521        <section xml:id='various-specific.set-tremolo-atomdata'>
     2522          <title xml:id='various-specific.set-tremolo-atomdata.title'>Tremolo
     2523          specific options and potential files</title>
    24622524
    24632525          <para><productname>TREMOLO</productname>'s configuration files start
    … …  
    24922554    </section>
    24932555
    2494     <section>
    2495       <title>Text menu</title>
     2556    <section xml:id='textmenu-interface'>
     2557      <title xml:id='textmenu-interface.title'>Text menu</title>
    24962558
    24972559      <para>We now discuss how to use the text menu interface.</para>
    … …  
    25112573    </section>
    25122574
    2513     <section>
    2514       <title linkend="GUI">Graphical user interface</title>
     2575    <section xml:id='graphical-user-interface'>
     2576      <title xml:id='graphical-user-interface.title'>Graphical user interface
     2577      </title>
    25152578
    25162579      <para>The main point of the GUI is that it renders the atoms and
    … …  
    25272590      various derived or slightly modified structures.</para>
    25282591
    2529       <section>
    2530         <title>Basic view</title>
     2592      <section xml:id='graphical-user-interface.basic-view'>
     2593        <title xml:id='graphical-user-interface.basic-view.title'>Basic view
     2594        </title>
    25312595
    25322596        <para>Let us first give an impression of the basic view of the gui
    … …  
    25442608        </figure>
    25452609
    2546         <section>
    2547           <title>3D view</title>
     2610        <section xml:id='graphical-user-interface.3d-view'>
     2611          <title xml:id='graphical-user-interface.3d-view.title'>3D view
     2612          </title>
    25482613
    25492614          <para>In the above figure, you see the stick-and-ball representation
    … …  
    25522617        </section>
    25532618
    2554         <section>
    2555           <title>Information Tabs</title>
     2619        <section xml:id='graphical-user-interface.information-tabs'>
     2620          <title xml:id='graphical-user-interface.information-tabs.title'>
     2621          Information Tabs</title>
    25562622
    25572623          <para>Beneath this 3D view that you can rotate at will your mouse
    … …  
    25662632        </section>
    25672633
    2568         <section>
    2569           <title>Shape section</title>
     2634        <section xml:id='graphical-user-interface.shape'>
     2635          <title xml:id='graphical-user-interface.shape.title'>Shape section
     2636          </title>
    25702637
    25712638          <para>Beneath these information tabs you find the shape sections.
    … …  
    25742641        </section>
    25752642
    2576         <section>
    2577           <title>Timeline</title>
     2643        <section xml:id='graphical-user-interface.timeline'>
     2644          <title xml:id='graphical-user-interface.timeline.title'>Timeline
     2645          </title>
    25782646
    25792647          <para>Directly below the 3D view there is a long slider. If a loaded
    … …  
    25852653        </section>
    25862654
    2587         <section>
    2588           <title>Selection tables</title>
     2655        <section xml:id='graphical-user-interface.tables'>
     2656          <title xml:id='graphical-user-interface.tables.title'>Selection
     2657          tables</title>
    25892658
    25902659          <para>Underneath the time line there is another place for
    … …  
    26082677      </section>
    26092678
    2610       <section>
    2611         <title>Selections</title>
     2679      <section xml:id='graphical-user-interface.selections'>
     2680        <title xml:id='graphical-user-interface.selections.title'>Selections
     2681        </title>
    26122682
    26132683        <para>Selections work generally always by selecting the respective
    … …  
    26302700      </section>
    26312701
    2632       <section>
    2633         <title>Dialogs</title>
     2702      <section xml:id='graphical-user-interface.dialogs'>
     2703        <title xml:id='graphical-user-interface.dialogs.title'>Dialogs</title>
    26342704
    26352705        <para>Most essential, however, to the GUI are the dialogs. Each action
    … …  
    26452715        </note>
    26462716
    2647         <section>
    2648           <title>Domain query</title>
     2717        <section xml:id='graphical-user-interface.dialogs.domain'>
     2718          <title xml:id='graphical-user-interface.dialogs.domain.title'>Domain
     2719          query</title>
    26492720
    26502721          <figure>
    … …  
    26652736        </section>
    26662737
    2667         <section>
    2668           <title>Element query</title>
     2738        <section xml:id='graphical-user-interface.dialogs.element'>
     2739          <title xml:id='graphical-user-interface.dialogs.element.title'>
     2740          Element query</title>
    26692741
    26702742          <figure>
    … …  
    26862758        </section>
    26872759
    2688         <section>
    2689           <title>Complex query</title>
     2760        <section xml:id='graphical-user-interface.dialogs.action'>
     2761          <title xml:id='graphical-user-interface.dialogs.action.title'>
     2762          Complex query</title>
    26902763
    26912764          <figure>
    … …  
    27062779        </section>
    27072780
    2708         <section>
    2709           <title>Exit query</title>
     2781        <section xml:id='graphical-user-interface.dialogs.exit'>
     2782          <title xml:id='graphical-user-interface.dialogs.exit.title'>Exit
     2783          query</title>
    27102784
    27112785          <figure>
    … …  
    27282802    </section>
    27292803
    2730     <section>
    2731       <title>Python interface</title>
     2804    <section xml:id='python-interface'>
     2805      <title xml:id='python-interface.title'>Python interface</title>
    27322806
    27332807      <para>Last but not least we elaborate on the python interface. We have
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