[Debian Wiki] Update of "BOINC/Server/Projects/AutoDock" by SteffenMoeller

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The "BOINC/Server/Projects/AutoDock" page has been changed by SteffenMoeller:
https://wiki.debian.org/BOINC/Server/Projects/AutoDock?action=diff&rev1=46&rev2=47

Comment:
auto-enumeration of sections

  
  Our ambition is to bring all components directly into a regular Debian package or present it as a dependency. The authors of this page have their own in-house BOINC-based AutoDock project going, with all components available on Debian, but to round it all up, the development is still ongoing - and particularly so is this documentation. For joining in, please contact us.
  
- == 1. Conceptional Overview ==
+ == Conceptional Overview ==
  
  The project is centered around Debian as the sole source of all software tools required for the project and for an automated retrieval of data. The BOINC client is shipping with Debian-proper since a long time. The BOINC Server we decided to leave in the experimental section of Debian, so we can update this publicly exposed software at any time.
  
@@ -20, +20 @@

  {{attachment:BOINC_Server_AutoDock_Overview.png}}
  
  In the following, we describe the yellow arrow of above figure, i.e. how to get from the boinc-server-autodock Debian package with the help of what is shipping with boinc-server-maker to a web site that invites users to contribute and to a repository of ligand evaluations that can be interpreted by Raccoon. All scripts described or referenced below (if not referenced directly) are available from the [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=summary|git repository]]. 
- == 2. Preparation of BOINC side ==
+ == Preparation of BOINC side ==
  
  The AutoDock BOINC project first of all is a regular BOINC project. All tools one knows about how to set up BOINC projects are working completely the same. We prepared a script to set up the AutoDock project at a predefined location with no human intervention. As nice as it is, please take the extra time to mentally follow the [[BOINC/ServerGuide]]. This transports a bit - not too much - of an extra understanding on how BOINC works internally, which we consider to help you all in helping us to improve the workflow. The current implementation is working solely with AutoDock Vina. Support for the classical AutoDock 4.x was once described on [[BOINC/ServerGuide/AutoDockApp]] and has yet to be updated and incorporated into our scripts.
  
  The executable scripts all reside in /usr/share/boinc-server-autodock/bin. All BOINC-specific preparation is completed with the script "[[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/install.sh|install.sh]]" in that directory. Caveat: This first cleans the database, do not use it inadvertedly. Then, it invokes separate scripts to perform steps 2.1 and 2.2 as described below.
  
- === 2.1. Install BOINC web server ===
+ === Install BOINC web server ===
  
  The tool [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/autodockvina_install_project.sh|autodockvina_install_project.sh]] performs
   * project creation with BOINC's make_project script
@@ -37, +37 @@

   
  At this point, users can subscribe to the project and wait for work units.
  
- === 2.2. Prepare AutoDock Vina binaries and inform BOINC about them ===
+ === Prepare AutoDock Vina binaries and inform BOINC about them ===
  
  To script [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/autodockvina_install_project.sh|autodockvina_install_apps.sh]] continues with
   * retrieval of wrappers for Linux (from Debian) and Windows (from BOINC_
@@ -48, +48 @@

  
  The project is functional now, except for the missing workunits.
  
- === 2.x. Comments ===
+ === Comments ===
  
  In a perfect world there would be no need wrappers. Instead, we would patch the AutoDock application to learn how to use the BOINC file descriptors. Also, we should indicate the progress in a file for BOINC to display to the user. For single ligands, though, AutoDock Vina is so quick, that this seems not to be required to help the user experience, much. For multiple ligands to be executed within the same work unit, the granularity of the progress indication is with the percentage of ligands evaluated.
  
  
- == 3. Preparation of Docking side ==
+ == Preparation of Docking side ==
  
  It may be convenient to keep AutoDock Vina configuration files, receptor and ligands models on the same machine that runs BOINC server to avoid large data transmission over network. PDBQT files for the receptors and ligands of interest may be prepared with use of utilites from AutoDockTools. A number of prepared ligand sets can be downloaded from http://zinc.docking.org/pdbqt/.  To automate the retrieval, install the [[wiki.debian.org/getData|getData]] Debian package. The one-time configuration of the receptor for the docking is performed as for every docking project with AutoDock and is supported by the [[http://mgltools.scripps.edu|MGLTools]]. Debian supports the CADD tool "Raccoon", which also features an interface to perform this preparation.
  
- === 3.1. Make a database of receptor models for screening ===
+ === Make a database of receptor models for screening ===
  
  For the bash commands below we will suppose that receptor files, in PDBQT format, are kept in ''/home/boincadm/my_autodock_vina_library/receptors''. 
  
- === 3.2. Make a database of ligand models for screening ===
+ === Make a database of ligand models for screening ===
  
  For the bash commands below we will suppose that ligand files, also in PDBQT format, are kept in ''/home/boincadm/my_autodock_vina_library/ligands''. 
  
- === 3.3. Set configuration parameters for docking ===
+ === Set configuration parameters for docking ===
  
  For the bash commands below we will suppose that configuration files are kept in ''/home/boincadm/my_autodock_vina_library/configs''. 
  
- == 4. Management of running project ==
+ == Management of running project ==
  
  Results are collected without human intervention. The challenge is to create the right set of work units.
  
- === 4.1. Assimilator program for collecting docking results ===
+ === Assimilator program for collecting docking results ===
  
  We suggest to use the [[http://boinc.berkeley.edu/trac/wiki/AssimilateIntro#Thesampleassimilator|sample assimilator]] as provided by BOINC itself and already installed by above described ''install.sh'' script. It collects the output files as returned from the boinc-clients into a folder named ''sample_results'' under the main project directory. With literally millions of ligands tested against several structures, this takes considerable disk space. As an optimisation, a more sophisticated assimilator could possibly extract only the predicted energy values and coordinate files. Alternatively, one just buys another hard disk - we decided not to care and to be happy about the possibility to characterise the involvement of side chains in the binding and otherwise interpret the molecular data.
  
- === 4.2. BASH script to generates workunits ===
+ === BASH script to generates workunits ===
  
  Every scientific application has its own - sometimes multiple - ways it may be used. For AutoDock Vina, the script
  [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/autodockvina_generatework.sh|autodockvina_generatework.sh]]
@@ -86, +86 @@

  
  The workflow template [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=share/autodockvina_templates/raccoon-autodockvina_wu_template.xml|raccoon-autodockvina_wu_template.xml]] specifies the receptor as invariant between compute jobs to avoid redundant downloads. The short compute time of single ligands with vina invites to have multiple ligands submitted together as a workflow. For the moment this is not implemented - it works as it is and the handling of results on the server side seems easier. Also, when changing the technology, e.g. back to the classical AutoDock 4.x, compute time is likely to increase again.
  
- == 5. Result Collection ==
+ == Result Collection ==
  
  {{attachment:Figure_BOINC_Wiki_Dataflow.png}}
  
- === 5.1. Create a bash script to filter out docking results ===
+ === Create a bash script to filter out docking results ===
  
  Having the simplest assimilator implementation, it requires additional effort to process the work results. The "top" best compounds names may be extracted from the output files with use of convenient Linux utilites. We propose the following example.