FlexX Installation Guide

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1. Preconditions

 At this time, the GUI in FlexX is available under Linux and Windows. We
 have tested several flavors of Linux distributions. Please contact us in
 case you need other operating systems to be supported. 

 1.1 Required: 
  - the executable 
  - a license (for docking only); please see the manual (p. 31) for more
    details or visit http://www.biosolveit.de/license 
  (Linux only:) 
  - glibc in version 2.2 or higher. 
  - OpenGL libraries installed; see the troubleshooting section in the user
    guide (p. 289) in case you encounter problems here. 

 1.2 Highly desirable: 
  - a ring conformer generation tool such as corina from Molecular Networks
    to enable FlexX to also dock ligands containing flexible ring systems. 
  - any minimization tool to dock only low-energy conformations of ligands.
    (This can be achieved using corina as well.)
  Please contact support@biosolveit.com in case you do lack a tool. More
  information about corina in combination with FlexX can be obtained from
  our FAQ & Knowledge Base at http://www.biosolveit.de/faq/questions/77/. 
 
 1.3 Optional: 
  Optionally, the GUI can work with special 3D hardware. Please refer to
  Section 5.2.2 in the manual for details.
  If you want to dock using pharmacophore constraints, you will need an
  extra PHARM license. Demo and evaluation licenses, however, certainly
  cover the PHARM functionality.
 
 
2. Quick Installation for Interactive and Batch Mode Usage 
 
 Installation is easy: 

 A.
    - Windows: Start the installer package. It should be fairly
      self-explanatory.
    - Linux: Unpack the tar ball in one place or use the rpm install
      mechanism (depending on what you have downloaded. FlexX is an
      executable. If it does not have the 'x' flag, then please set it with
      'chmod +x flexx'.

 B. Start the GUIby calling 'flexx' (Windows) or './bin/flexx' (Unix/Linux)
    at the console (preferred), or double-clicking the executable's icon in
    your operating system's desktop. The GUI will appear. Go to the
    troubleshooting section of the manual if you encounter problems here
    (p. 289).
    After the standard installation procedure of FlexX, you should have the
    following files and directories:

    Files: 
      flexv
      flexx-> flexx-3.1.2-Linux
      flexx-3.1.2-Linux
      flexx_pbc.sh
      settings.pxx
      corina

    Directories: 
      doc/
      examples/
      predict/
      tmp/

    At a later date the console will presumable be merged into the GUI.
    However, this will not affect scriptability and output re-direction
    etc., which will still be possible. 

 C. The GUI will check whether some paths are set correctly. This affects:
    - a ring conformer generator 
    - the parallel computing scratch files directory (PVM-based, currently
      supported for Linux only)
    - the temporary files directory (recommended to be a local disk
      directory) 
    - the results output directory 

    In case any of this contains invalid paths, the GUI will pop up a
    dialog box which assists you in defining valid locations (invalid
    locations will be highlighted in red while you type). Once valid
    entries have been made, the program will store the respective
    information, and there is no need to fill in the dialog box again. 

    Finally, to enable direct download of pdb files from your local (for
    example firewall-protected) corporate location, you can specify a proxy
    in 'File' -> 'Global Preference' in the tab 'Proxy'.


3. Installing FlexX for Python Embedded Usage

 The Python Interface requires a special installation which is along the
 lines of the former FlexX versions: Besides its module(s), it requires the
 configuration file 'config.dat' and the so-called 'static_data'-files,
 both as flat files. (Please note that this will change in the future.) 

 The second entry in the configuration file is the so-called ROOT
 directory. All paths specified later in the file are relative to this path
 except those starting with '/' or './'. In the '@DIRECTORIES' section,
 you can define default paths to various data locations. The '@STATIC_DATA'
 section contains paths and filenames of the static data files of FlexX and
 the '@PROGRAMS' section contains paths and filenames of executables. 
 For a simple installation in the current directory, you can enter the path
 to the installation directory after the keyword '@ROOTDIR' and just leave
 all the rest as it is. You can customize the configuration of FlexX later
 on, and also individually for each user. We recommend that you already
 include the paths for 'RCGENERATOR' and '3DGENERATOR' at this time. 

 The actual usage of the Python Interface is further explained in the 
 manual's Scripting section on page 277.