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Technical Information

Preface

Thank you for your interest in WODCA and CACTVS. WODCA is a computer program of the newest generation for the interactive planning of organic syntheses. Together with the CACTVS tools it allows powerful planning studies for organic syntheses on UNIX-workstations with IRIX and Solaris or on Personal Computers with Linux as operating system.
Before you begin the installation process read this document carefully for a successful installation of WODCA and CACTVS. A detailed description of the installation is given in the section "Installation - Step by Step".

Test License

If you are interested in a test version of WODCA or your test license of WODCA has expired, send an email to gasteiger@chemie.uni-erlangen.de and ask for a license extension. Please tell us on which hardware environment you wish to install the program. Usually, the evaluation license of WODCA is limited to a period of three months. After this period the program will not start any more.

About the Installation Media

WODCA is delivered on a single CD-ROM. The CD-ROM contains all necessary files for a WODCA / CACTVS evaluation installation. Additionally, the CD provides the Janssen and FLUKA catalogs of chemicals in electronical form. Further catalogs of chemicals are available on inquiry.
The following files and directories can be found on the CD-ROM:

README.TXT
Installation guide in english
/wodca
This directory contains two files. The middle part of the name of the *.tar.gz files depends on the UNIX system of the WODCA CD distribution, e.g., the following files are for IRIX 5.3 or later:
tcl-tk-IRIX5.3.tar.gz
wodca-4.00-IRIX5.3.tar.gz
/janssen
This directory contains all files for the JANSSEN catalog of chemicals. The file JANDIR-2.0.tar.gz serves as a backup file of the /janssen directory and is not necessary for working with this catalog. It is only there to enable a complete restore of the /janssen directory.
/fluka
This directory contains all files for the FLUKA catalog of chemicals. The file Fluka-1.0.tar.gz serves as a backup file of the /fluka directory and is not necessary for working with the catalog. It is only provided to enable a complete restore of the /fluka directory.
/cactvs
This directory contains severable CACTVS distribution. The highest 3.XX number indicates the latest release and should be selected for installation. The name of the *.tar.gz files depends on the UNIX system of the WODCA CD distribution, e.g.:
cactvstools-IRIX5.3-3.19.tar.gz
cactvstools-IRIX5.3-3.23.tar.gz
...
cactvstools-IRIX5.3-3.32.tar.gz
cactvstools-IRIX5.3-3.37.tar.gz
cactvstools-IRIX5.3-3.99.tar.gz
/tools_irix
This directory contains two utility programs for IRIX 5.3 or higher:
gunzip
tar
If you have not installed these two programs in your UNIX environment, you can use them from the CD-ROM. These utilities are necessary to restore the installation from the *.tar.gz files.
/examples
This directory contains example files taken from different synthesis planning studies with WODCA. The following structure files are included:
g1.ctx
g1m.ctx
g2.ctx
g3.ctx
g4.ctx
g5.ctx
prec1.ctx
prec2a.ctx
prec2b.ctx
prec3.ctx
riboflavin.ctx
target.ctx
tibo.ctx
trioxifene.ctx

These files can be loaded by WODCA or the CACTVS Editor/Browser for a later use.
/html
This directory contains the complete online manual for WODCA written in HTML. To view the manual you need a WWW browser like Netscape Navigator 2.02 or higher. The online manual is composed of the following HTML files which are listed in a chronological order:
index.html
first.html
example.html
tutorial-b.html
contents.html
intro.html
gui.html
simsearch.html
subsearch.html
sbonds.html
cactvs.html
(sorry, not yet written)
install.html
whatsnew.html
lectures.html

reference.html
end.html

It is recommended to use the online manual from within WODCA (see Help Menu), because this provides you with the most current manual. However, if your company has an internet firewall and no connection to the WODCA Home Page is possible, you can use the manual on the CD-ROM as a substitute. In this case, it is recommended to copy the complete directory /html to your local hard disk and adapt the configuration file .wodcarc (see Adaptation of WODCA).
/manuals

In this directory you can find the latest WODCA 4 manuals in different file formats.

File Name

File Size

Word Processor

Remark

W3MAN08.DOC

7MB

MS Word 6.0


w4man12.sdw

1MB

StarWriter 5.0

recommended

To view the StarWriter manual for WODCA 3 you need StarOffice 5.0 which is available for free for non-commercial use on different computer plattforms (Windows 95/98/NT, OS/2, Linux, Apple Macintosh, Sun Solaris).

To download StarOffice 5.0 please visit the international StarDivision home page at http://www.stardivision.com.

Hardware and Software Requirements

For a successful installation of WODCA and CACTVS from the CD-ROM you need at least one of the following environments:
WODCA was tested on workstations with IRIX 5.3, IRIX 6.3, IRIX 6.4, IRIX6.5, Solaris 2.4, Solaris 2.5, Solaris 5.6 and SunOS 4.1, and on Personal Computers with Linux on a kernel 2.0 (libc5) and 2.2 (libc5 and libc6).

Attention: If you run WODCA on a Linux system it is necessary that the library 'libc5' is installed! For more information contact your Linux administrator.

Installation - Step by Step

The following example describes the installation of WODCA and CACTVS on a SGI workstation running IRIX 6.5.

Installation of the CACTVS tools

The entire installation process of WODCA and CACTVS should be done as "root" to install WODCA and CACTVS in a network environment.

Installation of WODCA with the JANSSEN and FLUKA catalogs of chemicals

The following lines show the contents of the file wodca.sh:
#!/bin/sh
# `wodca.sh' - Bourne shell script to invoke the graphical based wodca
# system version 4.X
#
# Set environment variables necessary for the wodca system.
#
# WODCAHOME - where the WODCA distribution is installed
WODCAHOME=

OS=`uname -s``uname -r |sed 's/\([^.]*\.[^.]*\).*/\1/'`
TCL_LIBRARY=${WODCAHOME}/tcl7.6
TK_LIBRARY=${WODCAHOME}/tk4.2
LD_LIBRARY_PATH=${WODCAHOME}/lib
WODCA_HOME_DIR=${WODCA:=$HOME/WODCA}
WODCA_LIB_DIR=${WODCAHOME}
WODCA_TRAFO_DIR=${WODCAHOME}/trafos
export TCL_LIBRARY TK_LIBRARY WODCA_HOME_DIR WODCA_LIB_DIR WODCA_TRAFO_DIR LD_LIBRARY_PATH
#
# The application will be started by default in the $WODCA_HOME_DIR directory.
# Make sure that this directory exists and copy some configuration files into
# it.
#
if [ ! -d $WODCA_HOME_DIR ]
then
mkdir $WODCA_HOME_DIR
cp $WODCAHOME/profile $WODCA_HOME_DIR
cp $WODCAHOME/.wodcarc $WODCA_HOME_DIR
fi
#
# Clean up WODCA's working directory
#
if [ -f $WODCA_HOME_DIR/VMEM01 ]
then
rm $WODCA_HOME_DIR/VMEM*
fi
if [ -f $WODCA_HOME_DIR/tmp_file ]
then
rm $WODCA_HOME_DIR/tmp_file
fi
#
# Define the program components.
#
PGM=${WODCAHOME}/wodcaserver
GUI=${WODCA_LIB_DIR}/wodca.gui
#
# Start it in background.
#
${PGM} ${GUI} &

Note, that at this time the installation process is NOT yet finished! Before WODCA is ready to be used, a few things still have to be adapted (see Adaptation of WODCA).

WODCA's working directory

If WODCA is started for the first time, a WODCA subdirectory in the user's home directory is automatically created, e.g., /home/user/WODCA. Furthermore, two configuation files are copied from /usr/local/wodca to WODCA's working directory /home/user/WODCA. The first one is the hidden file .wodcarc, the second file is named profile. With these two configuration files each user of WODCA is able to adapt WODCA to his / her needs.
It is recommended to use WODCA's working directory to organize all the files of chemical structures, which are generated during working. For each new synthesis planning study the user should create a new subdirectory, where the synthesis target, precursors and match lists are saved, e.g.
/home/user/WODCA/study1
/home/user/WODCA/study2
/home/user/WODCA/study3

Adaptation of WODCA

.wodcarc

The hidden file .wodcarc enables the adaptation of WODCA's color scheme of the graphical user interface, the configuration of the display of strategic bonds, and the setup of the paths to the external programs of the CACTVS system. Furthermore, it defines the location of the online manual, which is to be used during working with WODCA.
The hidden file .wodcarc is located in WODCA's installation directory /usr/local/wodca. It is copied during the first start of WODCA to WODCA's working directory /home/user/WODCA. The first path has a lower priority than the second one. Thus, it is possible that each user of WODCA adapts the file .wodcarc, located in /home/user/WODCA to his / her needs.
It is recommended that the system administrator sets the default values to the file .wodcarc located in WODCA's installation directory before WODCA is started for the first time. In this case, the adapted file .wodcarc is copied to the user's working directory of WODCA and there will be no need to adapt the file again unless the user wants to define his / her own color palette for WODCA.
The following lines show the structure of the file .wodcarc:
! `.wodcarc'
!
! A general X resource file for tk based applications.
! This one is for the WODCA3 core system.
!
! General widget colors:
!
Wodca*Foreground: black
Wodca*Background: light steel blue
Wodca*activeForeground: white
Wodca*activeBackground: steel blue
Wodca*highlightBackground: light steel blue
Wodca*troughColor: pale turquoise
Wodca*Canvas.Background: gray35
Wodca*Entry.Background: pale turquoise
Wodca*Listbox.Background: ivory
Wodca*Text.Foreground: black
Wodca*Text.Background: ivory
Wodca*Radiobutton.activeBackground: steel blue
Wodca*Scrollbar.activeBackground: steel blue
Wodca*Listbox.selectForeground: white
Wodca*Listbox.selectBackground: steel blue
!Wodca*Scrollbar.Foreground: Light Steel Blue
!Wodca*Scrollbar.activeForeground: LightPink1
Wodca*selectColor: deep pink
! standard: #b03060
!
! Special widget colors:
!
Wodca*pic.Background: light steel blue
!
! Colors for molecular drawings:
!
*bondColor: white
*carbColor: white
*haloColor: green
*hydroColor: PaleTurquoise1
*nitroColor: deepskyblue
*oxColor: red
*phosColor: orchid
*sulfColor: yellow
*metColor: gray
*textColor4: white
!
! Special ressources for the display of strategic bonds:
!
*markerColor: yellow
*markerWidth: 3
*drawMode: ratings
!
! Resources to define the paths to the external CACTVS programs:
!
*editorCmd: csed
*browserCmd: csbr
*plannerCmd: /home/wodca3/bin/cspl
*subsearchCmd: /home/wodca3/bin/csss
*editorName: Cactvs/Editor
*browserName: Cactvs/Browser
*plannerName: Cactvs/Planner
*subsearchName: Cactvs/SubSearch
!
! Resources to configure the online help:
!
*manualBrowser:
*manualURL:
It is important to check the section »! Resources to define the paths to the external CACTVS programs«. If the CACTVS starting scripts are installed in /usr/local/bin and WODCA is installed in /usr/local/wodca, it is necessary to adapt the following entries as shown in the example:
*editorCmd: /usr/local/bin/csed
*browserCmd: /usr/local/bin/csbr
*plannerCmd: /usr/local/wodca/cspl
*subsearchCmd: /usr/local/wodca/csss

The section »! Resources to configure the online help« is used to define a WWW browser other than Netscape Navigator and another URL for the location of the online help. The default values for the variables *manualBrowser and *manualURL are netscape and http://www2.chemie.uni-erlangen.de/software/wodca/contents.html. Thus, if Netscape Navigator is installed in your UNIX environment and your firm has an unlimited access to the internet, then you will not need to change anything and the fields *manualBrowser: and *manualURL: can be empty.
But if a WWW browser other than Netscape Navigator is to be used accessing the online help, the variable *manualBrowser: has to be changed to the start script of the alternative WWW browser, e.g.

*manualBrowser: mosaic

If your firm has an internet firewall and the online manual is copied from the CD-ROM directory /html to a local network drive, e.g. /usr/local/html, then the variable *manualURL: has to be adapted, too.

*manualURL: file:/usr/local/html/contents.html

profile

The file profile enables the selection of a default catalog of chemicals which is to be automatically loaded during the launch of WODCA. Furthermore, it initializes a welcome message in the WODCA console after WODCA is started.
The file profile is located in WODCA's installation directory /usr/local/wodca. It is copied during the first start of WODCA to WODCA's working directory /home/user/WODCA. The first path has a lower priority than the second path. Thus, it is possible that each user of WODCA adapts the file profile, located in /home/user/WODCA to his / her needs.
It is recommended that the system administrator sets the default values to the file profile located in WODCA's installation directory before WODCA is used for the first time. In this case, the adapted file profile is copied to the user's working directory of WODCA and there will be no need to adapt the file again unless the user wants to define another catalog of chemicals than the default one.
The following lines show the contents of the file profile:
#
# `profile' - default start-up file for the Wodca core system
#
# Print a welcome message:
write2shell "\
        \n\t+---------------------------------------------------------------+\
        \n\t|                Welcome to the WODCA 3 system !                |\
        \n\t|                                                               |\
        \n\t|                     Face the challenge !                      |\
        \n\t+---------------------------------------------------------------+\n"
# Open a catalog of chemicals at startup time
set catalogdir /db/catalogs/FLUKA
set catalog Fluka
if [file isdirectory $catalogdir] {
        catalog -open $catalogdir/$catalog
} else {
        write2shell "\
        \nSorry, no catalog of chemicals available!\
        \nPlease, check the path to the catalog and load a catalog manually using the file menu.\n"
}
proc dbs {} {
        foreach db {VORHER MOLINF NACHER} {
                write2shell "$db: `[ens get $db A_LABEL]'"
        }
}
proc fs {} {
        foreach f [molfile list] {
                write2shell "$f: [molfile get $f format mode record name]"
        }
}
# EOF
        


Edit the file profile in the following manner to change the default catalog of chemicals. Define the desired catalog of chemicals by using the 'set-statement', e.g.


# Open a catalog of chemicals at startup time
set catalogdir /usr/local/janssen
set catalog JANDIR
if [file isdirectory $catalogdir] {
catalog -open catalogdir/$catalog
}
Now, WODCA automatically loads the JANSSEN catalog of chemicals during the launch.

Support

For further information referring to the installation of WODCA please contact:
Dr. Matthias Pförtner
Computer-Chemie-Centrum und Institut für Organische Chemie
Universität Erlangen-Nürnberg
Nägelsbachstr. 25
D-91052 Erlangen
Germany

Tel: +49-9131-85-2-6580
Fax: +49-9131-85-2-6566
Email: matthias.pfoertner@chemie.uni-erlangen.de


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Last change: 2000-06-28
Webmaster: matthias.pfoertner@chemie.uni-erlangen.de