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README.TXT/wodca*.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/janssenJANDIR-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-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./cactvscactvstools-IRIX5.3-3.19.tar.gzcactvstools-IRIX5.3-3.23.tar.gz...cactvstools-IRIX5.3-3.32.tar.gzcactvstools-IRIX5.3-3.37.tar.gzcactvstools-IRIX5.3-3.99.tar.gz/tools_irixgunziptar*.tar.gz files.
/examples
prec1.ctx
prec2a.ctx
prec2b.ctx
prec3.ctx
riboflavin.ctx
target.ctx
tibo.ctx
trioxifene.ctx/htmlindex.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/html to your local hard disk and adapt the
configuration file .wodcarc (see Adaptation
of WODCA).
/manualsIn this directory you can find the latest WODCA 4 manuals in different file formats.
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To download StarOffice 5.0 please visit the international StarDivision home page at http://www.stardivision.com.
SGI workstation with IRIX 5.3 or later
Sun workstation with SunOS 4.1 or later
Sun workstation with Solaris 2.4 or later
PC with Linux (kernel 2.0 or later)
libc5'
is installed! For more information contact your Linux administrator.The following example describes the installation of WODCA and CACTVS on a SGI workstation running IRIX 6.5.
Create a temporary directory (e.g. /demo/temp) and an
installation directory for WODCA and CACTVS (e.g. /usr/local)
on your local hard disk or network drive.
Put the CD-ROM in a CD-ROM drive and mount it from your UNIX
workstation. Go to the CD-ROM directory /cactvs and
copy the latest distribution file cactvstools-IRIX6.5-3.99.tar.gz
to the directory /demo/temp on your local hard disk,
e.g.cp cactvstools-IRIX6.5-3.99.tar.gz
/demo/temp
Go to the directory /demo/temp on your local
hard disk and unpack the file cactvstools-IRIX6.5-3.99.tar.gz
with the following command:gunzip <
cactvstools-IRIX6.5-3.99.tar.gz | tar xvf -
Start the installme script which has been
created in /demo/temp, e.g./demo/temp/installme
During the installation process two path names have to be
given. The first path is the place, where the subdirectory /cactvs
should be created (e.g. /usr/local), the second path is
the place, where the starting scripts should be created (e.g.
/usr/local/bin).
With these starting scripts the programs of the CACTVS system
can be started. To test the installation of the CACTVS tools, go to
the directory described before (e.g. /usr/local/bin)
and start the CACTVS programs with one of the following
commands:csed
(starts the CACTVS molecule
editor)csbr
(starts the CACTVS match list
browser)
After a successful installation of the CACTVS programs, the
directory /demo/temp on your local hard disk should be
deleted to save disk space.
Put the CD-ROM in a CD-ROM drive and mount it from your UNIX
workstation. Go to the root directory of the CD-ROM and copy the
directory /wodca to your local hard disk or network
drive, e.g.cp -r wodca /usr/local
Go to the directory /usr/local and set write
permission to the directory wodca, e.g.chmod +w wodca
Go to the directory /usr/local/wodca and unpack
the file tcl-tk-IRIX5.3.tar.gz with the following
command:gunzip < tcl-tk-IRIX5.3.tar.gz | tar xvf
-
Do the same with the file wodca-4.00-IRIX5.3.tar.gz,
e.g.gunzip < wodca-4.00-IRIX5.3.tar.gz
| tar xvf -
To install the JANSSEN catalog of chemicals, copy the
/janssen directory from the CD-ROM to your local hard
disk or network drive, e.g.:cp -r janssen
/usr/localThe file JANDIR-2.0.tar.gz
serves as a backup file of the /janssen directory and
is not necessary for working with the catalog. It enables a complete
restore of the /janssen directory. To save disk space,
it is recommended to delete the file JANDIR-2.0.tar.gz
from the directory /usr/local/janssen, e.g.:rm
/usr/local/janssen/JANDIR-2.0.tar.gz
To install the FLUKA catalog of chemicals, copy the /fluka
directory from the CD-ROM to your local hard disk or network drive,
e.g.:cp -r fluka /usr/localThe 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
enables a complete restore of the /fluka directory. To
save disk space, it is recommended to delete the file
Fluka-1.0.tar.gz from the directory /usr/local/fluka,
e.g.:rm /usr/local/fluka/Fluka-1.0.tar.gz
Now, it is necessary to set an environment variable to the
starting script of WODCA. Thus, go to the directory /usr/local/wodca
and edit the file wodca.sh. For the environment
variables WODCAHOME the corresponding absolute path has
to be set, e.g.: WODCAHOME=/usr/local/wodca
wodca.sh:
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cspl and csss are also
located in /usr/local/wodca. They are used to invoke
the external CACTVS Synthesis Planner and the Substructure Search.
Edit both files in the same way to set the environment variables
CACTVSHOME and WODCAHOME,
e.g.,CACTVSHOME=/usr/local/cactvs
WODCAHOME=/usr/local/wodcaThe file /usr/local/wodca/WLIBS contains the
absolute paths to the catalogs of chemicals implemented in WODCA.
All catalogs not included in this distribution should be deleted
from this file. However, the absolute path to the Janssen and the
FLUKA catalog has to be adapted,
e.g./usr/local/janssen/JANDIR
/usr/local/fluka/Fluka
The WODCA core program is now ready to start and can be
launched with the command wodca.sh from the directory
/usr/local/wodca, e.g. /usr/local/wodca/wodca.sh
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).
/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.
/home/user/WODCA/study1
/home/user/WODCA/study2
/home/user/WODCA/study3.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.
.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.
.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.
.wodcarc:
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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! 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.
*manualBrowser: mosaic/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.htmlprofile 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.
#
# `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
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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
}
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