Installation of the Molconn-Z software package on a Windows (95, 98, ME, 2000, XP) or UNIX/LINUX machine consists of (1) setting up the appropriate (sub)directory for Molconn-Z, (2) copying the files into that (sub)directory, (3) modifying the setup file that identifies the location of your executable, and (4) installing and setting the environment for your LICENSE file.

Windows Installation Procedure

Directory for Molconn-Z

Before the software is loaded into your system, setup the (sub)directory which will house the software materials, the executable module, and example input/output files. See the table below.

C:\> MKDIR C:\eduSoft\

Download (using FTP in BINARY mode) or copy the ZIP archive to this directory.

START/RUN/CMD
C:\> CD C:\eduSoft\
C:\eduSoft> FTP ftp.edusoft-lc.com 
<login with information provided by eduSoft>
ftp> bin
ftp> GET molconnz410_win2k.zip (make certain that binary file type is used, 
and watch case)

Extract the ZIP Archive

C:\eduSoft> Use WinZip or similar utility to "extract" molconnz410_win2k.zip 
and set the extract directory to your install directory C:\eduSoft\

See the directory listing for a copy of the contents of the software file directory.

C:\eduSoft> DIR C:\eduSoft\molconnz4.10_win2k

Setup Your Environment:

Windows 95/98/ME:  SET MCONN_LICENSE=C:\eduSoft\molconnz4.10_win2k\LICENSE.DAT (You may wish to add this to your AUTOEXEC.BAT, or you can edit and execute the "definemcz.BAT".)

Windows 2000/XP:  To set this value select the system icon from the control panel, then select the Environment Variables button located on the Advanced tab. Select New from the system variables to create this variable (note you may need to reboot).

In addition, you can add the directory that contains the Molconn-Z executable to your path (e.g., SET PATH=%path%;C:\eduSoft\molconnz4.10_win2k, or see comments about "definemcz.BAT" above) so that it can be found regardless of where your data is stored and calculations are performed. Windows 2000/XP path is modified by adding the directory containing the Molconn-Z executable to the PATH variable in the system variables.

License Keys

Install the Molconn-Z License Keys(s) as described on-line.

Test Run Molconn-Z

To determine that your software is properly executing, execute one or more test runs of Molconn-Z using demo input files. Note that Molconn-Z no longer has an interactive dialog. The syntax is:

MOLCONNZ DEMO_CONTROL.dat DEMO1.smi demo.S1

The input file type (SMILES, SDF, MOL2) and the output file content can be controlled by the "control file" (in this case demo_control.dat). See Chapter 4 for specific information on how to use the control file and Chapter 5 for details about the input file formats. 

In the software supplied with Molconn-Z, example output listing files are also included. Compare your output to the example output files to determine program performance. In the example files delivered in the Molconn-Z package, all the output options have been selected with the options provide in the demo_control.dat file. Please note that the files, demo*.S have been created under IRIX 6.5 on an R12K O2. There will be extremely small differences (in the fifth decimal place) for different CPU/OS due to different round-off errors. Therefore, if you run an automated "diff", you will need to look carefully at the differences.

Additional Information

It will be critical, in order to obtain maximum benefit from Molconn-Z, for the user to further analyze the Molconn-Z generated data using sophisticated statistical tools that are typically available from third party sources (and your company/site may already have a license for) like SAS and MATLAB.

Unix/Linux/Mac OS X Installation Procedure

Directory for Molconn-Z

Please create a directory, mkdir eduSoft under /usr or another convenient location which will be the root directory for this product:

%/usr: mkdir eduSoft
%/usr: cd eduSoft

Download the Molconn-Z software:

%/usr/eduSoft: ftp ftp.edusoft-lc.com
<login with information provided by eduSoft>
ftp> get molconnz410_irix.tar.gz <for SGI version>
ftp> get molconnz410_solaris.tar.gz <for SUN Solaris version, ASK>
ftp> get molconnz410_linux.tar.gz <for Intel LINUX version>
ftp> get molconnz410_macosx.tar.gz <for Macintosh OS X version, ASK>

Extract the GZIP archive

The UNIX distribution of Molconn-Z is a GZIP compressed "tar" archive. Extracting can be done by uncompressing with "gunzip" first then extracting with "tar", or in one process using GNU tar.

%/usr/eduSoft: gunzip molconnz410_irix.tar.gz; tar xvof molconnz410_irix.tar
%/usr/eduSoft: tar xvzf molconnz410_irix.tar.gz <if using GNU tar>

License Keys

Install the Molconn-Z License Keys(s) as described on-line.

Modify unix environment

Edit the appropriate file in /usr/eduSoft/molconnz4.10_platform/lib (i.e., the cshrc or profile shell files) to correct the entry for the actual location of $EDUSOFT_ROOT. The key environment variables to run Molconn-Z are $MCONN_LICENSE for the pointer to the eduSoft license, $DY_LICENSEDATA for the pointer to the Daylight toolkit license (if used), and $MCONN_RUN for the pointer to the location of the "molconnz" executable.

User Setup

Each user must:

"source" the above resource file; i.e., for cshell users add the line

source /usr/eduSoft/molconnz4.10_platform/lib/cshrc

to your $HOME/.cshrc.  To run Molconn-Z, type

$MCONN_RUN/molconnz
 

Test Molconn-Z as described above for Windows

$MCONN_RUN/molconnz demo_control.dat demo.smi demo.S

(Note that the unix filenames are all lowercase.)

Directory: Contents of the Molconn-Z Software

(Demo1) Sample files for Molconn-Z

1. Control File

demo_control.dat:

NORECORDS
ADD 1
ADD 3
ADD 4
ADD 8
ADD 9
HEADERS top
INPUTFORMAT oelibsmiles
WARNINGS off
ERRORS skip
GO

2. Input File

demo1.smi:

c1ccccc1 benzene

3. Output File

demo1.S:

 moleculenumber narecs nvx nedges nrings ncircuits nclass nelem ntpaths molweight molname formula
  X0   X1   X2   Xp3   Xp4   Xp5   Xp6   Xp7   Xp8   Xp9   Xp10
  Xv0  Xv1  Xv2  Xvp3  Xvp4  Xvp5  Xvp6  Xvp7  Xvp8  Xvp9  Xvp10
  dX0  dX1  dX2  dXp3  dXp4  dXp5  dXp6  dXp7  dXp8  dXp9  dXp10
 dXv0 dXv1 dXv2 dXvp3 dXvp4 dXvp5 dXvp6 dXvp7 dXvp8 dXvp9 dXvp10
1 1 6 6 1 1 1 2 30   78.113 benzene H(6)C(6)
4.242640 3.000000 2.121320 1.500000 1.060660 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000
3.464101 2.000000 1.154701 0.666667 0.384900 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000
-0.585787 0.085786 0.414213 0.542893 0.560660 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000
-1.364326 -0.914213 -0.552406 -0.290440 -0.115100 -0.006331 0.000000 0.000000 0.000000 0.000000 0.000000 

NOTE: All of the options for running Molconn-Z are in the control file. This file can be named anything you wish. The example provided has the arbitrary name demo_control.dat. The descriptors which have non-zero values will depend on the structure of the molecule. Also note that the files, demo*.S have been created under IRIX 6.5 on an R12K O2. There will be extreemly small differences (in the fifth decimal place) for different CPU/OS due to different round-off errors. Therefore, if you run an automated "diff", you will need to look carefully at the differences. For example, in demo2.S, for molecule 18485-76-2, the value of dX1 is -0.465054, however, it will be -0.465055 for a LINUX 2.2 machine running on an AMD K6-2 chip, and it will be -0.465053 for a Windows95 machine running on an AMD K6-2 chip.