Installation of the HintLogP software package
on a Windows (95, 98, ME, 2000, XP) or UNIX/LINUX machine consists of (1)
setting up the appropriate (sub)directory for HintLogP, (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.
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 www.edusoft-lc.com <login with information provided by eduSoft> ftp> bin ftp> GET hintlogp309win2k.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" hintlogp309win2k.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\hintlogp3.06_win2kSetup Your Environment:
Windows 95/98/ME: SET MCONN_LICENSE=C:\eduSoft\hintlogp3.06_win2k\LICENSE.DAT
(You may wish to add this to your AUTOEXEC.BAT, or you can edit and execute the "definehint.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 HintLogP executable to your path (e.g., SET PATH=%path%;C:\eduSoft\hintlogp3.06_win2k, or see comments about "definehint.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 HintLogP executable to the PATH variable in the system variables.
License Keys
Install the HintLogP License Keys(s) as described on-line.
Test Run HintLogP
To determine that your software is properly executing, execute one or more test runs of HintLogP using demo input files. Note that HintLogP no longer has an interactive dialog. The syntax is:
HINTLOGP DEMO_CONTROL.dat DEMO1.smi demo.OUT1The 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 Using HintLogP for specific information on how to use the control file and Input File Formats for details about the input file formats.
In the software supplied with HintLogP, 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 HintLogP package, all the output options have been selected with the options provide in the demo_control.dat file. Please note that the files, demo*.OUT 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 HintLogP, for the user to further analyze the HintLogP 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.
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 HintLogP software:
%/usr/eduSoft: ftp www.edusoft-lc.com
<login with information provided
by eduSoft>
ftp> get hintlogp306irix.gz
<for SGI version>
ftp> get hintlogp306solaris.gz
<for SUN Solaris version, ASK>
ftp> get hintlogp306linux.gz
<for Intel LINUX version>
ftp> get hintlogp306macosx.gz
<for Macintosh OS X version, ASK>
Extract the GZIP archive
The UNIX distribution of HintLogP 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 hintlogp306irix.gz; tar xvof
hintlogp306irix
%/usr/eduSoft: tar xvzf hintlogp306irix.gz <if
using GNU tar>
License Keys
Install the HintLogP License Keys(s) as described on-line.
Modify unix environment
Edit the appropriate file in /usr/eduSoft/hintlogp3.06_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 HintLogP are $MCONN_LICENSE for the pointer to the eduSoft license, $DY_LICENSEDATA for the pointer to the Daylight toolkit license (if used), and $HINT_RUN for the pointer to the location of the "hintlogp" executable.
User Setup
Each user must:
source /usr/eduSoft/hintlogp3.06_platform/lib/cshrc
to your $HOME/.cshrc. To run HintLogP, type
$HINT_RUN/hintlogp
$HINT_RUN/hintlogp demo_control.dat demo.smi demo.OUT
(Note that the unix filenames are all lowercase.)
| unix filename | Windows filename | description |
| bin/hintlogp | HINTLOGP.EXE | program executable |
| lib/cshrc | - | initialization script and environmentals (csh) |
| lib/profile | - | initialization script and environmentals (sh) |
| - | HINTSETUP.BAT | initialization script and environmentals |
| demo/demo_control.dat | demo\CONTROL.DAT | sample hintlogp control file |
| demo/demo1.smi | demo\DEMO1.SMI | simple demo file (benzene) in SMILES format |
| demo/demo1.OUT | demo\DEMO1.OUT | results for demo1 |
| demo/demo2.smi | demo\DEMO2.SMI | 200 molecule demo file in SMILES format |
| demo/demo2.OUT | demo\DEMO2.OUT | results for demo2 |
| demo/demo3.sdf | demo\DEMO3.SDF | 12 molecule demo file in SD Format |
| demo/demo3.OUT | demo\DEMO3.OUT | results for demo3 |
| demo/demo4.sdf | demo\DEMO4.SDF | 50 molecule demo file in SD Format |
| demo/demo4.OUT | demo\DEMO4.OUT | results for demo4 |
| demo/demo5.mol2 | demo\DEMO5.MOL2 | 10 molecule demo file in mol2 format |
| demo/demo5.OUT | demo\DEMO5.OUT | results for demo5 |
| license/HintLogPLicense.dat | LICENSE.DAT | text file for storage of license key string |
| docs/index.html | docs\INDEX.HTML | root document for html HintLogP manual |
demo_control.dat: DETAIL moleculelevel INPUTFORMAT oelibsmiles WARNINGS on ERRORS skip INDEX on OUTPUT record OUTPUT name OUTPUT formula OUTPUT weight OUTPUT logp DELIMITER space GO
demo1.smi: c1ccccc1 benzene
demo1.OUT:
1 benzene H(6)C(6) 78.113396 2.130000
demo_control.dat: DETAIL moleculelevel INPUTFORMAT oelibmol2 WARNINGS on ERRORS skip INDEX on OUTPUT record OUTPUT name OUTPUT formula OUTPUT weight OUTPUT logp DELIMITER space GO
demo5.mol2: See data file for details, contains the following molecules:1 B_ESTRADIOL 2 ACETYLCHOLINE 3 ARGININE 4 ASPIRIN 5 COCAINE 6 DOPAMINE 7 MORPHINE 8 ETHYLACETATE 9 PHENYLALANINE 10 TRIFLUOROMETHYLPHENYLETHER
demo5.OUT:
1 B_ESTRADIOL H(24)C(18)O(2) 272.386414 4.880000 2 ACETYLCHOLINE H(16)C(7)N(1)O(2) 146.208908 1.444200 3 ARGININE H(19)C(9)N(5)O(2) 229.281418 -6.661111 4 ASPIRIN H(7)C(9)O(4) 179.151901 1.217778 5 COCAINE H(21)C(17)N(1)O(4) 303.357178 4.237957 6 DOPAMINE H(11)C(8)N(1)O(2) 153.180405 0.328800 7 MORPHINE H(19)C(17)N(1)O(3) 285.341980 1.538764 8 ETHYLACETATE H(8)C(4)O(2) 88.105995 0.710000 9 PHENYLALANINE H(11)C(9)N(1)O(2) 165.191391 1.093000 10 TRIFLUOROMETHYLPHENYLETHER H(5)C(7)O(1)F(3) 162.111084 1.139000
NOTE: All of the options for running HintLogP 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*.OUT have been created under IRIX 6.5 on an R12K O2.