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<title>User manual for LigBuilder v1.2</title>
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<h2 align="center">How to install LigBuilder?</h2>

<hr>

<p>&nbsp;&nbsp;&nbsp; LigBuilder is written in C++ language and
has been tested on UNIX and LINUX platforms.</p>

<p>&nbsp;&nbsp;&nbsp; To compile LigBuilder, first you need to
decrypt the package. You can do this in a UNIX shell like this:</p>

<p align="left"><font color="#FF0000" size="4">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</font><font color="#FF0000" size="3">crypt&nbsp; the_key &lt;
LigBuilder.tar.Z.en &gt; LigBuilder.tar.Z</font></p>

<p align="left"><font color="#000000">&nbsp;&nbsp;&nbsp; Then,
uncompress the package:</font></p>

<p align="left"><font color="#FF0000" size="4">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</font><font color="#FF0000" size="3">uncompress &nbsp;
LigBuilder.tar.Z</font></p>

<p><font color="#000000">&nbsp;&nbsp;&nbsp; The third step is to
unpack the package:</font></p>

<p align="left"><font color="#FF0000" size="4">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</font><font
color="#FF0000" size="3"> tar&nbsp; xvf &nbsp;LigBuilder.tar</font></p>

<p><font color="#000000">&nbsp;&nbsp;&nbsp; Now a directory named
&quot;</font><font color="#0000FF">LigBuilder1.2</font><font
color="#000000">&quot; has been created in your working
directory. Under that directory, there are following
subdirectories: </font></p>

<ul>
    <li><font size="2" face="Courier New">bin/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        default working directory</font></li>
    <li><font size="2" face="Courier New">pocket/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        source codes of POCKET module</font></li>
    <li><font size="2" face="Courier New">grow/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        source codes of GROW module </font></li>
    <li><font size="2" face="Courier New">link/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;source
        codes of LINK module </font></li>
    <li><font size="2" face="Courier New">process/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;source
        codes of PROCESS module &nbsp;&nbsp; &nbsp;</font></li>
    <li><font size="2" face="Courier New">parameter/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        necessary parameters</font></li>
    <li><font size="2" face="Courier New">example/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;test
        examples</font></li>
    <li><font size="2" face="Courier New">manual/
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;user
        manual in HTML</font></li>
    <li><font size="2" face="Courier New">fragment.mdb/&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        building-block fragment library</font></li>
    <li><font size="2" face="Courier New">forbidden.mdb/&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        forbidden substructure library</font></li>
    <li><font size="2" face="Courier New">toxicity.mdb/&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        toxic substructure library</font></li>
</ul>

<p>&nbsp;&nbsp;&nbsp; LigBuilder has four main modules, i.e.
POCKET, GROW, LINK, and PROCESS. You need to compile them
respectively. You can do this by simply entering each
subdirectory, i.e. &quot;<font color="#0000FF">pocket/</font>&quot;,
&quot;<font color="#0000FF">grow/</font>&quot;, &quot;<font
color="#0000FF">link/</font>&quot;, and &quot;<font
color="#0000FF">process/</font>&quot;, and typing &quot;<font
color="#FF0000">make</font>&quot; to run the <font
color="#0000FF">Makefile</font> scripts. <font color="#000000">The
scripts will compile the source codes automatically and generate
the executable codes.</font> This can be described as:</p>

<p>&nbsp;&nbsp;&nbsp; To compile POCKET: </p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cd&nbsp; pocket/<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; make<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cp&nbsp; pocket&nbsp;
../bin</p>

<p>&nbsp;&nbsp;&nbsp; To compile GROW:</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cd&nbsp; grow/<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; make<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cp&nbsp; grow&nbsp;
../bin</p>

<p>&nbsp;&nbsp;&nbsp; To compile LINK:</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cd&nbsp; link/<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; make<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cp&nbsp; link&nbsp;
../bin</p>

<p>&nbsp;&nbsp;&nbsp; To compile PROCESS:</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cd&nbsp; process/<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; make<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cp&nbsp; process&nbsp;
../bin</p>

<p>&nbsp;&nbsp;&nbsp; Please notice:</p>

<p>&nbsp;&nbsp;&nbsp; (1) As indicated above, we suggest you to
copy all the resultant executable codes, i.e. &quot;<font
color="#0000FF">pocket</font>&quot;, &quot;<font color="#0000FF">grow</font>&quot;,
&quot;<font color="#0000FF">link</font>&quot;, and &quot;<font
color="#0000FF">process</font>&quot; to another directory. So you
will not spoil the source codes by accident. </p>

<p>&nbsp;&nbsp;&nbsp; (2) <font color="#000000">The default C++
compiler assigned in the Makefile script is SGI &quot;</font><font
color="#0000FF">CC</font><font color="#000000">&quot; compiler.
Therefore, if you are using a different C++ compiler on your
computer, for example &quot;</font><font color="#0000FF">g++</font><font
color="#000000">&quot;, you should modify the first line in
the&nbsp;&quot;</font><font color="#0000FF">Makefile</font><font
color="#000000">&quot; scripts as &quot;</font><font
color="#0000FF">CC = g++</font><font color="#000000">&quot;
before compiling. </font></p>

<p>&nbsp;&nbsp;&nbsp; (3) What if you do not have any C++
compiler on your computer? We have provided pre-compiled
executable codes in the directory &quot;<font color="#0000FF">bin</font>&quot;.
They are compiled on SGI O2/R10000 workstation running IRIX6.4.
So if you also use the same kind of computer, you will have a
good chance to run LigBuilder without compiling.</p>

<p>&nbsp;&nbsp;&nbsp; (4) For PC users, we have stopped providing
executable codes for DOS platforms since LINUX has become such
popular. LigBuilder has been tested on LINUX platforms.</p>

<hr>

<p align="center"><a href="index.html">[Content]</a> <a
href="intro.html">[Introduction]</a> <a href="download.html">[Download]</a>
[Install] <a href="overview.html">[Overview]</a> <a
href="pocket.html">[POCKET]</a> <a href="grow.html">[GROW]</a> <a
href="link.html">[LINK]</a> <a href="process.html">[PROCESS]</a> <a
href="skill.html">[Skills]</a> <a href="faq.html">[FAQs]</a></p>

<p align="center"><font size="2"><em>(These web pages are edited
by Dr. Renxiao Wang. Latest update: August, 2000)</em></font></p>
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