[Cdk-commits] CVS: cdk/packages/tar/cdk/man .cvsignore,NONE,1.1 Makefile.am,NONE,1.1 cdk-dbadmin.xml,NONE,1.1 cdk-download.xml,NONE,1.1 cdk-fileconvert.xml,NONE,1.1 cdk-view.xml,NONE,1.1

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/packages/tar/cdk/man
In directory usw-pr-cvs1:/tmp/cvs-serv7875/man

Added Files:
	.cvsignore Makefile.am cdk-dbadmin.xml cdk-download.xml 
	cdk-fileconvert.xml cdk-view.xml 
Log Message:
Uploaded files for making the "cdk" package which replaces
the other tar packages.


--- NEW FILE: .cvsignore ---
manpage.*
*.1
Makefile
Makefile.in

--- NEW FILE: Makefile.am ---
SUBDIRS= xsl

XML2MAN_RULE = \
        xsltproc xsl/db2man.xsl $< 

CHECK_XML_RULE = for f in $^; \
 do \
  echo -n "Checking $$f..."; \
  rm -f $$f.dbx; \
  echo "<?xml version=\"1.0\"?>" > $$f.dbx; \
  echo "<!DOCTYPE part PUBLIC \"-//OASIS//DTD DocBook XML V4.1.2//EN\"" >> $$f.dbx; \
  echo "        \"http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd\">" >> $$f.dbx; \
  echo "<part>" >> $$f.dbx; \
  echo "  <title>Man page for $$f</title>" >> $$f.dbx; \
  cat $$f >> $$f.dbx; \
  echo "</part>" >> $$f.dbx; \
  xmllint --noent --valid --noout $$f.dbx && echo ok; \
  rm -f $$f.dbx; \
 done

docbooks = cdk-fileconvert.xml cdk-dbadmin.xml cdk-view.xml cdk-download.xml

man_MANS = cdk-fileconvert.1 cdk-dbadmin.1 cdk-view.1 cdk-download.1

CLEANFILES = ${man_MANS}

EXTRA_DIST = $(docbooks) ${man_MANS}

cdk-fileconvert.1: cdk-fileconvert.xml
	$(XML2MAN_RULE)

cdk-dbadmin.1: cdk-dbadmin.xml
	$(XML2MAN_RULE)

cdk-view.1: cdk-view.xml
	$(XML2MAN_RULE)

cdk-download.1: cdk-download.xml
	$(XML2MAN_RULE)

check-xml: $(docbooks)
	$(CHECK_XML_RULE)



--- NEW FILE: cdk-dbadmin.xml ---
<refentry id="cdk-dbadmin">

  <refmeta>
    <refentrytitle>cdk-dbadmin</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>

  <refnamediv>
    <refname>cdk-dbadmin</refname>
    <refpurpose>administrate chemical database</refpurpose>
  </refnamediv>

  <refsynopsisdiv>
    <cmdsynopsis>
      <command>cdk-dbadmin</command>
      <arg>--useHost [hostname]</arg>
      <arg>--useDatabase [database name]</arg>
      <arg>--useDriver [mysql|postgresql]</arg>
      <arg>--username [username]</arg>
      <arg>--passwd [pwd]</arg>
      <arg>--createDefaultTables</arg>
      <arg>--listTables</arg>
      <arg>--deleteTables</arg>
    </cmdsynopsis>
  </refsynopsisdiv>

  <refsect1>
    <title>OPTIONS</title>
    <variablelist>
      <varlistentry>
        <term>--useHost [hostname]</term>
        <listitem>
          <para>sets the hostname of the machine on which the database is run</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--useDatabase [database name]</term>
        <listitem>
          <para>sets the name of the database in which the tables are stored</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--useDriver [mysql|postgresql]</term>
        <listitem>
          <para>sets the JDBC driver used to access the database (Only MySQL is currently working.)</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--username [username]</term>
        <listitem>
          <para>sets the username of the account with which the database can be accessed</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--passwd [pwd]</term>
        <listitem>
          <para>sets the password for the account with which the database can be accessed</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--createDefaultTables</term>
        <listitem>
          <para>create the default tables in the chemical database</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--listTables</term>
        <listitem>
          <para>lists all information on the tables in the chemical database</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--deleteTables</term>
        <listitem>
          <para>deletes all tables from the chemical database</para>
        </listitem>
      </varlistentry>
    </variablelist>
  </refsect1>

  <refsect1>
    <title>DESCRIPTION</title>
    <para>
      <command>cdk-dbadmin</command> is used to prepare and delete tables from
	  a chemical database.
    </para>
  </refsect1>

  <refsect1>
    <title>VERSION</title>
    <para>
      $Id: cdk-dbadmin.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $
    </para>
  </refsect1>

  <refsect1>
    <title>COPYRIGHT</title>
    <para>
      Copyright (C) 2001-2002 The CDK Project
    </para>
    <para>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
    </para>
    <para>
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
    </para>
  </refsect1>

  <refsect1>
    <title>AUTHOR</title>
    <para>
      Egon Willighagen <email>eg...@sc...</email>
    </para>
  </refsect1>

</refentry>


--- NEW FILE: cdk-download.xml ---
<refentry id="cdk-download">

  <refmeta>
    <refentrytitle>cdk-download</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>

  <refnamediv>
    <refname>cdk-download</refname>
    <refpurpose>download chemical information from the internet</refpurpose>
  </refnamediv>

  <refsynopsisdiv>
    <cmdsynopsis>
      <command>cdk-download</command>
      <arg>CAS NUMBER</arg>
    </cmdsynopsis>
  </refsynopsisdiv>

  <refsect1>
    <title>OPTIONS</title>
    <variablelist>
      <varlistentry>
        <term>CAS NUMBER</term>
        <listitem>
          <para>CAS number of the structure you want to download</para>
        </listitem>
      </varlistentry>
    </variablelist>
  </refsect1>

  <refsect1>
    <title>DESCRIPTION</title>
    <para>
      <command>cdk-download</command> retrieves the 2D coordiante file
      of the requested compound.
    </para>
  </refsect1>

  <refsect1>
    <title>VERSION</title>
    <para>
      $Id: cdk-download.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $
    </para>
  </refsect1>

  <refsect1>
    <title>COPYRIGHT</title>
    <para>
      Copyright (C) 2002 The CDK Project
    </para>
    <para>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
    </para>
    <para>
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
    </para>
  </refsect1>

  <refsect1>
    <title>AUTHOR</title>
    <para>
      Egon Willighagen <email>eg...@sc...</email>
    </para>
  </refsect1>

</refentry>

--- NEW FILE: cdk-fileconvert.xml ---
<refentry id="cdk-fileconvert">

  <refmeta>
    <refentrytitle>cdk-fileconvert</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>

  <refnamediv>
    <refname>cdk-fileconvert</refname>
    <refpurpose>converts one file format to another</refpurpose>
  </refnamediv>

  <refsynopsisdiv>
    <cmdsynopsis>
      <command>cdk-fileconvert</command>
      <arg>-i [format]</arg>
      <arg>-o [format]</arg>
    </cmdsynopsis>
  </refsynopsisdiv>

  <refsect1>
    <title>OPTIONS</title>
    <variablelist>
      <varlistentry>
        <term>-i</term>
        <listitem>
          <para>input format</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>-o</term>
        <listitem>
          <para>output format</para>
        </listitem>
      </varlistentry>
    </variablelist>
  </refsect1>

  <refsect1>
    <title>DESCRIPTION</title>
    <para>
      <command>cdk-fileconvert</command> reads a input file and converts
	  it to a new file with an other format.
	  Supported input formats are
	  <acronym>CML</acronym>,
	  <acronym>MDL Molfile</acronym>,
	  <acronym>PDB</acronym> and
	  <acronym>XYZ</acronym>.
	  Supported output formats are
	  <acronym>CML</acronym>,
	  <acronym>MDL Molfile</acronym> and
          <acronym>SMILES</acronym>.
    </para>
  </refsect1>

  <refsect1>
    <title>VERSION</title>
    <para>
      $Id: cdk-fileconvert.xml,v 1.1 2002/08/31 14:43:08 egonw Exp $
    </para>
  </refsect1>

  <refsect1>
    <title>COPYRIGHT</title>
    <para>
      Copyright (C) 2001-2002 The CDK Project
    </para>
    <para>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
    </para>
    <para>
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
    </para>
  </refsect1>

  <refsect1>
    <title>AUTHOR</title>
    <para>
      Egon Willighagen <email>eg...@sc...</email>
    </para>
  </refsect1>

</refentry>

--- NEW FILE: cdk-view.xml ---
<refentry id="cdk-view">

  <refmeta>
    <refentrytitle>cdk-view</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>

  <refnamediv>
    <refname>cdk-view</refname>
    <refpurpose>view content of chemical file</refpurpose>
  </refnamediv>

  <refsynopsisdiv>
    <cmdsynopsis>
      <command>cdk-view</command> <arg>--nojava3d</arg> <arg>--no3d</arg> <arg>file.xml</arg>
    </cmdsynopsis>
  </refsynopsisdiv>

  <refsect1>
    <title>OPTIONS</title>
    <variablelist>
      <varlistentry>
        <term>--nojava3d</term>
        <listitem>
          <para>do not try to use Java3D for viewing 3D coordinates</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term>--no3d</term>
        <listitem>
          <para>do not view 3D coordinates</para>
        </listitem>
      </varlistentry>
    </variablelist>
  </refsect1>

  <refsect1>
    <title>DESCRIPTION</title>
    <para>
      <command>cdk-view</command> displays to content of the file
      <filename>file.xml</filename> with the format PDB, XYZ, CML
      or MDLMol.
    </para>
  </refsect1>

  <refsect1>
    <title>VERSION</title>
    <para>
      $Id: cdk-view.xml,v 1.1 2002/08/31 14:43:08 egonw Exp $
    </para>
  </refsect1>

  <refsect1>
    <title>COPYRIGHT</title>
    <para>
      Copyright (C) 2001-2002 The CDK Project
    </para>
    <para>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
    </para>
    <para>
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
    </para>
  </refsect1>

  <refsect1>
    <title>AUTHOR</title>
    <para>
      Egon Willighagen <email>eg...@sc...</email>
    </para>
  </refsect1>

</refentry>