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debian/ant.properties deleted 100644 → 0
View file @ 1c4ac36f
jar=/usr/share/java
lib=/usr/share/java
devellib=/usr/share/java
nowarn=on
# CDK 1.0.x does not compile against Weka 2.5.7, see SF bug report #1895295
weka.jar=skip
# CDK 1.0.x is not tested againt Batik 1.7, see SF feature request #1895300
compile.batik=false
debian/cdk-manpages/cdk-dbadmin.xml deleted 100644 → 0
View file @ 1c4ac36f
<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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-download.xml deleted 100644 → 0
View file @ 1c4ac36f
<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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-fileconvert.xml deleted 100755 → 0
View file @ 1c4ac36f
<refentry id="cdk-fileconvert">
<refmeta>
<refentrytitle>cdk-fileconvert</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-fileconvert</refname>
<refpurpose>converts one or more files to another format</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-fileconvert</command>
<arg>OPTIONS</arg>
<arg>input files</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term>-h/--help</term>
<listitem>
<para>Print the help</para>
</listitem>
</varlistentry>
<varlistentry>
<term>-o[format]/--outputformat:[format]</term>
<listitem>
<para>Defines the output format to use. (See below for a list of
possible formats)</para>
</listitem>
</varlistentry>
<varlistentry>
<term>--quesion:[none|fewest|some|all]</term>
<listitem>
<para>Defines the level of customization of the file IO.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>--listoptions:[format]</term>
<listitem>
<para>Lists the options of customization of the given file format.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>--properties:[format]</term>
<listitem>
<para>Use a Java properties file to define the file IO option
values.</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>,
<acronym>PMP</acronym>,
<acronym>SHELX</acronym> and
<acronym>XYZ</acronym>. The input format is automatically detected.
</para>
<para>
Supported output formats are: cml, gin, mol, pdb, shelx, smi, svg and
xyz.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-fileconvert.xml,v 1.3 2003/07/03 08:48:56 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2001-2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-fingerprinter.xml deleted 100755 → 0
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<refentry id="cdk-fingerprinter">
<refmeta>
<refentrytitle>cdk-fingerprinter</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-fingerprinter</refname>
<refpurpose>generates CDK fingerprints for the given molecules</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-fingerprinter</command>
<arg>file</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-fingerprinter</command> reads one or more input files
and generates CDK fingerprints for all the molecules it finds.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-fingerprinter.xml,v 1.1 2004/01/12 11:50:58 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2003-2004 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-guessformat.xml deleted 100755 → 0
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<refentry id="cdk-guessformat">
<refmeta>
<refentrytitle>cdk-guessformat</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-guessformat</refname>
<refpurpose>guesses the file format of a file</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-guessformat</command>
<arg>file</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-guessformat</command> reads an input file and tries
to determine the file format.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-guessformat.xml,v 1.1 2003/05/27 14:33:52 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-iupacname.xml deleted 100755 → 0
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<refentry id="cdk-iupacname">
<refmeta>
<refentrytitle>cdk-iupacname</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-iupacname</refname>
<refpurpose>generates the IUPAC name for the given molecule</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-iupacname</command>
<arg>file</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-iupacname</command> reads an input file and tries
to generate a IUPAC name for this structure. Currently only
a few IUPAC rules are implemented, but simple alkane structures
can be named.
</para>
<para>
The output language can be set using <arg>--dutch</arg> or
<arg>--german</arg>.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-iupacname.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-substructure.xml deleted 100755 → 0
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<refentry id="cdk-substructure">
<refmeta>
<refentrytitle>cdk-substructure</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-substructure</refname>
<refpurpose>searches through a set of files to find a given
substructure</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-substructure</command>
<arg>SMILES</arg>
<arg>files</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-substructure</command> reads one or more an input files
and determines wether the structure given by the SMILES (after removal
of hydrogens) is a substructure of the input file.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-substructure.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-test.xml deleted 100644 → 0
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<refentry id="cdk-test">
<refmeta>
<refentrytitle>cdk-test</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-test</refname>
<refpurpose>perform JUnit tests on CDK classes</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-test</command> <arg>JUnit test</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-test</command> opens up a JUnit window for testing
CDK classes. The optional argument is used to set the JUnit test
that is loaded, e.g. org.openscience.cdk.test.CDKTests.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-test.xml,v 1.1 2003/01/01 16:42:09 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2001-2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-validate.xml deleted 100755 → 0
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<refentry id="cdk-validate">
<refmeta>
<refentrytitle>cdk-validate</refentrytitle>
<manvolnum>1</manvolnum>
</refmeta>
<refnamediv>
<refname>cdk-validate</refname>
<refpurpose>checks the chemical content of a file</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>cdk-validate</command>
<arg>file</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>
<command>cdk-validate</command> reads an input file and checks wether
the chemistry that is described in that file is correct, or might contain
problems.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-validate.xml,v 1.1 2003/07/14 20:57:59 egonw Exp $
</para>
</refsect1>
<refsect1>
<title>COPYRIGHT</title>
<para>
Copyright (C) 2003 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/cdk-manpages/cdk-view.xml deleted 100644 → 0
View file @ 1c4ac36f
<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>--useJmol</arg> <arg>file.xml</arg>
<command>cdk-view</command> <arg>--smiles</arg> <arg>SMILES</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>
<varlistentry>
<term>--smiles</term>
<listitem>
<para>show a 2D representation of the SMILES</para>
</listitem>
</varlistentry>
<varlistentry>
<term>--useTree</term>
<listitem>
<para>shows a ChemObjectTree of the loaded file</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 CML, IChI, MDLMol,
PDB and XYZ.
</para>
</refsect1>
<refsect1>
<title>VERSION</title>
<para>
$Id: cdk-view.xml,v 1.3 2003/01/01 16:42:09 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>egonw@sci.kun.nl</email>
</para>
</refsect1>
</refentry>
debian/compile.excludes deleted 100644 → 0
View file @ 1c4ac36f
**/Convertor.java
**/CMLWriter.java
**/RssWriter.java
**/PDBAtomCustomizer.java
**/MDMoleculeCustomizer.java
**/R/RModel.java
**/CNNClassificationModel.java
**/R/CNNRegressionModel.java
**/R/LinearRegressionModel.java
**/PLSRegressionModel.java
**/QSARCustomizer.java
debian/upstream/edam_ 0 → 100644
View file @ 8c07b71f
---
ontology: EDAM (1.16)
topic:
- Sequence analysis
scopes:
- name: summary
function:
- Multiple sequence alignment
input:
- data: Sequence
formats:
- EMBL format
- FASTA
- GCG
- GenBank format
- nbrf/pir
- PHYLIP format
- UniProtKB format
- data: Gene tree
output:
- data: Alignment
formats:
- FASTA-aln
- PHYLIP format
- selex
- Stockholm format
- Vienna local RNA secondary structure format
- data: Phylogenetic tree
formats: [Phylip tree format]
debian/upstream/metadata_ 0 → 100644
View file @ 8c07b71f
Reference:
Author:
Title:
Journal:
Year:
Volume:
Number:
Pages:
DOI:
PMID:
URL:
eprint: