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Fixed RDKit Book link in reaction nodes descriptions. rdkit#77
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@manuelschwarze
manuelschwarze committed May 7, 2020
1 parent fc2bbcc commit 0cb6331
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Showing 4 changed files with 72 additions and 64 deletions.
62 changes: 33 additions & 29 deletions ...cated/org/rdkit/knime/nodes/onecomponentreaction/RDKitOneComponentReactionNodeFactory.xml
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<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="one_comp_react.png" type="Manipulator" deprecated="true">
<name>RDKit One Component Reaction</name>

<shortDescription>
Applies a reaction to an input RDKit Mol column
</shortDescription>

<fullDescription>
<intro>Applies a reaction to an input RDKit Mol column.
<p>
The output table contains a row for each product produced by applying the reaction to the inputs.
<br />Each row contains the product molecule, index information, and the reactant molecule that was used.
</p>
</intro>

<option name="RDKit Mol column">The column containing reactant molecules</option>
<option name="Reaction SMARTS">A reaction SMARTS describing the reaction.
<br />For a description of the format, please see Chapter 2 of the <a href="http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Docs/Book/RDKit_Book.pdf" >RDKit Book</a>. </option>
<option name="Use Reaction from RXN file">If you want to use a reaction file rather than a smarts pattern, select this box and choose the RXN file in the file browser. </option>

</fullDescription>

<ports>
<inPort index="0" name="Data">Data with SMILES or RDKit Molecule column</inPort>
<outPort index="0" name="Product molecules">Product molecules</outPort>
</ports>
</knimeNode>
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="one_comp_react.png" type="Manipulator" deprecated="true">
<name>RDKit One Component Reaction</name>

<shortDescription>
Applies a reaction to an input RDKit Mol column
</shortDescription>

<fullDescription>
<intro>Applies a reaction to an input RDKit Mol column.
<p>
The output table contains a row for each product produced by applying the reaction to the inputs.
<br />Each row contains the product molecule, index information, and the reactant molecule that was used.
</p>
</intro>

<option name="RDKit Mol column">The column containing reactant molecules</option>
<option name="Reaction SMARTS">
A reaction SMARTS describing the reaction.
<br />
For a description of the format, please have a look in
<a href="http://rdkit.org/docs/RDKit_Book.html#reaction-smarts">The RDKit Book</a>.
</option>
<option name="Use Reaction from RXN file">If you want to use a reaction file rather than a smarts pattern, select this box and choose the RXN file in the file browser. </option>

</fullDescription>

<ports>
<inPort index="0" name="Data">Data with SMILES or RDKit Molecule column</inPort>
<outPort index="0" name="Product molecules">Product molecules</outPort>
</ports>
</knimeNode>
66 changes: 35 additions & 31 deletions ...cated/org/rdkit/knime/nodes/twocomponentreaction/RDKitTwoComponentReactionNodeFactory.xml
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<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="two_comp_react.png" type="Manipulator">
<name>RDKit Two Component Reaction</name>

<shortDescription>
Applies a reaction to two RDKit Mol columns
</shortDescription>
<fullDescription>
<intro>Applies a reaction to two RDKit Mol columns.
<p>
The output table contains a row for each product produced by applying the reaction to the inputs.
<br />Each row contains the product molecule, index information, and the reactant molecules that were used.
</p>
</intro>

<option name="Reactants 1 RDKit Mol column">The column containing the first reactant molecules</option>
<option name="Reactants 2 RDKit Mol column">The column containing the second reactant molecules</option>
<option name="Reaction SMARTS">A reaction SMARTS describing the reaction.
<br />For a description of the format, please see Chapter 2 of the <a href="http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Docs/Book/RDKit_Book.pdf" >RDKit Book</a>. </option>
<option name="Use Reaction from RXN file">If you want to use a reaction file rather than a smarts pattern, select this box and choose the RXN file in the file browser. </option>
<option name="Do Matrix Expansion">If checked, each reactant 1 will be combined with each reactant 2
yielding the combinatorial expansion of the reactants. If not checked, reactants 1 and 2 will be combined
sequentially, with the longer list determining the number of output rows.</option>
</fullDescription>
<ports>
<inPort index="0" name="Reactant 1">Data with RDKit Mol column</inPort>
<inPort index="1" name="Reactant 2">Data with RDKit Mol column</inPort>
<outPort index="0" name="Product molecules">Product molecules</outPort>
</ports>
</knimeNode>
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="two_comp_react.png" type="Manipulator">
<name>RDKit Two Component Reaction</name>

<shortDescription>
Applies a reaction to two RDKit Mol columns
</shortDescription>
<fullDescription>
<intro>Applies a reaction to two RDKit Mol columns.
<p>
The output table contains a row for each product produced by applying the reaction to the inputs.
<br />Each row contains the product molecule, index information, and the reactant molecules that were used.
</p>
</intro>

<option name="Reactants 1 RDKit Mol column">The column containing the first reactant molecules</option>
<option name="Reactants 2 RDKit Mol column">The column containing the second reactant molecules</option>
<option name="Reaction SMARTS">
A reaction SMARTS describing the reaction.
<br />
For a description of the format, please have a look in
<a href="http://rdkit.org/docs/RDKit_Book.html#reaction-smarts">The RDKit Book</a>.
</option>
<option name="Use Reaction from RXN file">If you want to use a reaction file rather than a smarts pattern, select this box and choose the RXN file in the file browser. </option>
<option name="Do Matrix Expansion">If checked, each reactant 1 will be combined with each reactant 2
yielding the combinatorial expansion of the reactants. If not checked, reactants 1 and 2 will be combined
sequentially, with the longer list determining the number of output rows.</option>
</fullDescription>
<ports>
<inPort index="0" name="Reactant 1">Data with RDKit Mol column</inPort>
<inPort index="1" name="Reactant 2">Data with RDKit Mol column</inPort>
<outPort index="0" name="Product molecules">Product molecules</outPort>
</ports>
</knimeNode>
4 changes: 2 additions & 2 deletions .../src/org/rdkit/knime/nodes/onecomponentreaction2/RDKitOneComponentReactionNodeFactory.xml
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<option name="Reaction SMARTS">
A reaction SMARTS describing the reaction.
<br />
For a description of the format, please see Chapter 2 of the
<a href="http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Docs/Book/RDKit_Book.pdf">RDKit Book</a>.
For a description of the format, please have a look in
<a href="http://rdkit.org/docs/RDKit_Book.html#reaction-smarts">The RDKit Book</a>.
</option>
</tab>
<tab name="Randomization">
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4 changes: 2 additions & 2 deletions .../src/org/rdkit/knime/nodes/twocomponentreaction2/RDKitTwoComponentReactionNodeFactory.xml
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Expand Up @@ -25,8 +25,8 @@
<option name="Reaction SMARTS">
A reaction SMARTS describing the reaction.
<br />
For a description of the format, please see Chapter 2 of the
<a href="http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Docs/Book/RDKit_Book.pdf">RDKit Book</a>.
For a description of the format, please have a look in
<a href="http://rdkit.org/docs/RDKit_Book.html#reaction-smarts">The RDKit Book</a>.
</option>
</tab>
<tab name="Randomization">
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