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Added documentation about using plugins.
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kliment-olechnovic committed Aug 29, 2023
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41 changes: 41 additions & 0 deletions README.md
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Expand Up @@ -260,14 +260,17 @@ Below is the breef description of 'ftdmp-all' interface.
--scoring-full-top number number of top complexes to keep after full scoring stage, default is 1000
--scoring-full-top-slow number number of top complexes to keep before slow full scoring stage, default is 9999999
--scoring-rank-names string * rank names to use, or name of a standard set of rank names
--scoring-rank-names-x string extra rank names to use, default is 'all_plugin' to use plugin output columns (if any)
--scoring-ranks-top number number of top complexes to consider for each ranking, default is 100
--scoring-jury-slices string slice sizes sequence definition for ranks jury scoring, default is '5 20'
--scoring-jury-cluster number clustering threshold for ranks jury scoring, default is 0.9
--scoring-jury-maxs number number of max values to use for ranks jury scoring, default is 1
--redundancy-threshold number minimal ordered redundancy value to accept, default is 0.9
--plugin-scoring-script string path to executable script that outputs a table of scores for a PDB structure
--build-complexes number number of top complexes to build, default is 0
--multiply-chains string options to multiply chains, default is ''
--relax-complexes string options to relax complexes, default is ''
--all-ranks-for-relaxed string flag to use both scoring ranks of both raw and relaxed structures, default is 'true'
--only-dock-and-score string flag to only dock, score and quit after scoring, default is 'false'
--diversify number step of CAD-score to diversify scoring results and exit, default is ''
--plot-jury-scores string flag to output plot of jury scores, default is 'false'
Expand Down Expand Up @@ -409,6 +412,44 @@ Main essential changes when compared with the protei-protein docking case:
--openmm-forcefield 'amber14-all-no-water' # now using a force field that is compatible with DNA and RNA
--relax-complexes '--max-iterations 10 --focus whole_interface' # now using iterations limit to not overdo the relaxation in absence of water

## Using a plugin script to score docking models

'ftdmp-all' can accept a plugin script that outputs one or more scoresa for an input model structure in PDB format.
Such a script must:

* accept two command line argument: input file, output file
* write an output file with two lines: first line with space-separated score names, second line with score values

Example of a plugin script:

#!/bin/bash

INFILE="$1"
OUTFILE="$2"

{
echo "Useful_Score1 Useful_Score2 Useful_Score3"
${HOME}/software/program_that outputs_three_scores "$INFILE"
} \
> "$OUTFILE"

Example of a plugin script output:

Useful_Score1 Useful_Score2 Useful_Score3
0.85 1.73 104.9

When providing a plugin script script file with

--plugin-scoring-script ./plugin.bash

and not providing anything with '--scoring-rank-names-x',
the default behaviour is to automatically use all the scores from the plugin script output.

Alternatively, space-separated score names with 'raw_' prefix can be provided, e.g.

--plugin-scoring-script ./plugin.bash --scoring-rank-names-x "raw_Useful_Score1 raw_Useful_Score3"

Important note - the plugin scores are assummed to be "the higher, the better", i.e. for ranking they are sorted in descending order.

# Using FTDMP for relaxing structures with OpenMM to remove clashes and improve interface interactions

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30 changes: 30 additions & 0 deletions index.html
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Expand Up @@ -34,6 +34,7 @@ <h1>FTDMP version 1.0</h1>
<li><a href="#command-line-user-interface-1">Command line user interface</a></li>
<li><a href="#example-of-protein-protein-docking-for-running-on-cluster">Example of protein-protein docking for running on cluster</a></li>
<li><a href="#example-of-protein-dna-docking-for-running-on-cluster">Example of protein-DNA docking for running on cluster</a></li>
<li><a href="#using-a-plugin-script-to-score-docking-models">Using a plugin script to score docking models</a></li>
</ul></li>
<li><a href="#using-ftdmp-for-relaxing-structures-with-openmm-to-remove-clashes-and-improve-interface-interactions">Using FTDMP for relaxing structures with OpenMM to remove clashes and improve interface interactions</a><ul>
<li><a href="#command-line-user-interface-2">Command line user interface</a></li>
Expand Down Expand Up @@ -253,14 +254,17 @@ <h2 id="command-line-user-interface-1">Command line user interface</h2>
--scoring-full-top number number of top complexes to keep after full scoring stage, default is 1000
--scoring-full-top-slow number number of top complexes to keep before slow full scoring stage, default is 9999999
--scoring-rank-names string * rank names to use, or name of a standard set of rank names
--scoring-rank-names-x string extra rank names to use, default is &#39;all_plugin&#39; to use plugin output columns (if any)
--scoring-ranks-top number number of top complexes to consider for each ranking, default is 100
--scoring-jury-slices string slice sizes sequence definition for ranks jury scoring, default is &#39;5 20&#39;
--scoring-jury-cluster number clustering threshold for ranks jury scoring, default is 0.9
--scoring-jury-maxs number number of max values to use for ranks jury scoring, default is 1
--redundancy-threshold number minimal ordered redundancy value to accept, default is 0.9
--plugin-scoring-script string path to executable script that outputs a table of scores for a PDB structure
--build-complexes number number of top complexes to build, default is 0
--multiply-chains string options to multiply chains, default is &#39;&#39;
--relax-complexes string options to relax complexes, default is &#39;&#39;
--all-ranks-for-relaxed string flag to use both scoring ranks of both raw and relaxed structures, default is &#39;true&#39;
--only-dock-and-score string flag to only dock, score and quit after scoring, default is &#39;false&#39;
--diversify number step of CAD-score to diversify scoring results and exit, default is &#39;&#39;
--plot-jury-scores string flag to output plot of jury scores, default is &#39;false&#39;
Expand Down Expand Up @@ -393,6 +397,32 @@ <h2 id="example-of-protein-dna-docking-for-running-on-cluster">Example of protei

--openmm-forcefield &#39;amber14-all-no-water&#39; # now using a force field that is compatible with DNA and RNA
--relax-complexes &#39;--max-iterations 10 --focus whole_interface&#39; # now using iterations limit to not overdo the relaxation in absence of water</code></pre>
<h2 id="using-a-plugin-script-to-score-docking-models">Using a plugin script to score docking models</h2>
<p>'ftdmp-all' can accept a plugin script that outputs one or more scoresa for an input model structure in PDB format. Such a script must:</p>
<ul>
<li>accept two command line argument: input file, output file</li>
<li>write an output file with two lines: first line with space-separated score names, second line with score values</li>
</ul>
<p>Example of a plugin script:</p>
<pre><code>#!/bin/bash

INFILE=&quot;$1&quot;
OUTFILE=&quot;$2&quot;

{
echo &quot;Useful_Score1 Useful_Score2 Useful_Score3&quot;
${HOME}/software/program_that outputs_three_scores &quot;$INFILE&quot;
} \
&gt; &quot;$OUTFILE&quot;</code></pre>
<p>Example of a plugin script output:</p>
<pre><code>Useful_Score1 Useful_Score2 Useful_Score3
0.85 1.73 104.9</code></pre>
<p>When providing a plugin script script file with</p>
<pre><code>--plugin-scoring-script ./plugin.bash</code></pre>
<p>and not providing anything with '--scoring-rank-names-x', the default behaviour is to automatically use all the scores from the plugin script output.</p>
<p>Alternatively, space-separated score names with 'raw_' prefix can be provided, e.g.</p>
<pre><code>--plugin-scoring-script ./plugin.bash --scoring-rank-names-x &quot;raw_Useful_Score1 raw_Useful_Score3&quot;</code></pre>
<p>Important note - the plugin scores are assummed to be &quot;the higher, the better&quot;, i.e. for ranking they are sorted in descending order.</p>
<h1 id="using-ftdmp-for-relaxing-structures-with-openmm-to-remove-clashes-and-improve-interface-interactions">Using FTDMP for relaxing structures with OpenMM to remove clashes and improve interface interactions</h1>
<h2 id="command-line-user-interface-2">Command line user interface</h2>
<p>Relaxing is done with the 'ftdmp-relax-with-openmm' script. After relaxing, model structures can be rescored and reranked with the 'ftdmp-qa-all' script. It is advised to do it on a machine with a nice GPU. Below is the breef description of 'ftdmp-relax-with-openmm' interface.</p>
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