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COMMANDS.html
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<html><head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8"></head><body>
<div class="plugin">
<a name="plugin-commons">
</a><div class="command"><a name="plugin-commons">
</a><a name="plugin-commons-command-fo">
<h3>fo</h3>
<pre class="short_description">Compute the fractional overlap of sel1 respective to sel2.</pre>
<pre class="long_description">FO = Nc/Nt
Nc is the number of atoms of sel1 in contact with sel2. Nt is the number of atoms
of sel1.
Hydrogen atoms are ignored.
If the contact radius is 0 then the VdW radii will be used.
The states are for select a single state from a multi-state objects.
OPTIONS:
sel1 ligand object.
sel2 hotspot object.
radius the radius so two atoms are in contact (default: 2).
state1 state of sel1.
state2 state of sel2.
EXAMPLES:
fo ref_lig, ftmap1234.D.003
fo ref_lig, ftmap1234.CS.000_016</pre>
</a></div><a name="plugin-commons-command-fo">
</a><div class="command"><a name="plugin-commons-command-fo">
</a><a name="plugin-commons-command-fo2">
<h3>fo2</h3>
<pre class="short_description">Compute the fractional overlap.</pre>
<pre class="long_description">SEE:
fo</pre>
</a></div><a name="plugin-commons-command-fo2">
</a><div class="command"><a name="plugin-commons-command-fo2">
</a><a name="plugin-commons-command-bsia">
<h3>bsia</h3>
<pre class="short_description">Bind site identity analysis.</pre>
<pre class="long_description">Compute the coefficient between aminoacids ids nearby two selections.
OPTIONS
sel1 Selection or object 1.
sel2 Selection or object 2.
polymer1 protein of sel1.
polymer2 protein of sel2.
radius Radius to look for nearby aminoacids.
method 'overlap' or 'sorensen–dice'
EXAMPLES
nearby_aminoacids_similarity *CS.000_*, *CS.002_*, radius=4
nearby_aminoacids_similarity *D.001*, *D.002*, polymer1='obj1', polymer2='obj2'
nearby_aminoacids_similarity 6y84.Bs.001, 6y84.B.004, method=sorensen-dice</pre>
</a></div><a name="plugin-commons-command-bsia">
</a></div><a name="plugin-commons-command-bsia">
</a><div class="plugin"><a name="plugin-commons-command-bsia">
</a><a name="plugin-__init__">
</a></div><a name="plugin-__init__">
</a><div class="plugin"><a name="plugin-__init__">
</a><a name="plugin-shape3d">
</a><div class="command"><a name="plugin-shape3d">
</a><a name="plugin-shape3d-command-fetch_similar_shape3d">
<h3>fetch_similar_shape3d</h3>
<pre class="short_description">Fetch similar structures using the 3D-Shape algorithm.</pre>
<pre class="long_description">https://search.rcsb.org/
OPTIONS:
pdb_id Reference PDB id.
min_similarity 3D-Shape score threshold.
max_resolution Fetch only structures up to such resolution.
ligand Refrence ligand PDB id for apo evaluation.
dist Distance cut-off around reference ligand for apo
evaluation. Only used when ligand is given.
compounds Selection that shold be considered ligands upon apo
evaluation. Only used when ligand is given.
prosthetic_groups List of ligands to be ignored when evaluating apo.
EXAMPLES:
fetch_similar_shape3d 2XY9
SEE ALSO:
fetch_similar_blast</pre>
</a></div><a name="plugin-shape3d-command-fetch_similar_shape3d">
</a></div><a name="plugin-shape3d-command-fetch_similar_shape3d">
</a><div class="plugin"><a name="plugin-shape3d-command-fetch_similar_shape3d">
</a><a name="plugin-blast_gui">
</a></div><a name="plugin-blast_gui">
</a><div class="plugin"><a name="plugin-blast_gui">
</a><a name="plugin-shape3d_gui">
</a></div><a name="plugin-shape3d_gui">
</a><div class="plugin"><a name="plugin-shape3d_gui">
</a><a name="plugin-__init__">
</a></div><a name="plugin-__init__">
</a><div class="plugin"><a name="plugin-__init__">
</a><a name="plugin-blast">
</a><div class="command"><a name="plugin-blast">
</a><a name="plugin-blast-command-fetch_similar_blast_update">
<h3>fetch_similar_blast_update</h3>
<pre class="short_description">The cluster database needs to be updated before the first use of the</pre>
<pre class="long_description">fetch_similar_blast feature. The database ftp://resources.rcsb.org/sequence/clusters/
is updated weekly, for new data is prudent to run this command weekly.</pre>
</a></div><a name="plugin-blast-command-fetch_similar_blast_update">
</a><div class="command"><a name="plugin-blast-command-fetch_similar_blast_update">
</a><a name="plugin-blast-command-fetch_similar_blast">
<h3>fetch_similar_blast</h3>
<pre class="short_description">Fetch sequence similar structures from RCSB PDB and optionally keep only</pre>
<pre class="long_description">apo structures. Apo are evaluated respective to a choosen ligand on the
reference chain.
On the first use update the database with the command `update_cluster_data`.
Update the database weekly.
OPTIONS
chain_id Reference structure chain id.
similarity Sequence similarity threshold (one of the available
from RCSB PDB).
ligand Reference ligand PDB id.
dist Distance cut-off around reference ligand for apo
evaluation.
compounds Selection that should be considered ligands upon apo
computation. Only used when ligand is given.
prothestic_groups List of ligands to be ignored when evaluating apo.
max_resolution Fetch only X-ray structures with up to such
resolution.
max_structures Fetch at most n structures. 0 for all structures.
EXAMPLES
fetch_similar_blast 2XY9_A, 100
fetch_similar_blast 2XY9_A, 95, 3ES, 3, organic
fetch_similar_blast 6Y2F_A, max_structures=0
SEE ALSO
update_cluster_data
fetch_similar_shape3d</pre>
</a></div><a name="plugin-blast-command-fetch_similar_blast">
</a></div><a name="plugin-blast-command-fetch_similar_blast">
</a><div class="plugin"><a name="plugin-blast-command-fetch_similar_blast">
</a><a name="plugin-core">
</a><div class="command"><a name="plugin-core">
</a><a name="plugin-core-command-load_ftmap">
<h3>load_ftmap</h3>
<pre class="short_description">Load a FTMap PDB file and classify hotspot ensembles in accordance to</pre>
<pre class="long_description">Kozakov et al. (2015).
https://doi.org/10.1021/acs.jmedchem.5b00586
OPTIONS
path PDB file path, glob or server result id.
group optional group name to put objects in.
max_cs the maximum number of consensus sites to consider.
plot plot similarity matrix.
plot_annot remove numbers on similarity matrix.
plot_class filter to show only a specific hotspot class.
plot_method see `help nearby_aminoacids_similarity`.
EXAMPLES
load_ftmap fftmap.1234.pdb
load_ftmap fftmap.1111.pdb, fftmap.2222.pdb, group=GRP, max_cs=4
load_ftmap fftmap_*.pdb, plot_annot=0, plot_class=D</pre>
</a></div><a name="plugin-core-command-load_ftmap">
</a><div class="command"><a name="plugin-core-command-load_ftmap">
</a><a name="plugin-core-command-load_atlas">
<h3>load_atlas</h3>
<pre class="short_description">Load an Atlas PDB file. See `help load_ftmap`.</pre>
</a></div><a name="plugin-core-command-load_atlas">
</a><div class="command"><a name="plugin-core-command-load_atlas">
</a><a name="plugin-core-command-kozakov2015">
<h3>kozakov2015</h3>
<pre class="short_description">Calculate a hotspot following Kozakov et al (2015).</pre>
<pre class="long_description">USAGE
calculate_kozakov2015 sel1, ...
EXAMPLES
calculate_kozakov2015 *CS.000_*, *CS.002_*
calculate_kozakov2015 *.000_*, *.001_*</pre>
</a></div><a name="plugin-core-command-kozakov2015">
</a></div><a name="plugin-core-command-kozakov2015">
</a><div class="plugin"><a name="plugin-core-command-kozakov2015">
</a><a name="plugin-__init__">
</a></div><a name="plugin-__init__">
</a><div class="plugin"><a name="plugin-__init__">
</a><a name="plugin-gui">
</a></div><a name="plugin-gui">
</a></body></html>