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Merge branch 'main' of https://github.com/adaptyvbio/proteinflow
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@elkoz
elkoz committed Dec 29, 2023
2 parents 5fbf6a1 + 28a0988 commit 683adce
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24 changes: 12 additions & 12 deletions docs/index.html
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Expand Up @@ -593,8 +593,8 @@ <h2 id="proteinflow-stable-releases">ProteinFlow Stable Releases</h2>
the sequence similarity threshold for excluding chains
exclude_clusters : bool, default False
if `True`, exclude clusters that contain chains similar to chains in the `exclude_chains` list
exclude_based_on_cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters
exclude_based_on_cdr : list, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from &#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;)
load_ligands : bool, default False
if `True`, load ligands from the PDB files
exclude_chains_without_ligands : bool, default False
Expand Down Expand Up @@ -760,8 +760,8 @@ <h2 id="proteinflow-stable-releases">ProteinFlow Stable Releases</h2>
the sequence similarity threshold for excluding chains
exclude_clusters : bool, default False
if `True`, exclude clusters that contain chains similar to chains in the `exclude_chains` list
exclude_based_on_cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters
exclude_based_on_cdr : list, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from &#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;)
random_seed : int, default 42
random seed for reproducibility (set to `None` to use a random seed)
exclude_chains_without_ligands : bool, default False
Expand Down Expand Up @@ -1136,8 +1136,8 @@ <h2 id="parameters">Parameters</h2>
<dd>the sequence similarity threshold for excluding chains</dd>
<dt><strong><code>exclude_clusters</code></strong> :&ensp;<code>bool</code>, default <code>False</code></dt>
<dd>if <code>True</code>, exclude clusters that contain chains similar to chains in the <code>exclude_chains</code> list</dd>
<dt><strong><code>exclude_based_on_cdr</code></strong> :&ensp;<code>{"H1", "H2", "H3", "L1", "L2", "L3"}</code>, optional</dt>
<dd>if given and <code>exclude_clusters</code> is <code>True</code> + the dataset is SAbDab, exclude files based on only the given CDR clusters</dd>
<dt><strong><code>exclude_based_on_cdr</code></strong> :&ensp;<code>list</code>, optional</dt>
<dd>if given and <code>exclude_clusters</code> is <code>True</code> + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from "H1", "H2", "H3", "L1", "L2", "L3")</dd>
<dt><strong><code>load_ligands</code></strong> :&ensp;<code>bool</code>, default <code>False</code></dt>
<dd>if <code>True</code>, load ligands from the PDB files</dd>
<dt><strong><code>exclude_chains_without_ligands</code></strong> :&ensp;<code>bool</code>, default <code>False</code></dt>
Expand Down Expand Up @@ -1277,8 +1277,8 @@ <h2 id="returns">Returns</h2>
the sequence similarity threshold for excluding chains
exclude_clusters : bool, default False
if `True`, exclude clusters that contain chains similar to chains in the `exclude_chains` list
exclude_based_on_cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters
exclude_based_on_cdr : list, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from &#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;)
load_ligands : bool, default False
if `True`, load ligands from the PDB files
exclude_chains_without_ligands : bool, default False
Expand Down Expand Up @@ -1454,8 +1454,8 @@ <h2 id="parameters">Parameters</h2>
<dd>the sequence similarity threshold for excluding chains</dd>
<dt><strong><code>exclude_clusters</code></strong> :&ensp;<code>bool</code>, default <code>False</code></dt>
<dd>if <code>True</code>, exclude clusters that contain chains similar to chains in the <code>exclude_chains</code> list</dd>
<dt><strong><code>exclude_based_on_cdr</code></strong> :&ensp;<code>{"H1", "H2", "H3", "L1", "L2", "L3"}</code>, optional</dt>
<dd>if given and <code>exclude_clusters</code> is <code>True</code> + the dataset is SAbDab, exclude files based on only the given CDR clusters</dd>
<dt><strong><code>exclude_based_on_cdr</code></strong> :&ensp;<code>list</code>, optional</dt>
<dd>if given and <code>exclude_clusters</code> is <code>True</code> + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from "H1", "H2", "H3", "L1", "L2", "L3")</dd>
<dt><strong><code>random_seed</code></strong> :&ensp;<code>int</code>, default <code>42</code></dt>
<dd>random seed for reproducibility (set to <code>None</code> to use a random seed)</dd>
<dt><strong><code>exclude_chains_without_ligands</code></strong> :&ensp;<code>bool</code>, default <code>False</code></dt>
Expand Down Expand Up @@ -1537,8 +1537,8 @@ <h2 id="returns">Returns</h2>
the sequence similarity threshold for excluding chains
exclude_clusters : bool, default False
if `True`, exclude clusters that contain chains similar to chains in the `exclude_chains` list
exclude_based_on_cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters
exclude_based_on_cdr : list, optional
if given and `exclude_clusters` is `True` + the dataset is SAbDab, exclude files based on only the given CDR clusters (choose from &#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;)
random_seed : int, default 42
random seed for reproducibility (set to `None` to use a random seed)
exclude_chains_without_ligands : bool, default False
Expand Down

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