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elkoz committed Dec 28, 2023
2 parents 4fdbda2 + b8cb468 commit 93c76eb
Showing 1 changed file with 26 additions and 16 deletions.
42 changes: 26 additions & 16 deletions docs/data/torch.html
Original file line number Diff line number Diff line change
Expand Up @@ -938,12 +938,15 @@ <h1 class="title">Module <code>proteinflow.data.torch</code></h1>

Parameters
----------
cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}
The CDR to be iterated over. Set to `None` to go back to iterating over all chains.
cdr : list | str | None
The CDR to be iterated over (choose from H1, H2, H3, L1, L2, L3).
Set to `None` to go back to iterating over all chains.

&#34;&#34;&#34;
if not self.sabdab:
cdr = None
if isinstance(cdr, str):
cdr = [cdr]
if cdr == self.cdr:
return
self.cdr = cdr
Expand All @@ -954,12 +957,12 @@ <h1 class="title">Module <code>proteinflow.data.torch</code></h1>
print(f&#34;Setting CDR to {cdr}...&#34;)
for i, data in tqdm(enumerate(self.data)):
if self.clusters is not None:
if data.split(&#34;__&#34;)[1] == cdr:
if data.split(&#34;__&#34;)[1] in cdr:
self.indices.append(i)
else:
add = False
for chain in self.files[data]:
if chain.split(&#34;__&#34;)[1] == cdr:
if chain.split(&#34;__&#34;)[1] in cdr:
add = True
break
if add:
Expand Down Expand Up @@ -1091,7 +1094,7 @@ <h1 class="title">Module <code>proteinflow.data.torch</code></h1>
id = self.data[idx] # data is already filtered by length
chain_id = random.choice(list(self.files[id].keys()))
if self.cdr is not None:
while self.cdr != chain_id.split(&#34;__&#34;)[1]:
while chain_id.split(&#34;__&#34;)[1] not in self.cdr:
chain_id = random.choice(list(self.files[id].keys()))
else:
cluster = self.data[idx]
Expand Down Expand Up @@ -1937,12 +1940,15 @@ <h2 id="parameters">Parameters</h2>

Parameters
----------
cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}
The CDR to be iterated over. Set to `None` to go back to iterating over all chains.
cdr : list | str | None
The CDR to be iterated over (choose from H1, H2, H3, L1, L2, L3).
Set to `None` to go back to iterating over all chains.

&#34;&#34;&#34;
if not self.sabdab:
cdr = None
if isinstance(cdr, str):
cdr = [cdr]
if cdr == self.cdr:
return
self.cdr = cdr
Expand All @@ -1953,12 +1959,12 @@ <h2 id="parameters">Parameters</h2>
print(f&#34;Setting CDR to {cdr}...&#34;)
for i, data in tqdm(enumerate(self.data)):
if self.clusters is not None:
if data.split(&#34;__&#34;)[1] == cdr:
if data.split(&#34;__&#34;)[1] in cdr:
self.indices.append(i)
else:
add = False
for chain in self.files[data]:
if chain.split(&#34;__&#34;)[1] == cdr:
if chain.split(&#34;__&#34;)[1] in cdr:
add = True
break
if add:
Expand Down Expand Up @@ -2090,7 +2096,7 @@ <h2 id="parameters">Parameters</h2>
id = self.data[idx] # data is already filtered by length
chain_id = random.choice(list(self.files[id].keys()))
if self.cdr is not None:
while self.cdr != chain_id.split(&#34;__&#34;)[1]:
while chain_id.split(&#34;__&#34;)[1] not in self.cdr:
chain_id = random.choice(list(self.files[id].keys()))
else:
cluster = self.data[idx]
Expand Down Expand Up @@ -2210,8 +2216,9 @@ <h3>Methods</h3>
<div class="desc"><p>Set the CDR to be iterated over (only for SAbDab datasets).</p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>cdr</code></strong> :&ensp;<code>{"H1", "H2", "H3", "L1", "L2", "L3"}</code></dt>
<dd>The CDR to be iterated over. Set to <code>None</code> to go back to iterating over all chains.</dd>
<dt><strong><code>cdr</code></strong> :&ensp;<code>list | str | None</code></dt>
<dd>The CDR to be iterated over (choose from H1, H2, H3, L1, L2, L3).
Set to <code>None</code> to go back to iterating over all chains.</dd>
</dl></div>
<details class="source">
<summary>
Expand All @@ -2222,12 +2229,15 @@ <h2 id="parameters">Parameters</h2>

Parameters
----------
cdr : {&#34;H1&#34;, &#34;H2&#34;, &#34;H3&#34;, &#34;L1&#34;, &#34;L2&#34;, &#34;L3&#34;}
The CDR to be iterated over. Set to `None` to go back to iterating over all chains.
cdr : list | str | None
The CDR to be iterated over (choose from H1, H2, H3, L1, L2, L3).
Set to `None` to go back to iterating over all chains.

&#34;&#34;&#34;
if not self.sabdab:
cdr = None
if isinstance(cdr, str):
cdr = [cdr]
if cdr == self.cdr:
return
self.cdr = cdr
Expand All @@ -2238,12 +2248,12 @@ <h2 id="parameters">Parameters</h2>
print(f&#34;Setting CDR to {cdr}...&#34;)
for i, data in tqdm(enumerate(self.data)):
if self.clusters is not None:
if data.split(&#34;__&#34;)[1] == cdr:
if data.split(&#34;__&#34;)[1] in cdr:
self.indices.append(i)
else:
add = False
for chain in self.files[data]:
if chain.split(&#34;__&#34;)[1] == cdr:
if chain.split(&#34;__&#34;)[1] in cdr:
add = True
break
if add:
Expand Down

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