Merge pull request #127 from adaptyvbio/improve_splitting

Fix docs
adaptyvbio · Dec 21, 2023 · 951a57f · 951a57f
2 parents 08165b8 + 5c38cf6
commit 951a57f
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diff --git a/docs/data/index.html b/docs/data/index.html
diff --git a/docs/data/torch.html b/docs/data/torch.html
diff --git a/docs/index.html b/docs/index.html
@@ -45,7 +45,7 @@ <h2 id="installation">Installation</h2>
 <pre><code class="language-bash">docker pull adaptyvbio/proteinflow
 </code></pre>
 <p>By default installing <code><a title="proteinflow" href="#proteinflow">proteinflow</a></code> with conda or pip will only load the dependencies that are required for the main functions of the package: downloading, generating and splitting datasets. If you are interested in using other functions like visualization, metrics and other data processing methods, please install the package with <code>pip install <a title="proteinflow" href="#proteinflow">proteinflow</a>[<a title="proteinflow.processing" href="processing/index.html">proteinflow.processing</a>]</code> or use the docker image.</p>
-<p>Some metric functions also have separate requirements, see the documentation for details.</p>
+<p>Some metric functions also have separate requirements, see the documentation for details. All of them are installed in the docker image.</p>
 <h3 id="troubleshooting">Troubleshooting</h3>
 <ul>
 <li>If you are using python 3.10 and encountering installation problems, try running <code>python -m pip install prody==2.4.0</code> before installing <code><a title="proteinflow" href="#proteinflow">proteinflow</a></code>.</li>
@@ -269,7 +269,7 @@ <h2 id="proteinflow-stable-releases">ProteinFlow Stable Releases</h2>
 
 By default installing `proteinflow` with conda or pip will only load the dependencies that are required for the main functions of the package: downloading, generating and splitting datasets. If you are interested in using other functions like visualization, metrics and other data processing methods, please install the package with `pip install proteinflow[processing]` or use the docker image.
 
-Some metric functions also have separate requirements, see the documentation for details.
+Some metric functions also have separate requirements, see the documentation for details. All of them are installed in the docker image.
 
 ### Troubleshooting
 - If you are using python 3.10 and encountering installation problems, try running `python -m pip install prody==2.4.0` before installing `proteinflow`.

diff --git a/docs/metrics/index.html b/docs/metrics/index.html
diff --git a/proteinflow/__init__.py b/proteinflow/__init__.py
@@ -31,7 +31,7 @@
 
 By default installing `proteinflow` with conda or pip will only load the dependencies that are required for the main functions of the package: downloading, generating and splitting datasets. If you are interested in using other functions like visualization, metrics and other data processing methods, please install the package with `pip install proteinflow[processing]` or use the docker image.
 
-Some metric functions also have separate requirements, see the documentation for details.
+Some metric functions also have separate requirements, see the documentation for details. All of them are installed in the docker image.
 
 ### Troubleshooting
 - If you are using python 3.10 and encountering installation problems, try running `python -m pip install prody==2.4.0` before installing `proteinflow`.

diff --git a/proteinflow/data/__init__.py b/proteinflow/data/__init__.py
@@ -142,7 +142,7 @@ def __init__(
         seqs : list of str
             Amino acid sequences of the protein (one-letter code)
         crds : list of np.ndarray
-            Coordinates of the protein, `'numpy'` arrays of shape `(L, 4, 3)`,
+            Coordinates of the protein, `numpy` arrays of shape `(L, 14, 3)`,
             in the order of `N, C, CA, O`
         masks : list of np.ndarray
             Mask arrays where 1 indicates residues with known coordinates and 0

diff --git a/proteinflow/extra.py b/proteinflow/extra.py
@@ -6,6 +6,7 @@
     pass
 
 import sys
+from functools import wraps
 
 
 def requires_extra(module_name, install_name=None):
@@ -23,6 +24,7 @@ def requires_extra(module_name, install_name=None):
         install_name = module_name
 
     def decorator(func):
+        @wraps(func)
         def wrapper(*args, **kwargs):
             if module_name not in sys.modules:
                 raise ImportError(

diff --git a/proteinflow/metrics/__init__.py b/proteinflow/metrics/__init__.py
@@ -61,6 +61,7 @@ def blosum62_score(seq_before, seq_after):
     return score
 
 
+@requires_extra("blosum")
 def long_repeat_num(seq, thr=5):
     """Calculate the number of long repeats in a sequence.