Added desc of usage

python/chemiscope/explore.py

@@ -69,7 +69,7 @@ def explore(frames, featurize=None, properties=None, environments=None, mode="de
 
 
         # Define a function for dimensionality reduction
-        def soap_kpca_featurize(frames):
+        def soap_kpca_featurize(frames, _environments):
             # Compute descriptors
             soap = dscribe.descriptors.SOAP(
                 species=["C"],
@@ -175,6 +175,12 @@ def soap_pca_featurize(frames, centers=None):
 
 
 def _pick_env_frames(envs, frames):
+    """
+    Get environment indices par structures and pick corresponding frames
+
+    :param: list envs: each element is a list of [env_index, atom_index, cutoff]
+    :param: list frames: list of frames
+    """
     grouped_envs = {}
     picked_frames = []
     for [env_index, atom_index, _cutoff] in envs:

python/examples/6-explore.py

@@ -69,10 +69,7 @@ def fetch_dataset(filename, base_url="https://zenodo.org/records/12748925/files/
 #
 # Provide the frames to the :py:func:`chemiscope.explore`. It will generate a Chemiscope
 # interactive widget with the reduced dimensionality of data.
-envs = [(0, 0, 3.5),
- (1, 1, 3.5),
- (2, 2, 3.5)]
-chemiscope.explore(frames, environments=envs)
+chemiscope.explore(frames)
 
 # %%
 #
@@ -87,6 +84,18 @@ def fetch_dataset(filename, base_url="https://zenodo.org/records/12748925/files/
 # properties to be used in visualization.
 
 
+# %%
+#
+# Besides this, it is possible to run the dimentionality reduction algorithm and display
+# specific atom-centered environments. They can be manually defined by specifying a list
+# of tuples in the format ``[index of structure, index of atom, cutoff]``, as shown in
+# this example.
+#
+# Alternatively, the environments can be extracted from the frames using the function
+# :py:func:`all_atomic_environments` or :py:func:`librascal_atomic_environments`.
+
+chemiscope.explore(frames, environments=[(0, 0, 3.5), (1, 0, 3.5), (2, 1, 3.5)])
+
 # %%
 #
 # Example with custom featurizer and custom properties
@@ -105,10 +114,11 @@ def fetch_dataset(filename, base_url="https://zenodo.org/records/12748925/files/
 
 # %%
 #
-# Define the function ``soap_kpca_featurize`` which takes one argument
-# (``frames``). This argument contains the structures provided to
-# :py:func:`chemiscope.explore` and is internally
-# passed to the ``featurize`` function.
+# Define the function ``soap_kpca_featurize`` which takes two arguments
+# (``frames``, which contains the structures provided to
+# :py:func:`chemiscope.explore` and internally passed to the ``featurize`` function;
+# ``environments``,  optional aurgument with the atom-centered environments,
+# if they were provided to the :py:func:`chemiscope.explore`.
 
 
 def soap_kpca_featurize(frames, _environments):