Add docs to workflow of conformer_generation

Add rst files and clean up docstrings

docs/source/reference/conformer_generation/index.rst

@@ -12,4 +12,5 @@ rdmc.conformer_generation
    embedding_geometries/index
    geometry_optimization/index
    postprocessing/index
+   workflow/index
    utils

docs/source/reference/conformer_generation/workflow/generators.rst

@@ -0,0 +1,7 @@
+rdmc.conformer_generation.generators
+=====================================
+
+.. automodule:: rdmc.conformer_generation.generators
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/reference/conformer_generation/workflow/index.rst

@@ -0,0 +1,10 @@
+Workflow
+=====================
+
+.. toctree::
+   :maxdepth: 2
+
+   generators
+   ts_generators
+   metrics
+   sampler

docs/source/reference/conformer_generation/workflow/metrics.rst

@@ -0,0 +1,7 @@
+rdmc.conformer_generation.metrics
+=====================================
+
+.. automodule:: rdmc.conformer_generation.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/reference/conformer_generation/workflow/sampler.rst

@@ -0,0 +1,7 @@
+rdmc.conformer_generation.sampler
+=======================================
+
+.. automodule:: rdmc.conformer_generation.sampler
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/reference/conformer_generation/workflow/ts_generators.rst

@@ -0,0 +1,7 @@
+rdmc.conformer_generation.ts_generators
+=======================================
+
+.. automodule:: rdmc.conformer_generation.ts_generators
+   :members:
+   :undoc-members:
+   :show-inheritance:

rdmc/conformer_generation/metrics.py

@@ -6,40 +6,57 @@
 """
 
 import numpy as np
-from typing import Optional
+from typing import List, Optional
 
 R = 0.0019872  # kcal/(K*mol)
 
 
 class SCGMetric:
     """
     A class to calculate and track the given metric ("entropy", "partition function", or "total conformers") for a molecule over time.
+
+    Args:
+        metric (str, optional): Metric to be calculated. Options are ``"entropy"``, ``"partition function"``, or ``"total conformers"``.
+                                Defaults to ``"entropy"``.
+        window (int, optional): Window size to compute the change in metric (doesn't work when the metric is "total conformers").
+                                Defaults to ``5``.
+        threshold (float, optional): Threshold for the change in metric to decide when to stop generating conformers.
+                                     Defaults to ``0.01``.
+        T (float, optional): Temperature for entropy or partition function calculations. Defaults to ``298`` K.
     """
 
-    def __init__(
-        self,
-        metric: Optional[str] = "entropy",
-        window: Optional[int] = 5,
-        threshold: Optional[float] = 0.01,
-        T: Optional[float] = 298,
-    ):
+    def __init__(self,
+                 metric: Optional[str] = "entropy",
+                 window: Optional[int] = 5,
+                 threshold: Optional[float] = 0.01,
+                 T: Optional[float] = 298,
+                 ):
         """
         Generate an SCGMetric instance.
 
         Args:
-            metric (str): Metric to be calculated.
-            window (int): Window size to compute the change in metric (doesn't work when the metric is "total conformers").
-            threshold (float): Threshold for the change in metric to decide when to stop generating conformers.
-            T (float): Temperature for entropy or partition function calculations.
+            metric (str, optional): Metric to be calculated. Options are ``"entropy"``, ``"partition function"``, or ``"total conformers"``.
+                                    Defaults to ``"entropy"``.
+            window (int, optional): Window size to compute the change in metric (doesn't work when the metric is "total conformers").
+                                    Defaults to ``5``.
+            threshold (float, optional): Threshold for the change in metric to decide when to stop generating conformers.
+                                        Defaults to ``0.01``.
+            T (float, optional): Temperature for entropy or partition function calculations. Defaults to ``298`` K.
         """
         self.metric = metric
         self.window = window
         self.threshold = threshold
         self.T = T
         self.metric_history = []
 
-    def calculate_metric(self, mol_data):
+    def calculate_metric(self,
+                         mol_data: List[dict]):
+        """
+        Calculate the metric for a given molecule. The calculated value will be appended to the ``metric_history`` list.
 
+        Args:
+            mol_data (List[dict]): A list of dictionaries with molecule conformers.
+        """
         if self.metric == "entropy":
             metric_val = self.calculate_entropy(mol_data)
 
@@ -55,7 +72,12 @@ def calculate_metric(self, mol_data):
         self.metric_history.append(metric_val)
 
     def check_metric(self):
+        """
+        Check if the change in metric is below the threshold.
 
+        Returns:
+            bool: ``True`` if the change in metric is below the threshold, ``False`` otherwise.
+        """
         if self.metric == "total conformers":
             return False
         else:
@@ -66,17 +88,29 @@ def check_metric(self):
             )
             return True if change <= self.threshold else False
 
-    def calculate_entropy(self, mol_data):
+    def calculate_entropy(self,
+                          mol_data: List[dict]):
+        """
+        Calculate the entropy of a molecule.
 
+        Args:
+            mol_data (List[dict]): A list of dictionaries with molecule conformers.
+        """
         energies = np.array([c["energy"] for c in mol_data])
         energies = energies - energies.min()
         _prob = np.exp(-energies / (R * self.T))
         prob = _prob / _prob.sum()
         entropy = -R * np.sum(prob * np.log(prob))
         return entropy
 
-    def calculate_partition_function(self, mol_data):
+    def calculate_partition_function(self,
+                                     mol_data: List[dict]):
+        """
+        Calculate the partition function of a molecule.
 
+        Args:
+            mol_data (List[dict]): A list of dictionaries with molecule conformers.
+        """
         energies = np.array([c["energy"] for c in mol_data])
         energies = energies - energies.min()
         prob = np.exp(-energies / (R * self.T))