wip: documentation on knot theory

GazzolaLab · Mar 16, 2022 · 2324574 · 2324574
1 parent 25ffb8a
commit 2324574
Showing 1 changed file with 25 additions and 2 deletions.
diff --git a/elastica/rod/knot_theory.py b/elastica/rod/knot_theory.py
@@ -1,5 +1,5 @@
 __docs__ = """
-This script is for computing the link-writhe-twist of a rod using the method 1a from Klenin & Langowski 2000 paper.
+This script is for computing the link-writhe-twist of a rod using the method from Klenin & Langowski 2000 paper.
 
 Following codes are adapted from section S2 of Charles et. al. PRL 2019 paper.
 """
@@ -24,6 +24,11 @@
 
 
 class KnotTheoryCompatibleProtocol(Protocol):
+    """ KnotTheoryCompatibleProtocol
+
+    Required properties to use KnotTheory mixin
+    """
+
     @property
     def position_collection(self) -> np.ndarray:
         ...
@@ -46,6 +51,8 @@ class KnotTheory:
     MIXIN_PROTOCOL = Union[RodBase, KnotTheoryCompatibleProtocol]
 
     def compute_twist(self: MIXIN_PROTOCOL):
+        """compute_twist
+        """
         total_twist, local_twist = compute_twist(
             self.position_collection[None, ...],
             self.director_collection[0][None, ...],
@@ -55,6 +62,14 @@ def compute_twist(self: MIXIN_PROTOCOL):
     def compute_writhe(
         self: MIXIN_PROTOCOL, type_of_additional_segment: str = "next_tangent"
     ):
+        """compute_writhe
+
+        Parameters
+        ----------
+        type_of_additional_segment : str
+            Determines the method to compute new segments (elements) added to the rod.
+            Valid inputs are "next_tangent", "end_to_end", "net_tangent", otherwise program uses the center line.
+        """
         return compute_writhe(
             self.position_collection[None, ...],
             self.rest_lengths.sum(),
@@ -64,6 +79,14 @@ def compute_writhe(
     def compute_link(
         self: MIXIN_PROTOCOL, type_of_additional_segment: str = "next_tangent"
     ):
+        """compute_link
+
+        Parameters
+        ----------
+        type_of_additional_segment : str
+            Determines the method to compute new segments (elements) added to the rod.
+            Valid inputs are "next_tangent", "end_to_end", "net_tangent", otherwise program uses the center line.
+        """
         return compute_link(
             self.position_collection[None, ...],
             self.director_collection[0][None, ...],
@@ -88,7 +111,7 @@ def compute_twist(center_line, normal_collection):
         Time history of rod elements normal direction.
 
     Warnings
-    -------
+    --------
     If center line is straight, although the normals of each element is pointing different direction computed twist
     will be zero.