Fix docstrings for commands

biotite-dev · Jun 8, 2020 · 61b0691 · 61b0691
1 parent 393e9d7
commit 61b0691
Showing 1 changed file with 72 additions and 48 deletions.
diff --git a/src/ammolite/object.py b/src/ammolite/object.py
@@ -363,8 +363,9 @@ def alter(self, selection, expression):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
         expression : str
@@ -396,8 +397,9 @@ def cartoon(self, type, selection=None):
             - ``'arrow'`` or
             - ``'dumbbell'``.
         
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -416,8 +418,9 @@ def center(self, selection=None, state=None, origin=True):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -452,8 +455,9 @@ def clip(self, mode, distance, selection=None, state=None):
 
         distance : float
             The meaning of this parameter depends on `mode`.
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -479,8 +483,9 @@ def color(self, color, selection=None):
         color : str or tuple(float, float, float)
             Either a *PyMOL* color name or a tuple containing an RGB
             value (0.0 to 1.0).
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -514,8 +519,9 @@ def desaturate(self, selection=None, a=0.5):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -535,8 +541,9 @@ def disable(self, selection=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -557,8 +564,9 @@ def distance(self, name, selection1, selection2, cutoff=None, mode=None,
         ----------
         name : str
             Name of the distance object to create.
-        selection1, selection2 : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection1, selection2 : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
         cutoff : float, optional
@@ -600,8 +608,9 @@ def dss(self, selection=None, state=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -624,8 +633,9 @@ def enable(self, selection=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -661,8 +671,9 @@ def hide(self, representation, selection=None):
             - ``'slice'`` or
             - ``'cell'``.
 
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -680,8 +691,9 @@ def indicate(self, selection=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -699,8 +711,9 @@ def label(self, selection, text):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
         text : str
@@ -719,8 +732,9 @@ def orient(self, selection=None, state=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -743,8 +757,9 @@ def origin(self, selection=None, state=None):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -771,8 +786,9 @@ def select(self, name, selection=None):
         ----------
         name : str
             Name of the selection object to create.
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -806,8 +822,9 @@ def set(self, name, value, selection=None, state=None):
 
         value : object
             The new value for the given setting name.
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -845,8 +862,9 @@ def set_bond(self, name, value, selection1=None, selection2=None,
 
         value : object
             The new value for the given setting name.
-        selection1, selection2 : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection1, selection2 : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, `selection1` applies to all atoms of this
@@ -893,8 +911,9 @@ def show(self, representation, selection=None):
             - ``'slice'`` or
             - ``'cell'``.
 
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -931,8 +950,9 @@ def show_as(self, representation, selection=None):
             - ``'slice'`` or
             - ``'cell'``.
 
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -951,8 +971,9 @@ def smooth(self, selection=None, passes=1, window=5,
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -998,8 +1019,9 @@ def unset(self, name, selection=None, state=None):
             - ``'transparency'`` (for surfaces) or
             - ``'sphere_transparency'``.
 
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this
@@ -1034,8 +1056,9 @@ def unset_bond(self, name, selection1=None, selection2=None, state=None):
             - ``'stick_color'`` or
             - ``'stick_transparency'``.
 
-        selection1, selection2 : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection1, selection2 : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, `selection1` applies to all atoms of this
@@ -1065,8 +1088,9 @@ def zoom(self, selection=None, buffer=0.0, state=None, complete=False):
 
         Parameters
         ----------
-        selection : str or ndarray, dtype=bool, optional
-            A boolean mask or a *PyMOL* selection expression that
+        selection : str or int or slice or ndarray, dtype=bool or ndarray, dtype=int, optional
+            A *Biotite* compatible atom selection index,
+            e.g. a boolean mask, or a *PyMOL* selection expression that
             selects the atoms of this *PyMOL* object to apply the
             command on.
             By default, the command is applied on all atoms of this