From 3daeb36bafc810d03e5e746fe66ce03f0fe261d6 Mon Sep 17 00:00:00 2001 From: Patrick Kunzmann Date: Mon, 8 Jun 2020 16:41:44 +0200 Subject: [PATCH] Fix docstrings for commands --- src/ammolite/object.py | 74 ++++++++++++++++++++++++++++-------------- 1 file changed, 49 insertions(+), 25 deletions(-) diff --git a/src/ammolite/object.py b/src/ammolite/object.py index b2d884d..5296757 100644 --- a/src/ammolite/object.py +++ b/src/ammolite/object.py @@ -364,7 +364,8 @@ def alter(self, selection, expression): Parameters ---------- selection : str or ndarray, dtype=bool - A boolean mask or a *PyMOL* selection expression that + 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 ndarray, dtype=bool + 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 @@ -417,7 +419,8 @@ 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 + 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 @@ -453,7 +456,8 @@ 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 + 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 @@ -480,7 +484,8 @@ def color(self, color, selection=None): 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 + 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 @@ -515,7 +520,8 @@ 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 + 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 @@ -536,7 +542,8 @@ def disable(self, selection=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -558,7 +565,8 @@ 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 + 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 @@ -601,7 +609,8 @@ def dss(self, selection=None, state=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -625,7 +634,8 @@ def enable(self, selection=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -662,7 +672,8 @@ def hide(self, representation, selection=None): - ``'cell'``. selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -681,7 +692,8 @@ def indicate(self, selection=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -700,7 +712,8 @@ def label(self, selection, text): Parameters ---------- selection : str or ndarray, dtype=bool - A boolean mask or a *PyMOL* selection expression that + 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 @@ -720,7 +733,8 @@ def orient(self, selection=None, state=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -744,7 +758,8 @@ def origin(self, selection=None, state=None): Parameters ---------- selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -772,7 +787,8 @@ 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 + 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 @@ -807,7 +823,8 @@ 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 + 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 @@ -846,7 +863,8 @@ 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 + 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 @@ -894,7 +912,8 @@ def show(self, representation, selection=None): - ``'cell'``. selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -932,7 +951,8 @@ def show_as(self, representation, selection=None): - ``'cell'``. selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -952,7 +972,8 @@ 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 + 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 @@ -999,7 +1020,8 @@ def unset(self, name, selection=None, state=None): - ``'sphere_transparency'``. selection : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -1035,7 +1057,8 @@ def unset_bond(self, name, selection1=None, selection2=None, state=None): - ``'stick_transparency'``. selection1, selection2 : str or ndarray, dtype=bool, optional - A boolean mask or a *PyMOL* selection expression that + 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 @@ -1066,7 +1089,8 @@ 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 + 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