diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py index cf9b49256ecd67dadbf18d4b61b3d04570a86d1b..625ee4ea15be6e0654a1048efb42d0b64cf86726 100644 --- a/modules/mol/alg/pymod/stereochemistry.py +++ b/modules/mol/alg/pymod/stereochemistry.py @@ -342,10 +342,10 @@ class ClashInfo: Constructor arguments are available as attributes: - * a1 - * a2 - * dist - * tolerated_dist + * a1 (:class:`ost.mol.AtomHandle`) + * a2 (:class:`ost.mol.AtomHandle`) + * dist (:class:`float`) + * tolerated_dist (:class:`float`) """ def __init__(self, a1, a2, dist, tolerated_dist): self.a1 = a1 @@ -367,11 +367,11 @@ class BondViolationInfo: Constructor arguments are available as attributes: - * a1 - * a2 - * length - * exp_length - * std + * a1 (:class:`ost.mol.AtomHandle`) + * a2 (:class:`ost.mol.AtomHandle`) + * length (:class:`float`) + * exp_length (:class:`float`) + * std (:class:`float`) """ def __init__(self, a1, a2, length, exp_length, std): self.a1 = a1 @@ -395,12 +395,12 @@ class AngleViolationInfo: Constructor arguments are available as attributes: - * a1 - * a2 - * a3 - * angle - * exp_angle - * std + * a1 (:class:`ost.mol.AtomHandle`) + * a2 (:class:`ost.mol.AtomHandle`) + * a3 (:class:`ost.mol.AtomHandle`) + * angle (:class:`float`) + * exp_angle (:class:`float`) + * std (:class:`float`) """ def __init__(self, a1, a2, a3, angle, exp_angle, std): self.a1 = a1 @@ -457,8 +457,8 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03, f"Got {ele}") # it would be elegant to just do a selection by the ele property. However, - # thats case sensitive so someone could define a vdw radius for Cl but - # the element of the atom is CL. + # thats case sensitive. So the element could be Cl but the vdw radii + # are all caps. elements = set([ele.upper() for ele in vdw_radii.keys()]) for a in ent.atoms: if a.GetElement().upper() in elements: