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Commit b40b875f authored by Studer Gabriel's avatar Studer Gabriel
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stereocheck: docu updates

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......@@ -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:
......
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