From da71670bbb6e1ade93dd25facae5d7466fed0fdf Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 17 Nov 2022 11:05:23 +0100
Subject: [PATCH] Introduce ClashInfo, BondViolationInfo, AngleViolationInfo
used as return values for the respective stereochemistry checks
---
modules/mol/alg/pymod/stereochemistry.py | 119 +++++++++++++++++++----
1 file changed, 101 insertions(+), 18 deletions(-)
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index fa74b1ef6..a05b74a4f 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -335,6 +335,90 @@ def GetAngleParam(a1, a2, a3, stereo_data = None, stereo_link_data = None):
return (None, None)
+class ClashInfo:
+ """ Object to hold info on clash
+
+ Constructor arguments are available as attributes:
+
+ * a1
+ * a2
+ * dist
+ * tolerated_dist
+ """
+ def __init__(self, a1, a2, dist, tolerated_dist):
+ self.a1 = a1
+ self.a2 = a2
+ self.dist = dist
+ self.tolerated_dist = tolerated_dist
+
+ def ToJSON(self):
+ """ Return JSON serializable dict
+ """
+ return {"a1": self.a1.GetQualifiedName(),
+ "a2": self.a2.GetQualifiedName(),
+ "dist": self.dist,
+ "tolerated_dist": self.tolerated_dist}
+
+
+class BondViolationInfo:
+ """ Object to hold info on bond violation
+
+ Constructor arguments are available as attributes:
+
+ * a1
+ * a2
+ * length
+ * exp_length
+ * std
+ """
+ def __init__(self, a1, a2, length, exp_length, std):
+ self.a1 = a1
+ self.a2 = a2
+ self.length = length
+ self.exp_length = exp_length
+ self.std = std
+
+ def ToJSON(self):
+ """ Return JSON serializable dict
+ """
+ return {"a1": self.a1.GetQualifiedName(),
+ "a2": self.a2.GetQualifiedName(),
+ "length": self.length,
+ "exp_length": self.exp_length,
+ "std": self.std}
+
+
+class AngleViolationInfo:
+ """ Object to hold info on angle violation
+
+ Constructor arguments are available as attributes:
+
+ * a1
+ * a2
+ * a3
+ * angle
+ * exp_angle
+ * std
+ """
+ def __init__(self, a1, a2, a3, angle, exp_angle, std):
+ self.a1 = a1
+ self.a2 = a2
+ self.a3 = a3
+ self.angle = angle
+ self.exp_angle = exp_angle
+ self.std = std
+
+ def ToJSON(self):
+ """ Return JSON serializable dict
+ """
+ return {"a1": self.a1.GetQualifiedName(),
+ "a2": self.a2.GetQualifiedName(),
+ "a3": self.a3.GetQualifiedName(),
+ "angle": self.angle,
+ "exp_angle": self.exp_angle,
+ "std": self.std}
+
+
def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
disulfid_tolerance = 1.0):
""" Identifies clashing atoms
@@ -359,8 +443,7 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
:type disulfid_dist: :class:`float`
:param disulfid_tolerance: The respective tolerance
:type disulfid_dist: :class:`float`
- :returns: A :class:`list` of pairs. Each pair consists of two
- :class:`ost.mol.AtomHandle` from *ent* that are clashing.
+ :returns: A :class:`list` of :class:`ClashInfo`
"""
if vdw_radii is None:
@@ -405,7 +488,8 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
hash_pair = (min(a_hash, ca_hash), max(a_hash, ca_hash))
if hash_pair not in done:
done.add(hash_pair)
- return_list.append((a.handle, ca.handle))
+ return_list.append(ClashInfo(a.handle, ca.handle, d,
+ thresh))
return return_list
@@ -423,8 +507,7 @@ def GetBadBonds(ent, stereo_data = None, stereo_link_data = None, tolerance=12):
:param tolerance: Bonds that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
:type tolerance: :class:`int`
- :returns: :class:`list` of pairs. Each pair consists of two
- :class:`ost.mol.AtomHandle` from *ent* that represent bad bonds.
+ :returns: :class:`list` :class:`BondViolationInfo`
"""
if stereo_data is None:
@@ -438,9 +521,9 @@ def GetBadBonds(ent, stereo_data = None, stereo_link_data = None, tolerance=12):
mean, std = GetBondParam(a1, a2, stereo_data = stereo_data,
stereo_link_data = stereo_link_data)
if None not in [mean, std]:
- diff = abs(mean-b.length)
- if diff > tolerance*std:
- return_list.append((a1, a2))
+ l = b.length
+ if abs(mean-l) > tolerance*std:
+ return_list.append(BondViolationInfo(a1, a2, l, mean, std))
return return_list
@@ -459,8 +542,7 @@ def GetBadAngles(ent, stereo_data = None, stereo_link_data = None,
:param tolerance: Angles that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
:type tolerance: :class:`int`
- :returns: :class:`list` of tuples. Each tuple consists of three
- :class:`ost.mol.AtomHandle` from *ent* that represent bad angles.
+ :returns: :class:`list` of :class:`AngleViolationInfo`
"""
if stereo_data is None:
stereo_data = GetDefaultStereoData()
@@ -476,7 +558,8 @@ def GetBadAngles(ent, stereo_data = None, stereo_link_data = None,
angle = angle/np.pi*180 # stereo params are in degrees
diff = abs(mean-angle)
if diff > tolerance*std:
- return_list.append(a)
+ return_list.append(AngleViolationInfo(a[0], a[1], a[2], angle,
+ mean, std))
return return_list
@@ -518,17 +601,17 @@ def StereoCheck(ent, stereo_data = None, stereo_link_data = None):
# set stereo problems as properties on an atom level
for clash in clashes:
- clash[0].SetIntProp("stereo_problem", 1)
- clash[1].SetIntProp("stereo_problem", 1)
+ clash.a1.SetIntProp("stereo_problem", 1)
+ clash.a2.SetIntProp("stereo_problem", 1)
for bond in bad_bonds:
- bond[0].SetIntProp("stereo_problem", 1)
- bond[1].SetIntProp("stereo_problem", 1)
+ bond.a1.SetIntProp("stereo_problem", 1)
+ bond.a2.SetIntProp("stereo_problem", 1)
for angle in bad_angles:
- angle[0].SetIntProp("stereo_problem", 1)
- angle[1].SetIntProp("stereo_problem", 1)
- angle[2].SetIntProp("stereo_problem", 1)
+ angle.a1.SetIntProp("stereo_problem", 1)
+ angle.a2.SetIntProp("stereo_problem", 1)
+ angle.a3.SetIntProp("stereo_problem", 1)
# set stereo problems as properties on a residue level
bad_ent = ent.Select("gastereo_problem:0=1")
--
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