2 Functions to calculate helix kinks: bend, face shift and wobble angles
10 def __FindProline(sele,proline):
11 if not sele.IsValid():
12 print(
'selection is not valid')
15 proline=sele.Select(
'rname=PRO')
16 if not proline.GetResidueCount()==1:
17 print(proline.GetResidueCount(),
'prolines in the selection. One proline is needed')
19 proline=proline.residues[0]
20 proline_ca=proline.FindAtom(
'CA')
21 if not proline_ca.IsValid():
22 print(
'proline has no CA atom')
24 return (proline,proline_ca)
25 proline.GetNumber().num
27 def __SelectPreAndPostProline(sele,proline_num):
28 pre_proline=sele.Select(
'rnum<'+str(proline_num))
29 post_proline=sele.Select(
'rnum>'+str(proline_num))
30 print(
'pre-proline residues')
31 for res
in pre_proline.residues:
33 print(
'post-proline residues')
34 for res
in post_proline.residues:
36 if pre_proline.GetResidueCount()<4
or post_proline.GetResidueCount()<4:
37 print(
'pre and post proline helices should be at least 4 residues long, 7 for better stability')
39 return (pre_proline,post_proline)
41 def __FindCa3AndCa4(sele,proline_ca,proline_num):
42 ca_3=sele.FindAtom(proline_ca.GetHandle().GetChain().GetName(),proline_num-3,
'CA')
43 ca_4=sele.FindAtom(proline_ca.GetHandle().GetChain().GetName(),proline_num-4,
'CA')
44 if not (ca_3.IsValid()
and ca_4.IsValid()):
45 print(
'CA not found in (i-4) or (i-3) residue')
50 def __CalculateBendAngle(pre_proline_axis,post_proline_axis):
51 return ost.geom.Angle(pre_proline_axis,post_proline_axis)
53 def __CalculateWobbleAngle(pre_proline_axis,post_proline_axis,post_proline_centers,proline_pos):
54 p1=proline_pos-post_proline_centers
55 n1=p1-ost.geom.Dot(p1,post_proline_axis)*post_proline_axis
57 n2=p2-ost.geom.Dot(p2,post_proline_axis)*post_proline_axis
58 sign=ost.geom.Dot(ost.geom.Cross(pre_proline_axis,n2),n2-n1)
60 return sign*ost.geom.Angle(n1,n2)
62 def __CalculateFaceShift(pre_proline_axis,post_proline_axis,pre_proline_centers,post_proline_centers,proline_pos,ca3_pos,ca4_pos,bend_angle):
63 p1=proline_pos-post_proline_centers
64 n1=p1-ost.geom.Dot(p1,post_proline_axis)*post_proline_axis
65 p2=(ca3_pos+ca4_pos)/2.0-pre_proline_centers
66 n2=p2-ost.geom.Dot(p2,pre_proline_axis)*pre_proline_axis
68 R=ost.geom.AxisRotation(ost.geom.Cross(post_proline_axis,pre_proline_axis),bend_angle)
71 sign=ost.geom.Dot(ost.geom.Cross(pre_proline_axis,n2),n2-n1)
73 return sign*ost.geom.Angle(n1,n2)
78 This function calculates the bend, wobble and face-shift angles in an alpha-
79 helix over a trajectory. The determination is more stable if there are at
80 least 4 residues on each side (8 is even better) of the proline around which
81 the helix is kinked. The selection should contain all residues in the correct
82 order and with no gaps and no missing C-alphas.
84 :param t: The trajectory to be analyzed
85 :type t: :class:`~ost.mol.CoordGroup`
86 :param sele: A selection containing the alpha helix to be analyzed
87 :type sele: :class:`~ost.mol.EntityView`
88 :param proline: A selection containing only the proline (or another residue)
89 around which the helix is kinked. If False, the proline will
90 be searched for automatically
91 :type proline: :class:`ost.mol.EntityView`
93 :return: A tuple (bend_angle, face_shift, wobble_angle).
94 :rtype: (FloatList, FLoatList, FloatList)
96 n_frames=t.GetFrameCount()
97 (proline,proline_ca)=__FindProline(sele,proline)
98 proline_num=proline.GetNumber().num
99 (pre_proline,post_proline)=__SelectPreAndPostProline(sele,proline_num)
100 (ca_3,ca_4)=__FindCa3AndCa4(sele,proline_ca,proline_num)
102 pre_proline_axis=ost.geom.Vec3List()
103 post_proline_axis=ost.geom.Vec3List()
104 pre_proline_centers=ost.geom.Vec3List()
105 post_proline_centers=ost.geom.Vec3List()
112 bend_angle=ost.FloatList()
113 face_shift=ost.FloatList()
114 wobble_angle=ost.FloatList()
115 for i
in range(n_frames):
116 bend_angle.append(__CalculateBendAngle(pre_proline_axis[i],post_proline_axis[i]))
117 face_shift.append(__CalculateFaceShift(pre_proline_axis[i],post_proline_axis[i],pre_proline_centers[i],post_proline_centers[i],proline_pos[i],ca3_pos[i],ca4_pos[i],bend_angle[i]))
118 wobble_angle.append(__CalculateWobbleAngle(pre_proline_axis[i],post_proline_axis[i],post_proline_centers[i],proline_pos[i]))
119 return (bend_angle,face_shift,wobble_angle)
124 This function calculates the bend, wobble and face-shift angles in an alpha-
125 helix of an EntityView. The determination is more stable if there are at least
126 4 residues on each side (8 is even better) of the proline around which the
127 helix is kinked. The selection should contain all residues in the correct
128 order and with no gaps and no missing C-alphas.
130 :param sele: A selection containing the alpha helix to be analyzed
131 :type sele: :class:`~ost.mol.EntityView`
132 :param proline: A selection containing only the proline (or another residue)
133 around which the helix is kinked. If False, the proline will
134 be searched for automatically
135 :type proline: :class:`ost.mol.EntityView`
137 :return: A tuple (bend_angle, face_shift, wobble_angle).
138 :rtype: (float, float, float)
140 (proline,proline_ca)=__FindProline(sele,proline)
141 proline_num=proline.GetNumber().num
142 (pre_proline,post_proline)=__SelectPreAndPostProline(sele,proline_num)
143 (ca_3,ca_4)=__FindCa3AndCa4(sele,proline_ca,proline_num)
147 prepa=pre_proline_axis.GetDirection()
148 prepc=pre_proline_axis.GetOrigin()
149 postpa=post_proline_axis.GetDirection()
150 postpc=post_proline_axis.GetOrigin()
152 bend=__CalculateBendAngle(prepa,postpa)
153 wobble=__CalculateWobbleAngle(prepa,postpa,postpc,proline_ca.pos)
154 shift=__CalculateFaceShift(prepa,postpa,prepc,postpc,proline_ca.pos,ca_3.pos,ca_4.pos,bend)
155 return (bend,shift,wobble)
geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeAtomPos(const CoordGroupHandle &traj, const AtomHandle &a1, unsigned int stride=1)
void DLLEXPORT_OST_MOL_ALG AnalyzeAlphaHelixAxis(const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List ¢ers, unsigned int stride=1)