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"""
Some functions for analyzing structures
Author: Niklaus Johner (Niklaus.Johner@unibas.ch)
"""
import os
import ost
def GetFrameFromEntity(eh):
"""
This function returns a CoordFrame from an EntityHandle
:param eh:
:type eh: :class:`~ost.mol.EntityHandle`
:return: :class:`ost.mol.CoordFrame`
"""
return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
def GetDistanceBetwCenterOfMass(sele1,sele2):
"""
This function calculates the distance between the centers of mass
of **sele1** and **sele2**, two selections from the same Entity.
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: :class:`float`
"""
if not sele1.IsValid() and sele2.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetDistanceBetwCenterOfMass(sele1,sele2)
def GetMinDistanceBetweenViews(sele1,sele2):
"""
This function calculates the minimal distance between
**sele1** and **sele2**, two selections from the same Entity.
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: :class:`float`
"""
if not sele1.IsValid() and sele2.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetMinDistance(sele1,sele2)
def GetMinDistBetwCenterOfMassAndView(sele1,sele2):
"""
This function calculates the minimal distance between **sele2** and
the center of mass of **sele1**, two selections from the same Entity.
:param sele1: The selection from which the center of mass is taken
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: distance (\\ :class:`float`\\ )
"""
if not sele1.IsValid() and sele2.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
if not eh==sele2.GetHandle():
print('The two views must be from the same entity')
return
f=GetFrameFromEntity(eh)
return f.GetMinDistBetwCenterOfMassAndView(sele1,sele2)
def GetAlphaHelixContent(sele1):
"""
This function calculates the content of alpha helix in a view.
All residues in the view have to ordered and adjacent (no gaps allowed)
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`float`
"""
if not sele1.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
return f.GetAlphaHelixContent(sele1)
def CalculateBestFitLine(sele1):
"""
This function calculates the best fit line to the atoms in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Line3`
"""
if not sele1.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
return f.GetODRLine(sele1)
def CalculateBestFitPlane(sele1):
"""
This function calculates the best fit plane to the atoms in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Plane`
"""
if not sele1.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
return f.GetODRPlane(sele1)
def CalculateHelixAxis(sele1):
"""
This function calculates the best fit cylinder to the CA atoms in **sele1**,
and returns its axis. Residues should be ordered correctly
in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Line3`
"""
if not sele1.IsValid():
print('invalid view')
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
return f.FitCylinder(sele1)[0]
def CalculateDistanceDifferenceMatrix(sele1,sele2):
"""
This function calculates the pairwise distance differences between two selections (\\ :class:`~ost.mol.EntityView`\\ ).
The two selections should have the same number of atoms
It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1)
where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)||
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: NxN numpy matrix
"""
try:import numpy as npy
except ImportError:
LogError("Function needs numpy, but I could not import it.")
raise
if not sele1.IsValid() and sele2.IsValid():
print('invalid view')
return
if not sele1.GetAtomCount()==sele2.GetAtomCount():
print('The two views must have the same number of atoms')
return
n_atoms=sele1.GetAtomCount()
M=npy.zeros([n_atoms,n_atoms])
for i,a1 in enumerate(sele1.atoms):
for j,a2 in enumerate(sele1.atoms):
if i>=j:continue
d1=ost.geom.Distance(a1.pos,a2.pos)
d2=ost.geom.Distance(sele2.atoms[i].pos,sele2.atoms[j].pos)
M[i,j]=d2-d1
M[j,i]=d2-d1
return M
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