00001 """
00002 Some functions for analyzing structures
00003
00004 Author: Niklaus Johner (Niklaus.Johner@unibas.ch)
00005 """
00006 import os
00007 import ost
00008
00009 def GetFrameFromEntity(eh):
00010 """
00011 This function returns a CoordFrame from an EntityHandle
00012
00013 :param eh:
00014 :type eh: :class:`~ost.mol.EntityHandle`
00015
00016 :return: :class:`ost.mol.CoordFrame`
00017 """
00018 return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
00019
00020 def GetDistanceBetwCenterOfMass(sele1,sele2):
00021 """
00022 This function calculates the distance between the centers of mass
00023 of **sele1** and **sele2**, two selections from the same Entity.
00024
00025 :param sele1:
00026 :param sele2:
00027 :type sele1: :class:`~ost.mol.EntityView`
00028 :type sele2: :class:`~ost.mol.EntityView`
00029
00030 :return: :class:`float`
00031 """
00032 if not sele1.IsValid() and sele2.IsValid():
00033 print 'invalid view'
00034 return
00035 eh=sele1.GetHandle()
00036 if not eh==sele2.GetHandle():
00037 print 'The two views must be from the same entity'
00038 return
00039 f=GetFrameFromEntity(eh)
00040 return f.GetDistanceBetwCenterOfMass(sele1,sele2)
00041
00042 def GetMinDistanceBetweenViews(sele1,sele2):
00043 """
00044 This function calculates the minimal distance between
00045 **sele1** and **sele2**, two selections from the same Entity.
00046
00047 :param sele1:
00048 :param sele2:
00049 :type sele1: :class:`~ost.mol.EntityView`
00050 :type sele2: :class:`~ost.mol.EntityView`
00051
00052 :return: :class:`float`
00053 """
00054 if not sele1.IsValid() and sele2.IsValid():
00055 print 'invalid view'
00056 return
00057 eh=sele1.GetHandle()
00058 if not eh==sele2.GetHandle():
00059 print 'The two views must be from the same entity'
00060 return
00061 f=GetFrameFromEntity(eh)
00062 return f.GetMinDistance(sele1,sele2)
00063
00064 def GetMinDistBetwCenterOfMassAndView(sele1,sele2):
00065 """
00066 This function calculates the minimal distance between **sele2** and
00067 the center of mass of **sele1**, two selections from the same Entity.
00068
00069 :param sele1: The selection from which the center of mass is taken
00070 :param sele2:
00071 :type sele1: :class:`~ost.mol.EntityView`
00072 :type sele2: :class:`~ost.mol.EntityView`
00073
00074 :return: distance (\ :class:`float`\ )
00075 """
00076 if not sele1.IsValid() and sele2.IsValid():
00077 print 'invalid view'
00078 return
00079 eh=sele1.GetHandle()
00080 if not eh==sele2.GetHandle():
00081 print 'The two views must be from the same entity'
00082 return
00083 f=GetFrameFromEntity(eh)
00084 return f.GetMinDistBetwCenterOfMassAndView(sele1,sele2)
00085
00086
00087 def GetAlphaHelixContent(sele1):
00088 """
00089 This function calculates the content of alpha helix in a view.
00090 All residues in the view have to ordered and adjacent (no gaps allowed)
00091
00092 :param sele1:
00093 :type sele1: :class:`~ost.mol.EntityView`
00094
00095 :return: :class:`float`
00096 """
00097 if not sele1.IsValid():
00098 print 'invalid view'
00099 return
00100 eh=sele1.GetHandle()
00101 f=GetFrameFromEntity(eh)
00102 return f.GetAlphaHelixContent(sele1)
00103
00104
00105 def CalculateBestFitLine(sele1):
00106 """
00107 This function calculates the best fit line to the atoms in **sele1**.
00108
00109 :param sele1:
00110 :type sele1: :class:`~ost.mol.EntityView`
00111
00112 :return: :class:`~ost.geom.Line3`
00113 """
00114 if not sele1.IsValid():
00115 print 'invalid view'
00116 return
00117 eh=sele1.GetHandle()
00118 f=GetFrameFromEntity(eh)
00119 return f.GetODRLine(sele1)
00120
00121 def CalculateBestFitPlane(sele1):
00122 """
00123 This function calculates the best fit plane to the atoms in **sele1**.
00124
00125 :param sele1:
00126 :type sele1: :class:`~ost.mol.EntityView`
00127
00128 :return: :class:`~ost.geom.Plane`
00129 """
00130 if not sele1.IsValid():
00131 print 'invalid view'
00132 return
00133 eh=sele1.GetHandle()
00134 f=GetFrameFromEntity(eh)
00135 return f.GetODRPlane(sele1)
00136
00137 def CalculateHelixAxis(sele1):
00138 """
00139 This function calculates the best fit cylinder to the CA atoms in **sele1**,
00140 and returns its axis. Residues should be ordered correctly
00141 in **sele1**.
00142
00143 :param sele1:
00144 :type sele1: :class:`~ost.mol.EntityView`
00145
00146 :return: :class:`~ost.geom.Line3`
00147 """
00148 if not sele1.IsValid():
00149 print 'invalid view'
00150 return
00151 eh=sele1.GetHandle()
00152 f=GetFrameFromEntity(eh)
00153 return f.FitCylinder(sele1)[0]
00154
00155
00156 def CalculateDistanceDifferenceMatrix(sele1,sele2):
00157 """
00158 This function calculates the pairwise distance differences between two selections (\ :class:`~ost.mol.EntityView`\ ).
00159 The two selections should have the same number of atoms
00160 It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1)
00161 where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)||
00162
00163 :param sele1:
00164 :param sele2:
00165 :type sele1: :class:`~ost.mol.EntityView`
00166 :type sele2: :class:`~ost.mol.EntityView`
00167
00168 :return: NxN numpy matrix
00169 """
00170 try:import numpy as npy
00171 except ImportError:
00172 LogError("Function needs numpy, but I could not import it.")
00173 raise
00174 if not sele1.IsValid() and sele2.IsValid():
00175 print 'invalid view'
00176 return
00177 if not sele1.GetAtomCount()==sele2.GetAtomCount():
00178 print 'The two views must have the same number of atoms'
00179 return
00180 n_atoms=sele1.GetAtomCount()
00181 M=npy.zeros([n_atoms,n_atoms])
00182 for i,a1 in enumerate(sele1.atoms):
00183 for j,a2 in enumerate(sele1.atoms):
00184 if i>=j:continue
00185 d1=ost.geom.Distance(a1.pos,a2.pos)
00186 d2=ost.geom.Distance(sele2.atoms[i].pos,sele2.atoms[j].pos)
00187 M[i,j]=d2-d1
00188 M[j,i]=d2-d1
00189 return M
00190
00191
