def set_sample_points(self, sample_factor = 1./4) :
   sample_spacing = sample_factor*self.resolution
   base = {}
   rn = self.residue.resname.strip().upper()
   if rn in ['DA', 'DG'] :
     base['C2'] = self.xyz.C2
     base['N1'] = self.xyz.N1
     base['C6'] = self.xyz.C6
   elif rn in ['DT', 'DC'] :
     base['N3'] = self.xyz.C2
     base['C4'] = self.xyz.N1
     base['C5'] = self.xyz.C6
   self.sample_points = box_base.get_points_around_base(base,rn,sample_spacing)
Exemplo n.º 2
0
 def set_sample_points(self, sample_factor=1. / 4):
     sample_spacing = sample_factor * self.resolution
     base = {}
     rn = self.residue.resname.strip().upper()
     if rn in ['DA', 'DG']:
         base['C2'] = self.xyz.C2
         base['N1'] = self.xyz.N1
         base['C6'] = self.xyz.C6
     elif rn in ['DT', 'DC']:
         base['N3'] = self.xyz.C2
         base['C4'] = self.xyz.N1
         base['C5'] = self.xyz.C6
     self.sample_points = box_base.get_points_around_base(
         base, rn, sample_spacing)
  def set_sample_points(self, sample_factor = 1./4) :
    sample_spacing = sample_factor*self.resolution
    base = {}
#     print self.get_string_id()
    rn = self.res_type.strip().upper()
    if rn in ['DA', 'DG'] :
      base['C2'] = self.xyz.C2
      base['N1'] = self.xyz.N1
      base['C6'] = self.xyz.C6
      # test_points is where we test for positive density when looking for 
      # potential decoys. 
      tp = box_base.get_test_points(base,rn,sample_spacing)
      vars(self.xyz)['test_1'] = tp.point_1
      vars(self.xyz)['test_2'] = tp.point_2
    elif rn in ['DT', 'DC'] :
      base['N3'] = self.xyz.C2
      base['C4'] = self.xyz.N1
      base['C5'] = self.xyz.C6
    self.sample_points = box_base.get_points_around_base(base,rn,sample_spacing)
Exemplo n.º 4
0
 def set_sample_points(self, sample_factor=1. / 4):
     sample_spacing = sample_factor * self.resolution
     base = {}
     #     print self.get_string_id()
     rn = self.res_type.strip().upper()
     if rn in ['DA', 'DG']:
         base['C2'] = self.xyz.C2
         base['N1'] = self.xyz.N1
         base['C6'] = self.xyz.C6
         # test_points is where we test for positive density when looking for
         # potential decoys.
         tp = box_base.get_test_points(base, rn, sample_spacing)
         vars(self.xyz)['test_1'] = tp.point_1
         vars(self.xyz)['test_2'] = tp.point_2
     elif rn in ['DT', 'DC']:
         base['N3'] = self.xyz.C2
         base['C4'] = self.xyz.N1
         base['C5'] = self.xyz.C6
     self.sample_points = box_base.get_points_around_base(
         base, rn, sample_spacing)