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def Bio::PDB::HSExposure::HSExposure::_get_rotran_list_from_cb (   self,
  residue_list 
) [private]

Return a list of (translation, rotation, ca, residue)
tuples (using CB). 

The translation and rotation are calculated 
using the CA-CB coordinates.

This list is used in the following way:

A certain atom is found within radius of a given position.
The coordinates are translated by -translation.
The coordinates are rotated by rotation.
If the z coordinate is >0 it lies in the side-chain sphere.
Otherwise it lies in the backbone sphere.

Definition at line 96 of file HSExposure.py.

00096                                                     :
        """
        Return a list of (translation, rotation, ca, residue)
        tuples (using CB). 
        
        The translation and rotation are calculated 
        using the CA-CB coordinates.

        This list is used in the following way:

        A certain atom is found within radius of a given position.
        The coordinates are translated by -translation.
        The coordinates are rotated by rotation.
        If the z coordinate is >0 it lies in the side-chain sphere.
        Otherwise it lies in the backbone sphere.
        """
        # list of (translation, rotation, ca, residue) tuples
        rotran_list=[]
        for residue in residue_list:
            if is_aa(residue):
                ca=residue["CA"]
                ca_v=ca.get_vector()
                if residue.has_id("CB"):
                    cb=residue["CB"]
                    cb_v=cb.get_vector()
                    # Call _get_gly_cb_vector here for PyMol output
                    # self._get_gly_cb_vector(residue)
                else:
                    # GLY has no CB - calculate pseudo CB position
                    # based on N/CA/C positions
                    cb_v=self._get_gly_cb_vector(residue)
                # CB-CA vector
                cb_ca_v=cb_v-ca_v
                # Rotate CB-CA vector to unit vector along Z
                rotation=rotmat(cb_ca_v, self._unit_z)
                translation=ca.get_coord()
                rotran_list.append((translation, rotation, ca, residue))
        return rotran_list

    def _get_rotran_list_from_ca(self, model):


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