biopython v1.71.0 Bio.PDB.FragmentMapper.Fragment

Represent a polypeptide C-alpha fragment.

Link to this section Summary

Initialize fragment object

Return lengt of the fragment

String representing the fragment object

Return rmsd between two fragments

Add a residue

Get the CA coordinates in the fragment

Get identifier for the fragment

Get residue list

__init__()

Initialize fragment object.

:param length: length of the fragment :type length: int

:param fid: id for the fragment :type fid: int

__len__()

Return lengt of the fragment.

__repr__()

String representing the fragment object.

Returns where L=length of fragment and ID the identifier (rank in the library).

__sub__()

Return rmsd between two fragments.

Example:

     >>> rmsd=fragment1-fragment2

:return: rmsd between fragments :rtype: float

add_residue()

Add a residue.

:param resname: residue name (eg. GLY). :type resname: string

:param ca_coord: the c-alpha coorinates of the residues :type ca_coord: Numeric array with length 3

get_coords()

Get the CA coordinates in the fragment.

:return: the CA coords in the fragment :rtype: Numeric (Nx3) array

get_id()

Get identifier for the fragment.

:return: id for the fragment :rtype: int

get_resname_list()

Get residue list.

:return: the residue names :rtype: [string, string,…]