Package Bio :: Package PDB :: Module FragmentMapper' :: Class Fragment
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Class Fragment

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object --+
         |
        Fragment

Represent a polypeptide C-alpha fragment.
Instance Methods [hide private]
 
__init__(self, length, fid)
@param length: length of the fragment @type length: int
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__len__(self)
@return: length of fragment @rtype: int
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__repr__(self)
Returns <Fragment length=L id=ID> where L=length of fragment and ID the identifier (rank in the library).
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__sub__(self, other)
Return rmsd between two fragments.
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add_residue(self, resname, ca_coord)
@param resname: residue name (eg.
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get_coords(self)
@return: the CA coords in the fragment @rtype: Numeric (Nx3) array
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get_id(self)
@return: id for the fragment @rtype: int
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get_resname_list(self)
@return: the residue names @rtype: [string, string,...]
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, length, fid)
(Constructor)

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

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

Overrides: object.__init__

__repr__(self)
(Representation operator)

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Returns <Fragment length=L id=ID> where L=length of fragment and ID the identifier (rank in the library).
Overrides: object.__repr__

__sub__(self, other)
(Subtraction operator)

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Return rmsd between two fragments.

Example:
>>> rmsd=fragment1-fragment2

@return: rmsd between fragments @rtype: float

add_residue(self, resname, ca_coord)

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@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