Package Bio :: Package PDB :: Module FragmentMapper' :: Class Fragment
[hide private]
[frames] | no frames]

Class Fragment

source code

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
source code
 
__len__(self)
@return: length of fragment...
source code
 
__repr__(self)
Returns <Fragment length=L id=ID> where L=length of fragment and ID the identifier (rank in the library).
source code
 
__sub__(self, other)
Return rmsd between two fragments.
source code
 
add_residue(self, resname, ca_coord)
@param resname: residue name (eg.
source code
 
get_coords(self)
@return: the CA coords in the fragment...
source code
 
get_id(self)
@return: id for the fragment...
source code
 
get_resname_list(self)
@return: the residue names...
source code

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)

source code 

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

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

Overrides: object.__init__

__len__(self)
(Length operator)

source code 

@return: length of fragment
@rtype: int

__repr__(self)
(Representation operator)

source code 

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)

source code 

Return rmsd between two fragments.

Example:
    >>> rmsd=fragment1-fragment2

@return: rmsd between fragments
@rtype: float

add_residue(self, resname, ca_coord)

source code 

@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(self)

source code 

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

get_id(self)

source code 

@return: id for the fragment
@rtype: int

get_resname_list(self)

source code 

@return: the residue names
@rtype: [string, string,...]