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

source code

object --+
         |
        Fragment

Represent a polypeptide C-alpha fragment.

Instance Methods [hide private]
 
__init__(self, length, fid)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
int
__len__(self)
Returns: 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
float
__sub__(self, other)
Return rmsd between two fragments.		 source code
 
add_residue(self, resname, ca_coord) source code
Numeric (Nx3) array
get_coords(self)
Returns: the CA coords in the fragment		 source code
int
get_id(self)
Returns: id for the fragment		 source code
[string, string,...]
get_resname_list(self)
Returns: 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 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • length (int) - length of the fragment
  • fid (int) - id for the fragment
Overrides: object.__init__

__len__(self)
(Length operator)

source code 
Returns: int
length of fragment

__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
Returns: float
rmsd between fragments

add_residue(self, resname, ca_coord)

source code 
Parameters:
  • resname (string) - residue name (eg. GLY).
  • ca_coord (Numeric array with length 3) - the c-alpha coorinates of the residues

get_coords(self)

source code 
Returns: Numeric (Nx3) array
the CA coords in the fragment

get_id(self)

source code 
Returns: int
id for the fragment

get_resname_list(self)

source code 
Returns: [string, string,...]
the residue names

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