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Biskit :: Ramachandran :: Ramachandran :: Class Ramachandran
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Class Ramachandran

source code

Instance Methods [hide private]
  __init__(self, models, name=None, profileName='relAS', verbose=1)
  calc(self, models)
Calculate angles, profiles and other things needed.
  calcProfiles(self, m)
Calculate needed profiles.
  phi_and_psi(self, model)
Calculate phi and psi torsion angles for all residues in model:
  dihedral(self, coor1, coor2, coor3, coor4)
Calculates the torsion angle of a set of four atom coordinates.
[ biggles.Point ], biggles.Inset ramachandran(self)
Create all the ramachandran plot points.
[ biggles.Point ] ramachandran_background(self)
Creates a background (favoured regions) for a ramachandran plot.
  show(self, fileName=None)
Show ramachandran plot.

Method Details [hide private]

__init__(self, models, name=None, profileName='relAS', verbose=1)
(Constructor)

source code 
Parameters:
  • models ([ PDBModel ] OR PDBModel) - List of models display a Ramachandran plot for
  • name (str) - model name, will show up in plot
  • profileName (str) - name of profile to use for coloring (default: 'relAS')
  • verbose (1|0) - verbosity level (default: 1)

calc(self, models)

source code 

Calculate angles, profiles and other things needed.
Parameters:
  • models ([ PDBModel ]) - List of models

calcProfiles(self, m)

source code 

Calculate needed profiles.
Parameters:
  • m (PDBModel) - PDBModel to calculate data for

phi_and_psi(self, model)

source code 

Calculate phi and psi torsion angles for all residues in model: 
 phi - rotation about the N-CA bond
     - last position in a chain = None
 psi - rotation about CA-C
     - first position in a chain = None
Parameters:
  • model (PDBModel) - PDBModel

dihedral(self, coor1, coor2, coor3, coor4)

source code 

Calculates the torsion angle of a set of four atom coordinates. The dihedral angle returned is the angle between the projection of i1-i2 and the projection of i4-i3 onto a plane normal to i2-i3.
Parameters:
  • coor1 ([float]) - coordinates
  • coor2 ([float]) - coordinates
  • coor3 ([float]) - coordinates
  • coor4 ([float]) - coordinates

ramachandran(self)

source code 

Create all the ramachandran plot points.
Returns: [ biggles.Point ], biggles.Inset
list of biggles.Point objects (all the points of the plot)and a biggles.Inset object (property scale).

ramachandran_background(self)

source code 

Creates a background (favoured regions) for a ramachandran plot.
Returns: [ biggles.Point ]
list of biggles.Point objects

show(self, fileName=None)

source code 

Show ramachandran plot.

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