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Biskit :: Dock :: ComplexRandomizer :: ComplexRandomizer :: Class ComplexRandomizer
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Class ComplexRandomizer

source code

Create Biskit.Dock.Complex(es) with random orientation

Instance Methods [hide private]
  __init__(self, mrec, mlig, rec_out=None, lig_out=None, debug=0)
PDBModel __center_model(self, model)
translate PDBModel so that it's center is in 0,0,0
float __max_distance(self, model)
largest center to any other atom distance
array __random_translation(self)
Random translation on a sphere around 0,0,0 with fixed radius The radius is the sum of the (max) radius of receptor and ligand
array __random_matrix(self)
Random rotation matrix.
Complex random_complex_remote(self)
Create a complex where the recrptor and ligand have random orientations but are spaced within contact distance.
  __minimize_complex(self, com)
Use Xplor to rigid body minimize the random complex.
Complex random_complex(self, inp_mirror=None)
Returns randomized and minimized complex

Method Details [hide private]

__init__(self, mrec, mlig, rec_out=None, lig_out=None, debug=0)
(Constructor)

source code 
Parameters:
  • mrec (PCRModel) - receptor model
  • mlig (PCRModel) - ligand model
  • rec_out (str) - rec output(default: None)
  • lig_out (str) - lig output (default: None)
  • debug (1|0) - 1, keep temporary xplor files (default: 0)

__center_model(self, model)

source code 

translate PDBModel so that it's center is in 0,0,0
Parameters:
  • model (PDBModel) - model to center
Returns: PDBModel
PDBModel (clone of model)

__max_distance(self, model)

source code 

largest center to any other atom distance
Parameters:
  • model (PDBModel) - model with centered coordinates
Returns: float
largest distance

__random_translation(self)

source code 

Random translation on a sphere around 0,0,0 with fixed radius The radius is the sum of the (max) radius of receptor and ligand
Returns: array
translation array 3 x 1 of float

__random_matrix(self)

source code 

Random rotation matrix.
Returns: array
4 x 4 array of float, random rotation and translation matrix

random_complex_remote(self)

source code 

Create a complex where the recrptor and ligand have random orientations but are spaced within contact distance.
Returns: Complex
rec & lig spaced r_rec + r_lig apart in random orientation

__minimize_complex(self, com)

source code 

Use Xplor to rigid body minimize the random complex.
Parameters:
  • com (Complex) - random complex

random_complex(self, inp_mirror=None)

source code 
Returns: Complex
randomized and minimized complex

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