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Package Biskit :: Package Mod :: Module Benchmark :: Class Benchmark
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Class Benchmark

source code

This class regroups the different methods to analyse the output files of interest from modeller

Instance Methods [hide private]
  __init__(self, outFolder='.', verbose=1)
  prepareFolders(self)
Create folders needed by this class.
PDBModel, PDBModel output_fittedStructures(self, pdb, reference, index, atom_mask, output_folder=None)
Takes a model and a reference structure, performs both a normal fillting to the reference and an itterative fitting.
  calc_rmsd(self, fitted_model_if, fitted_model_wo_if, reference, model)
Takes the two fitted structures (with and without iterative fitting), the known structure (reference), and the associated model inside the pdb_list.
  output_rmsd_aa(self, pdb_list, output_file=None)
Write a file rmsd_aa.dat that contains all the global heavy atom rmsd values.
  output_rmsd_ca(self, pdb_list, output_file=None)
Write a file rmsd_ca.dat that contains all the global c_alpha rmsd values.
[float] rmsd_res(self, coord1, coord2)
Calculate the rsmd on residue level for c-alpha between a model and its reference.
  output_rmsd_res(self, pdb_list, output_folder=None)
Write a file that contains the rmsd profile on a residue level for c_alpha.
  cad(self, reference, model)
Calculates the CAD Contact Area Difference between the model and its reference structure and set a profile for the model
  write_PDBModels(self, pdb_list, output_file=None)
Pickles the list of PDBModels to disc.
  go(self, model_list=None, reference=None)
Run benchmarking.

Class Variables [hide private]
  F_INPUT_FOLDER = Modeller.F_RESULT_FOLDER
  F_RESULT_FOLDER = '/benchmark'
  F_INPUT_REFERENCE = '/reference.pdb'
  F_PDBModels = F_INPUT_FOLDER+ '/PDBModels.list'
  F_RMSD_AA = F_RESULT_FOLDER+ '/rmsd_aa.out'
  F_RMSD_CA = F_RESULT_FOLDER+ '/rmsd_ca.out'
  F_RMSD_RES = '/rmsd_res'
  F_PDBModels_OUT = F_RESULT_FOLDER+ '/PDBModels.list'
  F_FINAL_REFERENCE = F_RESULT_FOLDER+ '/reference_final.pdb'

Method Details [hide private]

__init__(self, outFolder='.', verbose=1)
(Constructor)

source code 
Parameters:
  • outFolder (str) - folder for output (default: .)
  • verbose (1|0) - write intermediary files (default: 1)

prepareFolders(self)

source code 

Create folders needed by this class.

output_fittedStructures(self, pdb, reference, index, atom_mask, output_folder=None)

source code 

Takes a model and a reference structure, performs both a normal fillting to the reference and an itterative fitting. Then returns the two fitted models.
Parameters:
  • pdb (PDBModel) - model
  • reference (PDBModel) - reference model
  • index (int) - index number
  • atom_mask ([int]) - atom mask for discharding certain atoms
  • output_folder (str) - output folder (default: None → outFolder/F_RESULT_FOLDER
Returns: PDBModel, PDBModel
pdb_if, pdb - model, fitted iteratively (n=10), model, without iterative fitting

calc_rmsd(self, fitted_model_if, fitted_model_wo_if, reference, model)

source code 

Takes the two fitted structures (with and without iterative fitting), the known structure (reference), and the associated model inside the pdb_list. Calculates the different RMSD and set the profiles
Parameters:
  • fitted_model_if (PDBModel) - itteratively fitted model
  • fitted_model_wo_if (PDBModel) - normaly fitted model
  • reference (PDBModel) - reference model
  • model (PDBModel) - model

output_rmsd_aa(self, pdb_list, output_file=None)

source code 

Write a file rmsd_aa.dat that contains all the global heavy atom rmsd values.
Parameters:
  • pdb_list (ModelList) - list of models
  • output_file (str) - output file (default: None → outFolder/F_RMSD_AA)

output_rmsd_ca(self, pdb_list, output_file=None)

source code 

Write a file rmsd_ca.dat that contains all the global c_alpha rmsd values.
Parameters:
  • pdb_list (ModelList) - list of models
  • output_file (str) - output file (default: None → outFolder/F_RMSD_CA)

rmsd_res(self, coord1, coord2)

source code 

Calculate the rsmd on residue level for c-alpha between a model and its reference.
Parameters:
  • coord1 (array) - first set of coordinates
  • coord2 (array) - second set of coordinates
Returns: [float]
rmsd_res: rmsd per c-alpha

output_rmsd_res(self, pdb_list, output_folder=None)

source code 

Write a file that contains the rmsd profile on a residue level for c_alpha.
Parameters:
  • pdb_list (ModelList) - list of models
  • output_folder (str) - output folder (default: None → outFolder/ F_RESULT_FOLDER/F_RMSD_RES)

cad(self, reference, model)

source code 

Calculates the CAD Contact Area Difference between the model and its reference structure and set a profile for the model
Parameters:
  • reference (PDBModel) - reference model
  • model (PDBModel) - model

write_PDBModels(self, pdb_list, output_file=None)

source code 

Pickles the list of PDBModels to disc.
Parameters:
  • pdb_list (ModelList) - list of models
  • output_file (str) - output file (default: None → outFolder/F_PDBModels_OUT)

go(self, model_list=None, reference=None)

source code 

Run benchmarking.
Parameters:
  • model_list (ModelList) - list of models (default: None → outFolder/F_PDBModels)
  • reference (PDBModel) - reference model (default: None → outFolder/F_INPUT_REFERENCE)

Class Variable Details [hide private]

F_INPUT_FOLDER

Value:
Modeller.F_RESULT_FOLDER

F_RESULT_FOLDER

Value:
'/benchmark'

F_INPUT_REFERENCE

Value:
'/reference.pdb'

F_PDBModels

Value:
F_INPUT_FOLDER+ '/PDBModels.list'

F_RMSD_AA

Value:
F_RESULT_FOLDER+ '/rmsd_aa.out'

F_RMSD_CA

Value:
F_RESULT_FOLDER+ '/rmsd_ca.out'

F_RMSD_RES

Value:
'/rmsd_res'

F_PDBModels_OUT

Value:
F_RESULT_FOLDER+ '/PDBModels.list'

F_FINAL_REFERENCE

Value:
F_RESULT_FOLDER+ '/reference_final.pdb'

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