Fred2.EpitopeSelection Module

EpitopeSelection.OptiTope

class Fred2.EpitopeSelection.OptiTope.OptiTope(results, threshold=None, k=10, solver='glpk', verbosity=0)

Bases: object

This class implements the epitope selection functionality of OptiTope published by Toussaint et al. [1].

This module builds upon Pyomo, an embedded algebraic modeling languages [2].

It allows to (de)select specific constraints of the underlying ILP and to solve the specific problem with a MIP solver of choice

Note

[1] N. C. Toussaint and O. Kohlbacher. OptiTope–a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res, 2009, 37, W617-W622 [2] Pyomo - Optimization Modeling in Python. William E. Hart, Carl Laird, Jean-Paul Watson and David L. Woodruff. Springer, 2012.

activate_allele_coverage_const(minCoverage)

Enables the allele coverage constraint

Parameters:minCoverage (float) – Percentage of alleles which have to be covered [0,1]
Raises:ValueError – If the input variable is not in the same domain as the parameter
activate_antigen_coverage_const(t_var)

Activates the variation coverage constraint

Parameters:t_var (int) – The number of epitopes which have to come from each variation
Raises:ValueError – If the input variable is not in the same domain as the parameter
activate_epitope_conservation_const(t_c, conservation=None)

Activates the epitope conservation constraint

Parameters:t_c (float) – The percentage of conservation an epitope has to have [0.0,1.0].
Param:conservation: A dict with key=:class:~Fred2.Core.Peptide.Peptide specifying a different conservation score for each Peptide
Raises:ValueError – If the input variable is not in the same domain as the parameter
deactivate_allele_coverage_const()

Deactivates the allele coverage constraint

deactivate_antigen_coverage_const()

Deactivates the variation coverage constraint

deactivate_epitope_conservation_const()

Deactivates epitope conservation constraint

set_k(k)

Sets the number of epitopes to select

Parameters:k (int) – The number of epitopes
Raises:ValueError – If the input variable is not in the same domain as the parameter
solve(options=None)

Invokes the selected solver and solves the problem

Parameters:options (dict(str,str)) – A dictionary of solver specific options as keys and their parameters as values

:return Returns the optimal epitopes as list of Peptide objectives :rtype: list(Peptide) :raise RuntimeError: If the solver raised a problem or the solver is not accessible via the PATH

environmental variable.