Fred2.EpitopeSelection Module¶
EpitopeSelection.OptiTope¶
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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.
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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
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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
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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
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deactivate_allele_coverage_const
()¶ Deactivates the allele coverage constraint
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deactivate_antigen_coverage_const
()¶ Deactivates the variation coverage constraint
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deactivate_epitope_conservation_const
()¶ Deactivates epitope conservation constraint
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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
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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 PATHenvironmental variable.
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