EpitopeAssembly fails for instances > 50 peptides

[mattheiter]

Solving the EpitopeAssembly fails for larger instances with roughly more than 50 peptides. The error occurs while retrieving "immutable param values" for the peptide pairs

Minimal example:

from Fred2.CleavagePrediction import CleavageSitePredictorFactory
from Fred2.EpitopeAssembly import EpitopeAssembly
from Fred2.Core import Peptide

cleavage_predictor = CleavageSitePredictorFactory("PCM")
peptides = [
"YANRNRFLY",
"AGDSGFAAY",
"ATSRTLSYY",
"SSDNIALLV",
"VAGDSGFAAY",
"RVAGDSGFAAY",
"VATSRTLSY",
"FTSDYYQLY",
"ISEHDYQIGGY",
"TSDYYQLY",
"TTSPISEHDY",
"STDTGVEHVTF",
"HSYFTSDYY",
"STDTGVEHV",
"IVDEPEEHV",
"LSKSLTENKY",
"VVDDPCPIHFY",
"VDDPCPIHFY",
"VVDDPCPIHF",
"CSFYEDFLEY",
"YIDIGNYTV",
"SFYEDFLEY",
"NSSPDDQIGYY",
"SSPDDQIGYY",
"NSSPDDQIGY",
"VTPSGTWLTY",
"SSPDDQIGY",
"SPDDQIGYY",
"GTGPEAGLPY",
"LLNKHIDAY",
"EVTPSGTWLTY",
"DLSPRWYFY",
"ITLATCELY",
"RQEEVQELY",
"ATCELYHY",
"VSLVKPSFY",
"LTALRLCAY",
"LTDEMIAQY",
"STECSNLLLQY",
"LADAGFIKQY",
"LIDLQELGKY",
"TSNQVAVLY",
"NIDGYFKIY",
"NLDSKVGGNY",
"NTSNQVAVLY",
"YSSANNCTFEY",
"SANNCTFEY",
"YTNSFTRGVYY",
"VADYSVLY",
"MTKTSVDCTMY",
"YTNSFTRGVY",
"RVDFCGKGY",
"SSANNCTFEY"]

peptides = [Peptide(peptide) for peptide in peptides]

opti_result = EpitopeAssembly(
        peptides, cleavage_predictor, solver="cbc"
    ).solve()

Log:

ERROR: Rule failed when generating expression for objective obj: ValueError:
    Error retrieving immutable Param value (w_ab[('SSPDDQIGYY',
    'SSANNCTFEY')]):
        The Param value is undefined and no default value is specified.
ERROR: Constructing component 'obj' from data=None failed: ValueError: Error
    retrieving immutable Param value (w_ab[('SSPDDQIGYY', 'SSANNCTFEY')]):
        The Param value is undefined and no default value is specified.
Traceback (most recent call last):
  File "code_no_alleles.py", line 64, in <module>
    peptides, cleavage_predictor, solver="cbc"
  File "/usr/local/lib/python2.7/site-packages/Fred2/EpitopeAssembly/EpitopeAssembly.py", line 132, in __init__
    sense=minimize)
  File "/usr/local/lib/python2.7/site-packages/pyomo/core/base/block.py", line 544, in __setattr__
    self.add_component(name, val)
  File "/usr/local/lib/python2.7/site-packages/pyomo/core/base/block.py", line 1089, in add_component
    val.construct(data)
  File "/usr/local/lib/python2.7/site-packages/pyomo/core/base/objective.py", line 357, in construct
    tmp = _init_rule(_self_parent)
  File "/usr/local/lib/python2.7/site-packages/Fred2/EpitopeAssembly/EpitopeAssembly.py", line 130, in <lambda>
    rule=lambda mode: sum( model.w_ab[a,b]*model.x[a,b] for a in model.E_prime
  File "/usr/local/lib/python2.7/site-packages/Fred2/EpitopeAssembly/EpitopeAssembly.py", line 131, in <genexpr>
    for b in model.E_prime if a != b),
  File "/usr/local/lib/python2.7/site-packages/pyomo/core/base/indexed_component.py", line 426, in __getitem__
    return self._getitem_when_not_present(index)
  File "/usr/local/lib/python2.7/site-packages/pyomo/core/base/param.py", line 518, in _getitem_when_not_present
    % ( idx_str,) )
ValueError: Error retrieving immutable Param value (w_ab[('SSPDDQIGYY', 'SSANNCTFEY')]):
        The Param value is undefined and no default value is specified.