X-lab-3D / PANDORA

MODELLER-based, anchor restrained, Peptide-MHC Modelling pipeline
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setting the anchor points to '0,8' does not lead to an exception #280

Open cbaakman opened 1 week ago

cbaakman commented 1 week ago

Code:

 28 def run_case(args):
 29 
 30     id_, peptide = args
 31 
 32     allele_type = "HLA-A*0201"
 33 
 34     _log.debug(f"run case {allele_type} {peptide}")
 35 
 36     target = Target(
 37         id_,
 38         allele_type=allele_type,
 39         peptide=peptide,
 40         MHC_class="I",
 41         use_netmhcpan=True,
 42         output_dir="/home/cbaakman/pandora-models",
 43         anchors=[0,8],
 44     )
 45 
 46     forbidden_cluster = cluster_per_peptide[peptide]
 47 
 48     find_template_result, find_template_scores, keep_IL = find_template(target, db, best_n_templates=1000)
 49     templates = []
 50     for template in find_template_result:
 51         if template.peptide not in cluster_per_peptide or cluster_per_peptide[template.peptide] != forbidden_cluster:
 52             templates.append(template)
 53 
 54     case = Pandora(target, db, template=templates[0])
 55 
 56     case.model()

When I use this function, PANDORA builds the model, but the anchor isn't restrained.

DarioMarzella commented 1 week ago

Thanks for reporting this @cbaakman . Will add an exception for the new version release.