Rosetta  2020.37
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Functions
tcrmodel Namespace Reference

Functions

BooleanOptionKey const tcrmodel ("tcrmodel")
 
FileOptionKey const ignore_list ("tcrmodel:ignore_list")
 
RealOptionKey const blastp_identity_cutoff ("tcrmodel:blastp_identity_cutoff")
 
RealOptionKey const template_identity_cutoff ("tcrmodel:template_identity_cutoff")
 
BooleanOptionKey const include_ab_templates ("tcrmodel:include_ab_templates")
 
BooleanOptionKey const dump_templates ("tcrmodel:dump_templates")
 
BooleanOptionKey const skip_modeling ("tcrmodel:skip_modeling")
 
StringOptionKey const ab_template_db_path ("tcrmodel:ab_template_db_path")
 
StringOptionKey const tcr_template_db_path ("tcrmodel:tcr_template_db_path")
 
BooleanOptionKey const minimize_model ("tcrmodel:minimize_model")
 
BooleanOptionKey const relax_model ("tcrmodel:relax_model")
 
BooleanOptionKey const remodel_loop_cdr3a ("tcrmodel:remodel_loop_cdr3a")
 
BooleanOptionKey const remodel_loop_cdr3b ("tcrmodel:remodel_loop_cdr3b")
 
BooleanOptionKey const remodel_tcr_cdr3a_loop ("tcrmodel:remodel_tcr_cdr3a_loop")
 
BooleanOptionKey const remodel_tcr_cdr3b_loop ("tcrmodel:remodel_tcr_cdr3b_loop")
 
BooleanOptionKey const refine_tcr_cdr3a_loop ("tcrmodel:refine_tcr_cdr3a_loop")
 
BooleanOptionKey const refine_tcr_cdr3b_loop ("tcrmodel:refine_tcr_cdr3b_loop")
 
BooleanOptionKey const remodel_tcr_cdr3_loops ("tcrmodel:remodel_tcr_cdr3_loops")
 
BooleanOptionKey const refine_tcr_cdr3_loops ("tcrmodel:refine_tcr_cdr3_loops")
 
BooleanOptionKey const refine_all_tcr_cdr_loops ("tcrmodel:refine_all_tcr_cdr_loops")
 
BooleanOptionKey const use_user_templates ("tcrmodel:use_user_templates")
 
StringOptionKey const alpha_framework_template_id ("tcrmodel:alpha_framework_template_id")
 
StringOptionKey const beta_framework_template_id ("tcrmodel:beta_framework_template_id")
 
StringOptionKey const alpha_germline_template_id ("tcrmodel:alpha_germline_template_id")
 
StringOptionKey const beta_germline_template_id ("tcrmodel:beta_germline_template_id")
 
StringOptionKey const alpha_cdr1_template_id ("tcrmodel:alpha_cdr1_template_id")
 
StringOptionKey const beta_cdr1_template_id ("tcrmodel:beta_cdr1_template_id")
 
StringOptionKey const alpha_cdr2_template_id ("tcrmodel:alpha_cdr2_template_id")
 
StringOptionKey const beta_cdr2_template_id ("tcrmodel:beta_cdr2_template_id")
 
StringOptionKey const alpha_cdr3_template_id ("tcrmodel:alpha_cdr3_template_id")
 
StringOptionKey const beta_cdr3_template_id ("tcrmodel:beta_cdr3_template_id")
 
StringOptionKey const alpha_orientation_template_id ("tcrmodel:alpha_orientation_template_id")
 
StringOptionKey const beta_orientation_template_id ("tcrmodel:beta_orientation_template_id")
 
StringOptionKey const alpha_framework_template_pdb ("tcrmodel:alpha_framework_template_pdb")
 
StringOptionKey const beta_framework_template_pdb ("tcrmodel:beta_framework_template_pdb")
 
StringOptionKey const alpha_germline_template_pdb ("tcrmodel:alpha_germline_template_pdb")
 
StringOptionKey const beta_germline_template_pdb ("tcrmodel:beta_germline_template_pdb")
 
StringOptionKey const alpha_cdr1_template_pdb ("tcrmodel:alpha_cdr1_template_pdb")
 
StringOptionKey const beta_cdr1_template_pdb ("tcrmodel:beta_cdr1_template_pdb")
 
StringOptionKey const alpha_cdr2_template_pdb ("tcrmodel:alpha_cdr2_template_pdb")
 
StringOptionKey const beta_cdr2_template_pdb ("tcrmodel:beta_cdr2_template_pdb")
 
StringOptionKey const alpha_cdr3_template_pdb ("tcrmodel:alpha_cdr3_template_pdb")
 
StringOptionKey const beta_cdr3_template_pdb ("tcrmodel:beta_cdr3_template_pdb")
 
StringOptionKey const alpha_orientation_template_pdb ("tcrmodel:alpha_orientation_template_pdb")
 
StringOptionKey const beta_orientation_template_pdb ("tcrmodel:beta_orientation_template_pdb")
 
BooleanOptionKey const use_alpha_germline_templates ("tcrmodel:use_alpha_germline_templates")
 
BooleanOptionKey const use_beta_germline_templates ("tcrmodel:use_beta_germline_templates")
 
BooleanOptionKey const assign_cdr ("tcrmodel:assign_cdr")
 
StringOptionKey const assign_cdr1a ("tcrmodel:assign_cdr1a")
 
StringOptionKey const assign_cdr2a ("tcrmodel:assign_cdr2a")
 
StringOptionKey const assign_cdr3a ("tcrmodel:assign_cdr3a")
 
StringOptionKey const assign_cdr1b ("tcrmodel:assign_cdr1b")
 
StringOptionKey const assign_cdr2b ("tcrmodel:assign_cdr2b")
 
StringOptionKey const assign_cdr3b ("tcrmodel:assign_cdr3b")
 
StringOptionKey const anarci_path ("tcrmodel:anarci_path")
 

Function Documentation

StringOptionKey const tcrmodel::ab_template_db_path ( "tcrmodel:ab_template_db_path"  )
StringOptionKey const tcrmodel::alpha_cdr1_template_id ( "tcrmodel:alpha_cdr1_template_id"  )
StringOptionKey const tcrmodel::alpha_cdr1_template_pdb ( "tcrmodel:alpha_cdr1_template_pdb"  )
StringOptionKey const tcrmodel::alpha_cdr2_template_id ( "tcrmodel:alpha_cdr2_template_id"  )
StringOptionKey const tcrmodel::alpha_cdr2_template_pdb ( "tcrmodel:alpha_cdr2_template_pdb"  )
StringOptionKey const tcrmodel::alpha_cdr3_template_id ( "tcrmodel:alpha_cdr3_template_id"  )
StringOptionKey const tcrmodel::alpha_cdr3_template_pdb ( "tcrmodel:alpha_cdr3_template_pdb"  )
StringOptionKey const tcrmodel::alpha_framework_template_id ( "tcrmodel:alpha_framework_template_id"  )
StringOptionKey const tcrmodel::alpha_framework_template_pdb ( "tcrmodel:alpha_framework_template_pdb"  )
StringOptionKey const tcrmodel::alpha_germline_template_id ( "tcrmodel:alpha_germline_template_id"  )
StringOptionKey const tcrmodel::alpha_germline_template_pdb ( "tcrmodel:alpha_germline_template_pdb"  )
StringOptionKey const tcrmodel::alpha_orientation_template_id ( "tcrmodel:alpha_orientation_template_id"  )
StringOptionKey const tcrmodel::alpha_orientation_template_pdb ( "tcrmodel:alpha_orientation_template_pdb"  )
StringOptionKey const tcrmodel::anarci_path ( "tcrmodel:anarci_path"  )
BooleanOptionKey const tcrmodel::assign_cdr ( "tcrmodel:assign_cdr"  )
StringOptionKey const tcrmodel::assign_cdr1a ( "tcrmodel:assign_cdr1a"  )
StringOptionKey const tcrmodel::assign_cdr1b ( "tcrmodel:assign_cdr1b"  )
StringOptionKey const tcrmodel::assign_cdr2a ( "tcrmodel:assign_cdr2a"  )
StringOptionKey const tcrmodel::assign_cdr2b ( "tcrmodel:assign_cdr2b"  )
StringOptionKey const tcrmodel::assign_cdr3a ( "tcrmodel:assign_cdr3a"  )
StringOptionKey const tcrmodel::assign_cdr3b ( "tcrmodel:assign_cdr3b"  )
StringOptionKey const tcrmodel::beta_cdr1_template_id ( "tcrmodel:beta_cdr1_template_id"  )
StringOptionKey const tcrmodel::beta_cdr1_template_pdb ( "tcrmodel:beta_cdr1_template_pdb"  )
StringOptionKey const tcrmodel::beta_cdr2_template_id ( "tcrmodel:beta_cdr2_template_id"  )
StringOptionKey const tcrmodel::beta_cdr2_template_pdb ( "tcrmodel:beta_cdr2_template_pdb"  )
StringOptionKey const tcrmodel::beta_cdr3_template_id ( "tcrmodel:beta_cdr3_template_id"  )
StringOptionKey const tcrmodel::beta_cdr3_template_pdb ( "tcrmodel:beta_cdr3_template_pdb"  )
StringOptionKey const tcrmodel::beta_framework_template_id ( "tcrmodel:beta_framework_template_id"  )
StringOptionKey const tcrmodel::beta_framework_template_pdb ( "tcrmodel:beta_framework_template_pdb"  )
StringOptionKey const tcrmodel::beta_germline_template_id ( "tcrmodel:beta_germline_template_id"  )
StringOptionKey const tcrmodel::beta_germline_template_pdb ( "tcrmodel:beta_germline_template_pdb"  )
StringOptionKey const tcrmodel::beta_orientation_template_id ( "tcrmodel:beta_orientation_template_id"  )
StringOptionKey const tcrmodel::beta_orientation_template_pdb ( "tcrmodel:beta_orientation_template_pdb"  )
RealOptionKey const tcrmodel::blastp_identity_cutoff ( "tcrmodel:blastp_identity_cutoff"  )
BooleanOptionKey const tcrmodel::dump_templates ( "tcrmodel:dump_templates"  )
FileOptionKey const tcrmodel::ignore_list ( "tcrmodel:ignore_list"  )
BooleanOptionKey const tcrmodel::include_ab_templates ( "tcrmodel:include_ab_templates"  )
BooleanOptionKey const tcrmodel::minimize_model ( "tcrmodel:minimize_model"  )
BooleanOptionKey const tcrmodel::refine_all_tcr_cdr_loops ( "tcrmodel:refine_all_tcr_cdr_loops"  )
BooleanOptionKey const tcrmodel::refine_tcr_cdr3_loops ( "tcrmodel:refine_tcr_cdr3_loops"  )
BooleanOptionKey const tcrmodel::refine_tcr_cdr3a_loop ( "tcrmodel:refine_tcr_cdr3a_loop"  )
BooleanOptionKey const tcrmodel::refine_tcr_cdr3b_loop ( "tcrmodel:refine_tcr_cdr3b_loop"  )
BooleanOptionKey const tcrmodel::relax_model ( "tcrmodel:relax_model"  )
BooleanOptionKey const tcrmodel::remodel_loop_cdr3a ( "tcrmodel:remodel_loop_cdr3a"  )
BooleanOptionKey const tcrmodel::remodel_loop_cdr3b ( "tcrmodel:remodel_loop_cdr3b"  )
BooleanOptionKey const tcrmodel::remodel_tcr_cdr3_loops ( "tcrmodel:remodel_tcr_cdr3_loops"  )
BooleanOptionKey const tcrmodel::remodel_tcr_cdr3a_loop ( "tcrmodel:remodel_tcr_cdr3a_loop"  )
BooleanOptionKey const tcrmodel::remodel_tcr_cdr3b_loop ( "tcrmodel:remodel_tcr_cdr3b_loop"  )
BooleanOptionKey const tcrmodel::skip_modeling ( "tcrmodel:skip_modeling"  )
StringOptionKey const tcrmodel::tcr_template_db_path ( "tcrmodel:tcr_template_db_path"  )
BooleanOptionKey const tcrmodel::tcrmodel ( "tcrmodel"  )
RealOptionKey const tcrmodel::template_identity_cutoff ( "tcrmodel:template_identity_cutoff"  )
BooleanOptionKey const tcrmodel::use_alpha_germline_templates ( "tcrmodel:use_alpha_germline_templates"  )
BooleanOptionKey const tcrmodel::use_beta_germline_templates ( "tcrmodel:use_beta_germline_templates"  )
BooleanOptionKey const tcrmodel::use_user_templates ( "tcrmodel:use_user_templates"  )