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mutant_modeler.MutantModeler Class Reference

Public Member Functions

def __init__
 
def set_wt_RNA_secstruct
 
def set_run_locally
 
def get_mut_positions
 
def add_mutant
 
def set_cmd_opts
 
def set_sfxn
 
def set_protein_pack_reps
 
def set_rosetta_prefix
 
def write_mutfile
 
def figure_out_protein_pack_reps
 
def get_low_res_command_lines
 
def get_med_res_command_lines
 
def get_high_res_command_lines
 
def make_high_res_subsets_and_cmd_lines
 
def get_command_lines
 

Public Attributes

 wt_struct
 
 method
 
 run_local
 
 mutant_seqs
 
 high_res_WT_rebuild
 
 med_res_WT_rebuild
 
 compare_to_full_WT
 
 wt_pdb_tag
 
 wt_RNA_secstruct
 
 mutant_index
 
 cmd_opts
 
 sfxn
 
 protein_pack_reps
 
 rosetta_prefix
 
 wt_base_pairs
 
 map_RNA_index_to_full
 
 mutant_subsets
 

Detailed Description

Class in charge of making mutants of a given WT structure
Generates commands that will make mutant structures
starting from a 'WT' structure
Uses either the low-res, med-res, or high-res protocols

Constructor & Destructor Documentation

def mutant_modeler.MutantModeler.__init__ (   self,
  method,
  wt_struct 
)

Member Function Documentation

def mutant_modeler.MutantModeler.add_mutant (   self,
  seq 
)
def mutant_modeler.MutantModeler.figure_out_protein_pack_reps (   self,
  index 
)
def mutant_modeler.MutantModeler.get_command_lines (   self,
  index 
)
def mutant_modeler.MutantModeler.get_high_res_command_lines (   self,
  index 
)
def mutant_modeler.MutantModeler.get_low_res_command_lines (   self,
  index 
)
def mutant_modeler.MutantModeler.get_med_res_command_lines (   self,
  index 
)
def mutant_modeler.MutantModeler.get_mut_positions (   self,
  seq 
)
def mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines (   self,
  index,
  mut_subsets,
  mutant_seq_full,
  native_pdb,
  mut_depends 
)
def mutant_modeler.MutantModeler.set_cmd_opts (   self,
  cmd_opts 
)
def mutant_modeler.MutantModeler.set_protein_pack_reps (   self,
  protein_pack_reps 
)
def mutant_modeler.MutantModeler.set_rosetta_prefix (   self,
  prefix 
)
def mutant_modeler.MutantModeler.set_run_locally (   self,
  value 
)
def mutant_modeler.MutantModeler.set_sfxn (   self,
  sfxn 
)
def mutant_modeler.MutantModeler.set_wt_RNA_secstruct (   self,
  secstruct 
)
def mutant_modeler.MutantModeler.write_mutfile (   self,
  mut_indices,
  mutant_seq,
  input_file,
  mfil_name 
)

Member Data Documentation

mutant_modeler.MutantModeler.cmd_opts
mutant_modeler.MutantModeler.compare_to_full_WT
mutant_modeler.MutantModeler.high_res_WT_rebuild
mutant_modeler.MutantModeler.map_RNA_index_to_full
mutant_modeler.MutantModeler.med_res_WT_rebuild
mutant_modeler.MutantModeler.method
mutant_modeler.MutantModeler.mutant_index
mutant_modeler.MutantModeler.mutant_seqs
mutant_modeler.MutantModeler.mutant_subsets
mutant_modeler.MutantModeler.protein_pack_reps
mutant_modeler.MutantModeler.rosetta_prefix
mutant_modeler.MutantModeler.run_local
mutant_modeler.MutantModeler.sfxn
mutant_modeler.MutantModeler.wt_base_pairs
mutant_modeler.MutantModeler.wt_pdb_tag
mutant_modeler.MutantModeler.wt_RNA_secstruct
mutant_modeler.MutantModeler.wt_struct

The documentation for this class was generated from the following file: