mutant_modeler.MutantModeler Class Reference

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

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

__init__() [1/2]

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

Referenced by mutant_modeler.MutantModeler.__init__(), and pyrosetta.distributed.tasks.taskbase.TaskBase.__setstate__().

__init__() [2/2]

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

References mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.figure_out_WT_seq(), mutant_modeler.find_pairs(), mutant_modeler.MutantModeler.high_res_WT_rebuild, ObjexxFCL.len(), 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, range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), mutant_modeler.MutantModeler.sfxn, mutant_modeler.MutantModeler.wt_base_pairs, mutant_modeler.MutantModeler.wt_pdb_tag, mutant_modeler.MutantModeler.wt_RNA_secstruct, and mutant_modeler.MutantModeler.wt_struct.

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase.__setstate__().

Member Function Documentation

add_mutant() [1/2]

def mutant_modeler.MutantModeler.add_mutant	(		self,
			seq
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.get_mut_positions(), ObjexxFCL.len(), mutant_modeler.MutantModeler.mutant_index, and mutant_modeler.MutantModeler.mutant_seqs.

Referenced by mutant_modeler.MutantModeler.add_mutant().

add_mutant() [2/2]

def mutant_modeler.MutantModeler.add_mutant	(		self,
			seq
	)

References mutant_modeler.MutantModeler.add_mutant(), mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.get_mut_positions(), ObjexxFCL.len(), mutant_modeler.MutantModeler.mutant_index, and mutant_modeler.MutantModeler.mutant_seqs.

figure_out_protein_pack_reps() [1/2]

def mutant_modeler.MutantModeler.figure_out_protein_pack_reps	(		self,
			index
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, ObjexxFCL.len(), mutant_modeler.MutantModeler.mutant_seqs, and mutant_modeler.MutantModeler.protein_pack_reps.

Referenced by mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

figure_out_protein_pack_reps() [2/2]

def mutant_modeler.MutantModeler.figure_out_protein_pack_reps	(		self,
			index
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), ObjexxFCL.len(), mutant_modeler.MutantModeler.mutant_seqs, and mutant_modeler.MutantModeler.protein_pack_reps.

Referenced by mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

get_command_lines() [1/2]

def mutant_modeler.MutantModeler.get_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.method, and str().

Referenced by mutant_modeler.MutantModeler.get_command_lines().

get_command_lines() [2/2]

def mutant_modeler.MutantModeler.get_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.get_command_lines(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.method, and str().

get_high_res_command_lines() [1/2]

def mutant_modeler.MutantModeler.get_high_res_command_lines	(		self,
			index
	)

References numeric.add(), mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.high_res_WT_rebuild, enumerate_junctions.int, join(), ObjexxFCL.len(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), mutant_modeler.MutantModeler.map_RNA_index_to_full, mutant_modeler.MutantModeler.mutant_seqs, mutant_modeler.MutantModeler.mutant_subsets, basic::database.open(), range, mutant_modeler.MutantModeler.rosetta_prefix, set(), str(), test.T040_Types.values, mutant_modeler.MutantModeler.write_mutfile(), mutant_modeler.MutantModeler.wt_RNA_secstruct, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines(), and mutant_modeler.MutantModeler.get_high_res_command_lines().

get_high_res_command_lines() [2/2]

def mutant_modeler.MutantModeler.get_high_res_command_lines	(		self,
			index
	)

References numeric.add(), mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), util.get_surrounding_res(), mutant_modeler.MutantModeler.high_res_WT_rebuild, enumerate_junctions.int, join(), ObjexxFCL.len(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), mutant_modeler.MutantModeler.map_RNA_index_to_full, mutant_modeler.MutantModeler.mutant_seqs, mutant_modeler.MutantModeler.mutant_subsets, basic::database.open(), print(), range, mutant_modeler.MutantModeler.rosetta_prefix, set(), str(), test.T040_Types.values, mutant_modeler.MutantModeler.write_mutfile(), mutant_modeler.MutantModeler.wt_RNA_secstruct, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines().

get_low_res_command_lines() [1/2]

def mutant_modeler.MutantModeler.get_low_res_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.mutant_seqs, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.write_mutfile(), and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

get_low_res_command_lines() [2/2]

def mutant_modeler.MutantModeler.get_low_res_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.mutant_seqs, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.write_mutfile(), and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines(), mutant_modeler.MutantModeler.get_high_res_command_lines(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

get_med_res_command_lines() [1/2]

def mutant_modeler.MutantModeler.get_med_res_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_low_res_command_lines(), join(), ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, mutant_modeler.list_NC_BPs(), mutant_modeler.MutantModeler.map_RNA_index_to_full, mutant_modeler.MutantModeler.med_res_WT_rebuild, mutant_modeler.MutantModeler.mutant_seqs, basic::database.open(), range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, set(), InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), mutant_modeler.MutantModeler.sfxn, str(), test.T040_Types.values, mutant_modeler.MutantModeler.write_mutfile(), mutant_modeler.MutantModeler.wt_base_pairs, mutant_modeler.MutantModeler.wt_RNA_secstruct, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

get_med_res_command_lines() [2/2]

def mutant_modeler.MutantModeler.get_med_res_command_lines	(		self,
			index
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), join(), ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, mutant_modeler.list_NC_BPs(), mutant_modeler.MutantModeler.map_RNA_index_to_full, mutant_modeler.MutantModeler.med_res_WT_rebuild, mutant_modeler.MutantModeler.mutant_seqs, basic::database.open(), range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, set(), InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), mutant_modeler.MutantModeler.sfxn, str(), test.T040_Types.values, mutant_modeler.MutantModeler.write_mutfile(), mutant_modeler.MutantModeler.wt_base_pairs, mutant_modeler.MutantModeler.wt_RNA_secstruct, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_command_lines().

get_mut_positions() [1/2]

def mutant_modeler.MutantModeler.get_mut_positions	(		self,
			seq
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, ObjexxFCL.len(), and range.

Referenced by mutant_modeler.MutantModeler.add_mutant(), and mutant_modeler.MutantModeler.get_mut_positions().

get_mut_positions() [2/2]

def mutant_modeler.MutantModeler.get_mut_positions	(		self,
			seq
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, mutant_modeler.MutantModeler.get_mut_positions(), ObjexxFCL.len(), and range.

Referenced by mutant_modeler.MutantModeler.add_mutant().

make_high_res_subsets_and_cmd_lines() [1/2]

def mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines	(		self,
			index,
			mut_subsets,
			mutant_seq_full,
			native_pdb,
			mut_depends
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), join(), ObjexxFCL.len(), DRRAFTER_util.make_tag_with_dashes(), basic::database.open(), range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), mutant_modeler.MutantModeler.sfxn, str(), mutant_modeler.MutantModeler.wt_pdb_tag, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines(), and mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

make_high_res_subsets_and_cmd_lines() [2/2]

def mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines	(		self,
			index,
			mut_subsets,
			mutant_seq_full,
			native_pdb,
			mut_depends
	)

References mutant_modeler.MutantModeler.cmd_opts, mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), join(), ObjexxFCL.len(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), DRRAFTER_util.make_tag_with_dashes(), basic::database.open(), range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), mutant_modeler.MutantModeler.sfxn, str(), mutant_modeler.MutantModeler.wt_pdb_tag, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines().

set_cmd_opts() [1/2]

def mutant_modeler.MutantModeler.set_cmd_opts	(		self,
			cmd_opts
	)

References mutant_modeler.MutantModeler.cmd_opts.

Referenced by mutant_modeler.MutantModeler.set_cmd_opts().

set_cmd_opts() [2/2]

def mutant_modeler.MutantModeler.set_cmd_opts	(		self,
			cmd_opts
	)

References mutant_modeler.MutantModeler.cmd_opts, and mutant_modeler.MutantModeler.set_cmd_opts().

set_protein_pack_reps() [1/2]

def mutant_modeler.MutantModeler.set_protein_pack_reps	(		self,
			protein_pack_reps
	)

References mutant_modeler.MutantModeler.protein_pack_reps.

Referenced by mutant_modeler.MutantModeler.set_protein_pack_reps().

set_protein_pack_reps() [2/2]

def mutant_modeler.MutantModeler.set_protein_pack_reps	(		self,
			protein_pack_reps
	)

References mutant_modeler.MutantModeler.protein_pack_reps, and mutant_modeler.MutantModeler.set_protein_pack_reps().

set_rosetta_prefix() [1/2]

def mutant_modeler.MutantModeler.set_rosetta_prefix	(		self,
			prefix
	)

References mutant_modeler.MutantModeler.rosetta_prefix.

Referenced by mutant_modeler.MutantModeler.set_rosetta_prefix().

set_rosetta_prefix() [2/2]

def mutant_modeler.MutantModeler.set_rosetta_prefix	(		self,
			prefix
	)

References mutant_modeler.MutantModeler.rosetta_prefix, and mutant_modeler.MutantModeler.set_rosetta_prefix().

set_run_locally() [1/2]

def mutant_modeler.MutantModeler.set_run_locally	(		self,
			value
	)

References mutant_modeler.MutantModeler.run_local.

Referenced by mutant_modeler.MutantModeler.set_run_locally().

set_run_locally() [2/2]

def mutant_modeler.MutantModeler.set_run_locally	(		self,
			value
	)

References mutant_modeler.MutantModeler.run_local, and mutant_modeler.MutantModeler.set_run_locally().

set_sfxn() [1/2]

def mutant_modeler.MutantModeler.set_sfxn	(		self,
			sfxn
	)

References InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), and mutant_modeler.MutantModeler.sfxn.

Referenced by mutant_modeler.MutantModeler.set_sfxn().

set_sfxn() [2/2]

def mutant_modeler.MutantModeler.set_sfxn	(		self,
			sfxn
	)

References mutant_modeler.MutantModeler.set_sfxn(), InterfaceDDGMover.sfxn(), ScoreFunctionFingerprintMover.sfxn(), and mutant_modeler.MutantModeler.sfxn.

set_wt_RNA_secstruct() [1/2]

def mutant_modeler.MutantModeler.set_wt_RNA_secstruct	(		self,
			secstruct
	)

References mutant_modeler.find_pairs(), mutant_modeler.MutantModeler.wt_base_pairs, and mutant_modeler.MutantModeler.wt_RNA_secstruct.

Referenced by mutant_modeler.MutantModeler.set_wt_RNA_secstruct().

set_wt_RNA_secstruct() [2/2]

def mutant_modeler.MutantModeler.set_wt_RNA_secstruct	(		self,
			secstruct
	)

References mutant_modeler.find_pairs(), mutant_modeler.MutantModeler.set_wt_RNA_secstruct(), mutant_modeler.MutantModeler.wt_base_pairs, and mutant_modeler.MutantModeler.wt_RNA_secstruct.

write_mutfile() [1/2]

def mutant_modeler.MutantModeler.write_mutfile	(		self,
			mut_indices,
			mutant_seq,
			input_file,
			mfil_name
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, ObjexxFCL.len(), mutant_modeler.MutantModeler.map_RNA_index_to_full, and basic::database.open().

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.write_mutfile().

write_mutfile() [2/2]

def mutant_modeler.MutantModeler.write_mutfile	(		self,
			mut_indices,
			mutant_seq,
			input_file,
			mfil_name
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, ObjexxFCL.len(), mutant_modeler.MutantModeler.map_RNA_index_to_full, basic::database.open(), and mutant_modeler.MutantModeler.write_mutfile().

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

Member Data Documentation

cmd_opts

mutant_modeler.MutantModeler.cmd_opts

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_cmd_opts().

compare_to_full_WT

mutant_modeler.MutantModeler.compare_to_full_WT

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.add_mutant(), mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.get_mut_positions(), and mutant_modeler.MutantModeler.write_mutfile().

high_res_WT_rebuild

mutant_modeler.MutantModeler.high_res_WT_rebuild

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.get_high_res_command_lines().

map_RNA_index_to_full

mutant_modeler.MutantModeler.map_RNA_index_to_full

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.write_mutfile().

med_res_WT_rebuild

mutant_modeler.MutantModeler.med_res_WT_rebuild

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

method

mutant_modeler.MutantModeler.method

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.get_command_lines().

mutant_index

mutant_modeler.MutantModeler.mutant_index

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.add_mutant().

mutant_seqs

mutant_modeler.MutantModeler.mutant_seqs

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.add_mutant(), mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

mutant_subsets

mutant_modeler.MutantModeler.mutant_subsets

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.get_high_res_command_lines().

protein_pack_reps

mutant_modeler.MutantModeler.protein_pack_reps

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.figure_out_protein_pack_reps(), and mutant_modeler.MutantModeler.set_protein_pack_reps().

rosetta_prefix

mutant_modeler.MutantModeler.rosetta_prefix

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_rosetta_prefix().

run_local

mutant_modeler.MutantModeler.run_local

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_run_locally().

sfxn

mutant_modeler.MutantModeler.sfxn

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_med_res_command_lines(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_sfxn().

wt_base_pairs

mutant_modeler.MutantModeler.wt_base_pairs

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.set_wt_RNA_secstruct().

wt_pdb_tag

mutant_modeler.MutantModeler.wt_pdb_tag

Referenced by mutant_modeler.MutantModeler.__init__(), and mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

wt_RNA_secstruct

mutant_modeler.MutantModeler.wt_RNA_secstruct

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.set_wt_RNA_secstruct().

wt_struct

mutant_modeler.MutantModeler.wt_struct

Referenced by mutant_modeler.MutantModeler.__init__(), mutant_modeler.MutantModeler.get_high_res_command_lines(), mutant_modeler.MutantModeler.get_low_res_command_lines(), mutant_modeler.MutantModeler.get_med_res_command_lines(), and mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

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

• src/apps/pilot/kkappel/old_ddg_scripts/mutant_modeler.py