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
	)

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

Member Function Documentation

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.

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

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(), and mutant_modeler.MutantModeler.method.

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(), util.get_surrounding_res(), mutant_modeler.MutantModeler.high_res_WT_rebuild, fmt.join(), ObjexxFCL.len(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), mutant_modeler.MutantModeler.mutant_seqs, mutant_modeler.MutantModeler.mutant_subsets, basic::database.open(), basic::options::OptionKeys::relax::range.range, mutant_modeler.MutantModeler.rosetta_prefix, 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().

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(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

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(), fmt.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(), basic::options::OptionKeys::relax::range.range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, mutant_modeler.MutantModeler.sfxn, 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().

def mutant_modeler.MutantModeler.get_mut_positions	(		self,
			seq
	)

References mutant_modeler.MutantModeler.compare_to_full_WT, ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.

Referenced by mutant_modeler.MutantModeler.add_mutant().

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(), fmt.join(), ObjexxFCL.len(), DRRAFTER_util.make_tag_with_dashes(), basic::database.open(), basic::options::OptionKeys::relax::range.range, mutant_modeler.MutantModeler.rosetta_prefix, mutant_modeler.MutantModeler.run_local, mutant_modeler.MutantModeler.sfxn, mutant_modeler.MutantModeler.wt_pdb_tag, and mutant_modeler.MutantModeler.wt_struct.

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines().

def mutant_modeler.MutantModeler.set_cmd_opts	(		self,
			cmd_opts
	)

References mutant_modeler.MutantModeler.cmd_opts.

def mutant_modeler.MutantModeler.set_protein_pack_reps	(		self,
			protein_pack_reps
	)

References mutant_modeler.MutantModeler.protein_pack_reps.

def mutant_modeler.MutantModeler.set_rosetta_prefix	(		self,
			prefix
	)

References mutant_modeler.MutantModeler.rosetta_prefix.

def mutant_modeler.MutantModeler.set_run_locally	(		self,
			value
	)

References mutant_modeler.MutantModeler.run_local.

def mutant_modeler.MutantModeler.set_sfxn	(		self,
			sfxn
	)

References mutant_modeler.MutantModeler.sfxn.

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.

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(), and mutant_modeler.MutantModeler.get_med_res_command_lines().

Member Data Documentation

mutant_modeler.MutantModeler.cmd_opts

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(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_cmd_opts().

mutant_modeler.MutantModeler.compare_to_full_WT

Referenced by 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().

mutant_modeler.MutantModeler.high_res_WT_rebuild

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines().

mutant_modeler.MutantModeler.map_RNA_index_to_full

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

mutant_modeler.MutantModeler.med_res_WT_rebuild

Referenced by mutant_modeler.MutantModeler.get_med_res_command_lines().

mutant_modeler.MutantModeler.method

Referenced by mutant_modeler.MutantModeler.get_command_lines().

mutant_modeler.MutantModeler.mutant_index

Referenced by mutant_modeler.MutantModeler.add_mutant().

mutant_modeler.MutantModeler.mutant_seqs

Referenced by 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_modeler.MutantModeler.mutant_subsets

Referenced by mutant_modeler.MutantModeler.get_high_res_command_lines().

mutant_modeler.MutantModeler.protein_pack_reps

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

mutant_modeler.MutantModeler.rosetta_prefix

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(), mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines(), and mutant_modeler.MutantModeler.set_rosetta_prefix().

mutant_modeler.MutantModeler.run_local

Referenced by 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().

mutant_modeler.MutantModeler.sfxn

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

mutant_modeler.MutantModeler.wt_base_pairs

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

mutant_modeler.MutantModeler.wt_pdb_tag

Referenced by mutant_modeler.MutantModeler.make_high_res_subsets_and_cmd_lines().

mutant_modeler.MutantModeler.wt_RNA_secstruct

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

mutant_modeler.MutantModeler.wt_struct

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.make_high_res_subsets_and_cmd_lines().

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

• src/apps/public/rnp_ddg/mutant_modeler.py