Public Member Functions
def	__init__ (self)

def	read_cmdline_full (self, argv)

def	read_cmdline_erraser (self, argv)

def	read_cmdline_erraser_single_res (self, argv)

def	finalize (self)

Public Attributes
	input_pdb

	map_file

	out_pdb

	out_prefix

	map_reso

	rosetta_folder

	debug

	verbose

	kept_temp_folder

	use_existing_temp_folder

	new_torsional_potential

	corrected_geo

	rna_prot_erraser

	rosetta_bin

	rosetta_database

	log_out

	log_err

	nproc

	multiproc_minimize

	guarantee_no_DNA

	n_iterate

	rebuild_rmsd

	rebuild_all

	fixed_res

	cutpoint

	extra_res

	fixed_res_rs

	cutpoint_rs

	rebuild_res_pdb

	skip_single_res_minimize

	vary_geometry

	skip_minimize

	attempt_pyrimidine_flip

	constrain_phosphate

	res_slice

	native_screen_RMSD

	use_native_edensity_cutoff

	native_edensity_cutoff

	ideal_geometry

	allow_syn_pyrimidine

	include_native

	slice_nearby

	rebuild_res

	scoring_file

	cluster_RMSD

	is_append

	num_pose_kept

	num_pose_kept_cluster

	rebuild_res_list

	search_syn_pyrimidine_only_when_native_syn

	constrain_chi

	o2prime_legacy_mode

	use_2prime_OH_potential

	fcc2012_new_torsional_potential

	fcc2012_scoring_file

	enlarge_H_lj

Constructor & Destructor Documentation

◆ init()

def erraser_option.erraser_option.__init__ ( self )

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

Member Function Documentation

◆ finalize()

def erraser_option.erraser_option.finalize ( self )

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ read_cmdline_erraser()

def erraser_option.erraser_option.read_cmdline_erraser	(	self,
		argv
	)

◆ read_cmdline_erraser_single_res()

def erraser_option.erraser_option.read_cmdline_erraser_single_res	(	self,
		argv
	)

◆ read_cmdline_full()

def erraser_option.erraser_option.read_cmdline_full	(	self,
		argv
	)

Member Data Documentation

◆ allow_syn_pyrimidine

erraser_option.erraser_option.allow_syn_pyrimidine

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ attempt_pyrimidine_flip

erraser_option.erraser_option.attempt_pyrimidine_flip

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ cluster_RMSD

erraser_option.erraser_option.cluster_RMSD

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ constrain_chi

erraser_option.erraser_option.constrain_chi

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ constrain_phosphate

erraser_option.erraser_option.constrain_phosphate

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ corrected_geo

erraser_option.erraser_option.corrected_geo

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ cutpoint

erraser_option.erraser_option.cutpoint

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ cutpoint_rs

erraser_option.erraser_option.cutpoint_rs

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ debug

erraser_option.erraser_option.debug

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ enlarge_H_lj

erraser_option.erraser_option.enlarge_H_lj

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ extra_res

erraser_option.erraser_option.extra_res

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ fcc2012_new_torsional_potential

erraser_option.erraser_option.fcc2012_new_torsional_potential

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ fcc2012_scoring_file

erraser_option.erraser_option.fcc2012_scoring_file

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ fixed_res

erraser_option.erraser_option.fixed_res

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ fixed_res_rs

erraser_option.erraser_option.fixed_res_rs

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ guarantee_no_DNA

erraser_option.erraser_option.guarantee_no_DNA

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ ideal_geometry

erraser_option.erraser_option.ideal_geometry

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ include_native

erraser_option.erraser_option.include_native

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ input_pdb

erraser_option.erraser_option.input_pdb

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ is_append

erraser_option.erraser_option.is_append

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ kept_temp_folder

erraser_option.erraser_option.kept_temp_folder

Referenced by erraser_option.erraser_option.finalize(), and erraser_option.erraser_option.read_cmdline_full().

◆ log_err

erraser_option.erraser_option.log_err

◆ log_out

erraser_option.erraser_option.log_out

◆ map_file

erraser_option.erraser_option.map_file

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ map_reso

erraser_option.erraser_option.map_reso

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ multiproc_minimize

erraser_option.erraser_option.multiproc_minimize

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ n_iterate

erraser_option.erraser_option.n_iterate

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ native_edensity_cutoff

erraser_option.erraser_option.native_edensity_cutoff

Referenced by erraser_option.erraser_option.finalize(), and erraser_option.erraser_option.read_cmdline_full().

◆ native_screen_RMSD

erraser_option.erraser_option.native_screen_RMSD

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ new_torsional_potential

erraser_option.erraser_option.new_torsional_potential

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ nproc

erraser_option.erraser_option.nproc

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ num_pose_kept

erraser_option.erraser_option.num_pose_kept

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ num_pose_kept_cluster

erraser_option.erraser_option.num_pose_kept_cluster

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ o2prime_legacy_mode

erraser_option.erraser_option.o2prime_legacy_mode

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ out_pdb

erraser_option.erraser_option.out_pdb

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ out_prefix

erraser_option.erraser_option.out_prefix

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ rebuild_all

erraser_option.erraser_option.rebuild_all

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ rebuild_res

erraser_option.erraser_option.rebuild_res

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ rebuild_res_list

erraser_option.erraser_option.rebuild_res_list

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ rebuild_res_pdb

erraser_option.erraser_option.rebuild_res_pdb

Referenced by erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ rebuild_rmsd

erraser_option.erraser_option.rebuild_rmsd

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), and erraser_option.erraser_option.read_cmdline_full().

◆ res_slice

erraser_option.erraser_option.res_slice

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ rna_prot_erraser

erraser_option.erraser_option.rna_prot_erraser

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ rosetta_bin

erraser_option.erraser_option.rosetta_bin

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ rosetta_database

erraser_option.erraser_option.rosetta_database

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ rosetta_folder

erraser_option.erraser_option.rosetta_folder

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ scoring_file

erraser_option.erraser_option.scoring_file

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ search_syn_pyrimidine_only_when_native_syn

erraser_option.erraser_option.search_syn_pyrimidine_only_when_native_syn

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ skip_minimize

erraser_option.erraser_option.skip_minimize

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ skip_single_res_minimize

erraser_option.erraser_option.skip_single_res_minimize

Referenced by erraser_option.erraser_option.read_cmdline_erraser_single_res().

◆ slice_nearby

erraser_option.erraser_option.slice_nearby

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ use_2prime_OH_potential

erraser_option.erraser_option.use_2prime_OH_potential

Referenced by erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ use_existing_temp_folder

erraser_option.erraser_option.use_existing_temp_folder

Referenced by erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ use_native_edensity_cutoff

erraser_option.erraser_option.use_native_edensity_cutoff

Referenced by erraser_option.erraser_option.finalize(), erraser_option.erraser_option.read_cmdline_erraser(), erraser_option.erraser_option.read_cmdline_erraser_single_res(), and erraser_option.erraser_option.read_cmdline_full().

◆ vary_geometry

erraser_option.erraser_option.vary_geometry

Referenced by erraser_option.erraser_option.read_cmdline_full().

◆ verbose

erraser_option.erraser_option.verbose

Referenced by erraser_option.erraser_option.finalize(), and erraser_option.erraser_option.read_cmdline_full().

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

src/apps/public/ERRASER/erraser_option.py

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ finalize()

◆ read_cmdline_erraser()

◆ read_cmdline_erraser_single_res()

◆ read_cmdline_full()

Member Data Documentation

◆ allow_syn_pyrimidine

◆ attempt_pyrimidine_flip

◆ cluster_RMSD

◆ constrain_chi

◆ constrain_phosphate

◆ corrected_geo

◆ cutpoint

◆ cutpoint_rs

◆ debug

◆ enlarge_H_lj

◆ extra_res

◆ fcc2012_new_torsional_potential

◆ fcc2012_scoring_file

◆ fixed_res

◆ fixed_res_rs

◆ guarantee_no_DNA

◆ ideal_geometry

◆ include_native

◆ input_pdb

◆ is_append

◆ kept_temp_folder

◆ log_err

◆ log_out

◆ map_file

◆ map_reso

◆ multiproc_minimize

◆ n_iterate

◆ native_edensity_cutoff

◆ native_screen_RMSD

◆ new_torsional_potential

◆ nproc

◆ num_pose_kept

◆ num_pose_kept_cluster

◆ o2prime_legacy_mode

◆ out_pdb

◆ out_prefix

◆ rebuild_all

◆ rebuild_res

◆ rebuild_res_list

◆ rebuild_res_pdb

◆ rebuild_rmsd

◆ res_slice

◆ rna_prot_erraser

◆ rosetta_bin

◆ rosetta_database

◆ rosetta_folder

◆ scoring_file

◆ search_syn_pyrimidine_only_when_native_syn

◆ skip_minimize

◆ skip_single_res_minimize

◆ slice_nearby

◆ use_2prime_OH_potential

◆ use_existing_temp_folder

◆ use_native_edensity_cutoff

◆ vary_geometry

◆ verbose

◆ init()