erraser_option.erraser_option Class Reference

Public Member Functions
def	__init__
def	read_cmdline_full
def	read_cmdline_erraser
def	read_cmdline_erraser_single_res
def	finalize

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

def erraser_option.erraser_option.__init__

(

self

)

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

Member Function Documentation

def erraser_option.erraser_option.finalize

(

self

)

References basic::options::OptionKeys::ProQ.basename, erraser_util.check_path_exist(), erraser_option.erraser_option.debug, erraser_util.error_exit(), erraser_option.erraser_option.fcc2012_scoring_file, erraser_option.erraser_option.input_pdb, erraser_option.erraser_option.kept_temp_folder, erraser_option.erraser_option.map_file, erraser_option.erraser_option.native_edensity_cutoff, erraser_option.erraser_option.nproc, erraser_option.erraser_option.num_pose_kept_cluster, erraser_option.erraser_option.out_pdb, erraser_option.erraser_option.out_prefix, erraser_util.remove(), binder.replace(), erraser_option.erraser_option.rosetta_bin, erraser_option.erraser_option.rosetta_database, erraser_option.erraser_option.rosetta_folder, erraser_option.erraser_option.scoring_file, erraser_option.erraser_option.use_native_edensity_cutoff, and erraser_option.erraser_option.verbose.

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().

def erraser_option.erraser_option.read_cmdline_erraser	(		self,
			argv
	)

References erraser_option.erraser_option.constrain_chi, erraser_option.erraser_option.debug, erraser_option.erraser_option.enlarge_H_lj, erraser_option.erraser_option.extra_res, erraser_option.erraser_option.fcc2012_new_torsional_potential, erraser_option.erraser_option.fcc2012_scoring_file, erraser_option.erraser_option.finalize(), erraser_option.erraser_option.fixed_res, erraser_option.erraser_option.guarantee_no_DNA, erraser_option.erraser_option.input_pdb, erraser_option.erraser_option.map_file, erraser_option.erraser_option.map_reso, erraser_option.erraser_option.multiproc_minimize, erraser_option.erraser_option.n_iterate, erraser_option.erraser_option.native_screen_RMSD, erraser_option.erraser_option.nproc, erraser_option.erraser_option.num_pose_kept, erraser_option.erraser_option.num_pose_kept_cluster, erraser_option.erraser_option.o2prime_legacy_mode, erraser_option.erraser_option.out_pdb, erraser_util.parse_options(), erraser_option.erraser_option.rebuild_all, erraser_option.erraser_option.rebuild_rmsd, erraser_option.erraser_option.rna_prot_erraser, erraser_option.erraser_option.rosetta_bin, erraser_option.erraser_option.rosetta_database, erraser_option.erraser_option.rosetta_folder, erraser_option.erraser_option.scoring_file, erraser_option.erraser_option.search_syn_pyrimidine_only_when_native_syn, erraser_option.erraser_option.use_2prime_OH_potential, and erraser_option.erraser_option.use_native_edensity_cutoff.

def erraser_option.erraser_option.read_cmdline_erraser_single_res	(		self,
			argv
	)

References erraser_option.erraser_option.constrain_chi, erraser_option.erraser_option.debug, erraser_option.erraser_option.enlarge_H_lj, erraser_option.erraser_option.fcc2012_new_torsional_potential, erraser_option.erraser_option.fcc2012_scoring_file, erraser_option.erraser_option.finalize(), erraser_option.erraser_option.input_pdb, erraser_option.erraser_option.map_file, erraser_option.erraser_option.map_reso, erraser_option.erraser_option.multiproc_minimize, erraser_option.erraser_option.native_screen_RMSD, erraser_option.erraser_option.nproc, erraser_option.erraser_option.num_pose_kept, erraser_option.erraser_option.num_pose_kept_cluster, erraser_option.erraser_option.o2prime_legacy_mode, erraser_option.erraser_option.out_prefix, erraser_util.parse_options(), erraser_option.erraser_option.rebuild_res_pdb, erraser_option.erraser_option.rna_prot_erraser, erraser_option.erraser_option.rosetta_bin, erraser_option.erraser_option.rosetta_database, erraser_option.erraser_option.rosetta_folder, erraser_option.erraser_option.scoring_file, erraser_option.erraser_option.search_syn_pyrimidine_only_when_native_syn, erraser_option.erraser_option.skip_single_res_minimize, erraser_option.erraser_option.use_2prime_OH_potential, erraser_option.erraser_option.use_existing_temp_folder, and erraser_option.erraser_option.use_native_edensity_cutoff.

def erraser_option.erraser_option.read_cmdline_full	(		self,
			argv
	)

References erraser_option.erraser_option.allow_syn_pyrimidine, erraser_option.erraser_option.attempt_pyrimidine_flip, erraser_option.erraser_option.cluster_RMSD, erraser_option.erraser_option.constrain_chi, erraser_option.erraser_option.constrain_phosphate, erraser_option.erraser_option.corrected_geo, erraser_option.erraser_option.cutpoint, erraser_option.erraser_option.cutpoint_rs, erraser_option.erraser_option.debug, erraser_option.erraser_option.enlarge_H_lj, erraser_option.erraser_option.extra_res, erraser_option.erraser_option.fcc2012_new_torsional_potential, erraser_option.erraser_option.fcc2012_scoring_file, erraser_option.erraser_option.finalize(), erraser_option.erraser_option.fixed_res, erraser_option.erraser_option.fixed_res_rs, erraser_option.erraser_option.guarantee_no_DNA, erraser_option.erraser_option.ideal_geometry, erraser_option.erraser_option.include_native, erraser_option.erraser_option.input_pdb, erraser_option.erraser_option.is_append, erraser_option.erraser_option.kept_temp_folder, erraser_option.erraser_option.map_file, erraser_option.erraser_option.map_reso, erraser_option.erraser_option.multiproc_minimize, erraser_option.erraser_option.n_iterate, erraser_option.erraser_option.native_edensity_cutoff, erraser_option.erraser_option.native_screen_RMSD, erraser_option.erraser_option.new_torsional_potential, erraser_option.erraser_option.nproc, erraser_option.erraser_option.num_pose_kept, erraser_option.erraser_option.num_pose_kept_cluster, erraser_option.erraser_option.o2prime_legacy_mode, erraser_option.erraser_option.out_pdb, erraser_option.erraser_option.out_prefix, erraser_util.parse_options(), erraser_option.erraser_option.rebuild_all, erraser_option.erraser_option.rebuild_res, erraser_option.erraser_option.rebuild_res_list, erraser_option.erraser_option.rebuild_res_pdb, erraser_option.erraser_option.rebuild_rmsd, erraser_option.erraser_option.res_slice, erraser_option.erraser_option.rna_prot_erraser, erraser_option.erraser_option.rosetta_bin, erraser_option.erraser_option.rosetta_database, erraser_option.erraser_option.rosetta_folder, erraser_option.erraser_option.scoring_file, erraser_option.erraser_option.search_syn_pyrimidine_only_when_native_syn, erraser_option.erraser_option.skip_minimize, erraser_option.erraser_option.slice_nearby, erraser_option.erraser_option.use_2prime_OH_potential, erraser_option.erraser_option.use_existing_temp_folder, erraser_option.erraser_option.use_native_edensity_cutoff, erraser_option.erraser_option.vary_geometry, and erraser_option.erraser_option.verbose.

Member Data Documentation

erraser_option.erraser_option.allow_syn_pyrimidine

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.attempt_pyrimidine_flip

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.cluster_RMSD

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

erraser_option.erraser_option.constrain_phosphate

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.corrected_geo

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.cutpoint

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.cutpoint_rs

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

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().

erraser_option.erraser_option.extra_res

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

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().

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().

erraser_option.erraser_option.fixed_res

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

erraser_option.erraser_option.fixed_res_rs

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.guarantee_no_DNA

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

erraser_option.erraser_option.ideal_geometry

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.include_native

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

erraser_option.erraser_option.is_append

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.kept_temp_folder

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

erraser_option.erraser_option.log_err

erraser_option.erraser_option.log_out

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().

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().

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().

erraser_option.erraser_option.n_iterate

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

erraser_option.erraser_option.native_edensity_cutoff

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

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().

erraser_option.erraser_option.new_torsional_potential

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

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().

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().

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().

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().

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().

erraser_option.erraser_option.rebuild_all

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

erraser_option.erraser_option.rebuild_res

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.rebuild_res_list

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

erraser_option.erraser_option.rebuild_rmsd

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

erraser_option.erraser_option.res_slice

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

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().

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().

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().

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().

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().

erraser_option.erraser_option.skip_minimize

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.skip_single_res_minimize

Referenced by erraser_option.erraser_option.read_cmdline_erraser_single_res().

erraser_option.erraser_option.slice_nearby

Referenced by erraser_option.erraser_option.read_cmdline_full().

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().

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().

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().

erraser_option.erraser_option.vary_geometry

Referenced by erraser_option.erraser_option.read_cmdline_full().

erraser_option.erraser_option.verbose

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

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

• src/apps/public/ERRASER/erraser_option.py