erraser_wrapper Namespace Reference

Functions
def	erraser (option)
	erraser start#################################################### More...
def	outlier_rebuild_if_necessary (step, rebuild_res_error, rebuild_option)
	erraser end ##################################################### More...
def	rmsd_rebuild_if_necessary (step, rebuild_res_rmsd, rebuild_option)
def	erraser_single_res (option)
	erraser_single_res start ######################################## More...
def	erraser_minimize (option)
	erraser_single_res end ######################################## More...
def	SWA_rebuild_erraser_async (SWA_option)
	erraser_minimize end ########################################## More...
def	SWA_rebuild_erraser_postproc (SWA_option)
	synchronous SWA_rebuild_erraser (post processing) ####################### More...
def	SWA_rebuild_erraser_multiproc (SWA_option)
	multiprocess SWA_rebuild_erraser (multiproc wrapper) #################### More...
def	rebuild_completed (file)
def	seq_rebuild_new (option, output_minimized_pose_list=False)
def	seq_rebuild (option)
	seq_rebuild start ############################################### More...
def	SWA_rebuild_erraser (option)
	seq_rebuild end ############################################### More...

Variables
	file_path = os.path.split( os.path.abspath(__file__) ) [0]

Function Documentation

erraser()

def erraser_wrapper.erraser

(

option

)

erraser start####################################################

References basename, erraser_util.copy(), erraser_minimize(), erraser_util.error_exit(), erraser_util.find_error_res(), run_backbone.float, erraser_util.get_total_res(), enumerate_junctions.int, ObjexxFCL.len(), basic::database.open(), outlier_rebuild_if_necessary(), erraser_util.pdb2rosetta(), range, erraser_util.regularize_OP1_OP2(), erraser_util.regularize_pdb(), erraser_util.remove(), binder.replace(), erraser_util.res_num_convert(), erraser_util.res_wise_rmsd(), rmsd_rebuild_if_necessary(), erraser_util.rosetta2phenix_merge_back(), and erraser_util.rosetta2std_pdb().

erraser_minimize()

def erraser_wrapper.erraser_minimize

(

option

)

erraser_single_res end ########################################

erraser_minimize start ##########################################

References erraser_util.copy(), erraser_util.get_fasta(), join(), ObjexxFCL.len(), test_terpenes.lower, basic::options::OptionKeys::stepwise.move, basic::database.open(), erraser_util.rosetta_bin_path(), erraser_util.rosetta_database_path(), str(), and erraser_util.subprocess_call().

Referenced by erraser(), and erraser_single_res().

erraser_single_res()

def erraser_wrapper.erraser_single_res

(

option

)

erraser_single_res start ########################################

References basename, basic::options::OptionKeys::stepwise.enumerate, erraser_minimize(), filter, run_backbone.float, erraser_util.get_total_res(), enumerate_junctions.int, ObjexxFCL.len(), basic::database.open(), erraser_util.pdb2rosetta(), range, erraser_util.regularize_OP1_OP2(), erraser_util.regularize_pdb(), erraser_util.remove(), binder.replace(), erraser_util.res_num_convert(), erraser_util.rosetta2phenix_merge_back(), erraser_util.sliced2orig_merge_back(), binder.split(), and SWA_rebuild_erraser().

outlier_rebuild_if_necessary()

def erraser_wrapper.outlier_rebuild_if_necessary	(		step,
			rebuild_res_error,
			rebuild_option
	)

erraser end #####################################################

References erraser_util.copy(), ObjexxFCL.len(), and seq_rebuild_new().

Referenced by erraser().

rebuild_completed()

def erraser_wrapper.rebuild_completed

(

file

)

References basic::database.open().

Referenced by seq_rebuild(), seq_rebuild_new(), and SWA_rebuild_erraser_multiproc().

rmsd_rebuild_if_necessary()

def erraser_wrapper.rmsd_rebuild_if_necessary	(		step,
			rebuild_res_rmsd,
			rebuild_option
	)

References erraser_util.copy(), ObjexxFCL.len(), and seq_rebuild_new().

Referenced by erraser().

seq_rebuild()

def erraser_wrapper.seq_rebuild

(

option

)

seq_rebuild start ###############################################

References basename, erraser_util.copy(), filter, basic::database.open(), rebuild_completed(), erraser_util.remove(), binder.replace(), SWA_rebuild_erraser(), and SWA_rebuild_erraser_multiproc().

seq_rebuild_new()

def erraser_wrapper.seq_rebuild_new	(		option,
			output_minimized_pose_list = False
	)

References basename, erraser_util.copy(), pyrosetta.tests.distributed.test_dask.format, erraser_util.get_total_res(), ObjexxFCL.len(), test_terpenes.lower, basic::database.open(), rebuild_completed(), binder.replace(), erraser_util.rosetta_bin_path(), str(), and erraser_util.subprocess_call().

Referenced by outlier_rebuild_if_necessary(), and rmsd_rebuild_if_necessary().

SWA_rebuild_erraser()

def erraser_wrapper.SWA_rebuild_erraser

(

option

)

seq_rebuild end ###############################################

SWA_rebuild_erraser start #######################################

References basename, erraser_util.copy(), erraser_util.extract_pdb(), erraser_util.find_chi_angle(), erraser_util.get_total_res(), if(), enumerate_junctions.int, ObjexxFCL.len(), test_terpenes.lower, basic::database.open(), erraser_util.pdb2fasta(), erraser_util.pdb_slice(), erraser_util.pdb_slice_with_patching(), range, erraser_util.remove(), binder.replace(), erraser_util.rosetta_bin_path(), erraser_util.rosetta_database_path(), erraser_util.sliced2orig_merge_back(), str(), erraser_util.subprocess_call(), and erraser_util.subprocess_out().

Referenced by erraser_single_res(), seq_rebuild(), and SWA_rebuild_erraser_async().

SWA_rebuild_erraser_async()

def erraser_wrapper.SWA_rebuild_erraser_async

(

SWA_option

)

erraser_minimize end ##########################################

asynchronous SWA_rebuild_erraser (asynch process) #######################

References erraser_util.copy(), and SWA_rebuild_erraser().

SWA_rebuild_erraser_multiproc()

def erraser_wrapper.SWA_rebuild_erraser_multiproc

(

SWA_option

)

multiprocess SWA_rebuild_erraser (multiproc wrapper) ####################

References rebuild_completed(), erraser_util.remove(), and SWA_rebuild_erraser_postproc().

Referenced by seq_rebuild().

SWA_rebuild_erraser_postproc()

def erraser_wrapper.SWA_rebuild_erraser_postproc

(

SWA_option

)

synchronous SWA_rebuild_erraser (post processing) #######################

References erraser_util.copy(), erraser_util.get_total_res(), join(), ObjexxFCL.len(), range, erraser_util.remove(), and erraser_util.sliced2orig_merge_back().

Referenced by SWA_rebuild_erraser_multiproc().

Variable Documentation

file_path

erraser_wrapper.file_path = os.path.split( os.path.abspath(__file__) ) [0]