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Public Member Functions | Public Attributes | List of all members
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)

Member Function Documentation

def erraser_option.erraser_option.finalize (   self)
def erraser_option.erraser_option.read_cmdline_erraser (   self,
  argv 
)
def erraser_option.erraser_option.read_cmdline_erraser_single_res (   self,
  argv 
)
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
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.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.log_err
erraser_option.erraser_option.log_out
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_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.skip_single_res_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
erraser_option.erraser_option.verbose

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