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| def | erraser_util.error_exit (message="") |
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| def | erraser_util.rosetta_bin_path (exe_file, rosetta_folder="") |
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| def | erraser_util.initialize_rna_tools (rosetta_folder="") |
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| def | erraser_util.get_fasta (pdb_file, out_file, rosetta_folder="") |
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| def | erraser_util.rosetta_database_path (rosetta_folder="") |
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| def | erraser_util.subprocess_call (command, out=sys.stdout, err=sys.stderr, is_append_file=False) |
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| def | erraser_util.subprocess_out (command, err=sys.stderr) |
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| def | erraser_util.grep (pattern, input_file) |
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| def | erraser_util.remove (pattern, ignore_errors=True) |
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| def | erraser_util.copy (file1, dst) |
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| def | erraser_util.move (file1, dst) |
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| def | erraser_util.get_total_res (pdbname) |
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| def | erraser_util.find_nearby_res (input_pdb, input_res, dist_cutoff, reload=True) |
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| def | erraser_util.parse_options (argv, tag, default) |
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| def | erraser_util.parse_option_int_list (argv, tag) |
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| def | erraser_util.parse_option_string_list (argv, tag) |
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| def | erraser_util.parse_option_chain_res_list (argv, tag) |
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| def | erraser_util.rna_rosetta_ready_set (input_pdb, out_name, option, rosetta_bin="", rosetta_database="", rna_prot_erraser=False) |
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| def | erraser_util.extract_pdb (silent_file, output_folder_name, rosetta_bin="", rosetta_database="", extract_first_only=False, output_virtual=False, rna_prot_erraser=False) |
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| def | erraser_util.phenix_release_tag () |
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| def | erraser_util.phenix_rna_validate (input_pdb, outliers_only=True) |
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| def | erraser_util.find_error_res (input_pdb) |
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| def | erraser_util.pdb2fasta (input_pdb, fasta_out, using_protein=False) |
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| def | erraser_util.pdb_slice (input_pdb, out_name, segment) |
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| def | erraser_util.check_path_exist (path_name) |
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| def | erraser_util.load_pdb_coord_old (input_pdb) |
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| def | erraser_util.load_pdb_coord (input_pdb) |
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| def | erraser_util.regularize_pdb (input_pdb, out_name) |
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| def | erraser_util.regularize_OP1_OP2 (input_pdb, out_name) |
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| def | erraser_util.rosetta2phenix_merge_back (orig_pdb, rs_pdb, out_name) |
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| def | erraser_util.rosetta2std_pdb (input_pdb, out_name, cryst1_line="") |
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| def | erraser_util.pdb2rosetta (input_pdb, out_name, alter_conform='A', PO_dist_cutoff=2.0, use_rs_atom_res_name=False, using_protein=False, renumbering=True) |
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| def | erraser_util.res_num_convert (res_conversion_list, res_pdb) |
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| def | erraser_util.res_wise_rmsd (pdb1, pdb2) |
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| def | erraser_util.pdb_slice_into_chunks (input_pdb, n_chunk) |
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| def | erraser_util.pdb_slice_with_patching (input_pdb, out_name, slice_res_list) |
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| def | erraser_util.sliced2orig_merge_back (orig_pdb, new_pdb, out_name, res_list) |
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| def | erraser_util.find_chi_angle (input_pdb, res) |
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