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Rosetta
3.8
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Rosetta
3.8
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Functions | |
| def | erraser |
| erraser start#################################################### More... | |
| def | outlier_rebuild_if_necessary |
| erraser end ##################################################### More... | |
| def | rmsd_rebuild_if_necessary |
| def | erraser_single_res |
| erraser_single_res start ######################################## More... | |
| def | erraser_minimize |
| erraser_single_res end ######################################## More... | |
| def | SWA_rebuild_erraser_async |
| erraser_minimize end ########################################## More... | |
| def | SWA_rebuild_erraser_postproc |
| synchronous SWA_rebuild_erraser (post processing) ####################### More... | |
| def | SWA_rebuild_erraser_multiproc |
| multiprocess SWA_rebuild_erraser (multiproc wrapper) #################### More... | |
| def | rebuild_completed |
| def | seq_rebuild_new |
| def | seq_rebuild |
| seq_rebuild start ############################################### More... | |
| def | SWA_rebuild_erraser |
| seq_rebuild end ############################################### More... | |
Variables | |
| tuple | file_path = os.path.split( os.path.abspath(__file__) ) |
| def erraser_wrapper.erraser | ( | option | ) |
erraser start####################################################
References basic::options::OptionKeys::ProQ.basename, erraser_util.copy(), erraser_minimize(), erraser_util.error_exit(), erraser_util.find_error_res(), erraser_util.get_total_res(), ObjexxFCL.len(), basic::database.open(), outlier_rebuild_if_necessary(), erraser_util.pdb2rosetta(), basic::options::OptionKeys::relax::range.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().
| def erraser_wrapper.erraser_minimize | ( | option | ) |
erraser_single_res end ########################################
erraser_minimize start ##########################################
References ObjexxFCL.len(), basic::options::OptionKeys::stepwise.move, basic::database.open(), erraser_util.rosetta_bin_path(), erraser_util.rosetta_database_path(), and erraser_util.subprocess_call().
Referenced by erraser(), and erraser_single_res().
| def erraser_wrapper.erraser_single_res | ( | option | ) |
erraser_single_res start ########################################
References basic::options::OptionKeys::ProQ.basename, erraser_minimize(), basic::options::OptionKeys::mh::filter.filter, erraser_util.get_total_res(), ObjexxFCL.len(), basic::database.open(), erraser_util.pdb2rosetta(), basic::options::OptionKeys::relax::range.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().
| 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().
| def erraser_wrapper.rebuild_completed | ( | file | ) |
References basic::database.open().
Referenced by seq_rebuild(), seq_rebuild_new(), and SWA_rebuild_erraser_multiproc().
| 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().
| def erraser_wrapper.seq_rebuild | ( | option | ) |
seq_rebuild start ###############################################
References basic::options::OptionKeys::ProQ.basename, erraser_util.copy(), basic::options::OptionKeys::mh::filter.filter, basic::database.open(), rebuild_completed(), erraser_util.remove(), binder.replace(), SWA_rebuild_erraser(), and SWA_rebuild_erraser_multiproc().
| def erraser_wrapper.seq_rebuild_new | ( | option | ) |
References basic::options::OptionKeys::ProQ.basename, erraser_util.copy(), erraser_util.get_total_res(), basic::database.open(), rebuild_completed(), erraser_util.remove(), binder.replace(), erraser_util.rosetta_bin_path(), and erraser_util.subprocess_call().
Referenced by outlier_rebuild_if_necessary(), and rmsd_rebuild_if_necessary().
| def erraser_wrapper.SWA_rebuild_erraser | ( | option | ) |
seq_rebuild end ###############################################
SWA_rebuild_erraser start #######################################
References basic::options::OptionKeys::ProQ.basename, erraser_util.copy(), erraser_util.extract_pdb(), erraser_util.find_chi_angle(), erraser_util.get_total_res(), ObjexxFCL.len(), basic::database.open(), erraser_util.pdb2fasta(), erraser_util.pdb_slice(), erraser_util.pdb_slice_with_patching(), basic::options::OptionKeys::relax::range.range, erraser_util.remove(), binder.replace(), erraser_util.rosetta_bin_path(), erraser_util.rosetta_database_path(), erraser_util.sliced2orig_merge_back(), erraser_util.subprocess_call(), and erraser_util.subprocess_out().
Referenced by erraser_single_res(), seq_rebuild(), and 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().
| 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().
| def erraser_wrapper.SWA_rebuild_erraser_postproc | ( | SWA_option | ) |
synchronous SWA_rebuild_erraser (post processing) #######################
References erraser_util.copy(), erraser_util.get_total_res(), utility.join(), ObjexxFCL.len(), basic::options::OptionKeys::relax::range.range, erraser_util.remove(), and erraser_util.sliced2orig_merge_back().
Referenced by SWA_rebuild_erraser_multiproc().
| tuple erraser_wrapper.file_path = os.path.split( os.path.abspath(__file__) ) |
1.8.7