Bindings for protocols::cyclic_peptide_predict namespace

Classes
		builtins.object SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE SimpleCycpepPredictApplication SimpleCycpepPredictApplication_MPI_JobResultsSummary   class SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE, rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE, int) -> NoneType   2. __init__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE, rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.cyclic_peptide_predict.SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE) -> str Data and other attributes defined here: SORT_BY_ENERGIES = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_ENERGIES SORT_BY_HBONDS = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_HBONDS SORT_BY_RMSD = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_RMSD   class SimpleCycpepPredictApplication(builtins.object)     Application-level code for simple_cycpep_predict application.     Also called by the BOINC minirosetta app.     Vikram K. Mulligan, Baker laboratory (vmullig.edu)     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> NoneType   doc   2. __init__(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, allow_file_read : bool) -> NoneType   3. __init__(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, src : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication,  : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication initialize_from_options(...) from builtins.PyCapsule initialize_from_options(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> NoneType   Initialize the application.      Initializes using the option system. register_options(...) from builtins.PyCapsule register_options() -> NoneType   Register the set of options that this application uses (for the help menu). run(...) from builtins.PyCapsule run(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication) -> NoneType   Actually run the application.      The initialize_from_options() function must be called before calling this.  (Called by default constructor.) set_D_alpha_compfile_contents(...) from builtins.PyCapsule set_D_alpha_compfile_contents(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in : str) -> NoneType   Allows external code to set the file contents for the D-alpha aa_composition file. set_D_beta_compfile_contents(...) from builtins.PyCapsule set_D_beta_compfile_contents(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in : str) -> NoneType   Allows external code to set the file contents for the D-beta aa_composition file. set_L_alpha_compfile_contents(...) from builtins.PyCapsule set_L_alpha_compfile_contents(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in : str) -> NoneType   Allows external code to set the file contents for the L-alpha aa_composition file. set_L_beta_compfile_contents(...) from builtins.PyCapsule set_L_beta_compfile_contents(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in : str) -> NoneType   Allows external code to set the file contents for the L-beta aa_composition file. set_abba_bins_binfile_contents(...) from builtins.PyCapsule set_abba_bins_binfile_contents(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, contents_in : str) -> NoneType   Allows external code to set the ABBA bin parameters without having to read the  bin params file directly from disk. set_allowed_residues_by_position(...) from builtins.PyCapsule set_allowed_residues_by_position(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, allowed_canonicals : rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals : rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) -> NoneType   Allows external code to set the allowed residues by position, so that this needn't be read directly  from disk. set_my_rank(...) from builtins.PyCapsule set_my_rank(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, rank_in : int) -> NoneType   If called by MPI code, the rank of the current process can be stored here.      Used for output of job summaries. set_native(...) from builtins.PyCapsule set_native(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, native : rosetta.core.pose.Pose) -> NoneType   Allows external code to provide a native, so that the SimpleCycpepPredictApplication doesn't have to read  directly from disk. set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, nstruct_in : int) -> NoneType   Allows external code to override the number of structures that this should generate (otherwise  set by options system. set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, sfxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType   Sets the default scorefunction to use.      The scorefunction is cloned.  The high-hbond version is constructed  from this one.  If necessary, the aa_composition score term will be turned on  in that one; it needn't be turned on in this one. set_sequence(...) from builtins.PyCapsule set_sequence(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, seq : str) -> NoneType   Allows external code to provide a sequence, so that the SimpleCycpepPredictApplication doesn't have to read  directly from disk. set_suppress_checkpoints(...) from builtins.PyCapsule set_suppress_checkpoints(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication, suppress_checkpoints : bool) -> NoneType   Allows external code to suppress checkpointing, to prevent direct file I/O from disk.      Useful on Blue Gene.   class SimpleCycpepPredictApplication_MPI_JobResultsSummary(builtins.object)     A class for summarizing the result of an MPI-mode job run with the SimpleCycpepPredictApplication.     Vikram K. Mulligan, Baker laboratory (vmullig.edu)     Methods defined here: MPI_ranks_handling_message(...) from builtins.PyCapsule MPI_ranks_handling_message(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> rosetta.utility.vector1_int   Get the list of procs that transmitted this JobResultsSummary.      Whenever a proc sends it to someone else, the receiving proc appends the sender's rank here.  This allows the emperor  node to address an output request to the correct proc. __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> NoneType   2. __init__(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, originating_node_MPI_rank : int, jobindex_on_originating_node : int, pose_energy : float, rmsd : float, hbonds : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_MPI_rank_handling_message(...) from builtins.PyCapsule add_MPI_rank_handling_message(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, new_proc : int) -> NoneType   Add a proc that handled this message to the list of procs that transmitted this JobResultsSummary.      Whenever a proc sends it to someone else, the receiving proc appends the sender's rank here.  This allows the emperor  node to address an output request to the correct proc. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary,  : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary hbonds(...) from builtins.PyCapsule hbonds(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> float   Get the number of hbonds of the pose generated by this job. jobindex_on_originating_node(...) from builtins.PyCapsule jobindex_on_originating_node(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> int   Get the local index of the job on the node on which it was carried out. originating_node_MPI_rank(...) from builtins.PyCapsule originating_node_MPI_rank(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> int   Get the MPI rank of the process that initially carried out this job. pose_energy(...) from builtins.PyCapsule pose_energy(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> float   Get the energy of the pose generated by this job. rmsd(...) from builtins.PyCapsule rmsd(rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary) -> float   Get the RMSD of the pose generated by this job to native. set_hbonds(...) from builtins.PyCapsule set_hbonds(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val : float) -> NoneType   Set the number of hbonds of the pose generated by this job. set_jobindex_on_originating_node(...) from builtins.PyCapsule set_jobindex_on_originating_node(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, index : int) -> NoneType   Set the local index of the job on the node on which it was carried out. set_originating_node_MPI_rank(...) from builtins.PyCapsule set_originating_node_MPI_rank(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, rank : int) -> NoneType   Set the MPI rank of the process that initially carried out this job. set_pose_energy(...) from builtins.PyCapsule set_pose_energy(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val : float) -> NoneType   Set the energy of the pose generated by this job. set_rmsd(...) from builtins.PyCapsule set_rmsd(self : rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary, val : float) -> NoneType   Set the RMSD of the pose generated by this job to native.

Functions
		is_canonical(...) method of builtins.PyCapsule instance is_canonical(resname : str) -> bool   Given a residue name, return true if this is one of the 20  canonical amino acids, false otherwise. read_file_into_string(...) method of builtins.PyCapsule instance read_file_into_string(output_string : str, filename : str, from_database : bool) -> NoneType   Given an ASCII file name, read the contents into a string.  If from_database is true, the read is from the database.      The string that will be filled with the file contents.  Overwritten by this operation.      The name of the file to read.  If from_database is true, this is a relative database path.      If true, the file is assumed to be in the database.  If false, the path is relative the execution  directory, or is absolute. read_peptide_design_file(...) method of builtins.PyCapsule instance read_peptide_design_file(filename : str, allowed_canonicals_by_position : rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t, allowed_noncanonicals_by_position : rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t) -> NoneType   Given a filename, read and parse the file, returning a list of canonical residues allowed at each position  and a list of noncanonicals allowed at each position.      This does the actual file read.  It is NOT THREADSAFE.  The file format is a series of lines with the pattern:  residue_index residuetype_1_fullname residuetype_2_fullname residuetype_3_fullname ...  Anything after a pound sign should be ignored.  A line with DEFAULT in place of the resiude index should be interpreted  as providing default values, which should be stored as map key 0.      The file name from which we'll read.      A map of [position->vector of strings of full names] listing the allowed canonical  residue types at each position.  Reset and populated by this function.  Key 0 indicates default settings applied anywhere  that lacks a map key.      A map of [position->vector of strings of full names] listing the allowed noncanonical  residue types at each position.  Reset and populated by this function.  Key 0 indicates default settings applied anywhere  that lacks a map key.

Data
		SORT_BY_ENERGIES = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_ENERGIES SORT_BY_HBONDS = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_HBONDS SORT_BY_RMSD = SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE.SORT_BY_RMSD