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- builtins.object
-
- DynamicProfileThis
- Emitter
-
- JsonEmitter
- YamlEmitter
- ExecutionResult
- MetricValueBase
- ProfTag
- ProfileThis
- Report
- Reporter
- TracerManager
- TracerOptions
- TracerPriority
- basic_otstream_char_std_char_traits_char_t
-
- ComparingTracer
- PyTracer
- Tracer
-
- MemTracer
- TracerToFile
class Emitter(builtins.object) |
| |
Lightweight class to ease writting YAML documents (http://yaml.org)
YAML is a structured data format, a more human-readable
alternative to XML.
I use the terms "map" and "list" here, but you may also see "mapping" and "sequence".
The former is a series of key : value pairs, while the latter is a simple series of items.
This class is not entirely able to enforce the generation of valid YAML --
you can still e.g. write a key : value pair in the middle of a list.
It will print a warning message but will otherwise try to continue on.
YAML documents have optional explicit start/end markers; if the emitter
supports them, they will be auto-generated when the class is initialized
and when you're finished and you call end().
Whitespace is YAML documents is semi-significant. By default, this class
will try to pretty-print, showing the depth of nesting through indentation.
When starting a new list or map, you can request that it not be indented
(i.e., be printed all on one line), but all lists and maps nested inside it
will also be printed without linebreaks, regardless of the requested indentation.
YAML refers to these two styles as "block" and "flow", respectively.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.basic.Emitter, out : std::ostream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- depth(...) from builtins.PyCapsule
- depth(rosetta.basic.Emitter) -> int
Number of closing brackets/braces required to end document (non-negative)
- end(...) from builtins.PyCapsule
- end(*args, **kwargs)
Overloaded function.
1. end(rosetta.basic.Emitter) -> NoneType
By default, closes all open maps/lists, ending the document.
2. end(self : rosetta.basic.Emitter, desired_depth : int) -> NoneType
By default, closes all open maps/lists, ending the document.
- end_list(...) from builtins.PyCapsule
- end_list(rosetta.basic.Emitter) -> NoneType
Counterpart to start_list() -- writes closing bracket.
- end_map(...) from builtins.PyCapsule
- end_map(rosetta.basic.Emitter) -> NoneType
Counterpart to start_map() -- writes closing brace.
- flush(...) from builtins.PyCapsule
- flush(rosetta.basic.Emitter) -> NoneType
Flush the underlying output stream.
- set_indent(...) from builtins.PyCapsule
- set_indent(self : rosetta.basic.Emitter, num_spaces : int) -> NoneType
Number of spaces used for indenting. Default is one.
- start_doc(...) from builtins.PyCapsule
- start_doc(rosetta.basic.Emitter) -> NoneType
Start a new document, ending the previous one first if necessary.
A no-op for some types of output (e.g. JSON) that don't allow multiple documents.
- start_list(...) from builtins.PyCapsule
- start_list(*args, **kwargs)
Overloaded function.
1. start_list(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_list(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
- start_map(...) from builtins.PyCapsule
- start_map(*args, **kwargs)
Overloaded function.
1. start_map(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_map(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
|
class JsonEmitter(Emitter) |
| |
Lightweight class to ease writting JSON documents, a subset of YAML (http://json.org)
Using this class is not recommended -- use YamlEmitter instead.
JSON is JavaScript Object Notation, the format for
object and array literals in the JavaScript language.
It also looks a great deal like nested Python dicts and lists,
except for the special JSON values true, false, and null.
(Python uses True, False, and None instead.
Otherwise, JSON can be embedded directly into Python scripts.)
JSON is legal subset of YAML, but leaves out much of YAML's complexity and advanced features.
At the present time, there appears to be more library support
for JSON than for YAML, especially for reading and parsing.
(Both are fairly easy to write, as demonstrated here.)
The topmost level of every valid JSON document consists of exactly one map,
which is automatically started for you when the class is initialized.
When you're finished you should call end(), and then probably flush().
Whitespace is JSON documents is not significant. By default, this class
will try to pretty-print, showing the depth of nesting through indentation.
When starting a new list or map, you can request that it not be indented
(i.e., be printed all on one line), but all lists and maps nested inside it
will also be printed without linebreaks, regardless of the requested indentation.
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| |
- Method resolution order:
- JsonEmitter
- Emitter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, out : std::ostream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- start_doc(...) from builtins.PyCapsule
- start_doc(rosetta.basic.JsonEmitter) -> NoneType
JSON doesn't support multiple documents, so this just calls end(1)
to return you to the top (least-nested) level.
Methods inherited from Emitter:
- depth(...) from builtins.PyCapsule
- depth(rosetta.basic.Emitter) -> int
Number of closing brackets/braces required to end document (non-negative)
- end(...) from builtins.PyCapsule
- end(*args, **kwargs)
Overloaded function.
1. end(rosetta.basic.Emitter) -> NoneType
By default, closes all open maps/lists, ending the document.
2. end(self : rosetta.basic.Emitter, desired_depth : int) -> NoneType
By default, closes all open maps/lists, ending the document.
- end_list(...) from builtins.PyCapsule
- end_list(rosetta.basic.Emitter) -> NoneType
Counterpart to start_list() -- writes closing bracket.
- end_map(...) from builtins.PyCapsule
- end_map(rosetta.basic.Emitter) -> NoneType
Counterpart to start_map() -- writes closing brace.
- flush(...) from builtins.PyCapsule
- flush(rosetta.basic.Emitter) -> NoneType
Flush the underlying output stream.
- set_indent(...) from builtins.PyCapsule
- set_indent(self : rosetta.basic.Emitter, num_spaces : int) -> NoneType
Number of spaces used for indenting. Default is one.
- start_list(...) from builtins.PyCapsule
- start_list(*args, **kwargs)
Overloaded function.
1. start_list(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_list(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
- start_map(...) from builtins.PyCapsule
- start_map(*args, **kwargs)
Overloaded function.
1. start_map(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_map(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
|
class MemTracer(Tracer) |
| | |
- Method resolution order:
- MemTracer
- Tracer
- basic_otstream_char_std_char_traits_char_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, rosetta.basic.TracerPriority) -> NoneType
doc
3. __init__(self : handle, priority : rosetta.basic.TracerPriority, muted_by_default : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
Methods inherited from Tracer:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.basic.Tracer, priority : int) -> rosetta.basic.Tracer
- calculate_tracer_visibilities(...) from builtins.PyCapsule
- calculate_tracer_visibilities() -> NoneType
This function should be invoked after the options system has been
initialized, so that the visibility for all tracers that have so far been
constructed and have been waiting for the options system to be initialized
can now have their visibility calculated. After this function completes,
all newly-constructed Tracers will calculate their visibility in their
constructors. Visibility is no longer be calculated on a just-in-time
basis and stored in mutable data members.
- channel(...) from builtins.PyCapsule
- channel(rosetta.basic.Tracer) -> str
- channel_color(...) from builtins.PyCapsule
- channel_color(*args, **kwargs)
Overloaded function.
1. channel_color(rosetta.basic.Tracer) -> str
Get the channel color.
2. channel_color(self : rosetta.basic.Tracer, color : str) -> NoneType
Set the channel color.
This can be done in a stream like this:
TR << TR.bgWhite << TR.Black << "Example" << TR.Reset << std::endl;
- channel_name_color(...) from builtins.PyCapsule
- channel_name_color(*args, **kwargs)
Overloaded function.
1. channel_name_color(rosetta.basic.Tracer) -> str
2. channel_name_color(self : rosetta.basic.Tracer, color : str) -> NoneType
- final_stream(...) from builtins.PyCapsule
- final_stream() -> std::ostream
set ios hook for final tracer stream (deafult is std::cout).
- flush_all_channels(...) from builtins.PyCapsule
- flush_all_channels(rosetta.basic.Tracer) -> NoneType
flush tracer buffer and flush buffers of all
sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace
- flush_all_tracers(...) from builtins.PyCapsule
- flush_all_tracers() -> NoneType
- get_all_channels_string(...) from builtins.PyCapsule
- get_all_channels_string() -> str
- init(...) from builtins.PyCapsule
- init(self : rosetta.basic.Tracer, tr : rosetta.basic.Tracer) -> NoneType
re-init using data from another tracer object.
- priority(...) from builtins.PyCapsule
- priority(*args, **kwargs)
Overloaded function.
1. priority(rosetta.basic.Tracer) -> int
get/set tracer priority level.
2. priority(self : rosetta.basic.Tracer, priority : int) -> NoneType
- set_default_final_stream(...) from builtins.PyCapsule
- set_default_final_stream() -> NoneType
- set_ios_hook(...) from builtins.PyCapsule
- set_ios_hook(*args, **kwargs)
Overloaded function.
1. set_ios_hook(tr : rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list : str) -> NoneType
2. set_ios_hook(tr : rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list : str, raw : bool) -> NoneType
- super_mute(...) from builtins.PyCapsule
- super_mute(*args, **kwargs)
Overloaded function.
1. super_mute() -> bool
global super mute flag that allow to mute all io no matter what.
2. super_mute(f : bool) -> NoneType
- tracer_options(...) from builtins.PyCapsule
- tracer_options() -> rosetta.basic.TracerOptions
get/set tracer options - global options for Tracer IO.
- visible(...) from builtins.PyCapsule
- visible(*args, **kwargs)
Overloaded function.
1. visible(rosetta.basic.Tracer) -> bool
Is this tracer currently visible?.
2. visible(self : rosetta.basic.Tracer, priority : int) -> bool
is this tracer visible, if it used the given priority value?
Methods inherited from basic_otstream_char_std_char_traits_char_t:
- is_flushed(...) from builtins.PyCapsule
- is_flushed(rosetta.basic.basic_otstream_char_std_char_traits_char_t) -> bool
|
class ProfTag(builtins.object) |
| | |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.basic.ProfTag, rosetta.basic.ProfTag) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.basic.ProfTag) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.basic.ProfTag, int) -> NoneType
2. __init__(rosetta.basic.ProfTag, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.basic.ProfTag) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.basic.ProfTag, rosetta.basic.ProfTag) -> 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.basic.ProfTag) -> str
Data and other attributes defined here:
- ABINITIO = ProfTag.ABINITIO
- APPLY_BB_MOVE = ProfTag.APPLY_BB_MOVE
- APPLY_MOVE = ProfTag.APPLY_MOVE
- APPLY_SC_MOVE = ProfTag.APPLY_SC_MOVE
- ARCHIVE_BLOCK_FILE = ProfTag.ARCHIVE_BLOCK_FILE
- ARCHIVE_CRITICAL_JOBSCOMPLETE = ProfTag.ARCHIVE_CRITICAL_JOBSCOMPLETE
- ARCHIVE_EVALUATORS = ProfTag.ARCHIVE_EVALUATORS
- ARCHIVE_EVAL_DECOYS = ProfTag.ARCHIVE_EVAL_DECOYS
- ARCHIVE_FILL_POSE = ProfTag.ARCHIVE_FILL_POSE
- ARCHIVE_GEN_BATCH = ProfTag.ARCHIVE_GEN_BATCH
- ARCHIVE_JOBSCOMPLETE = ProfTag.ARCHIVE_JOBSCOMPLETE
- ARCHIVE_READ_DECOYS = ProfTag.ARCHIVE_READ_DECOYS
- ARCHIVE_SCORE_POSE = ProfTag.ARCHIVE_SCORE_POSE
- ARCHIVE_SYNC_BATCHES = ProfTag.ARCHIVE_SYNC_BATCHES
- ATOM_TREE_UPDATE_INTERNAL_COORDS = ProfTag.ATOM_TREE_UPDATE_INTERNAL_COORDS
- ATOM_TREE_UPDATE_XYZ_COORDS = ProfTag.ATOM_TREE_UPDATE_XYZ_COORDS
- BACKRUB_MOVER = ProfTag.BACKRUB_MOVER
- CANONICALMOVER_WRITE_TO_FILE = ProfTag.CANONICALMOVER_WRITE_TO_FILE
- CA_DME_EVALUATION = ProfTag.CA_DME_EVALUATION
- CA_RMSD_EVALUATION = ProfTag.CA_RMSD_EVALUATION
- CCD_CLOSE = ProfTag.CCD_CLOSE
- CHECK_COMM_SIZE = ProfTag.CHECK_COMM_SIZE
- CHEMICAL_MAKE_POSE = ProfTag.CHEMICAL_MAKE_POSE
- COMM_REDUCE_SIZE = ProfTag.COMM_REDUCE_SIZE
- CONFORMATION_COPY = ProfTag.CONFORMATION_COPY
- CONFORMATION_DETECT_DISULF = ProfTag.CONFORMATION_DETECT_DISULF
- CONFORMATION_FIX_DISULF = ProfTag.CONFORMATION_FIX_DISULF
- CONSTRAINT_SCORE = ProfTag.CONSTRAINT_SCORE
- CONSTRAINT_SET_COPY = ProfTag.CONSTRAINT_SET_COPY
- CONSTRUCT_DISTANCE_MATRIX = ProfTag.CONSTRUCT_DISTANCE_MATRIX
- COPY_COORDS = ProfTag.COPY_COORDS
- DALPHABALL = ProfTag.DALPHABALL
- DALPHABALL_DERIV = ProfTag.DALPHABALL_DERIV
- DATA_STORAGE = ProfTag.DATA_STORAGE
- DFUNC = ProfTag.DFUNC
- ENERGIES_COPY = ProfTag.ENERGIES_COPY
- ENERGY_ENVPAIR_POTENTIAL = ProfTag.ENERGY_ENVPAIR_POTENTIAL
- ENERGY_GRAPH_COPY = ProfTag.ENERGY_GRAPH_COPY
- FACTS_GET_ALL_BORN_RADII = ProfTag.FACTS_GET_ALL_BORN_RADII
- FACTS_ROTAMER_BACKGROUND_ENERGIES = ProfTag.FACTS_ROTAMER_BACKGROUND_ENERGIES
- FACTS_ROTAMER_PAIR_ENERGIES = ProfTag.FACTS_ROTAMER_PAIR_ENERGIES
- FACTS_SETUP_FOR_PACKING = ProfTag.FACTS_SETUP_FOR_PACKING
- FARRAY_MANIPULATION = ProfTag.FARRAY_MANIPULATION
- FINALIZE = ProfTag.FINALIZE
- FIND_SUGAR_AND_SUITE_FRAGS_I = ProfTag.FIND_SUGAR_AND_SUITE_FRAGS_I
- FIND_SUGAR_AND_SUITE_FRAGS_II = ProfTag.FIND_SUGAR_AND_SUITE_FRAGS_II
- FRAGMENTPICKING = ProfTag.FRAGMENTPICKING
- FRAGMENTPICKING_ATOMPAIR_SCORE = ProfTag.FRAGMENTPICKING_ATOMPAIR_SCORE
- FRAGMENTPICKING_CANDIDATES_COLLECTING = ProfTag.FRAGMENTPICKING_CANDIDATES_COLLECTING
- FRAGMENTPICKING_CS_SCORE = ProfTag.FRAGMENTPICKING_CS_SCORE
- FRAGMENTPICKING_DIHEDRALCONSTR_SCORE = ProfTag.FRAGMENTPICKING_DIHEDRALCONSTR_SCORE
- FRAGMENTPICKING_PHIPSI_SCORE = ProfTag.FRAGMENTPICKING_PHIPSI_SCORE
- FRAGMENTPICKING_PROFILE_CAHING = ProfTag.FRAGMENTPICKING_PROFILE_CAHING
- FRAGMENTPICKING_PROFILE_SCORE = ProfTag.FRAGMENTPICKING_PROFILE_SCORE
- FRAGMENTPICKING_READ_VALL = ProfTag.FRAGMENTPICKING_READ_VALL
- FRAGMENTPICKING_SECONDARY_SCORE = ProfTag.FRAGMENTPICKING_SECONDARY_SCORE
- FRAGMENT_MOVER = ProfTag.FRAGMENT_MOVER
- FUNC = ProfTag.FUNC
- GB_GET_ALL_BORN_RADII = ProfTag.GB_GET_ALL_BORN_RADII
- GB_SETUP_FOR_PACKING = ProfTag.GB_SETUP_FOR_PACKING
- GEN_BORN_ROTAMER_BACKGROUND_ENERGIES = ProfTag.GEN_BORN_ROTAMER_BACKGROUND_ENERGIES
- GEN_BORN_ROTAMER_PAIR_ENERGIES = ProfTag.GEN_BORN_ROTAMER_PAIR_ENERGIES
- GET_ENERGIES = ProfTag.GET_ENERGIES
- HIERARCHICAL_ADD = ProfTag.HIERARCHICAL_ADD
- HIERARCHICAL_ADD_ELEM_TO_CACHE = ProfTag.HIERARCHICAL_ADD_ELEM_TO_CACHE
- HIERARCHICAL_EVALUATE = ProfTag.HIERARCHICAL_EVALUATE
- HIERARCHICAL_FIND = ProfTag.HIERARCHICAL_FIND
- HIERARCHICAL_FIND_ADDRESS = ProfTag.HIERARCHICAL_FIND_ADDRESS
- HIERARCHICAL_POOL_SIZE = ProfTag.HIERARCHICAL_POOL_SIZE
- HIERARCHICAL_ROUND = ProfTag.HIERARCHICAL_ROUND
- HIERARCHICAL_SORT_ADDRESSES = ProfTag.HIERARCHICAL_SORT_ADDRESSES
- HIERARCHY_FIND_ADDRESS = ProfTag.HIERARCHY_FIND_ADDRESS
- HIERARCHY_GET_NEXT_CANDIDATE = ProfTag.HIERARCHY_GET_NEXT_CANDIDATE
- HIERARCHY_RECV_COORDS = ProfTag.HIERARCHY_RECV_COORDS
- HIERARCHY_SEND_COORDS = ProfTag.HIERARCHY_SEND_COORDS
- HIERARCHY_SETUP_TO_RECV = ProfTag.HIERARCHY_SETUP_TO_RECV
- INITIALIZE = ProfTag.INITIALIZE
- INITIALIZE_HIERARCHY = ProfTag.INITIALIZE_HIERARCHY
- INSERT_FRAGS = ProfTag.INSERT_FRAGS
- JD2 = ProfTag.JD2
- JD2_INIT_MOVER = ProfTag.JD2_INIT_MOVER
- JD2_OUTPUT = ProfTag.JD2_OUTPUT
- JD2_SILENT_OUTPUTTER = ProfTag.JD2_SILENT_OUTPUTTER
- KDTREE_CONSTRUCT = ProfTag.KDTREE_CONSTRUCT
- KDTREE_SEARCH = ProfTag.KDTREE_SEARCH
- LIB_FULL_PATH = ProfTag.LIB_FULL_PATH
- LOAD_HIERARCHY = ProfTag.LOAD_HIERARCHY
- MAKE_BASE_PAIR_MOVE = ProfTag.MAKE_BASE_PAIR_MOVE
- MAKE_BASE_STEP_MOVE = ProfTag.MAKE_BASE_STEP_MOVE
- MASTER_PROCESS_NEW_STRUCTURES = ProfTag.MASTER_PROCESS_NEW_STRUCTURES
- MC_ACCEPT = ProfTag.MC_ACCEPT
- MINMOVER_APPLY = ProfTag.MINMOVER_APPLY
- MPIBARRIER = ProfTag.MPIBARRIER
- MPIBARRIER_BEGIN = ProfTag.MPIBARRIER_BEGIN
- MPIBARRIER_END = ProfTag.MPIBARRIER_END
- MPICANONICALSAMPLING = ProfTag.MPICANONICALSAMPLING
- MPICOMMCREATION = ProfTag.MPICOMMCREATION
- MPIH_ADD_FIRST_STRUCTURE = ProfTag.MPIH_ADD_FIRST_STRUCTURE
- MPIH_EVAL_AGAINST_NBR = ProfTag.MPIH_EVAL_AGAINST_NBR
- MPIH_EVAL_CHECK_PROGRESS = ProfTag.MPIH_EVAL_CHECK_PROGRESS
- MPIH_EVAL_COMMUNICATE_NEW = ProfTag.MPIH_EVAL_COMMUNICATE_NEW
- MPIH_PREPARE_WRITE_STRUCTURES = ProfTag.MPIH_PREPARE_WRITE_STRUCTURES
- MPIH_UPDATE_EVAL = ProfTag.MPIH_UPDATE_EVAL
- MPIH_WRITE_STRUCT = ProfTag.MPIH_WRITE_STRUCT
- MPIPOOLCOMMUNICATION = ProfTag.MPIPOOLCOMMUNICATION
- MPI_FILE_BUF = ProfTag.MPI_FILE_BUF
- MPI_GATHER_BARRIER = ProfTag.MPI_GATHER_BARRIER
- MPI_JD2_WAITS_FOR_ARCHIVE = ProfTag.MPI_JD2_WAITS_FOR_ARCHIVE
- MPI_MASTER_BCAST_COORDS = ProfTag.MPI_MASTER_BCAST_COORDS
- MPI_MASTER_BCAST_NEW_COMM_SIZE = ProfTag.MPI_MASTER_BCAST_NEW_COMM_SIZE
- MPI_MASTER_BCAST_NEW_POOL_RANKS = ProfTag.MPI_MASTER_BCAST_NEW_POOL_RANKS
- MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD = ProfTag.MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD
- MPI_MASTER_BCAST_WINNING_RANKS = ProfTag.MPI_MASTER_BCAST_WINNING_RANKS
- MPI_MASTER_BCAST_WINNING_STRUCTURES = ProfTag.MPI_MASTER_BCAST_WINNING_STRUCTURES
- MPI_NOTIFY_ARCHIVE = ProfTag.MPI_NOTIFY_ARCHIVE
- MPI_POOL_MASTER_THINKS = ProfTag.MPI_POOL_MASTER_THINKS
- MPI_POOL_SLAVE_THINKS = ProfTag.MPI_POOL_SLAVE_THINKS
- MPI_SEND_ACCEPTED = ProfTag.MPI_SEND_ACCEPTED
- MPI_SEND_UPDATE = ProfTag.MPI_SEND_UPDATE
- MPI_SLAVE_REPORT_NEW_COORDS = ProfTag.MPI_SLAVE_REPORT_NEW_COORDS
- MPI_SLAVE_REPORT_SIZES = ProfTag.MPI_SLAVE_REPORT_SIZES
- MPI_SYNC_POOL_DIFF = ProfTag.MPI_SYNC_POOL_DIFF
- MULTIPOLE_ENERGIES = ProfTag.MULTIPOLE_ENERGIES
- MULTIPOLE_SETUP = ProfTag.MULTIPOLE_SETUP
- NOESY_ASSIGN_CALIBRATE = ProfTag.NOESY_ASSIGN_CALIBRATE
- NOESY_ASSIGN_CHEMSHIFT = ProfTag.NOESY_ASSIGN_CHEMSHIFT
- NOESY_ASSIGN_CP_GEN_CST = ProfTag.NOESY_ASSIGN_CP_GEN_CST
- NOESY_ASSIGN_DECOY_COMP = ProfTag.NOESY_ASSIGN_DECOY_COMP
- NOESY_ASSIGN_DIAGONAL = ProfTag.NOESY_ASSIGN_DIAGONAL
- NOESY_ASSIGN_DISTANCE = ProfTag.NOESY_ASSIGN_DISTANCE
- NOESY_ASSIGN_DIST_APPLY = ProfTag.NOESY_ASSIGN_DIST_APPLY
- NOESY_ASSIGN_DIST_CST_CAST = ProfTag.NOESY_ASSIGN_DIST_CST_CAST
- NOESY_ASSIGN_DIST_CST_EVAL = ProfTag.NOESY_ASSIGN_DIST_CST_EVAL
- NOESY_ASSIGN_DIST_INIT = ProfTag.NOESY_ASSIGN_DIST_INIT
- NOESY_ASSIGN_DIST_MAKE_POSE = ProfTag.NOESY_ASSIGN_DIST_MAKE_POSE
- NOESY_ASSIGN_DIST_PREP_SCORE = ProfTag.NOESY_ASSIGN_DIST_PREP_SCORE
- NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE = ProfTag.NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE
- NOESY_ASSIGN_ELIMINATE = ProfTag.NOESY_ASSIGN_ELIMINATE
- NOESY_ASSIGN_GEN_CST = ProfTag.NOESY_ASSIGN_GEN_CST
- NOESY_ASSIGN_INITIAL = ProfTag.NOESY_ASSIGN_INITIAL
- NOESY_ASSIGN_MAP2CB = ProfTag.NOESY_ASSIGN_MAP2CB
- NOESY_ASSIGN_MAP2CB_NEW = ProfTag.NOESY_ASSIGN_MAP2CB_NEW
- NOESY_ASSIGN_NETWORK = ProfTag.NOESY_ASSIGN_NETWORK
- NOESY_ASSIGN_NETWORK_COMPUTE_NK = ProfTag.NOESY_ASSIGN_NETWORK_COMPUTE_NK
- NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA = ProfTag.NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA
- NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN = ProfTag.NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN
- NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE = ProfTag.NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE
- NOESY_ASSIGN_NETWORK_PEAK_COUNT = ProfTag.NOESY_ASSIGN_NETWORK_PEAK_COUNT
- NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL = ProfTag.NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL
- NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN = ProfTag.NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN
- NOESY_ASSIGN_NETWORK_TOTAL = ProfTag.NOESY_ASSIGN_NETWORK_TOTAL
- NOESY_ASSIGN_NMR_STRING = ProfTag.NOESY_ASSIGN_NMR_STRING
- NOESY_ASSIGN_PA_GEN_CST = ProfTag.NOESY_ASSIGN_PA_GEN_CST
- NOESY_ASSIGN_READ_INPUT = ProfTag.NOESY_ASSIGN_READ_INPUT
- NOESY_ASSIGN_REQUIRES_CB_MAPPING = ProfTag.NOESY_ASSIGN_REQUIRES_CB_MAPPING
- NOESY_ASSIGN_SYMMETRY = ProfTag.NOESY_ASSIGN_SYMMETRY
- NOESY_ASSIGN_TOTAL = ProfTag.NOESY_ASSIGN_TOTAL
- NOESY_ASSIGN_UPDATE_PEAK_VOL = ProfTag.NOESY_ASSIGN_UPDATE_PEAK_VOL
- NOESY_ASSIGN_WRITE_ASSIGNMENTS = ProfTag.NOESY_ASSIGN_WRITE_ASSIGNMENTS
- NOESY_ASSIGN_WRITE_CST = ProfTag.NOESY_ASSIGN_WRITE_CST
- PACK_ROTAMERS = ProfTag.PACK_ROTAMERS
- POOL_RMSD_ADD_STRUCTURE = ProfTag.POOL_RMSD_ADD_STRUCTURE
- POOL_RMSD_EVALUATE = ProfTag.POOL_RMSD_EVALUATE
- POOL_RMSD_MASTER_EVALUATE = ProfTag.POOL_RMSD_MASTER_EVALUATE
- POSE_COPY = ProfTag.POSE_COPY
- RG = ProfTag.RG
- RG_LOCAL = ProfTag.RG_LOCAL
- ROTAMER_TRIALS = ProfTag.ROTAMER_TRIALS
- SAVE_ARCHIVE = ProfTag.SAVE_ARCHIVE
- SAXS = ProfTag.SAXS
- SCORE = ProfTag.SCORE
- SCORE_BEGIN_NOTIFY = ProfTag.SCORE_BEGIN_NOTIFY
- SCORE_DOT = ProfTag.SCORE_DOT
- SCORE_END_NOTIFY = ProfTag.SCORE_END_NOTIFY
- SCORE_FINALIZE = ProfTag.SCORE_FINALIZE
- SCORE_LONG_RANGE_ENERGIES = ProfTag.SCORE_LONG_RANGE_ENERGIES
- SCORE_NEIGHBOR_ENERGIES = ProfTag.SCORE_NEIGHBOR_ENERGIES
- SCORE_ONEBODY_ENERGIES = ProfTag.SCORE_ONEBODY_ENERGIES
- SCORE_SETUP = ProfTag.SCORE_SETUP
- SECONDARY_STRUCTURE_ENERGY = ProfTag.SECONDARY_STRUCTURE_ENERGY
- SECONDARY_STRUCTURE_HSPAIR_ENERGY = ProfTag.SECONDARY_STRUCTURE_HSPAIR_ENERGY
- SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY = ProfTag.SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY
- SECONDARY_STRUCTURE_SSPAIR_ENERGY = ProfTag.SECONDARY_STRUCTURE_SSPAIR_ENERGY
- SEQUENCE_COMPARISON = ProfTag.SEQUENCE_COMPARISON
- SETUP_NBLIST = ProfTag.SETUP_NBLIST
- SIDECHAINMCMOVER = ProfTag.SIDECHAINMCMOVER
- SIDECHAINMOVER = ProfTag.SIDECHAINMOVER
- SILENT_FILL_POSE = ProfTag.SILENT_FILL_POSE
- SILENT_FILL_STRUCT = ProfTag.SILENT_FILL_STRUCT
- SILENT_READ_TAG_TEST = ProfTag.SILENT_READ_TAG_TEST
- SILENT_SET_POSE_COORDS = ProfTag.SILENT_SET_POSE_COORDS
- SIMANNEALING = ProfTag.SIMANNEALING
- SIMPLEINTGRAPH = ProfTag.SIMPLEINTGRAPH
- SORT_POOL = ProfTag.SORT_POOL
- STAGE1 = ProfTag.STAGE1
- STAGE2 = ProfTag.STAGE2
- STAGE3 = ProfTag.STAGE3
- STAGE4 = ProfTag.STAGE4
- STAGE5 = ProfTag.STAGE5
- TEST1 = ProfTag.TEST1
- TEST2 = ProfTag.TEST2
- TEST3 = ProfTag.TEST3
- TEST4 = ProfTag.TEST4
- TEST5 = ProfTag.TEST5
- TOTAL = ProfTag.n_prof_tags
- TRUNCATED_SCORE_EVALUATOR = ProfTag.TRUNCATED_SCORE_EVALUATOR
- UPDATE_RESIDUE_COORDINATES = ProfTag.UPDATE_RESIDUE_COORDINATES
- UPDATE_RESIDUE_NEIGHBORS = ProfTag.UPDATE_RESIDUE_NEIGHBORS
- UPDATE_RESIDUE_TORSIONS = ProfTag.UPDATE_RESIDUE_TORSIONS
- VDW_ENERGY = ProfTag.VDW_ENERGY
- WRITE_DECOYS_TO_HIERARCHY = ProfTag.WRITE_DECOYS_TO_HIERARCHY
- WRITE_TO_FILE = ProfTag.WRITE_TO_FILE
- n_prof_tags = ProfTag.n_prof_tags
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class Tracer(basic_otstream_char_std_char_traits_char_t) |
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Class for handling user debug/warnings/errors.
Use instance of this class instead of 'std::cout' for all your regular io.
Channel argument must be related to the location of the source file. For example if you create
Tracer object in src/basic/scoring/myfile.cc,
then channel must be something like 'src.basic.scoring.myfile'
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- Method resolution order:
- Tracer
- basic_otstream_char_std_char_traits_char_t
- builtins.object
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.basic.Tracer, priority : int) -> rosetta.basic.Tracer
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, str) -> NoneType
doc
3. __init__(handle, str, rosetta.basic.TracerPriority) -> NoneType
doc
4. __init__(self : handle, channel : str, priority : rosetta.basic.TracerPriority, muted_by_default : bool) -> NoneType
5. __init__(handle, str, str) -> NoneType
doc
6. __init__(handle, str, str, str) -> NoneType
doc
7. __init__(handle, str, str, str, rosetta.basic.TracerPriority) -> NoneType
doc
8. __init__(self : handle, channel : str, channel_color : str, channel_name_color : str, priority : rosetta.basic.TracerPriority, muted_by_default : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- calculate_tracer_visibilities(...) from builtins.PyCapsule
- calculate_tracer_visibilities() -> NoneType
This function should be invoked after the options system has been
initialized, so that the visibility for all tracers that have so far been
constructed and have been waiting for the options system to be initialized
can now have their visibility calculated. After this function completes,
all newly-constructed Tracers will calculate their visibility in their
constructors. Visibility is no longer be calculated on a just-in-time
basis and stored in mutable data members.
- channel(...) from builtins.PyCapsule
- channel(rosetta.basic.Tracer) -> str
- channel_color(...) from builtins.PyCapsule
- channel_color(*args, **kwargs)
Overloaded function.
1. channel_color(rosetta.basic.Tracer) -> str
Get the channel color.
2. channel_color(self : rosetta.basic.Tracer, color : str) -> NoneType
Set the channel color.
This can be done in a stream like this:
TR << TR.bgWhite << TR.Black << "Example" << TR.Reset << std::endl;
- channel_name_color(...) from builtins.PyCapsule
- channel_name_color(*args, **kwargs)
Overloaded function.
1. channel_name_color(rosetta.basic.Tracer) -> str
2. channel_name_color(self : rosetta.basic.Tracer, color : str) -> NoneType
- final_stream(...) from builtins.PyCapsule
- final_stream() -> std::ostream
set ios hook for final tracer stream (deafult is std::cout).
- flush_all_channels(...) from builtins.PyCapsule
- flush_all_channels(rosetta.basic.Tracer) -> NoneType
flush tracer buffer and flush buffers of all
sub-channels ie: Fatal, Error, Warning, Info, Debug, Trace
- flush_all_tracers(...) from builtins.PyCapsule
- flush_all_tracers() -> NoneType
- get_all_channels_string(...) from builtins.PyCapsule
- get_all_channels_string() -> str
- init(...) from builtins.PyCapsule
- init(self : rosetta.basic.Tracer, tr : rosetta.basic.Tracer) -> NoneType
re-init using data from another tracer object.
- priority(...) from builtins.PyCapsule
- priority(*args, **kwargs)
Overloaded function.
1. priority(rosetta.basic.Tracer) -> int
get/set tracer priority level.
2. priority(self : rosetta.basic.Tracer, priority : int) -> NoneType
- set_default_final_stream(...) from builtins.PyCapsule
- set_default_final_stream() -> NoneType
- set_ios_hook(...) from builtins.PyCapsule
- set_ios_hook(*args, **kwargs)
Overloaded function.
1. set_ios_hook(tr : rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list : str) -> NoneType
2. set_ios_hook(tr : rosetta.basic.basic_otstream_char_std_char_traits_char_t, monitoring_channels_list : str, raw : bool) -> NoneType
- super_mute(...) from builtins.PyCapsule
- super_mute(*args, **kwargs)
Overloaded function.
1. super_mute() -> bool
global super mute flag that allow to mute all io no matter what.
2. super_mute(f : bool) -> NoneType
- tracer_options(...) from builtins.PyCapsule
- tracer_options() -> rosetta.basic.TracerOptions
get/set tracer options - global options for Tracer IO.
- visible(...) from builtins.PyCapsule
- visible(*args, **kwargs)
Overloaded function.
1. visible(rosetta.basic.Tracer) -> bool
Is this tracer currently visible?.
2. visible(self : rosetta.basic.Tracer, priority : int) -> bool
is this tracer visible, if it used the given priority value?
Methods inherited from basic_otstream_char_std_char_traits_char_t:
- is_flushed(...) from builtins.PyCapsule
- is_flushed(rosetta.basic.basic_otstream_char_std_char_traits_char_t) -> bool
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class YamlEmitter(Emitter) |
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Emitter for more classically formatted YAML
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- Method resolution order:
- YamlEmitter
- Emitter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, out : std::ostream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- start_doc(...) from builtins.PyCapsule
- start_doc(rosetta.basic.YamlEmitter) -> NoneType
Start a new YAML document, ending the previous one first if necessary
Methods inherited from Emitter:
- depth(...) from builtins.PyCapsule
- depth(rosetta.basic.Emitter) -> int
Number of closing brackets/braces required to end document (non-negative)
- end(...) from builtins.PyCapsule
- end(*args, **kwargs)
Overloaded function.
1. end(rosetta.basic.Emitter) -> NoneType
By default, closes all open maps/lists, ending the document.
2. end(self : rosetta.basic.Emitter, desired_depth : int) -> NoneType
By default, closes all open maps/lists, ending the document.
- end_list(...) from builtins.PyCapsule
- end_list(rosetta.basic.Emitter) -> NoneType
Counterpart to start_list() -- writes closing bracket.
- end_map(...) from builtins.PyCapsule
- end_map(rosetta.basic.Emitter) -> NoneType
Counterpart to start_map() -- writes closing brace.
- flush(...) from builtins.PyCapsule
- flush(rosetta.basic.Emitter) -> NoneType
Flush the underlying output stream.
- set_indent(...) from builtins.PyCapsule
- set_indent(self : rosetta.basic.Emitter, num_spaces : int) -> NoneType
Number of spaces used for indenting. Default is one.
- start_list(...) from builtins.PyCapsule
- start_list(*args, **kwargs)
Overloaded function.
1. start_list(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_list(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_list(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_list(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
- start_map(...) from builtins.PyCapsule
- start_map(*args, **kwargs)
Overloaded function.
1. start_map(rosetta.basic.Emitter) -> NoneType
Write method for use inside lists / arrays
2. start_map(self : rosetta.basic.Emitter, indent : bool) -> NoneType
Write method for use inside lists / arrays
3. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
4. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
5. start_map(self : rosetta.basic.Emitter, label : str) -> NoneType
Write method for use inside maps / dicts / objects
6. start_map(self : rosetta.basic.Emitter, label : str, indent : bool) -> NoneType
Write method for use inside maps / dicts / objects
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