jobdist

Bindings for protocols::jobdist namespace

class pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor

Bases: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor

Distributor for use with atomtree_diff silent files.

This class is deliberately designed for each process to work on its own silent file (and preferrably in its own directory); unlike Rosetta++, we DO NOT share silent files among multiple processes. First, true atomic file locking is impossible on most distributed file systems (e.g. NFS), meaning that files may be corrupted by multiple simultaneous writes. For long-running processes, collisions may be rare, but as we scale to more processors it becomes increasingly dangerous. Second, many processes writing to the same file (or even directory) can cause tremendous file system bottlenecks, possibly bringing down the cluster; ask Keith or Chance in the Baker lab for details.

begin_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::begin_critical_section() –> void

disable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_ignorefinished() –> void

disable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_inprogress() –> void

disable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_output() –> void

dump_pose(self: pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor, tag: str, scores: pyrosetta.rosetta.std.map_std_string_double, ref_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) None

Appends pose to the silent file

C++: protocols::jobdist::AtomTreeDiffJobDistributor::dump_pose(const std::string &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, const class core::pose::Pose &, const class core::pose::Pose &) –> void

dump_pose_and_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str, : pyrosetta.rosetta.core.pose.Pose) None

Virtual function for dump_pose that is needed for main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::dump_pose_and_map(const std::string &, class core::pose::Pose &) –> void

enable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_ignorefinished() –> void

enable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_inprogress() –> void

enable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_output() –> void

end_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::end_critical_section() –> void

get_current_output_tag(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

get output_tag for current job’s current nstruct

by default return current_job’s current_nstruct’ output_tag.

Overridden in derived PlainSilentFileJobDistributor to return names with “S_” at the beginning

C++: protocols::jobdist::BaseJobDistributor::get_current_output_tag() –> std::string

get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

C++: protocols::jobdist::BaseJobDistributor::get_output_filename() –> std::string

ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::ignorefinished() const –> bool

inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::inprogress() const –> bool

next_job(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) bool
If true, sets the next Job and nstruct number to be processed.

Deliberately not virtual: should not be overriden. Uses the “find_available_job” method, which is common to both MPI and standard protocols, but used in slightly different manners.

C++: protocols::jobdist::BaseJobDistributor::next_job(class std::shared_ptr<class protocols::jobdist::BasicJob> &, int &) –> bool

nooutput(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::nooutput() const –> bool

score_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : pyrosetta.rosetta.std.map_std_string_double) None
Virtual function for score_map that is needed for main_plain_mover

sets the score_map

C++: protocols::jobdist::BaseJobDistributor::score_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_precision(self: pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor, bb_precision: int, sc_precision: int, bondlen_precision: int) None

Sets number of digits used in writing atomtree diff.

C++: protocols::jobdist::AtomTreeDiffJobDistributor::set_precision(int, int, int) –> void

set_proc_id(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, proc_id: int, nproc: int) None

C++: protocols::jobdist::BaseJobDistributor::set_proc_id(unsigned long, unsigned long) –> void

shutdown(self: pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor) None

C++: protocols::jobdist::AtomTreeDiffJobDistributor::shutdown() –> void

startup(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client before first call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::startup() –> void

temp_file(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str) None

Virtual function for temp_file main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::temp_file(const std::string &) –> void

class pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor

Bases: pybind11_builtins.pybind11_object

Coordinates processing of jobs across multiple Rosetta processes.

Job distributors need to be customized in three different ways:
  • by cluster architecture (none/Condor, MPI, BOINC, etc)

  • by local test for job completion (PDB exists, tag already in silent file, etc)

  • by type of input (single PDB file, pair of PDB files, list of tag IDs, etc)

Cluster architecture is a GLOBAL COMPILE-TIME decision: it’s handled by scons, it’s the same for all executables built at that time, and it should be implemented using ifdef’s in this base class, by modifying the next_job() method directly.

Test for job completion is a PER-EXECUTABLE decision: it’s handled by subclassing BaseJobDistributor and implementing the is_finished() method. BaseJobDistributor will consult is_finished() in whatever way is appropriate for the current cluster architecture to ensure that jobs are not repeated.

Type of input is handled by templating the job distributor on a Job object. BasicJob has been provided already, but you can subclass it if you need to carry around additional information about the inputs.

begin_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::begin_critical_section() –> void

disable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_ignorefinished() –> void

disable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_inprogress() –> void

disable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_output() –> void

dump_pose_and_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str, : pyrosetta.rosetta.core.pose.Pose) None

Virtual function for dump_pose that is needed for main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::dump_pose_and_map(const std::string &, class core::pose::Pose &) –> void

enable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_ignorefinished() –> void

enable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_inprogress() –> void

enable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_output() –> void

end_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::end_critical_section() –> void

get_current_output_tag(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

get output_tag for current job’s current nstruct

by default return current_job’s current_nstruct’ output_tag.

Overridden in derived PlainSilentFileJobDistributor to return names with “S_” at the beginning

C++: protocols::jobdist::BaseJobDistributor::get_current_output_tag() –> std::string

get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

C++: protocols::jobdist::BaseJobDistributor::get_output_filename() –> std::string

ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::ignorefinished() const –> bool

inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::inprogress() const –> bool

next_job(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) bool
If true, sets the next Job and nstruct number to be processed.

Deliberately not virtual: should not be overriden. Uses the “find_available_job” method, which is common to both MPI and standard protocols, but used in slightly different manners.

C++: protocols::jobdist::BaseJobDistributor::next_job(class std::shared_ptr<class protocols::jobdist::BasicJob> &, int &) –> bool

nooutput(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::nooutput() const –> bool

score_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : pyrosetta.rosetta.std.map_std_string_double) None
Virtual function for score_map that is needed for main_plain_mover

sets the score_map

C++: protocols::jobdist::BaseJobDistributor::score_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_proc_id(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, proc_id: int, nproc: int) None

C++: protocols::jobdist::BaseJobDistributor::set_proc_id(unsigned long, unsigned long) –> void

shutdown(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client after last call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::shutdown() –> void

startup(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client before first call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::startup() –> void

temp_file(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str) None

Virtual function for temp_file main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::temp_file(const std::string &) –> void

class pyrosetta.rosetta.protocols.jobdist.BasicJob

Bases: pybind11_builtins.pybind11_object

Each Job object describes a particular input to Rosetta.

Ordinarily, an input is just a single PDB file. In other cases, e.g. docking, input might be a pair of PDB files. In still other cases, input might be a list of tags to extract from a silent file. And so on. One BasicJob class is defined below that should meet most needs, but if you need to carry additional information, you can subclass it.

Contains a map of strings to strings that can be used to store arbitrary extra data if you’re too lazy to make a subclass. Templated get/set functions accept anything that can be read from and written to a C++ stream with >> and << operators. All data is stored as strings internally. Some numeric data may experience slight round-off error, though I think we’re storing enough digits to avoid that.

Example:

BasicJob jobdata(“1abc.pdb”, 10); jobdata.set(“cmp_to”, “1xyz.pdb”); jobdata.set(“score”, 42.42);

std::string cmp_to; core::Real score; if( jobdata.get(“cmp_to”, cmp_to) ) std::cout << “cmp_to = ” << cmp_to << std::endl; else std::cout << “Unable to recover cmp_to!” << std::endl; if( jobdata.get(“score”, score) ) std::cout << “score = ” << score << std::endl; else std::cout << “Unable to recover score!” << std::endl;

Although Jobs are small objects, it is common for Rosetta to loop many times over the same input. In order to avoid creating (size of -s and -l) * (nstruct) JobData objects, each Job also has an nstruct counter.

So, each Job represents a unique input, and each tuple of (Job, struct_n) represents a unique output.

assign(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, : pyrosetta.rosetta.protocols.jobdist.BasicJob) pyrosetta.rosetta.protocols.jobdist.BasicJob

C++: protocols::jobdist::BasicJob::operator=(const class protocols::jobdist::BasicJob &) –> class protocols::jobdist::BasicJob &

get(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, key: str, value: str) bool

Specialization for strings.

C++: protocols::jobdist::BasicJob::get(const std::string &, std::string &) –> bool

input_tag(self: pyrosetta.rosetta.protocols.jobdist.BasicJob) str

The tag supplied at create time.

C++: protocols::jobdist::BasicJob::input_tag() const –> std::string

native_tag(self: pyrosetta.rosetta.protocols.jobdist.BasicJob) str

The tag supplied at create time.

C++: protocols::jobdist::BasicJob::native_tag() const –> std::string

nstruct(self: pyrosetta.rosetta.protocols.jobdist.BasicJob) int

The number of times this job should be repeated.

C++: protocols::jobdist::BasicJob::nstruct() const –> int

output_file_name(self: pyrosetta.rosetta.protocols.jobdist.BasicJob) str

The tag supplied at create time plus the nstruct number (from 1 to nstruct inclusive).

C++: protocols::jobdist::BasicJob::output_file_name() const –> std::string

output_tag(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, struct_n: int) str

The tag supplied at create time plus the nstruct number (from 1 to nstruct inclusive).

C++: protocols::jobdist::BasicJob::output_tag(int) const –> std::string

set(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, key: str, value: str) None

Specialization for strings.

C++: protocols::jobdist::BasicJob::set(const std::string &, const std::string &) –> void

set_output_file_name(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, str: str) None

The tag supplied at create time plus the nstruct number (from 1 to nstruct inclusive).

C++: protocols::jobdist::BasicJob::set_output_file_name(std::string) –> void

set_preserve_whole_input_tag(self: pyrosetta.rosetta.protocols.jobdist.BasicJob, setting: bool) None

C++: protocols::jobdist::BasicJob::set_preserve_whole_input_tag(bool) –> void

class pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor

Bases: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor

Distributor for use with plain old PDB files. Use is strongly discouraged in production environments!

This class is deliberately designed for each process to write its own PDB files in its own directory; it checks for pre-existing files only for use by stopped and re-started jobs, NOT for coordinating between processes. (To coordinate, it would have to “touch” the non-existant file in next_job() before starting to process it, but see AtomtreeDiffJobDistributor for an explanation of why coordinating processes via the filesystem is a bad idea.)

begin_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::begin_critical_section() –> void

disable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_ignorefinished() –> void

disable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_inprogress() –> void

disable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_output() –> void

dump_pose_and_map(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor, tag: str, pose: pyrosetta.rosetta.core.pose.Pose) None

Writes pose and basic score data to a standard PDB file.

C++: protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map(const std::string &, class core::pose::Pose &) –> void

enable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_ignorefinished() –> void

enable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_inprogress() –> void

enable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_output() –> void

end_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::end_critical_section() –> void

get_current_output_tag(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

get output_tag for current job’s current nstruct

by default return current_job’s current_nstruct’ output_tag.

Overridden in derived PlainSilentFileJobDistributor to return names with “S_” at the beginning

C++: protocols::jobdist::BaseJobDistributor::get_current_output_tag() –> std::string

get_output_filename(*args, **kwargs)

Overloaded function.

  1. get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor) -> str

  2. get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor, tag: str) -> str

Translates an output tag name to an output PDB file name.

C++: protocols::jobdist::PlainPdbJobDistributor::get_output_filename(const std::string &) –> std::string

ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::ignorefinished() const –> bool

inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::inprogress() const –> bool

next_job(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) bool
If true, sets the next Job and nstruct number to be processed.

Deliberately not virtual: should not be overriden. Uses the “find_available_job” method, which is common to both MPI and standard protocols, but used in slightly different manners.

C++: protocols::jobdist::BaseJobDistributor::next_job(class std::shared_ptr<class protocols::jobdist::BasicJob> &, int &) –> bool

nooutput(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::nooutput() const –> bool

score_map(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor, score_map_in: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jobdist::PlainPdbJobDistributor::score_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_proc_id(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, proc_id: int, nproc: int) None

C++: protocols::jobdist::BaseJobDistributor::set_proc_id(unsigned long, unsigned long) –> void

shutdown(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client after last call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::shutdown() –> void

startup(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor) None

Allows setting of inprogress.

C++: protocols::jobdist::PlainPdbJobDistributor::startup() –> void

temp_file(self: pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor, tag: str) None

Opens a temp file (.in_progress)

C++: protocols::jobdist::PlainPdbJobDistributor::temp_file(const std::string &) –> void

class pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor

Bases: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor

Distributor for use with raw files.

This class is deliberately designed for each process to work on its own silent file (and preferrably in its own directory); unlike Rosetta++, we DO NOT share silent files among multiple processes. First, true atomic file locking is impossible on most distributed file systems (e.g. NFS), meaning that files may be corrupted by multiple simultaneous writes. For long-running processes, collisions may be rare, but as we scale to more processors it becomes increasingly dangerous. Second, many processes writing to the same file (or even directory) can cause tremendous file system bottlenecks, possibly bringing down the cluster; ask Keith or Chance in the Baker lab for details.

begin_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::begin_critical_section() –> void

disable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_ignorefinished() –> void

disable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_inprogress() –> void

disable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_output() –> void

dump_pose_and_map(self: pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor, tag: str, pose: pyrosetta.rosetta.core.pose.Pose) None

Writes pose and basic score data to a standard silent file.

C++: protocols::jobdist::PlainRawJobDistributor::dump_pose_and_map(const std::string &, class core::pose::Pose &) –> void

enable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_ignorefinished() –> void

enable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_inprogress() –> void

enable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_output() –> void

end_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::end_critical_section() –> void

get_current_output_tag(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) str

get output_tag for current job’s current nstruct

by default return current_job’s current_nstruct’ output_tag.

Overridden in derived PlainSilentFileJobDistributor to return names with “S_” at the beginning

C++: protocols::jobdist::BaseJobDistributor::get_current_output_tag() –> std::string

get_output_filename(*args, **kwargs)

Overloaded function.

  1. get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor) -> str

  2. get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor, tag: str) -> str

Translates an output tag name to an output PDB file name.

C++: protocols::jobdist::PlainRawJobDistributor::get_output_filename(const std::string &) –> std::string

get_output_tag(self: pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor, struct_n: int) str

C++: protocols::jobdist::PlainRawJobDistributor::get_output_tag(const int &) –> std::string

ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::ignorefinished() const –> bool

inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::inprogress() const –> bool

next_job(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) bool
If true, sets the next Job and nstruct number to be processed.

Deliberately not virtual: should not be overriden. Uses the “find_available_job” method, which is common to both MPI and standard protocols, but used in slightly different manners.

C++: protocols::jobdist::BaseJobDistributor::next_job(class std::shared_ptr<class protocols::jobdist::BasicJob> &, int &) –> bool

nooutput(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::nooutput() const –> bool

score_map(self: pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor, score_map_in: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jobdist::PlainRawJobDistributor::score_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_proc_id(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, proc_id: int, nproc: int) None

C++: protocols::jobdist::BaseJobDistributor::set_proc_id(unsigned long, unsigned long) –> void

shutdown(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client after last call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::shutdown() –> void

startup(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Must be called by client before first call to next_job().

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::startup() –> void

temp_file(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str) None

Virtual function for temp_file main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::temp_file(const std::string &) –> void

class pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor

Bases: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor

Distributor for use with silent files.

This class is deliberately designed for each process to work on its own silent file (and preferrably in its own directory); unlike Rosetta++, we DO NOT share silent files among multiple processes. First, true atomic file locking is impossible on most distributed file systems (e.g. NFS), meaning that files may be corrupted by multiple simultaneous writes. For long-running processes, collisions may be rare, but as we scale to more processors it becomes increasingly dangerous. Second, many processes writing to the same file (or even directory) can cause tremendous file system bottlenecks, possibly bringing down the cluster; ask Keith or Chance in the Baker lab for details.

begin_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::begin_critical_section() –> void

disable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_ignorefinished() –> void

disable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_inprogress() –> void

disable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::disable_output() –> void

dump_pose(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor, job: protocols::jobdist::BasicJob, nstruct: int, fullatom: bool, pose: pyrosetta.rosetta.core.pose.Pose) None

Writes pose and basic score data to a standard silent file.

C++: protocols::jobdist::PlainSilentFileJobDistributor::dump_pose(const class std::shared_ptr<class protocols::jobdist::BasicJob> &, const int &, const bool &, class core::pose::Pose &) –> void

dump_pose_and_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str, : pyrosetta.rosetta.core.pose.Pose) None

Virtual function for dump_pose that is needed for main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::dump_pose_and_map(const std::string &, class core::pose::Pose &) –> void

dump_silent(*args, **kwargs)

Overloaded function.

  1. dump_silent(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor, struct_n: int, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

Writes the silent_struct to a silen file

C++: protocols::jobdist::PlainSilentFileJobDistributor::dump_silent(const int &, class core::io::silent::SilentStruct &) –> void

  1. dump_silent(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor, silent_file: pyrosetta.rosetta.core.io.silent.SilentFileData) -> None

C++: protocols::jobdist::PlainSilentFileJobDistributor::dump_silent(const class core::io::silent::SilentFileData &) –> void

enable_ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_ignorefinished() –> void

enable_inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_inprogress() –> void

enable_output(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None

C++: protocols::jobdist::BaseJobDistributor::enable_output() –> void

end_critical_section(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) None
Signal that if at all possible, we would like to not be killed while in the critical section.

If overriden by a subclass, it MUST call the superclass implementation.

C++: protocols::jobdist::BaseJobDistributor::end_critical_section() –> void

get_current_output_tag(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor) str

C++: protocols::jobdist::PlainSilentFileJobDistributor::get_current_output_tag() –> std::string

get_output_filename(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor) str

C++: protocols::jobdist::PlainSilentFileJobDistributor::get_output_filename() –> std::string

get_output_tag(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) str

C++: protocols::jobdist::PlainSilentFileJobDistributor::get_output_tag(const class std::shared_ptr<class protocols::jobdist::BasicJob> &, const int &) const –> std::string

ignorefinished(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::ignorefinished() const –> bool

inprogress(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::inprogress() const –> bool

next_job(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, job: protocols::jobdist::BasicJob, struct_n: int) bool
If true, sets the next Job and nstruct number to be processed.

Deliberately not virtual: should not be overriden. Uses the “find_available_job” method, which is common to both MPI and standard protocols, but used in slightly different manners.

C++: protocols::jobdist::BaseJobDistributor::next_job(class std::shared_ptr<class protocols::jobdist::BasicJob> &, int &) –> bool

nooutput(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor) bool

C++: protocols::jobdist::BaseJobDistributor::nooutput() const –> bool

score_map(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : pyrosetta.rosetta.std.map_std_string_double) None
Virtual function for score_map that is needed for main_plain_mover

sets the score_map

C++: protocols::jobdist::BaseJobDistributor::score_map(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_proc_id(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, proc_id: int, nproc: int) None

C++: protocols::jobdist::BaseJobDistributor::set_proc_id(unsigned long, unsigned long) –> void

shutdown(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor) None

C++: protocols::jobdist::PlainSilentFileJobDistributor::shutdown() –> void

startup(self: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor) None

C++: protocols::jobdist::PlainSilentFileJobDistributor::startup() –> void

temp_file(self: pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor, : str) None

Virtual function for temp_file main_plain_mover

C++: protocols::jobdist::BaseJobDistributor::temp_file(const std::string &) –> void

pyrosetta.rosetta.protocols.jobdist.get_output_tag(pose: pyrosetta.rosetta.core.pose.Pose) str

Helper function to safely get current output tag that’s cached in Pose.

C++: protocols::jobdist::get_output_tag(const class core::pose::Pose &) –> std::string

pyrosetta.rosetta.protocols.jobdist.get_score_map(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_double

Helper function to safely get score_map that’s cached in Pose.

C++: protocols::jobdist::get_score_map(const class core::pose::Pose &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.jobdist.load_s_and_l() pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_jobdist_BasicJob_t

Makes BasicJob objects from command line flags -s, -l, and -nstruct.

C++: protocols::jobdist::load_s_and_l() –> class utility::vector1<class std::shared_ptr<class protocols::jobdist::BasicJob>, class std::allocator<class std::shared_ptr<class protocols::jobdist::BasicJob> > >

pyrosetta.rosetta.protocols.jobdist.main_plain_mover(*args, **kwargs)

Overloaded function.

  1. main_plain_mover(mover: pyrosetta.rosetta.protocols.moves.Mover) -> int

  2. main_plain_mover(mover: pyrosetta.rosetta.protocols.moves.Mover, random_permutation: bool) -> int

Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files.

Supplied Mover is used to transform input structure into output structure.

C++: protocols::jobdist::main_plain_mover(class protocols::moves::Mover &, bool) –> int

pyrosetta.rosetta.protocols.jobdist.main_plain_pdb_mover(mover: pyrosetta.rosetta.protocols.moves.Mover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) int
Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files.

Supplied Mover is used to transform input structure into output structure.

C++: protocols::jobdist::main_plain_pdb_mover(class protocols::moves::Mover &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> int

pyrosetta.rosetta.protocols.jobdist.not_universal_main(mover: pyrosetta.rosetta.protocols.moves.Mover) int

C++: protocols::jobdist::not_universal_main(class protocols::moves::Mover &) –> int

pyrosetta.rosetta.protocols.jobdist.pose_matches_user_tag(pose: pyrosetta.rosetta.core.pose.Pose, user_tags: pyrosetta.rosetta.utility.vector1_std_string) bool

C++: protocols::jobdist::pose_matches_user_tag(class core::pose::Pose &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> bool

pyrosetta.rosetta.protocols.jobdist.register_options_universal_main() None
Handles loading and writing of silent files and or PDB files - superseeds the bottom two

functions.

C++: protocols::jobdist::register_options_universal_main() –> void

pyrosetta.rosetta.protocols.jobdist.universal_main(*args, **kwargs)

Overloaded function.

  1. universal_main(mover: pyrosetta.rosetta.protocols.moves.Mover) -> int

  2. universal_main(mover: pyrosetta.rosetta.protocols.moves.Mover, thinout_factor: float) -> int

C++: protocols::jobdist::universal_main(class protocols::moves::Mover &, float) –> int