comparative_modeling

• features

Bindings for protocols::comparative_modeling namespace

class pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator

Bases: pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator

creator for the AlignRmsdTargetEvaluatorCreator class

add_evaluators(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, : pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::operator=(const class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &) –> class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &

register_options(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → None

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::register_options() –> void

type_name(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → str

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter

Bases: pyrosetta.rosetta.protocols.jd2.JobInputter

This is the simplest implementation of JobInputter

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) → pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter

C++: protocols::comparative_modeling::GenericJobInputter::operator=(const class protocols::comparative_modeling::GenericJobInputter &) –> class protocols::comparative_modeling::GenericJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, jobs: pyrosetta.rosetta.protocols.jd2.JobsContainer) → None

this function determines what jobs exist

C++: protocols::comparative_modeling::GenericJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum

Return the type of input source that the GenericJobInputter is currently

using.

Always POSE.

C++: protocols::comparative_modeling::GenericJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) → str

call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) → None

this function is responsible for filling the pose reference with

the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

C++: protocols::comparative_modeling::GenericJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) → None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob

Bases: pyrosetta.rosetta.protocols.jd2.InnerJob

The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is. InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct. The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs). InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.

alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) → pyrosetta.rosetta.core.sequence.SequenceAlignment

the alignment for this Job

C++: protocols::comparative_modeling::ThreadingJob::alignment() const –> const class core::sequence::SequenceAlignment &

alignment_id(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) → str

convenience : alignment id

C++: protocols::comparative_modeling::ThreadingJob::alignment_id() const –> std::string

bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → bool

C++: protocols::jd2::InnerJob::bad() const –> bool

clone(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → pyrosetta.rosetta.protocols.jd2.InnerJob

Return an owning pointer to a copy of this object.

C++: protocols::jd2::InnerJob::clone() const –> class std::shared_ptr<class protocols::jd2::InnerJob>

current_job() → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob

Convenience function to get the current ThreadingJob from JD2

Will return a nullptr if we can’t get a ThreadingJob from JD2

C++: protocols::comparative_modeling::ThreadingJob::current_job() –> const class protocols::comparative_modeling::ThreadingJob *

extra_residues_to_steal(*args, **kwargs)

Overloaded function.

1. extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) -> pyrosetta.rosetta.utility.vector1_unsigned_long

returns list of extra residues to steal

C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

2. extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

get_pose(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → pyrosetta.rosetta.core.pose.Pose

return a COP to the input pose

DO NOT USE OUTSIDE OF JD2 NAMESPACE

C++: protocols::jd2::InnerJob::get_pose() const –> class std::shared_ptr<const class core::pose::Pose>

input_tag(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → str

return the input tag (a string of space separated PDB filenames)

C++: protocols::jd2::InnerJob::input_tag() const –> const std::string &

loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, nres: int) → pyrosetta.rosetta.protocols.loops.Loops

returns the “standard” loop definition (as conservative as possible)

C++: protocols::comparative_modeling::ThreadingJob::loops(unsigned long) const –> class protocols::loops::Loops

nstruct_max(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → int

C++: protocols::jd2::InnerJob::nstruct_max() const –> unsigned long

optional_output_name(*args, **kwargs)

Overloaded function.

1. optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> str

returns a job name controlled by the mover. Must be turned with the optional_output_name out flag. This flag is typically used in conjuction with a mover

C++: protocols::jd2::InnerJob::optional_output_name() const –> const std::string &

2. optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob, output_name: str) -> None

sets a job name controlled by the mover

C++: protocols::jd2::InnerJob::optional_output_name(class std::basic_string<char>) –> void

same(self: pyrosetta.rosetta.protocols.jd2.InnerJob, other: pyrosetta.rosetta.protocols.jd2.InnerJob) → bool

returns true if this is the same as other;

does not call other.same()

C++: protocols::jd2::InnerJob::same(const class protocols::jd2::InnerJob &) const –> bool

set_bad(*args, **kwargs)

Overloaded function.

1. set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> None
2. set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob, value: bool) -> None

C++: protocols::jd2::InnerJob::set_bad(bool) –> void

show(self: pyrosetta.rosetta.protocols.jd2.InnerJob, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::jd2::InnerJob::show(class std::basic_ostream<char> &) const –> void

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter

Bases: pyrosetta.rosetta.protocols.jd2.JobInputter

This is the simplest implementation of JobInputter

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter

C++: protocols::comparative_modeling::ThreadingJobInputter::operator=(const class protocols::comparative_modeling::ThreadingJobInputter &) –> class protocols::comparative_modeling::ThreadingJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, jobs: pyrosetta.rosetta.protocols.jd2.JobsContainer) → None

this function determines what jobs exist

C++: protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum

Return the type of input source that the ThreadingJobInputter is

currently using for template structures.

C++: protocols::comparative_modeling::ThreadingJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) → str

call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) → None

this function is responsible for filling the pose reference with

the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

C++: protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) → None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

pyrosetta.rosetta.protocols.comparative_modeling.alignments_from_cmd_line() → pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet

C++: protocols::comparative_modeling::alignments_from_cmd_line() –> class protocols::comparative_modeling::AlignmentSet

pyrosetta.rosetta.protocols.comparative_modeling.bounded_loops_from_alignment(num_residues: int, min_size: int, alignment: pyrosetta.rosetta.core.sequence.SequenceAlignment, unaligned_regions: pyrosetta.rosetta.protocols.loops.Loops) → None

Identifies consecutive stretches of unaligned residues by scanning

the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>.

C++: protocols::comparative_modeling::bounded_loops_from_alignment(const unsigned long, const unsigned long, const class core::sequence::SequenceAlignment &, class std::shared_ptr<class protocols::loops::Loops> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.cm_main() → None

Initiates LoopRelaxThreadingMover using the job distributor (jd2)

C++: protocols::comparative_modeling::cm_main() –> void

pyrosetta.rosetta.protocols.comparative_modeling.gather_coords(*args, **kwargs)

Overloaded function.

1. gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: ObjexxFCL::FArray2D<double>, p2a: ObjexxFCL::FArray2D<double>) -> None
2. gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: ObjexxFCL::FArray2D<double>, p2a: ObjexxFCL::FArray2D<double>, atom_name: str) -> None

C++: protocols::comparative_modeling::gather_coords(const class core::pose::Pose &, const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, int &, class ObjexxFCL::FArray2D<double> &, class ObjexxFCL::FArray2D<double> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.get_qt_mapping_general(query_pose: pyrosetta.rosetta.core.pose.Pose, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose, query_index: int, template_index: int) → pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::comparative_modeling::get_qt_mapping_general(const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> class core::id::SequenceMapping

pyrosetta.rosetta.protocols.comparative_modeling.initialize_ss(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::initialize_ss(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.loops_are_closed(pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::comparative_modeling::loops_are_closed(class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.comparative_modeling.loops_from_alignment(nres: int, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::loops_from_alignment(unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.loops_from_transitive_alignments(nres1: int, aln1: pyrosetta.rosetta.core.sequence.SequenceAlignment, nres2: int, aln2: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::loops_from_transitive_alignments(unsigned long, const class core::sequence::SequenceAlignment &, unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.pick_loops_chainbreak(query_pose: pyrosetta.rosetta.core.pose.Pose, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::pick_loops_chainbreak(class core::pose::Pose &, unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.pick_loops_unaligned(nres: int, unaligned_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::pick_loops_unaligned(unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.poses_from_cmd_line(fn_list: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.std.map_std_string_core_pose_Pose

C++: protocols::comparative_modeling::poses_from_cmd_line(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> class std::map<std::string, class core::pose::Pose, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::pose::Pose> > >

pyrosetta.rosetta.protocols.comparative_modeling.randomize_selected_atoms(query_pose: pyrosetta.rosetta.core.pose.Pose, selected: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) → None

C++: protocols::comparative_modeling::randomize_selected_atoms(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.rebuild_loops_until_closed(query_pose: pyrosetta.rosetta.core.pose.Pose, min_loop_size: int, max_times: int, loop_mover_name: str) → None

C++: protocols::comparative_modeling::rebuild_loops_until_closed(class core::pose::Pose &, const unsigned long, const unsigned long, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.steal_ligands(dest_pose: pyrosetta.rosetta.core.pose.Pose, source_pose_in: pyrosetta.rosetta.core.pose.Pose, anchor_atom_dest: pyrosetta.rosetta.core.id.NamedAtomID, anchor_atom_source: pyrosetta.rosetta.core.id.NamedAtomID, ligand_indices: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) → None

Function for stealing ligands from a given Pose

and adding them to source_pose.

: The parameters are:

dest_pose Pose to which ligands are added.

source_pose_in Pose from which ligands and orientations are taken.

anchor_atom_dest anchor atom providing reference in dest_pose for ligand orientation.

anchor_atom_source anchor atom providing reference in source_pose for ligand orientation.

ligand_indices list of AtomID entries for ligand, one per ligand. Ligand orientation is determined by orientation between anchor_atom_source and each ligand AtomID.

C++: protocols::comparative_modeling::steal_ligands(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::NamedAtomID &, const class core::id::NamedAtomID &, const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.templates_from_cmd_line() → pyrosetta.rosetta.utility.vector1_core_pose_Pose

C++: protocols::comparative_modeling::templates_from_cmd_line() –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >