hydrate

Bindings for protocols::hydrate namespace

class pyrosetta.rosetta.protocols.hydrate.Hydrate

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.hydrate.Hydrate, input_pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the corresponding move to <input_pose>.

C++: protocols::hydrate::Hydrate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.hydrate.Hydrate, hyd: pyrosetta.rosetta.protocols.hydrate.Hydrate) pyrosetta.rosetta.protocols.hydrate.Hydrate

C++: protocols::hydrate::Hydrate::operator=(const class protocols::hydrate::Hydrate &) –> class protocols::hydrate::Hydrate &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.hydrate.Hydrate) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::hydrate::Hydrate::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.hydrate.Hydrate) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::hydrate::Hydrate::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.hydrate.Hydrate) str

Return the name of the Mover.

C++: protocols::hydrate::Hydrate::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

pyrosetta.rosetta.protocols.hydrate.add_water_overcoordinated_hb_score(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::hydrate::add_water_overcoordinated_hb_score(class core::pose::Pose &, class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.protocols.hydrate.append_single_far_away_water(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::append_single_far_away_water(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.atom_is_hydratable(*args, **kwargs)

Overloaded function.

  1. atom_is_hydratable(pose: pyrosetta.rosetta.core.pose.Pose, residue: int, atom: str) -> bool

C++: protocols::hydrate::atom_is_hydratable(const class core::pose::Pose &, const unsigned long, const std::string &) –> bool

  1. atom_is_hydratable(pose: pyrosetta.rosetta.core.pose.Pose, residue: int, atom: int) -> bool

C++: protocols::hydrate::atom_is_hydratable(const class core::pose::Pose &, const unsigned long, const unsigned long) –> bool

pyrosetta.rosetta.protocols.hydrate.calculate_water_overcoordinated_hb_correction(pose: pyrosetta.rosetta.core.pose.Pose, water_hb_correction: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::hydrate::calculate_water_overcoordinated_hb_correction(const class core::pose::Pose &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.protocols.hydrate.enforce_all_waters(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::enforce_all_waters(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.get_ready_for_sew_packing(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::hydrate::get_ready_for_sew_packing(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

pyrosetta.rosetta.protocols.hydrate.hydrate_cavities(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::hydrate_cavities(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.hydrate_hyfile(pose: pyrosetta.rosetta.core.pose.Pose, hydrate_V: pyrosetta.rosetta.utility.vector1_bool, resfile: str) None

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

pyrosetta.rosetta.protocols.hydrate.is_inside(pose: pyrosetta.rosetta.core.pose.Pose, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) bool

C++: protocols::hydrate::is_inside(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> bool

pyrosetta.rosetta.protocols.hydrate.place_de_novo_wat_at_anchor(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::place_de_novo_wat_at_anchor(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.print_residues_near_water(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::print_residues_near_water(const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.read_hyfile(hyfile: str, enforced_V: pyrosetta.rosetta.utility.vector1_bool, hydrate_V: pyrosetta.rosetta.utility.vector1_bool) None

C++: protocols::hydrate::read_hyfile(const std::string &, class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) –> void

pyrosetta.rosetta.protocols.hydrate.remove_all_anchors_and_ENF(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::remove_all_anchors_and_ENF(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.remove_high_energy_water_molecules(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::hydrate::remove_high_energy_water_molecules(class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.protocols.hydrate.remove_non_buried_wat(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::remove_non_buried_wat(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.residue_near_water(pose: pyrosetta.rosetta.core.pose.Pose, ii: int) bool

C++: protocols::hydrate::residue_near_water(const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.protocols.hydrate.set_bb_movemap(pose: pyrosetta.rosetta.core.pose.Pose, mini_backbone_file_name: str, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::hydrate::set_bb_movemap(const class core::pose::Pose &, const std::string &, class core::kinematics::MoveMap &) –> void

pyrosetta.rosetta.protocols.hydrate.set_dew_waters_not_to_be_included(pose: pyrosetta.rosetta.core.pose.Pose, partial_hydrate_dew: float) None

C++: protocols::hydrate::set_dew_waters_not_to_be_included(class core::pose::Pose &, const double) –> void

pyrosetta.rosetta.protocols.hydrate.set_task_and_movemap(pose: pyrosetta.rosetta.core.pose.Pose, protein_flexibility: str, task: pyrosetta.rosetta.core.pack.task.PackerTask, mm: pyrosetta.rosetta.core.kinematics.MoveMap, minimize_bb_where_packing: bool) None

C++: protocols::hydrate::set_task_and_movemap(const class core::pose::Pose &, const std::string &, class std::shared_ptr<class core::pack::task::PackerTask> &, class core::kinematics::MoveMap &, const bool) –> void

pyrosetta.rosetta.protocols.hydrate.set_task_with_de_novo_water_using_resfile(pose: pyrosetta.rosetta.core.pose.Pose, resfile: str, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::hydrate::set_task_with_de_novo_water_using_resfile(class core::pose::Pose &, std::string, class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

pyrosetta.rosetta.protocols.hydrate.set_water_info_and_add_de_novo_water(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::hydrate::set_water_info_and_add_de_novo_water(class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.protocols.hydrate.show_water_hb_network(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::hydrate::show_water_hb_network(const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.hydrate.water_specific_hbond_energy(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::hydrate::water_specific_hbond_energy(class core::pose::Pose &, class core::scoring::ScoreFunction &) –> void