flexpep_docking

Bindings for protocols::flexpep_docking namespace

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::flexpep_docking::FlexPepDockingAbInitio::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio

C++: protocols::flexpep_docking::FlexPepDockingAbInitio::operator=(const class protocols::flexpep_docking::FlexPepDockingAbInitio &) –> class protocols::flexpep_docking::FlexPepDockingAbInitio &

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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.flexpep_docking.FlexPepDockingAbInitio) str

C++: protocols::flexpep_docking::FlexPepDockingAbInitio::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 &

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags

C++: protocols::flexpep_docking::FlexPepDockingFlags::operator=(const class protocols::flexpep_docking::FlexPepDockingFlags &) –> class protocols::flexpep_docking::FlexPepDockingFlags &

property backrub_opt
property boost_fa_atr
clone(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags

C++: protocols::flexpep_docking::FlexPepDockingFlags::clone() const –> class std::shared_ptr<class protocols::flexpep_docking::FlexPepDockingFlags>

property design_peptide
property dumpPDB_abinitio
property dumpPDB_hires
property dumpPDB_lowres
property extend
property frag3_weight
property frag5_weight
property frag9_weight
property hb_filter
property hotspot_filter
is_ligand_present(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::is_ligand_present(const class core::pose::Pose &) const –> bool

property lowres_abinitio
property lowres_preoptimize
property mcm_cycles
property min_only
property min_receptor_bb
property no_prepack1
property no_prepack2
property pSer2Asp_centroid
property pSer2Glu_centroid
property params_file
property pep_fold_only
property pep_refine
property peptide_anchors
peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str

C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain() const –> char

property peptide_cuts
peptide_first_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res() const –> unsigned long

peptide_last_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res() const –> unsigned long

property peptide_loop_model
peptide_nres(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres() const –> unsigned long

property place_peptide
property ppk_only
property ramp_fa_rep
property ramp_rama
property randomRBstart
property random_phi_psi_pert
property random_phi_psi_pert_size
property rbMCM
property rb_rot_size
property rb_trans_size
property recal_foldtree
property receptor_anchor_pos
receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str

C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain() const –> std::string

receptor_first_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res() const –> unsigned long

receptor_last_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res() const –> unsigned long

receptor_nres(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int

C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres() const –> unsigned long

ref_start_struct(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str

C++: protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct() const –> std::string

property rep_ramp_cycles
property sample_pc
property score_filter
property score_only
setDefaultAnchors(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(class core::pose::Pose &) –> void

set_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, ch: str) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::set_peptide_chain(char) –> void

set_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, ch: str) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain(std::string) –> void

set_user_defined_peptide(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, state: bool) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_peptide(bool) –> void

set_user_defined_receptor(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, state: bool) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_receptor(bool) –> void

property slideintocontact
property smove_angle_range
property torsionsMCM
updateChains(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::updateChains(const class core::pose::Pose &) –> void

updateChainsAndAnchors_fromParamsFile(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, params_file: str) None

C++: protocols::flexpep_docking::FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile(const std::string &) –> void

user_defined_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::user_defined_peptide_chain() const –> bool

user_defined_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::user_defined_receptor_chain() const –> bool

valid_anchors(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_anchors() const –> bool

valid_chain_info(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_info() const –> bool

valid_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain() const –> bool

valid_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain() const –> bool

valid_ref_start_struct(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool

C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct() const –> bool

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::flexpep_docking::FlexPepDockingLowRes::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes

C++: protocols::flexpep_docking::FlexPepDockingLowRes::operator=(const class protocols::flexpep_docking::FlexPepDockingLowRes &) –> class protocols::flexpep_docking::FlexPepDockingLowRes &

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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.flexpep_docking.FlexPepDockingLowRes) str

C++: protocols::flexpep_docking::FlexPepDockingLowRes::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 &

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::operator=(const class protocols::flexpep_docking::FlexPepDockingPoseMetrics &) –> class protocols::flexpep_docking::FlexPepDockingPoseMetrics &

calc_frac_native_contacts(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, native: pyrosetta.rosetta.core.pose.Pose, final: pyrosetta.rosetta.core.pose.Pose, threashold: float) float

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts(const class core::pose::Pose &, const class core::pose::Pose &, double) const –> double

calc_interface_metrics(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose: pyrosetta.rosetta.core.pose.Pose, rb_jump: int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(class core::pose::Pose &, unsigned long, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

calc_pep_scores(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose: pyrosetta.rosetta.core.pose.Pose, pepScore: float, pepScore_noref: float) None

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(const class core::pose::Pose &, double &, double &) const –> void

calc_phipsi_RMSD(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, res_subset: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) float

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(const class core::pose::Pose &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<bool> &) const –> double

isInContact(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, threashold: float) bool

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(const class core::conformation::Residue &, const class core::conformation::Residue &, double) const –> bool

set_flags(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, flags: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) None

C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::set_flags(class std::shared_ptr<const class protocols::flexpep_docking::FlexPepDockingFlags>) –> void

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::flexpep_docking::FlexPepDockingProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol

C++: protocols::flexpep_docking::FlexPepDockingProtocol::operator=(const class protocols::flexpep_docking::FlexPepDockingProtocol &) –> class protocols::flexpep_docking::FlexPepDockingProtocol &

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.flexpep_docking.FlexPepDockingProtocol) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::flexpep_docking::FlexPepDockingProtocol::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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.flexpep_docking.FlexPepDockingProtocol) str

C++: protocols::flexpep_docking::FlexPepDockingProtocol::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 mover_name() str

C++: protocols::flexpep_docking::FlexPepDockingProtocol::mover_name() –> std::string

static name() str

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::flexpep_docking::FlexPepDockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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_default(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol) None

setup that is called from constructor

C++: protocols::flexpep_docking::FlexPepDockingProtocol::set_default() –> 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 &

view(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, view_in: bool) None

setter

C++: protocols::flexpep_docking::FlexPepDockingProtocol::view(bool) –> void

class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator

C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::operator=(const class protocols::flexpep_docking::FlexPepDockingProtocolCreator &) –> class protocols::flexpep_docking::FlexPepDockingProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) str

C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void