glycan_docking

Bindings for protocols::glycan_docking namespace

class pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

TODO

Morgan L. Nance ()

apply(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the GlycanDockProtocol mover

C++: protocols::glycan_docking::GlycanDockProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

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.glycan_docking.GlycanDockProtocol) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

required in the context of the parser/scripting scheme

C++: protocols::glycan_docking::GlycanDockProtocol::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_full_packing_frequency(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) int

Get the number of times to apply the more costly PackRotamersMover

during the inner cycles of Stage 2 sampling and optimization.

Should be a factor of n_rb_rounds and n_tor_rounds. When the

PackRotamersMover is not used, the EnergyCutRotamerTrialsMover is

C++: protocols::glycan_docking::GlycanDockProtocol::get_full_packing_frequency() –> unsigned long

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_interface_packing_distance(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the distance in Ang. defining the protein-glycoligand interface

when performing packing during Stage 2 sampling and optimization

Uses less accurate neighbor atom distances to get interface

C++: protocols::glycan_docking::GlycanDockProtocol::get_interface_packing_distance() –> double

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_mc_kt(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the temperature (kT) used when applying the Metropolis

criterion via the MonteCarlo object to accept or a reject a move

C++: protocols::glycan_docking::GlycanDockProtocol::get_mc_kt() –> double

get_n_repeats(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) int

Get the number of times to repeat the GlycanDockProtocol

starting from the decoy conformation after Stage 1 (if applied)

if the decoy fails the docking filter at the end of the protocol

C++: protocols::glycan_docking::GlycanDockProtocol::get_n_repeats() –> unsigned long

get_n_rigid_body_rounds(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) int

Get the number of rigid-body sampling and optimization

rounds to perform during each inner cycle of Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::get_n_rigid_body_rounds() –> unsigned long

get_n_torsion_rounds(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) int

Get the number of glycosidic torsion angle sampling and optimization

rounds to perform during each inner cycle of Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::get_n_torsion_rounds() –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) str

C++: protocols::glycan_docking::GlycanDockProtocol::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_partners(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) str

Get the chain IDs identifying the protein-glycoligand complex

protein is chain A, glycoligand is chain X –> partners = A_X

C++: protocols::glycan_docking::GlycanDockProtocol::get_partners() const –> std::string

get_prepack_only(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get whether to apply only the GlycanDock pre-packing protocol

C++: protocols::glycan_docking::GlycanDockProtocol::get_prepack_only() –> bool

get_ramp_scorefxn(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get whether to ramp the fa_atr and fa_rep score terms of the

ScoreFunction used during Stage 2 sampling and optimization

C++: protocols::glycan_docking::GlycanDockProtocol::get_ramp_scorefxn() –> bool

get_rand_glycan_jump_res(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get whether to use a random, non-branch-point residue of the

glycoligand to set as the Jump residue for the docking FoldTree

C++: protocols::glycan_docking::GlycanDockProtocol::get_rand_glycan_jump_res() –> bool

get_refine_only(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get whether to skip Stage 1 of GlycanDockProtocol and perform more

conservative glycosidic torsion angle moves during Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::get_refine_only() –> bool

get_scorefunction(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction

Get the ScoreFunction used for the GlycanDockProtocol

C++: protocols::glycan_docking::GlycanDockProtocol::get_scorefunction() –> const class std::shared_ptr<class core::scoring::ScoreFunction>

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_slide_glycan_into_contact(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get wehter to ocassionally rigidly slide the glycoligand

toward the center-of-mass of its proteein docking partner

during Stage 2 rigid-body sampling and optimization cycles

C++: protocols::glycan_docking::GlycanDockProtocol::get_slide_glycan_into_contact() –> bool

get_stage1_perturb_glycan_com_rot_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the magnitude used when applying a random rotational

perturbation to the initial glycoligand conformation in Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage1_perturb_glycan_com_rot_mag() –> double

get_stage1_perturb_glycan_com_trans_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the magnitude used when applying a random translational

perturbation to the initial glycoligand conformation in Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage1_perturb_glycan_com_trans_mag() –> double

get_stage1_rotate_glycan_about_com(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Get whether the Stage 1 conformation initialization portion

of the GlycanDockProtocol is performed

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage1_rotate_glycan_about_com() –> bool

get_stage1_torsion_uniform_pert_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the magnitude used when applying a random perturbation to

each initial glycosidic torsion angle during Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage1_torsion_uniform_pert_mag() –> double

get_stage2_rot_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the magnitude used when applying a random rotational

perturbation to the glycoligand conformation in Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage2_rot_mag() –> double

get_stage2_trans_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) float

Get the magnitude used when applying a random translational

perturbation to the glycoligand conformation in Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::get_stage2_trans_mag() –> double

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

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

get_watch_in_pymol(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) bool

Send the conformation of the decoy to PyMOL at specific,

hard-coded points during the GlycanDockProtocol

TODO - currently not implemented

C++: protocols::glycan_docking::GlycanDockProtocol::get_watch_in_pymol() –> bool

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::glycan_docking::GlycanDockProtocol::mover_name() –> std::string

static name() str

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

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

parse XML tag

C++: protocols::glycan_docking::GlycanDockProtocol::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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::glycan_docking::GlycanDockProtocol::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_full_packing_frequency(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, full_pack_freq: int) None

Set the number of times to apply the more costly PackRotamersMover

during the inner cycles of Stage 2 sampling and optimization.

Should be a factor of n_rb_rounds and n_tor_rounds. When the

PackRotamersMover is not used, the EnergyCutRotamerTrialsMover is

C++: protocols::glycan_docking::GlycanDockProtocol::set_full_packing_frequency(const unsigned long) –> 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_interface_packing_distance(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, intf_pack_dist: float) None

Set the distance in Ang. defining the protein-glycoligand interface

when performing packing during Stage 2 sampling and optimization

Uses less accurate neighbor atom distances to get interface

C++: protocols::glycan_docking::GlycanDockProtocol::set_interface_packing_distance(const double) –> void

set_mc_kt(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, mc_kt: float) None

Set the temperature (kT) used when applying the Metropolis

criterion via the MonteCarlo object to accept or a reject a move

C++: protocols::glycan_docking::GlycanDockProtocol::set_mc_kt(const double) –> void

set_n_repeats(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, n_repeats: int) None

Set the number of times to repeat the GlycanDockProtocol

starting from the decoy conformation after Stage 1 (if applied)

if the decoy fails the docking filter at the end of the protocol

C++: protocols::glycan_docking::GlycanDockProtocol::set_n_repeats(const unsigned long &) –> void

set_n_rigid_body_rounds(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, rb_rounds: int) None

Set the number of rigid-body sampling and optimization

rounds to perform during each inner cycle of Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::set_n_rigid_body_rounds(const unsigned long) –> void

set_n_torsion_rounds(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, tor_rounds: int) None

Set the number of glycosidic torsion angle sampling and optimization

rounds to perform during each inner cycle of Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::set_n_torsion_rounds(const unsigned long) –> 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_partners(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, p: str) None

Set the chain IDs identifying the protein-glycoligand complex

protein is chain A, glycoligand is chain X –> partners = A_X

C++: protocols::glycan_docking::GlycanDockProtocol::set_partners(const std::string &) –> void

set_prepack_only(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, prepack_only: bool) None

Set whether to apply only the GlycanDock pre-packing protocol

C++: protocols::glycan_docking::GlycanDockProtocol::set_prepack_only(const bool) –> void

set_ramp_scorefxn(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, ramp_sf: bool) None

Set whether to ramp the fa_atr and fa_rep score terms of the

ScoreFunction used during Stage 2 sampling and optimization

C++: protocols::glycan_docking::GlycanDockProtocol::set_ramp_scorefxn(const bool) –> void

set_rand_glycan_jump_res(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, rand_glyc_jump: bool) None

Set whether to use a random, non-branch-point residue of the

glycoligand to set as the Jump residue for the docking FoldTree

C++: protocols::glycan_docking::GlycanDockProtocol::set_rand_glycan_jump_res(const bool) –> void

set_refine_only(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, refine_only: bool) None

Set whether to skip Stage 1 of GlycanDockProtocol and perform more

conservative glycosidic torsion angle moves during Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::set_refine_only(const bool) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, in_sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None
Set the ScoreFunction used for the GlycanDockProtocol

GlycanDock was benchmarked using the ref2015 scoring function with sugar_bb = 0.5 and fa_intra_rep_nonprotein 0.55 (fa_rep weight)

C++: protocols::glycan_docking::GlycanDockProtocol::set_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_slide_glycan_into_contact(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, slide: bool) None

Set wehter to ocassionally rigidly slide the glycoligand

toward the center-of-mass of its proteein docking partner

during Stage 2 rigid-body sampling and optimization cycles

C++: protocols::glycan_docking::GlycanDockProtocol::set_slide_glycan_into_contact(const bool) –> void

set_stage1_perturb_glycan_com_rot_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, rot_mag: float) None

Set the magnitude used when applying a random rotational

perturbation to the initial glycoligand conformation in Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage1_perturb_glycan_com_rot_mag(const double) –> void

set_stage1_perturb_glycan_com_trans_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, trans_mag: float) None

Set the magnitude used when applying a random translational

perturbation to the initial glycoligand conformation in Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage1_perturb_glycan_com_trans_mag(const double) –> void

set_stage1_rotate_glycan_about_com(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, sg1: bool) None

Set whether the Stage 1 conformation initialization portion

of the GlycanDockProtocol is performed

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage1_rotate_glycan_about_com(const bool) –> void

set_stage1_torsion_uniform_pert_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, pert_mag: float) None

Set the magnitude used when applying a random perturbation to

each initial glycosidic torsion angle during Stage 1

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage1_torsion_uniform_pert_mag(const double) –> void

set_stage2_rot_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, rot_mag: float) None

Set the magnitude used when applying a random rotational

perturbation to the glycoligand conformation in Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage2_rot_mag(const double) –> void

set_stage2_trans_mag(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, trans_mag: float) None

Set the magnitude used when applying a random translational

perturbation to the glycoligand conformation in Stage 2

C++: protocols::glycan_docking::GlycanDockProtocol::set_stage2_trans_mag(const double) –> 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

set_watch_in_pymol(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, pymol: bool) None

Send the conformation of the decoy to PyMOL at specific,

hard-coded points during the GlycanDockProtocol

TODO - currently not implemented

C++: protocols::glycan_docking::GlycanDockProtocol::set_watch_in_pymol(const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of GlycanDockProtocol

C++: protocols::glycan_docking::GlycanDockProtocol::show(std::ostream &) const –> void

  1. show(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol) -> None

PyRosetta-friendly version of show

C++: protocols::glycan_docking::GlycanDockProtocol::show() 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.glycan_docking.GlycanDockProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator, : pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator) pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator

C++: protocols::glycan_docking::GlycanDockProtocolCreator::operator=(const class protocols::glycan_docking::GlycanDockProtocolCreator &) –> class protocols::glycan_docking::GlycanDockProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator) str

C++: protocols::glycan_docking::GlycanDockProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

pyrosetta.rosetta.protocols.glycan_docking.calc_GlycanDock_intf_metrics(*args, **kwargs)

Overloaded function.

  1. calc_GlycanDock_intf_metrics(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, glycolig_subset: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.utility.vector1_double

  2. calc_GlycanDock_intf_metrics(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, glycolig_subset: pyrosetta.rosetta.utility.vector1_bool, dist_cutoff: float) -> pyrosetta.rosetta.utility.vector1_double

Calculate various metrics describing the protein-glycoligand interface

The return vector1 looks like so:

< num intf res, num intf res in the ref pose,

the fraction of ref pose intf res recovered in the decoy,

num intf contacts, num intf contacts in the ref pose,

the fraction of ref pose intf contacts recovered in the decoy >

C++: protocols::glycan_docking::calc_GlycanDock_intf_metrics(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.protocols.glycan_docking.calc_res_contact(rsd_ii: pyrosetta.rosetta.core.conformation.Residue, rsd_jj: pyrosetta.rosetta.core.conformation.Residue, dist_cutoff: float) bool

Determine if rsd_ii is in contact with rsd_jj

If any non-hydrogen atom of rsd_ii is within dist_cutoff

(generally 5 Ang) of any non-hydrogen atom of rsd_jj,

then the two residues are considered contacting

This does not check if an atom is virtual, but virtual

carbohydrate atoms should track their corresponding real atom

C++: protocols::glycan_docking::calc_res_contact(class std::shared_ptr<const class core::conformation::Residue>, class std::shared_ptr<const class core::conformation::Residue>, const double) –> bool

pyrosetta.rosetta.protocols.glycan_docking.do_stage1_conformation_initialization(pose: pyrosetta.rosetta.core.pose.Pose, stage1_rb_seqmover: pyrosetta.rosetta.protocols.moves.SequenceMover, glycolig_subset: pyrosetta.rosetta.utility.vector1_bool, glycolig_has_dihedrals: bool, stage1_tor_perturb_mag: float) None

Apply Stage 1 initial conformation perturbation to input Pose

Stage 1 serves to increase the conformational diversity of

a docking trajectory by injecting a little initial randomness

C++: protocols::glycan_docking::do_stage1_conformation_initialization(class core::pose::Pose &, class std::shared_ptr<class protocols::moves::SequenceMover>, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const double) –> void

pyrosetta.rosetta.protocols.glycan_docking.do_stage1_tor_uniform_perturbation(pose: pyrosetta.rosetta.core.pose.Pose, glycolig_subset: pyrosetta.rosetta.utility.vector1_bool, stage1_tor_perturb_mag: float) None

Apply small uniform perturbation on each glycosidic torsion angle

Stage 1 serves to increase the conformational diversity of

a docking trajectory by injecting a little initial randomness

C++: protocols::glycan_docking::do_stage1_tor_uniform_perturbation(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double) –> void

pyrosetta.rosetta.protocols.glycan_docking.do_stage2_sample_pack_min_cycle(pose: pyrosetta.rosetta.core.pose.Pose, stage2_mover: pyrosetta.rosetta.protocols.moves.RandomMover, n_rounds: int, full_packer: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, ecut_packer: protocols::minimization_packing::EnergyCutRotamerTrialsMover, full_pack_every_x_rounds: int, min_mover: pyrosetta.rosetta.protocols.minimization_packing.MinMover, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) int

Apply an inner cycle of Stage 2 sampling and optimization

Stage 2 is the main docking refinement portion of GlycanDock

C++: protocols::glycan_docking::do_stage2_sample_pack_min_cycle(class core::pose::Pose &, class std::shared_ptr<class protocols::moves::RandomMover>, const unsigned long, class std::shared_ptr<class protocols::minimization_packing::PackRotamersMover>, class std::shared_ptr<class protocols::minimization_packing::EnergyCutRotamerTrialsMover>, const unsigned long, class std::shared_ptr<class protocols::minimization_packing::MinMover>, class std::shared_ptr<class protocols::moves::MonteCarlo>) –> unsigned long

pyrosetta.rosetta.protocols.glycan_docking.gen_intf_contact_map(pose: pyrosetta.rosetta.core.pose.Pose, receptor_nbrhood_subset: pyrosetta.rosetta.utility.vector1_bool, glycolig_subset: pyrosetta.rosetta.utility.vector1_bool, dist_cutoff: float) pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t

Generate a map of Pose interface contacts between the

receptor_nbrhood_subset and the glycolig_subset

receptor_nbrhood_subset: A pre-filtered residue subset

of protein receptor residues at the interface based on

a cutoff of 10 Ang (using the tenA energy map)

glycolig_subset: Subset indicating the carbohydrate

residues of the glycoligand

C++: protocols::glycan_docking::gen_intf_contact_map(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const double) –> class ObjexxFCL::FArray2D<bool>

pyrosetta.rosetta.protocols.glycan_docking.get_GlycanDock_IAM(docking_partners: str, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover

Create an InterfaceAnalyzerMover appropriate for GlycanDock output

C++: protocols::glycan_docking::get_GlycanDock_IAM(const std::string &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::shared_ptr<class protocols::analysis::InterfaceAnalyzerMover>

pyrosetta.rosetta.protocols.glycan_docking.get_glycolig_subset_with_torsions(pose: pyrosetta.rosetta.core.pose.Pose, glycolig_selector: pyrosetta.rosetta.core.select.residue_selector.ChainSelector) pyrosetta.rosetta.utility.vector1_bool

Return a residue subset where carbohydrates of the glycoligand

that have (movable) glycosidic torsion angles

Reducing end carbohydrate does not have dihedrals

C++: protocols::glycan_docking::get_glycolig_subset_with_torsions(const class core::pose::Pose &, class std::shared_ptr<const class core::select::residue_selector::ChainSelector>) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.glycan_docking.setup_GlycanDock_movemap(pose: pyrosetta.rosetta.core.pose.Pose, glycolig_selector: pyrosetta.rosetta.core.select.residue_selector.ChainSelector, lock_rings: bool, dock_jump_num: int) pyrosetta.rosetta.core.kinematics.MoveMap

Create a MoveMap appropriate for structure minimization

Not affected by -prepack_only because minimization is not used

C++: protocols::glycan_docking::setup_GlycanDock_movemap(const class core::pose::Pose &, class std::shared_ptr<const class core::select::residue_selector::ChainSelector>, const bool, const unsigned long) –> class std::shared_ptr<class core::kinematics::MoveMap>

pyrosetta.rosetta.protocols.glycan_docking.setup_GlycanDock_stage1_rb_seqmover(pose: pyrosetta.rosetta.core.pose.Pose, docking_jump_num: int, stage1_rotation_magnitude: float, stage1_translation_magnitude: float, stage1_rotate_glycolig_about_com: bool) pyrosetta.rosetta.protocols.moves.SequenceMover

Create SequenceMover holding Stage 1 rigid-body perturbation Movers

C++: protocols::glycan_docking::setup_GlycanDock_stage1_rb_seqmover(const class core::pose::Pose &, const unsigned long, const double, const double, const bool) –> class std::shared_ptr<class protocols::moves::SequenceMover>

pyrosetta.rosetta.protocols.glycan_docking.setup_GlycanDock_stage2_rb_randmover(docking_jump_num: int, stage2_rotation_magnitude: float, stage2_translaation_magnitude: float, slide_glycolig_into_contact: bool) pyrosetta.rosetta.protocols.moves.RandomMover

Create RandomMover holding Stage 2 rigid-body perturbation Movers

C++: protocols::glycan_docking::setup_GlycanDock_stage2_rb_randmover(const unsigned long, const double, const double, const bool) –> class std::shared_ptr<class protocols::moves::RandomMover>

pyrosetta.rosetta.protocols.glycan_docking.setup_GlycanDock_stage2_tor_randmover(pose: pyrosetta.rosetta.core.pose.Pose, glycolig_subset_with_torsions: pyrosetta.rosetta.utility.vector1_bool, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, mc_kt: float, n_shear_moves: int, refine_only: bool) pyrosetta.rosetta.protocols.moves.RandomMover

Create RandomMover holding Stage 2 torsion angle perturbation Movers

C++: protocols::glycan_docking::setup_GlycanDock_stage2_tor_randmover(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::shared_ptr<class core::scoring::ScoreFunction>, const double, const unsigned long, const bool) –> class std::shared_ptr<class protocols::moves::RandomMover>

pyrosetta.rosetta.protocols.glycan_docking.setup_GlycanDock_taskfactory(docking_jump_num: int, interface_packing_distance: float, prepack_only: bool) pyrosetta.rosetta.core.pack.task.TaskFactory

Create a TaskFactory appropriate for the GlycanDockProtocol

If -prepack_only is true, TaskFactory is not restricted to interface

C++: protocols::glycan_docking::setup_GlycanDock_taskfactory(const unsigned long, const double, const bool) –> class std::shared_ptr<class core::pack::task::TaskFactory>

pyrosetta.rosetta.protocols.glycan_docking.setup_glycoligand_selector(docking_partners: str) pyrosetta.rosetta.core.select.residue_selector.ChainSelector

Creates a ChainSelector based on the downstream partner (glycoligand)

of the -docking:partners (e.g. AB_X) after some quality assurance

C++: protocols::glycan_docking::setup_glycoligand_selector(const std::string &) –> class std::shared_ptr<const class core::select::residue_selector::ChainSelector>