glycan_docking¶
Bindings for protocols::glycan_docking namespace
- class pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol¶
Bases:
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_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.
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
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- pyrosetta.rosetta.protocols.glycan_docking.calc_GlycanDock_intf_metrics(*args, **kwargs)¶
Overloaded function.
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
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>