constraints

Bindings for protocols::antibody::constraints namespace

class pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Add Cluster or General Dihedral CircularHarmonic constraints to a CDR. Cluster constraints currently only work for AHO renumbered CDRs.

(This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.)

apply(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, : pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::operator=(const class protocols::antibody::constraints::CDRDihedralConstraintMover &) –> class protocols::antibody::constraints::CDRDihedralConstraintMover &

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.antibody.constraints.CDRDihedralConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::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.antibody.constraints.CDRDihedralConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::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.antibody.constraints.CDRDihedralConstraintMover) str

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::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_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::antibody::constraints::CDRDihedralConstraintMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::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_cdr(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_cdr(enum protocols::antibody::CDRNameEnum) –> void

set_cluster_csts_data_cutoff(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cutoff: int) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_data_cutoff(unsigned long) –> void

set_cluster_csts_use_mean_cst_data(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_mean_cst_data: bool) None
Use constraints which have the means as the actual cluster means.

Setting this to false will use constraints that have the cst means set as cluster center data.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_use_mean_cst_data(bool) –> void

set_cluster_csts_use_outlier_data(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_outlier_data: bool) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_cluster_csts_use_outlier_data(bool) –> 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_force_cluster(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cluster: pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum) None

Do not use AntibodyInfo to for cluster - use this cluster instead

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_force_cluster(enum protocols::antibody::clusters::CDRClusterEnum) –> void

set_general_phi_sd(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, phi_sd: float) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_general_phi_sd(double) –> void

set_general_psi_sd(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, psi_sd: float) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_general_psi_sd(double) –> void

set_ignore_pose_datacache(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, ignore_pose_datacache: bool) None
By default, if cluster information is present in the datacache, we attempt to use that first.

Override this behavior by setting this option to true.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_ignore_pose_datacache(bool) –> 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_remove_any_set_forced_cluster(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) None

Remove any forced cluster settings.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_remove_any_set_forced_cluster() –> 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_use_cluster_csts(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_cluster_csts: bool) None
Attempt to add cluster-based dihedral constraints. If this is set to false will simply add General Dihedral constraints instead.

Default True

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_cluster_csts(bool) –> void

set_use_cluster_for_H3(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_cluster_for_H3: bool) None
Set to use H3 cluster data for constraints if we are doing cluster-based constraints.

Default False - H3 does not cluster well. If use_general_data_on_failure is false, we will skip H3.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_cluster_for_H3(bool) –> void

set_use_general_csts_on_cluster_failure(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_general_csts_on_failure: bool) None
If we are set to use cluster csts and:
  1. the cluster is NA,

  2. there is sparse data for the cluster, or

  3. The CDR is H3 and we have chosen not to use cluster data for H3 (default),

THEN add general dihedral constraints instead.

C++: protocols::antibody::constraints::CDRDihedralConstraintMover::set_use_general_csts_on_cluster_failure(bool) –> 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.antibody.constraints.CDRDihedralConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator, : pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator) pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator

C++: protocols::antibody::constraints::CDRDihedralConstraintMoverCreator::operator=(const class protocols::antibody::constraints::CDRDihedralConstraintMoverCreator &) –> class protocols::antibody::constraints::CDRDihedralConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody::constraints::CDRDihedralConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator) str

C++: protocols::antibody::constraints::CDRDihedralConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::antibody::constraints::CDRDihedralConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present.

If no paratope interface residues are given, detects the epitope at 10 A from antibody chain(s). Optionally constrain to paratope CDRs or a specific set of paratope residues. Uses a Linear Harmonic at 0, 1, 10 by default. Which means epitope will have penalty at greater than 10 A. Linear Harmonic distance tolerance (last number) is set at the interface distance.

apply(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, : pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::operator=(const class protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover &) –> class protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover &

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.antibody.constraints.ParatopeEpitopeSiteConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

constrain_to_epitope_residues(*args, **kwargs)

Overloaded function.

  1. constrain_to_epitope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, epitope_residues: pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Manually set the epitope residues via PDB Numbering

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_epitope_residues(const class utility::vector1<struct protocols::antibody::design::PDBNumbering, class std::allocator<struct protocols::antibody::design::PDBNumbering> > &, const class core::pose::Pose &) –> void

  1. constrain_to_epitope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, epitope_residues: pyrosetta.rosetta.utility.vector1_bool) -> None

Manually set the epitope residues via pose Numbering

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_epitope_residues(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

constrain_to_paratope_cdrs(*args, **kwargs)

Overloaded function.

  1. constrain_to_paratope_cdrs(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_cdrs: pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_cdrs(const class utility::vector1<enum protocols::antibody::CDRNameEnum, class std::allocator<enum protocols::antibody::CDRNameEnum> > &) –> void

  1. constrain_to_paratope_cdrs(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_cdrs: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

constrain_to_paratope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_residues: pyrosetta.rosetta.utility.vector1_bool) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::constrain_to_paratope_residues(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

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_epitope_residues(*args, **kwargs)

Overloaded function.

  1. get_epitope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_epitope_residues() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

  1. get_epitope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_epitope_residues(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

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.antibody.constraints.ParatopeEpitopeSiteConstraintMover) str

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::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_paratope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::get_paratope_residues(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

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_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::antibody::constraints::ParatopeEpitopeSiteConstraintMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::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

remove(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::remove(class core::pose::Pose &) –> void

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_constraint_func(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, constraint_func: pyrosetta.rosetta.core.scoring.func.Func) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_constraint_func(class std::shared_ptr<class core::scoring::func::Func>) –> 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_defaults(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_defaults() –> 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_distance(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, distance: float) None
The interface distance for antigen epitope auto-detection and the distance at which the default

at which the default flat-harmonic constraint will give a penalty. 10A default.

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_interface_distance(const double) –> 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.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator, : pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator) pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::operator=(const class protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator &) –> class protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator) str

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead.

apply(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them.

If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them. If they are missing, such as after a graft, add them.

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, : pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::operator=(const class protocols::antibody::constraints::ParatopeSiteConstraintMover &) –> class protocols::antibody::constraints::ParatopeSiteConstraintMover &

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.antibody.constraints.ParatopeSiteConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

constrain_to_antigen_chains(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, antigen_chains: pyrosetta.rosetta.utility.vector1_std_string) None

Optionally constrain to a set of antigen chains instead of all of them

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_antigen_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

constrain_to_paratope_cdrs(*args, **kwargs)

Overloaded function.

  1. constrain_to_paratope_cdrs(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_cdrs: pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> None

Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_cdrs(const class utility::vector1<enum protocols::antibody::CDRNameEnum, class std::allocator<enum protocols::antibody::CDRNameEnum> > &) –> void

  1. constrain_to_paratope_cdrs(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_cdrs: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

constrain_to_paratope_residues(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_residues: pyrosetta.rosetta.utility.vector1_bool) None

Optionally constrain to a set of pre-determined paratope residues

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::constrain_to_paratope_residues(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

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.antibody.constraints.ParatopeSiteConstraintMover) str

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::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_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::antibody::constraints::ParatopeSiteConstraintMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

provide_citation_info(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::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

remove(*args, **kwargs)

Overloaded function.

  1. remove(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. remove(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, pose: pyrosetta.rosetta.core.pose.Pose, reset_paratope_residues: bool) -> None

Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the

set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion.

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::remove(class core::pose::Pose &, bool) –> void

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_constraint_func(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, constraint_func: pyrosetta.rosetta.core.scoring.func.Func) None

Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::set_constraint_func(class std::shared_ptr<class core::scoring::func::Func>) –> 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_defaults(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) None

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::set_defaults() –> 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_distance(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, interface_distance: float) None
Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint

if no constraint func is set.

C++: protocols::antibody::constraints::ParatopeSiteConstraintMover::set_interface_distance(double) –> 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.antibody.constraints.ParatopeSiteConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator, : pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator) pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator

C++: protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator::operator=(const class protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator &) –> class protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator) str

C++: protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.antibody.constraints.add_harmonic_dihedral_cst_general(*args, **kwargs)

Overloaded function.

  1. add_harmonic_dihedral_cst_general(ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) -> None

  2. add_harmonic_dihedral_cst_general(ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, phi_sd_deg: float) -> None

  3. add_harmonic_dihedral_cst_general(ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, phi_sd_deg: float, psi_sd_deg: float) -> None

Add dihedral constraints to CDR with mean being the current phi/psi.

Values for avg SD for each cluster not including H3 were 16 and 16 degrees respectively. Using cluster outliers, values were at 21 and 23 degrees respectively.

Mean SD for both dihedrals was 16 and 22 for without/with outliers. Use this especially if doing cartesian-space minimization

C++: protocols::antibody::constraints::add_harmonic_dihedral_cst_general(class std::shared_ptr<const class protocols::antibody::AntibodyInfo>, class core::pose::Pose &, const enum protocols::antibody::CDRNameEnum, double, double) –> void

pyrosetta.rosetta.protocols.antibody.constraints.cdr_has_res_constraints(ab_info: pyrosetta.rosetta.protocols.antibody.AntibodyInfo, pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum, constraint_type: str) bool

Check if all residues already have a specific constraint type. Useful for coordinate and dihedral constraints.

C++: protocols::antibody::constraints::cdr_has_res_constraints(class std::shared_ptr<const class protocols::antibody::AntibodyInfo>, class core::pose::Pose &, const enum protocols::antibody::CDRNameEnum, const std::string &) –> bool