bcl

Bindings for protocols::drug_design::bcl namespace

class pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, POSE: pyrosetta.rosetta.core.pose.Pose) → None

apply BCLFragmentBaseMover

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, : pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover) → pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::operator=(const class protocols::drug_design::bcl::BCLFragmentBaseMover &) –> class protocols::drug_design::bcl::BCLFragmentBaseMover &

static base_attributes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::base_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

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.drug_design.bcl.BCLFragmentBaseMover) → pyrosetta.rosetta.protocols.moves.Mover

create copy constructor

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::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.drug_design.bcl.BCLFragmentBaseMover) → pyrosetta.rosetta.protocols.moves.Mover

create this type of objectt

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::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.drug_design.bcl.BCLFragmentBaseMover) → str

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::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 > > &

init_fragment_sample_confs(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover) → None

initial setup of conformer sampler upon object construction

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::init_fragment_sample_confs() –> void

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::drug_design::bcl::BCLFragmentBaseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, TAG: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parse xml file

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

provide_citation_info(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This mover is unpublished. Hopefully we can publish it soon and I can change this to a citation for an actual manuscript

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

set_conf_clash_resolution(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, clash_resolution: float) → None

set the conformer clash resolution

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_resolution(const double) –> void

set_conf_clash_tolerance(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, clash_tolerance: float) → None

set the conformer clash tolerance

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_tolerance(const double) –> void

set_conf_cluster(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, cluster: bool) → None

set leader-follower clustering during conf generation

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_cluster(const bool) –> void

set_conf_comparer(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, conformation_comparer: str) → None

set the fragment conformation comparer type

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_comparer(const std::string &) –> void

set_conf_generate_3d(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, generate_3d: bool) → None

set de novo conformer generation

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_generate_3d(const bool) –> void

set_conf_sample_bond_angles(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_bonds: bool) → None

set bond angle/length sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_bond_angles(const bool) –> void

set_conf_sample_dihed(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_dihed: bool) → None

set dihedral bin sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_dihed(const bool) –> void

set_conf_sample_rings(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_rings: bool) → None

set ring sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_rings(const bool) –> void

set_conf_tolerance(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, tolerance: float) → None

set the tolerance for different conformers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_tolerance(const double) –> void

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

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

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

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

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

setter for poses contained for rms

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

set_ligand(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, ligand_chain_id: str) → None

set the residue ID of the ligand to be mutated

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_ligand(const std::string &) –> void

set_n_max_conf_iterations(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, n_max_iterations: int) → None

set the max number of iterations for conformer sampling

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_conf_iterations(const unsigned long) –> void

set_n_max_confs(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, n_confs: int) → None

set the max number of desired fragment conformers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_confs(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_rand_dihed_prob(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, random_dihedral_change_prob: float) → None

set the probability of accepting a random dihedral

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_rand_dihed_prob(const double) –> void

set_sample_chirality(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, change_chirality: bool) → None

allow R/S sampling at chiral centers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_sample_chirality(const bool) –> 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

2. 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.drug_design.bcl.BCLFragmentMutateMover

Bases: BCLFragmentBaseMover

apply(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply BCLFragmentMutateMover

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, : pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover) → pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::operator=(const class protocols::drug_design::bcl::BCLFragmentMutateMover &) –> class protocols::drug_design::bcl::BCLFragmentMutateMover &

static base_attributes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::base_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

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.drug_design.bcl.BCLFragmentMutateMover) → pyrosetta.rosetta.protocols.moves.Mover

create copy constructor

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::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.drug_design.bcl.BCLFragmentMutateMover) → pyrosetta.rosetta.protocols.moves.Mover

create this type of objectt

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::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_mutate_label(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover) → None

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::get_mutate_label() const –> void

get_name(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover) → str

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::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_tag(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → str

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::get_tag(class core::pose::Pose &, unsigned long) const –> std::string

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 > > &

init_fragment_sample_confs(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover) → None

initial setup of conformer sampler upon object construction

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::init_fragment_sample_confs() –> void

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::drug_design::bcl::BCLFragmentMutateMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parse xml file

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

provide_citation_info(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This mover is unpublished. Hopefully we can publish it soon and I can change this to a citation for an actual manuscript

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::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_conf_clash_resolution(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, clash_resolution: float) → None

set the conformer clash resolution

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_resolution(const double) –> void

set_conf_clash_tolerance(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, clash_tolerance: float) → None

set the conformer clash tolerance

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_clash_tolerance(const double) –> void

set_conf_cluster(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, cluster: bool) → None

set leader-follower clustering during conf generation

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_cluster(const bool) –> void

set_conf_comparer(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, conformation_comparer: str) → None

set the fragment conformation comparer type

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_comparer(const std::string &) –> void

set_conf_generate_3d(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, generate_3d: bool) → None

set de novo conformer generation

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_generate_3d(const bool) –> void

set_conf_sample_bond_angles(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_bonds: bool) → None

set bond angle/length sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_bond_angles(const bool) –> void

set_conf_sample_dihed(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_dihed: bool) → None

set dihedral bin sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_dihed(const bool) –> void

set_conf_sample_rings(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, sample_rings: bool) → None

set ring sampling preference

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_sample_rings(const bool) –> void

set_conf_tolerance(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, tolerance: float) → None

set the tolerance for different conformers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_conf_tolerance(const double) –> void

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

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

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

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

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

setter for poses contained for rms

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

set_ligand(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, ligand_chain_id: str) → None

set the residue ID of the ligand to be mutated

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_ligand(const std::string &) –> void

set_mutate(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, object_data_label: str) → None

set the mutate using a BCL object data label string

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::set_mutate(const std::string &) –> void

set_n_max_conf_iterations(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, n_max_iterations: int) → None

set the max number of iterations for conformer sampling

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_conf_iterations(const unsigned long) –> void

set_n_max_confs(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, n_confs: int) → None

set the max number of desired fragment conformers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_n_max_confs(const unsigned long) –> void

set_n_max_mutate_attempts(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover, n_max_mutate_attempts: int) → None

set the maximum number of mutate attempts

C++: protocols::drug_design::bcl::BCLFragmentMutateMover::set_n_max_mutate_attempts(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_rand_dihed_prob(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, random_dihedral_change_prob: float) → None

set the probability of accepting a random dihedral

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_rand_dihed_prob(const double) –> void

set_sample_chirality(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover, change_chirality: bool) → None

allow R/S sampling at chiral centers

C++: protocols::drug_design::bcl::BCLFragmentBaseMover::set_sample_chirality(const bool) –> 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

2. 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.drug_design.bcl.BCLFragmentMutateMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator, : pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator) → pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator

C++: protocols::drug_design::bcl::BCLFragmentMutateMoverCreator::operator=(const class protocols::drug_design::bcl::BCLFragmentMutateMoverCreator &) –> class protocols::drug_design::bcl::BCLFragmentMutateMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::drug_design::bcl::BCLFragmentMutateMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator) → str

C++: protocols::drug_design::bcl::BCLFragmentMutateMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::drug_design::bcl::BCLFragmentMutateMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.drug_design.bcl.BCLReferenceSDFilesManager

Bases: SingletonBase_protocols_drug_design_bcl_BCLReferenceSDFilesManager_t

A singleton class for managing supplementary SDFs to ensure that they are loaded once and only once from disk.

Benjamin P. Brown (benjamin.p.brown17.com)

add_reference_fragment(self: pyrosetta.rosetta.protocols.drug_design.bcl.BCLReferenceSDFilesManager, reference_fragment_filename: str) → None

add a fragment to our collection of reference fragments

C++: protocols::drug_design::bcl::BCLReferenceSDFilesManager::add_reference_fragment(const std::string &) –> void

static get_instance() → protocols::drug_design::bcl::BCLReferenceSDFilesManager

C++: utility::SingletonBase<protocols::drug_design::bcl::BCLReferenceSDFilesManager>::get_instance() –> class protocols::drug_design::bcl::BCLReferenceSDFilesManager *

class pyrosetta.rosetta.protocols.drug_design.bcl.BCLSampleConfsManager

Bases: SingletonBase_protocols_drug_design_bcl_BCLSampleConfsManager_t

A singleton class for managing supplementary SDFs to ensure that they are loaded once and only once from disk.

Benjamin P. Brown (benjamin.p.brown17.com)

static get_instance() → protocols::drug_design::bcl::BCLSampleConfsManager

C++: utility::SingletonBase<protocols::drug_design::bcl::BCLSampleConfsManager>::get_instance() –> class protocols::drug_design::bcl::BCLSampleConfsManager *