match_enzdes_util¶

Bindings for protocols::toolbox::match_enzdes_util namespace

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover¶

Bases: Mover

small mover that takes an invrot tree

apply(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover¶: C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::operator=(const class protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover &) –> class protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

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

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) → str¶: C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::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 name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_add_target_to_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, setting: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_add_target_to_pose(const 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_geomcst_for_superposition_from_enz_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → None¶: C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) –> void

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

setter for poses contained for rms

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

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

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

setup_foldtree_around_anchor_invrot(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, pose: pyrosetta.rosetta.core.pose.Pose, anchor_seqpos: int, first_target_seqpos: int) → None¶

sets up a foldtree such that: the anchor residue doesn’t move, i.e. a backward edge from anchor to 1 and a forward edge from anchor to seqpos also need to setup the jumps at anchor res

C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot(class core::pose::Pose &, const unsigned long, const unsigned long) const –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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

switch_residue_type_set(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, residue: pyrosetta.rosetta.core.conformation.Residue, desired_restype_set: pyrosetta.rosetta.core.chemical.TypeSetMode) → pyrosetta.rosetta.core.conformation.Residue¶

silly helper function to get the equivalent: of a certain residue in a new residue type set note if the passed in residue is already of the required residue type set, nothing changes, just passes back input pointer

C++: protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::switch_residue_type_set(class std::shared_ptr<const class core::conformation::Residue>, enum core::chemical::TypeSetMode) const –> class std::shared_ptr<const class core::conformation::Residue>

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.toolbox.match_enzdes_util.AllowedSeqposForGeomCst¶

Bases: pybind11_object

a simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst¶: C++: protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::operator=(const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst &) –> class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst &

initialize_from_command_line(*args, **kwargs)¶

Overloaded function.

initialize_from_command_line(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> None
initialize_from_command_line(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst, pose: pyrosetta.rosetta.core.pose.Pose) -> None

this function used to live in the matcher task: pose can be passed in optionally to support the ALL tag in the pos file

C++: protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(class std::shared_ptr<const class core::pose::Pose>) –> void

num_seqpos_lists(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → int¶: C++: protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::num_seqpos_lists() const –> unsigned long

seqpos_for_geomcst(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst, geomcst: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst(unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo¶

Bases: pybind11_object

helper class to allow for removal of covalent constraints

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo¶: C++: protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::operator=(const class protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo &) –> class protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo &

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶: C++: protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remap_resid(const class core::id::SequenceMapping &) –> void

remove_covalent_connection_from_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions¶

Bases: ResInteractions

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions¶: C++: protocols::toolbox::match_enzdes_util::CstResInteractions::operator=(const class protocols::toolbox::match_enzdes_util::CstResInteractions &) –> class protocols::toolbox::match_enzdes_util::CstResInteractions &

cst_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions) → int¶: C++: protocols::toolbox::match_enzdes_util::CstResInteractions::cst_block() const –> unsigned long

dis(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::dis() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loop_ang(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loop_ang() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loop_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loop_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loopres_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

loopres_base2_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_base2_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

loopres_base_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_base_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

lt_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::lt_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

num_interactions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → int¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::num_interactions() const –> unsigned long

read_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions, data: pyrosetta.rosetta.utility.io.izstream) → bool¶: C++: protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(class utility::io::izstream &) –> bool

resA(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions) → bool¶: C++: protocols::toolbox::match_enzdes_util::CstResInteractions::resA() const –> bool

targ_ang(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_ang() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

targ_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_base2_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_base2_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_base_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_base_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

targ_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → int¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_res() const –> unsigned long

write_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions) → None¶: C++: protocols::toolbox::match_enzdes_util::CstResInteractions::write_data() const –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO¶

Bases: pybind11_object

add_constraints_to_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, accept_blocks_missing_header: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, bool) –> void

add_constraints_to_pose_for_block_without_clearing_and_header_processing(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, cst_block: int) → None¶

BE CAREFUL when using this function, it generates constraints

without clearing the internal data structures and reading in

the information in the pdb REMARKs

if you’re unsure use the above one

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, unsigned long) const –> void

add_pregenerated_constraints_to_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

convenience function that will add constraints to the pose if they have

been previously generated. BE CAREFUL when using this function, it relies on the

pose having the same residue types at the same constrained positions as in the pose

that was originally used to generate the constraints. If in doubt, it’s safer to

regenerate the constraints before adding (i.e. use the above add_constraints_to_pose

function.)

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>) const –> void

allowed_res_name3_at_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::allowed_res_name3_at_position(const class core::pose::Pose &, const unsigned long) const –> class utility::vector1<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::operator=(const class protocols::toolbox::match_enzdes_util::EnzConstraintIO &) –> class protocols::toolbox::match_enzdes_util::EnzConstraintIO &

clear_active_pose_constraints_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::clear_active_pose_constraints_for_block(class core::pose::Pose &, unsigned long) const –> void

contains_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → bool¶

are constraints specified for this position?

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::contains_position(const class core::pose::Pose &, const unsigned long) const –> bool

enz_cst_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block: int) → protocols::toolbox::match_enzdes_util::EnzConstraintParameters¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>

enz_cst_params_missing_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_missing_in_pose(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>, class std::allocator<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters> > >

enz_cst_params_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_size() –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

initialize_with_mcfi_list(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, mcfi_list_vec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_MatchConstraintFileInfoList_t) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::initialize_with_mcfi_list(class utility::vector1<class std::shared_ptr<class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList>, class std::allocator<class std::shared_ptr<class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList> > >) –> void

is_backbone_only_cst(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → bool¶

are the constraints specified at this position: mediated through backbone interactions only?

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::is_backbone_only_cst(const class core::pose::Pose &, const unsigned long) const –> bool

mcfi_list(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block: int) → protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_list(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList>

mcfi_lists_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_size() const –> unsigned long

num_mcfi_lists(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::num_mcfi_lists() const –> unsigned long

ordered_constrained_positions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

process_pdb_header(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, accept_missing_blocks: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(class core::pose::Pose &, bool) –> void

read_enzyme_cstfile(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, fname: str) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::read_enzyme_cstfile(std::string) –> void

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶

changing the constrained residues if the sequence length changes

C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remap_resid(const class core::id::SequenceMapping &) –> void

remove_constraints_from_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, keep_covalent: bool, fail_on_constraints_missing: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose(class core::pose::Pose &, const bool, const bool) const –> void

remove_constraints_from_pose_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int, fail_on_constraints_missing: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block(class core::pose::Pose &, unsigned long, const bool) const –> void

remove_position_from_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, pos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res(class core::pose::Pose &, unsigned long) const –> void

remove_position_from_template_res_for_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, pos: int, cst_block: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res_for_block(class core::pose::Pose &, unsigned long, unsigned long) const –> void

set_external_position_for_resA_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block: int, respos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resA_in_parameter_block(unsigned long, unsigned long) –> void

set_external_position_for_resB_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block: int, respos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resB_in_parameter_block(unsigned long, unsigned long) –> void

set_position_for_missing_res_in_parameter_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose, cst_block: int, respos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_position_for_missing_res_in_parameter_block(class core::pose::Pose &, unsigned long, unsigned long) const –> void

show_cst_definitions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::show_cst_definitions() const –> void

target_downstream_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res() const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

update_pdb_remarks_for_backbone_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintIO::update_pdb_remarks_for_backbone_params(class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters¶

Bases: pybind11_object

class that holds all the parameters for one specific constraint

allowed_res_name3_at_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → pyrosetta.rosetta.std.set_std_string_t¶

all residue names specified in the cstfile: returns an empty set if the constraints don’t apply to the specifed position

C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::allowed_res_name3_at_position(const class core::pose::Pose &, unsigned long) const –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::operator=(const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters &) –> class protocols::toolbox::match_enzdes_util::EnzConstraintParameters &

static convert_GeomSampleInfo_to_FuncOP(gsi: protocols::toolbox::match_enzdes_util::GeomSampleInfo, ideal_val: float) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::convert_GeomSampleInfo_to_FuncOP(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>, double &) –> class std::shared_ptr<class core::scoring::func::Func>

cst_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::cst_block() const –> unsigned long

enz_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::enz_io() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

generate_pose_specific_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_pose_specific_data(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>) const –> void

get_missing_template_other_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_other_res(const class core::pose::Pose &) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

get_missing_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_res(const class core::pose::Pose &) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_self_weak_ptr() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>

init(*args, **kwargs)¶

Overloaded function.

init(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, cst_block: int, src_restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, src_enz_io: pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t) -> None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::init(unsigned long, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) –> void

init(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> None

C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::init() –> void

is_covalent(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_covalent() const –> bool

is_empty(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_empty() const –> bool

missing_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::missing_in_pose(const class core::pose::Pose &) const –> bool

nonconst_resA(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resA() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

nonconst_resB(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resB() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remap_resid(const class core::id::SequenceMapping &) –> void

remove_covalent_connections_from_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remove_covalent_connections_from_pose(class core::pose::Pose &) const –> void

resA(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resA() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

resB(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → protocols::toolbox::match_enzdes_util::EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resB() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

set_cst_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, cst_block: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_cst_block(unsigned long) –> void

set_external_position_for_resA(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resA(unsigned long) –> void

set_external_position_for_resB(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resB(unsigned long) –> void

set_mcfi(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, mcfi: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_mcfi(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo>) –> void

show_definitions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::show_definitions() const –> void

update_pdb_remarks(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

updates the pdb remarks according to what is in the: EnzCstTemplateRes member data. returns false in case any error occured

C++: protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks(class core::pose::Pose &) const –> bool

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes¶

Bases: pybind11_object

helper class for class EnzConstraintParameters, gathers information

from cst input and pdb input

allowed_res_types(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

allowed_res_types_pointers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::allowed_res_types_pointers() const –> const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::operator=(const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes &) –> class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes &

atom_inds_for_restype(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, template_atom: int, restype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

clear_all(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::clear_all() –> void

compatible_restype(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, restype: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::compatible_restype(class std::shared_ptr<const class core::chemical::ResidueType>) const –> bool

corresponding_res_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::corresponding_res_block() const –> unsigned long

determine_atom_inds_for_restype(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, restype: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype(class std::shared_ptr<const class core::chemical::ResidueType>) const –> void

find_in_pose_if_missing_from_header(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(class core::pose::Pose &) –> bool

get_pose_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(class core::pose::Pose &) const –> void

get_template_atoms_at_pos(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_template_atoms_at_pos(const class core::pose::Pose &, unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms>

identical_info_consistency_check(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_info_consistency_check() const –> void

initialize_from_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, a1: str, a2: str, a3: str, allowed_3res: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::initialize_from_params(const std::string &, const std::string &, const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

is_backbone(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::is_backbone() const –> bool

param_index(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::param_index() const –> unsigned long

rb_minimizable(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::rb_minimizable() const –> bool

read_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, line_stream: pyrosetta.rosetta.std.istringstream) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(class std::basic_istringstream<char> &) –> void

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::remap_resid(const class core::id::SequenceMapping &) –> void

residue_conformations_redundant(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) → bool¶

checks whether the distance: between any of the template res atoms of res1 and res2 is below a certain cutoff.

C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

set_enzio_param(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_enz_io_param: pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_enzio_param(class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintParameters>) –> void

set_external_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, resnum: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_external_position(unsigned long) –> void

set_param_index(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, index: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::set_param_index(unsigned long) –> void

show_params(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::show_params() const –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms¶

Bases: pybind11_object

helper class for EnzCstTemplateRes, holds atom ids corresponding

to the residue types in a certain pose

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms::operator=(const class protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms &) –> class protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms &

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms::remap_resid(const class core::id::SequenceMapping &) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache¶

Bases: pybind11_object

add_position_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::add_position_in_pose(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::operator=(const class protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache &) –> class protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache &

contains_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos: int) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::contains_position(const unsigned long) const –> bool

not_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::not_in_pose() const –> bool

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶

remapping sequence positions

C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::remap_resid(const class core::id::SequenceMapping &) –> void

remove_seqpos(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos: int) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::remove_seqpos(unsigned long) –> bool

seqpos_map_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::seqpos_map_size() const –> unsigned long

set_position_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache::set_position_in_pose(unsigned long) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver¶

Bases: CacheableObserver

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver &) –> class protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

attach to Pose/Conformation: Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

cst_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → protocols::toolbox::match_enzdes_util::EnzdesCstCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::cst_cache() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesCstCache>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None¶

detach from Pose/Conformation

Derived classes do not overload this method – see
detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

enzdes_loops_file(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → protocols::toolbox::match_enzdes_util::EnzdesLoopsFile¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::enzdes_loops_file() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesLoopsFile>

erase_rigid_body_confs_for_lig(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seqpos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::erase_rigid_body_confs_for_lig(unsigned long) –> void

get_seq_recovery_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::get_seq_recovery_cache() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache>

is_attached(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::is_attached() const –> bool

lig_rigid_body_confs(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::lig_rigid_body_confs() const –> const class std::map<unsigned long, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > > > > &

remove_favor_native_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::remove_favor_native_constraints(class core::pose::Pose &) –> void

set_cst_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, cst_cache: protocols::toolbox::match_enzdes_util::EnzdesCstCache) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::set_cst_cache(class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesCstCache>) –> void

set_enzdes_loops_file(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, loopfile_in: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::set_enzdes_loops_file(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesLoopsFile>) –> void

set_rigid_body_confs_for_lig(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seqpos: int, rg_confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::set_rigid_body_confs_for_lig(unsigned long, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void

set_seq_recovery_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seq_recovery_cache: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::set_seq_recovery_cache(class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache>) –> void

setup_favor_native_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, native_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache¶

Bases: pybind11_object

a simple class to store the pose specific enzdes constraint information in the actual pose

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesCstCache &) –> class protocols::toolbox::match_enzdes_util::EnzdesCstCache &

contains_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, seqpos: int) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::contains_position(unsigned long) const –> bool

enzcst_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::enzcst_io() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>

ncsts(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::ncsts() const –> unsigned long

ordered_constrained_positions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

returns all seqpos present in the cache in order of the params: which they are in.

note: ligands are explicityly put at the end of the vector

C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::ordered_constrained_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

param_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, cst_block: int) → protocols::toolbox::match_enzdes_util::EnzdesCstParamCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::param_cache(unsigned long) –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesCstParamCache>

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶

remapping sequence positions

C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::remap_resid(const class core::id::SequenceMapping &) –> void

set_param_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, cst_block: int, param_cache: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstCache::set_param_cache(unsigned long, class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesCstParamCache>) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache¶

Bases: pybind11_object

active_pose_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::active_pose_constraints() –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesCstParamCache &) –> class protocols::toolbox::match_enzdes_util::EnzdesCstParamCache &

clear_active_pose_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::clear_active_pose_constraints() –> void

contains_position(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos: int) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::contains_position(unsigned long) const –> bool

covalent_connections(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_CovalentConnectionReplaceInfo_t¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::covalent_connections() const –> const class utility::vector1<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo>, class std::allocator<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo> > > &

missing_in_pose(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::missing_in_pose() const –> bool

remap_resid(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶

remapping sequence positions

C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::remap_resid(const class core::id::SequenceMapping &) –> void

remove_seqpos_from_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::remove_seqpos_from_template_res(unsigned long) –> void

set_active_pose_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, constraints: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::set_active_pose_constraints(const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &) –> void

set_position_for_missing_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::set_position_for_missing_res(unsigned long) –> void

template_res_cache(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, index: int) → protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache(unsigned long) –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache>

template_res_cache_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache_size() const –> unsigned long

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesLoopInfo &) –> class protocols::toolbox::match_enzdes_util::EnzdesLoopInfo &

check_data_consistency(*args, **kwargs)¶

Overloaded function.

check_data_consistency(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) -> bool
check_data_consistency(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo, report: bool) -> bool

C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::check_data_consistency(bool) const –> bool

contact_buried_problematic_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::contact_buried_problematic_res() const –> bool

cst_interactions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::cst_interactions() const –> const class utility::vector1<class protocols::toolbox::match_enzdes_util::CstResInteractions, class std::allocator<class protocols::toolbox::match_enzdes_util::CstResInteractions> > &

max_length(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::max_length() const –> unsigned long

min_length(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::min_length() const –> unsigned long

pdb_numb(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pdb_numb() const –> bool

pose_numb(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::pose_numb() const –> bool

preserve_buried_contacts(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::preserve_buried_contacts() const –> bool

read_loops_file_block(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo, data: pyrosetta.rosetta.utility.io.izstream) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(class utility::io::izstream &) –> bool

res_interactions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::res_interactions() const –> const class utility::vector1<class protocols::toolbox::match_enzdes_util::ResInteractions, class std::allocator<class protocols::toolbox::match_enzdes_util::ResInteractions> > &

ss_strings(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::ss_strings() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

ss_strings_specified(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::ss_strings_specified() const –> bool

start(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start() const –> unsigned long

start_pdb(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start_pdb() const –> unsigned long

start_pdb_chain(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → str¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::start_pdb_chain() const –> char

stop(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop() const –> unsigned long

stop_pdb(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop_pdb() const –> unsigned long

stop_pdb_chain(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo) → str¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::stop_pdb_chain() const –> char

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile¶

Bases: pybind11_object

class to process an enzdes loops file

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesLoopsFile &) –> class protocols::toolbox::match_enzdes_util::EnzdesLoopsFile &

clear(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::clear() –> void

file_read(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::file_read() const –> bool

loop_info(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile, l: int) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::loop_info(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesLoopInfo>

num_loops(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) → int¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::num_loops() const –> unsigned long

read_loops_file(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile, filename: str) → bool¶: C++: protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::read_loops_file(std::string) –> bool

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::operator=(const class protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache &) –> class protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache &

get_designable_residues(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::get_designable_residues() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

get_sequence(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache) → pyrosetta.rosetta.std.map_unsigned_long_char¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::get_sequence() –> class std::map<unsigned long, char, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, char> > >

remap_residues(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::remap_residues(const class core::id::SequenceMapping &) –> void

sequence_recovery(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache, designed_pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::sequence_recovery(const class core::pose::Pose &) const –> double

set_designable_residues(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache, des_res: pyrosetta.rosetta.std.set_unsigned_long_t) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_designable_residues(class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

set_sequence(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache, native_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_sequence(class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler¶

Bases: pybind11_object

The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner.

The external geom sampler holds the data for the six degrees of freedom that describe the downstream atoms relative to the upstream atoms. The naming of the 6 atoms involved and the 6 degrees of freedom involved is as follows:

Atoms U1, U2, and U3 are on the upstream partner. Atoms D1, D2, and D3 are on the downstream partner. The numbers indicate the distance the atoms have from the “break” between the upstream and downstream partners.

DOF 1: “tor_U3D1” is the torsion between atoms U3, U2, U1 and D1. DOF 2: “ang_U2D1” is angle between atoms U2, U1 and D1. DOF 3: “dis_U1D1” is the distance between atoms U1 and D1. DOF 4: “tor_U2D2” is the torsion between atoms U2, U1, D1 and D2. DOF 5: “ang_U1D2” is the angle between atoms U1, D1 and D3 DOF 6: “tor_U1D3” is the torsion between atoms U1, D1, D2 and D3

This naming convention describes a parameter by three letters followed by two atom names. The letter is “d” for distance, “a” for angle, and “t” for torsion. The two numbers describe the end points of that parameter assuming a continuous span of numbers between. E.g. t25 describes the geometry of 4 atoms starting at 2 and going to 5, hitting atoms 3 and 4 along the way.

ASCII art:

Fig 1. The 6 atoms that define the geometry between the upstream partner and the downstream partner. dis_U1D1 is the distance between atoms U1 and D1 U3

.
U2 — U1

dis_U1D1

D1 — D2

.
D3

Fig 2. The two angles U3

.

U2 — U1

ang_U2D1

.

ang_U1D2

D1 — D2

.
D3

Fig 3. The three torsions U3

tor_U3D1 tor_U3D1: torsion about U2-U1 axis starting at atom U3 and ending at D1
U2 — U1

tor_U2D2 tor_U2D2: torsion about U1-D1 axis starting at atom U2 and ending at D2

D1 — D2

tor_U1D3 tor_U1D3: torsion about D1-D2 axis starting at atom U1 and ending at D3
D3

There are three other parameters needed to construct the location of atoms 4, 5 and 6 from atoms 1, 2 and 3, but these are not considered DOFs as they are not allowed to vary. They are: Extra 1: the distance between atom D1 and atom D2 Extra 2: the distance between atom D2 and atom D3 Extra 3: the angle between atoms D1, D2 and D3.

These three parameters must be communicated to the ExternGeomSampler through its functions set_dis_D1D2, set_dis_D2D3 and set_ang_D1D2D3.

The ExternalGeomSampler holds the set of samples for each of the 6 DOFs. For each sample, it precomputes a HomogeneousTransform so that during the enumeration of all sample combinations the coordinate computation requires matrix multiplication only: the more expensive transcendental function evaluations evaluated before coordinate construction begins, their results stored, and are thereby avoided in the enumeration loops.

To build the coordinates of atoms D1, D2 and D3, given the sample id’s for the 6 DOFs as the 6-tuple [ i, j, k, l, m, n ]: start with a coordinate frame at atom U1 s.t. the z axis lies on the vector from atom U2 to atom U1, the y axis lies in the plane defined atoms U1, U2 and U3, and the x axis is the cross-product of y and z. Call the start frame “frame1.” frame2 is the product: frame1 * transform( HT_tor_U3D1, i ); frame3 is the product: frame2 * transform( HT_ang_U2D1, j ); frame4 is computed from frame3 by walking along frame3’s z-axis by dis_U1D1_samples( k ); frame4.point() is the coordinate for atom 4. frame5 is the product: frame4 * transform( HT_tor_U2D2, l ); frame6 is the product: frame5 * transform( HT_ang_U1D2, m ); frame6.point() is the coordinate for atom 5. NOTE: transform( HT_ang_U1D2, m ) is the product of the z-axis rotation by ang_U1D2_sample_[ m ] and the transformation HT along the z-axis by the distance between atoms D1 and D2. The ExternalGeomSampler pre-multiplies these matricies. frame7 is the product: frame6 * transform( HT_tor_U1D3, n ); frame7.point() is the coordinate for atom 6. NOTE: transform( HT_tor_U1D3, n ) is the product of three HTs: the HT representing the z-axis rotation by tor_U1D3_sample_[ n ], the HT representing the x-axis rotation by ( -1 * ( 180 - ang_D1D2D3 ) ) and the HT representing the z-axis translation by the distance between atoms D2 and D3. The ExternalGeomSampler pre-multiplies these matrices.

ang_U1D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::ang_U1D2_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

ang_U2D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::ang_U2D1_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, rhs: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::operator=(const class protocols::toolbox::match_enzdes_util::ExternalGeomSampler &) –> class protocols::toolbox::match_enzdes_util::ExternalGeomSampler &

dis_U1D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::dis_U1D1_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

flip_upstream_downstream_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → None¶

convenience function if one wants to change the meaning of: upstream and downstream

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::flip_upstream_downstream_samples() –> void

n_ang_U1D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U1D2_samples() const –> unsigned long

n_ang_U2D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U2D1_samples() const –> unsigned long

n_dis_U1D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_dis_U1D1_samples() const –> unsigned long

n_tor_U1D3_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U1D3_samples() const –> unsigned long

n_tor_U2D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U2D2_samples() const –> unsigned long

n_tor_U3D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → int¶

Accessors

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U3D1_samples() const –> unsigned long

precompute_transforms(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → None¶

Must be called after the samples are set, and the: internal geometry of the three downstream coordinates (point 4, 5, and 6) are described. Does nothing if the transforms are up to date.

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::precompute_transforms() –> void

set_ang_D1D2D3(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_in_degrees: float) → None¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_D1D2D3(double) –> void

set_ang_U1D2_samples(*args, **kwargs)¶

Overloaded function.

set_ang_U1D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U1D2_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_U1D2_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_ang_U1D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U1D2_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_U1D2_samples(const class std::list<double, class std::allocator<double> > &) –> void

set_ang_U2D1_samples(*args, **kwargs)¶

Overloaded function.

set_ang_U2D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U2D1_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_U2D1_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_ang_U2D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U2D1_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_ang_U2D1_samples(const class std::list<double, class std::allocator<double> > &) –> void

set_dis_D1D2(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, distance: float) → None¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(double) –> void

set_dis_D2D3(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, distance: float) → None¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D2D3(double) –> void

set_dis_U1D1_samples(*args, **kwargs)¶

Overloaded function.

set_dis_U1D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, dis_U1D1_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_U1D1_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_dis_U1D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, dis_U1D1_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_U1D1_samples(const class std::list<double, class std::allocator<double> > &) –> void

set_tor_U1D3_samples(*args, **kwargs)¶

Overloaded function.

set_tor_U1D3_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U1D3_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U1D3_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_tor_U1D3_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U1D3_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U1D3_samples(const class std::list<double, class std::allocator<double> > &) –> void

set_tor_U2D2_samples(*args, **kwargs)¶

Overloaded function.

set_tor_U2D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U2D2_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U2D2_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_tor_U2D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U2D2_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U2D2_samples(const class std::list<double, class std::allocator<double> > &) –> void

set_tor_U3D1_samples(*args, **kwargs)¶

Overloaded function.

set_tor_U3D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U3D1_samples: pyrosetta.rosetta.utility.vector1_double) -> None

Intialization routines: all initialization routines must be invoked before building may begin. Once each has been called, the function precompute_transforms() must be called.

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U3D1_samples(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_tor_U3D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U3D1_samples: pyrosetta.rosetta.std.list_double_t) -> None

C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_tor_U3D1_samples(const class std::list<double, class std::allocator<double> > &) –> void

tor_U1D3_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::tor_U1D3_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

tor_U2D2_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::tor_U2D2_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

tor_U3D1_samples(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::tor_U3D1_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

transform(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, id: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform, which_state: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::transform(enum protocols::toolbox::match_enzdes_util::ExternalTransform, unsigned long) const –> const class numeric::HomogeneousTransform<double> &

transforms_uptodate(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) → bool¶: C++: protocols::toolbox::match_enzdes_util::ExternalGeomSampler::transforms_uptodate() const –> bool

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform¶

Bases: pybind11_object

Members:

HT_tor_U3D1

HT_ang_U2D1

HT_tor_U2D2

HT_ang_U1D2

HT_tor_U1D3

n_external_transforms

HT_ang_U1D2 = <ExternalTransform.HT_ang_U1D2: 4>¶

HT_ang_U2D1 = <ExternalTransform.HT_ang_U2D1: 2>¶

HT_tor_U1D3 = <ExternalTransform.HT_tor_U1D3: 5>¶

HT_tor_U2D2 = <ExternalTransform.HT_tor_U2D2: 3>¶

HT_tor_U3D1 = <ExternalTransform.HT_tor_U3D1: 1>¶

n_external_transforms = <ExternalTransform.HT_tor_U1D3: 5>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo¶

Bases: pybind11_object

class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::operator=(const class protocols::toolbox::match_enzdes_util::GeomSampleInfo &) –> class protocols::toolbox::match_enzdes_util::GeomSampleInfo &

create_sample_vector(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → pyrosetta.rosetta.utility.vector1_double¶

creates an explicit sample vector from the input data: i.e. translates ideal value, tolerance, num_steps and periodicity into a vector of values

C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::create_sample_vector() const –> class utility::vector1<double, class std::allocator<double> >

force_const(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → float¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::force_const() const –> double

function_tag(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → str¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::function_tag() const –> std::string

ideal_val(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → float¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::ideal_val() const –> double

num_steps(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::num_steps() const –> unsigned long

periodicity(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → float¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::periodicity() const –> double

read_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, line_stream: pyrosetta.rosetta.std.istringstream) → bool¶

data reading routine

C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::read_data(class std::basic_istringstream<char> &) –> bool

step_size(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → float¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::step_size() const –> double

tag(*args, **kwargs)¶

Overloaded function.

tag(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, tag: str) -> None

C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::tag(const std::string &) –> void

tag(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> str

C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::tag() const –> std::string

tolerance(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) → float¶: C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::tolerance() const –> double

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector¶

Bases: pybind11_object

@ brief helper class for collecting all different definitions of invrots from a tree

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector¶: C++: protocols::toolbox::match_enzdes_util::InvrotCollector::operator=(const class protocols::toolbox::match_enzdes_util::InvrotCollector &) –> class protocols::toolbox::match_enzdes_util::InvrotCollector &

clone(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector¶: C++: protocols::toolbox::match_enzdes_util::InvrotCollector::clone() const –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::InvrotCollector>

invrots(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector) → pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotCollector::invrots() const –> const class std::vector<class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >, class std::allocator<class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > > > &

owner_nodes_and_locations(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector) → pyrosetta.rosetta.std.map_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_unsigned_long_std_less_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_std_allocator_std_pair_const_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_unsigned_long_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotCollector::owner_nodes_and_locations() const –> const class std::map<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>, unsigned long, struct std::less<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase> >, class std::allocator<struct std::pair<const class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>, unsigned long> > > &

set_invrots_for_listnum(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector, listnum: int, invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, tree_node: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase, location_in_node: int) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotCollector::set_invrots_for_listnum(unsigned long, const class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>, unsigned long) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget¶

Bases: InvrotTreeNodeBase

the ‘root’ target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity

all_target_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_res() const –> class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget¶: C++: protocols::toolbox::match_enzdes_util::InvrotTarget::operator=(const class protocols::toolbox::match_enzdes_util::InvrotTarget &) –> class protocols::toolbox::match_enzdes_util::InvrotTarget &

generate_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

generate constraints against a certain pose

C++: protocols::toolbox::match_enzdes_util::InvrotTarget::generate_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

initialize_tree_nodes_from_enzcst_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → bool¶

can initialize tree nodes according to: an enzcst io note that this function presumes that representative_target_res_for_geom_cst_ and all_target_res_ have been set through calling the generate_representative_target_res_for_geom_cst() function as implemented by the child class

C++: protocols::toolbox::match_enzdes_util::InvrotTarget::initialize_tree_nodes_from_enzcst_io(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) –> bool

location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::location_in_parent_node() const –> unsigned long

parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

set_location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location: int) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::set_location_in_parent_node(unsigned long) –> void

target_res_for_geom_cst(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, geom_cst: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: protocols::toolbox::match_enzdes_util::InvrotTarget::target_res_for_geom_cst(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree¶

Bases: pybind11_object

abstract base class for the inverse rotamer tree is abstract so that in the future inverse rots could be generated in different ways than throug the enz cst machinery

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree¶: C++: protocols::toolbox::match_enzdes_util::InvrotTree::operator=(const class protocols::toolbox::match_enzdes_util::InvrotTree &) –> class protocols::toolbox::match_enzdes_util::InvrotTree &

check_pose_tree_compatibility(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

important function 2:: after a chain/pose has been generated, check whether it’s compatible with the inverse rotamers in the tree this can change the pose again

C++: protocols::toolbox::match_enzdes_util::InvrotTree::check_pose_tree_compatibility(class core::pose::Pose &) const –> bool

collect_all_inverse_rotamers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotCollector_t¶

convenience access function: to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned

C++: protocols::toolbox::match_enzdes_util::InvrotTree::collect_all_inverse_rotamers() const –> class utility::vector1<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotCollector>, class std::allocator<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotCollector> > >

dump_invrots_tree_as_multimodel_pdbs(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, filename_base: str) → None¶

visualization: this can lead to several files being written, depending on the ambiguities in the tree

C++: protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(std::string) const –> void

generate_inverse_rotamer_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → None¶

the main function, generate the constraints

C++: protocols::toolbox::match_enzdes_util::InvrotTree::generate_inverse_rotamer_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) –> void

generate_targets_and_inverse_rotamers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → None¶

important function 1:: populate the tree should be called before folding a chain obviously see TheozymeInvrotTree below for example

C++: protocols::toolbox::match_enzdes_util::InvrotTree::generate_targets_and_inverse_rotamers() –> void

get_constraint_for_target_state(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, target_state: int) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: protocols::toolbox::match_enzdes_util::InvrotTree::get_constraint_for_target_state(unsigned long) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

num_target_states(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTree::num_target_states() const –> unsigned long

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode¶

Bases: InvrotTreeNodeBase

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::operator=(const class protocols::toolbox::match_enzdes_util::InvrotTreeNode &) –> class protocols::toolbox::match_enzdes_util::InvrotTreeNode &

generate_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

for each invrots/node pointer pair:
a.generate an ambigous constraint for the inverse rots for each node pointer to child nodes (only if there are child nodes, of course)
call the generate_constraints function on the pointers to child nodes
c. package the ambig constraint generated for the inverse rots and the constraints that come from the child nodes into one multicst caveat: if the child nodes send up a multi constraint and not an ambiguous constraint, ‘unpackage’ those multicst and generate a new multicst containing this nodes ambigcst and the member_csts from the child nodes’ multicsts

if there is more than one invrots/node pointer pair, throw all the generated multicsts into one ambig cst

return either the multicst (one pair) or the ambigcst

hope this works

C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::generate_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

get_fixed_pt(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.id.AtomID¶

this function returns the AtomID for an atom: in the pose that’s supposed to stay fixed during folding, i.e. the neighbor atom of the first target needed to generate the right backbone_stub constraints

C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(const class core::pose::Pose &) const –> class core::id::AtomID

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

initialize_from_enzcst_io(*args, **kwargs)¶

Overloaded function.

initialize_from_enzcst_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, target_residue: pyrosetta.rosetta.core.conformation.Residue, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst: int) -> bool
initialize_from_enzcst_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, target_residue: pyrosetta.rosetta.core.conformation.Residue, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst: int, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

generate invrots according to: an enzdes cstfile returns true if it was possible to build invrots, i.e. geometry correctly defined in cstfile and no clashes with any parent inverse rotamers

C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(const class core::conformation::Residue &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>, unsigned long, class std::shared_ptr<const class core::pose::Pose>) –> bool

initialize_from_enzcst_io_and_invrots(*args, **kwargs)¶

Overloaded function.

initialize_from_enzcst_io_and_invrots(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, all_invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst: int) -> bool
initialize_from_enzcst_io_and_invrots(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, all_invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst: int, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io_and_invrots(const class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>, unsigned long, class std::shared_ptr<const class core::pose::Pose>) –> bool

location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::location_in_parent_node() const –> unsigned long

parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

remove_invrots_clashing_with_parent_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, covalent: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, bool) const –> void

set_location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location: int) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::set_location_in_parent_node(unsigned long) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶

Bases: pybind11_object

abstract base class for an inverse rotamer tree node. Exists so that the target node (InvrotTreeTarget) and the different geom cst nodes (InvrotTreeNode) have a common base class. This is necessary so that a node can point at its parent node in a tree without having to worry about whether that is a target or a regular node

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::operator=(const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase &) –> class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase &

generate_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

nodes need to be able to generate constraints

C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::generate_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::location_in_parent_node() const –> unsigned long

parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

set_location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location: int) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::set_location_in_parent_node(unsigned long) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::operator=(const class protocols::toolbox::match_enzdes_util::LigandConformer &) –> class protocols::toolbox::match_enzdes_util::LigandConformer &

atom1_atom2_atom3_angle(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶

Returns an angle in degrees between the three downstream atoms.

C++: protocols::toolbox::match_enzdes_util::LigandConformer::atom1_atom2_atom3_angle() const –> double

atom1_atom2_distance(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::atom1_atom2_distance() const –> double

atom2_atom3_distance(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::atom2_atom3_distance() const –> double

collision_check_id_2_restype_id(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, coll_check_id: int) → int¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::collision_check_id_2_restype_id(unsigned long) const –> unsigned long

coordinate_in_D3_frame(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno: int, frame3: pyrosetta.rosetta.numeric.HomogeneousTransform_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::coordinate_in_D3_frame(unsigned long, const class numeric::HomogeneousTransform<double> &) const –> class numeric::xyzVector<double>

coordinate_in_global_frame(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno: int, orientation_frame: pyrosetta.rosetta.numeric.HomogeneousTransform_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::coordinate_in_global_frame(unsigned long, const class numeric::HomogeneousTransform<double> &) const –> class numeric::xyzVector<double>

coordinates_from_orientation(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, orientation: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, atom_indices: pyrosetta.rosetta.utility.vector1_core_id_AtomID, atom_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::coordinates_from_orientation(const class utility::fixedsizearray1<double, 6> &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> void

frame_from_global_orientation(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, orientation: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶

The orientation frame at orientation atom 3 given: orientation atom 3’s xyz coordinates and the euler angles describing the frame

C++: protocols::toolbox::match_enzdes_util::LigandConformer::frame_from_global_orientation(class utility::fixedsizearray1<double, 6>) const –> class numeric::HomogeneousTransform<double>

get_global_coords_as_FArray2D(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, coords: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, orientation_frame: pyrosetta.rosetta.numeric.HomogeneousTransform_double_t, restype_atomnos: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

@ brief helper function to get the coordinates in 2D FArray format

C++: protocols::toolbox::match_enzdes_util::LigandConformer::get_global_coords_as_FArray2D(class ObjexxFCL::FArray2D<double> &, const class numeric::HomogeneousTransform<double> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_lig_restype(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::get_lig_restype() const –> const class core::chemical::ResidueType &

global_orientation_from_frame3(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, frame3: pyrosetta.rosetta.numeric.HomogeneousTransform_double_t) → pyrosetta.rosetta.utility.fixedsizearray1_double_6_t¶

The orientaton frame at orientation atom 3 given: the coordinate frame at D3 (this frame is called frame3)

C++: protocols::toolbox::match_enzdes_util::LigandConformer::global_orientation_from_frame3(const class numeric::HomogeneousTransform<double> &) const –> class utility::fixedsizearray1<double, 6>

ignore_h_collisions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, setting: bool) → None¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::ignore_h_collisions(bool) –> void

initialize_from_residue(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, D1: int, D2: int, D3: int, orientation_atom1: int, orientation_atom2: int, orientation_atom3: int, residue: pyrosetta.rosetta.core.conformation.Residue) → None¶

Specify the residue, with coordinates, that’s being used as the downstream: partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm, and therefore the initialization routines are specific for that algorithm. In this initialization function, one must list atoms “D1, D2 and D3” in the convention of describing the rigid-body orientation between three atoms of the upstream partner (atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to define the orientation frame of the downstream ligand. It is essential to the matching algorithm that the same three orientation atoms are used for all LigandConformers.

C++: protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, const class core::conformation::Residue &) –> void

move_atoms_to_collcheck_begin(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atnos_to_move_early: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::move_atoms_to_collcheck_begin(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

n_collision_check_atoms(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → int¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::n_collision_check_atoms() const –> unsigned long

oatom1_oatom2_distance(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶

returns the distance between orientation atom 1 and orientation atom 2

C++: protocols::toolbox::match_enzdes_util::LigandConformer::oatom1_oatom2_distance() const –> double

oatom1_oatom2_oatom3_angle(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶

Returns an angle in degrees between the three orientation atoms.

C++: protocols::toolbox::match_enzdes_util::LigandConformer::oatom1_oatom2_oatom3_angle() const –> double

oatom2_oatom3_distance(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) → float¶

returns the distance between orientation atom 2 and orientation atom 3

C++: protocols::toolbox::match_enzdes_util::LigandConformer::oatom2_oatom3_distance() const –> double

restype_id_2_collision_check_id(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno: int) → int¶: C++: protocols::toolbox::match_enzdes_util::LigandConformer::restype_id_2_collision_check_id(unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo¶

Bases: pybind11_object

algorithm_inputs(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t¶

holds information read from ALGORITHM_INFO blocks: in the input file

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::algorithm_inputs() const –> const class std::map<std::string, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<std::string, class std::allocator<std::string > > > > > &

allowed_res_name3s(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres: int) → pyrosetta.rosetta.utility.vector1_std_string¶

what type of amino acids/ligands make this: constraint

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_res_name3s(unsigned long) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

allowed_restypes(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶

all chemically non-redundant restypes of the given restypes. Note – now sorted by name!

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_restypes(unsigned long) const –> const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

allowed_seqpos(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

all positions where a residue for this geometry: can be placed

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::allowed_seqpos() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::operator=(const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo &) –> class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo &

constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::constraints() const –> class utility::vector1<struct protocols::toolbox::match_enzdes_util::SingleConstraint, class std::allocator<struct protocols::toolbox::match_enzdes_util::SingleConstraint> >

diversify_backbone_only_rotamers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) → None¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> void

downstream_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → int¶

which one of the residues (1 or 2 ) in this block: is the upstream res. used for classic match algorithm hardcoded 1 for now

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::downstream_res() const –> unsigned long

enz_cst_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, template_res: int) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::enz_cst_template_res(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzCstTemplateRes>

index(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::index() const –> unsigned long

initialize_from_tag(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::initialize_from_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

inverse_rotamers_against_residue(*args, **kwargs)¶

Overloaded function.

inverse_rotamers_against_residue(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, target_template: int, target_conf: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t

function that takes all rotamers for the ResidueType(s): that interact with the target residues and places them according according to the geometry specified

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(const unsigned long, class std::shared_ptr<const class core::conformation::Residue>) const –> class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

inverse_rotamers_against_residue(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, target_conf: pyrosetta.rosetta.core.conformation.Residue, invrot_restype: pyrosetta.rosetta.core.chemical.ResidueType, target_ats: pyrosetta.rosetta.utility.vector1_unsigned_long, invrot_ats: pyrosetta.rosetta.utility.vector1_unsigned_long, flip_exgs_upstream_downstream_samples: bool, backbone_interaction: bool) -> pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(const class core::conformation::Residue &, class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool) const –> class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

is_backbone(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres: int) → bool¶

is this interaction a backbone interaction

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::is_backbone(unsigned long) const –> bool

is_covalent(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::is_covalent() const –> bool

native(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → bool¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::native() const –> bool

num_enz_cst_template_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → int¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::num_enz_cst_template_res() const –> unsigned long

process_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → None¶

processes the read data: right now this only generates the template atomnos for every restype

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::process_data() –> void

read_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, data: pyrosetta.rosetta.utility.io.izstream) → bool¶

data reading routine

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::read_data(class utility::io::izstream &) –> bool

static return_complex_type_for_MatcherConstraint(ssl: pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::return_complex_type_for_MatcherConstraint(class utility::tag::XMLSchemaSimpleSubelementList &, class utility::tag::XMLSchemaDefinition &) –> void

template_atom_inds(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres: int, which_template_atom: int, restype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

all atoms of restype to be used as template_atom: in the matcher/constraints

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::template_atom_inds(unsigned long, unsigned long, const class core::chemical::ResidueType &) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

upstream_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → int¶

which one of the residues (1 or 2 ) in this block: is the upstream res. used for classic match algorithm hardcoded 2 for now

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::upstream_res() const –> unsigned long

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList¶

Bases: pybind11_object

a simple container class to contain several MatchConstraintFileInfo instances. this can also query the MatchConstraintFileInfos for common upstream restypes and put all their geomsamples into one list

add_mcfi(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, mcfi: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) → None¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::add_mcfi(class std::shared_ptr<class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo>) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::operator=(const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList &) –> class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList &

inverse_rotamers_against_residue(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, target_template: int, target_conf: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t¶

function that takes all rotamers for the ResidueType(s): that interact with the target residues and places them according according to the geometry specified

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::inverse_rotamers_against_residue(const unsigned long, class std::shared_ptr<const class core::conformation::Residue>) const –> class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

mcfi(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, which_mcfi: int) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::mcfi(unsigned long) const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo>

num_mcfis(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList) → int¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::num_mcfis() const –> unsigned long

read_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, data: pyrosetta.rosetta.utility.io.izstream) → bool¶

data reading routine

C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::read_data(class utility::io::izstream &) –> bool

upstream_restypes(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶: C++: protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::upstream_restypes() const –> const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::operator=(const class protocols::toolbox::match_enzdes_util::ResInteractions &) –> class protocols::toolbox::match_enzdes_util::ResInteractions &

dis(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::dis() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loop_ang(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loop_ang() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loop_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loop_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

loopres_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

loopres_base2_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_base2_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

loopres_base_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::loopres_base_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

lt_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::lt_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

num_interactions(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → int¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::num_interactions() const –> unsigned long

read_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions, data: pyrosetta.rosetta.utility.io.izstream) → bool¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::read_data(class utility::io::izstream &) –> bool

targ_ang(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_ang() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

targ_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_base2_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_base2_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_base_atom_names(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_base_atom_names() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

targ_dih(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → protocols::toolbox::match_enzdes_util::GeomSampleInfo¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_dih() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::GeomSampleInfo>

targ_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → int¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::targ_res() const –> unsigned long

write_data(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions) → None¶: C++: protocols::toolbox::match_enzdes_util::ResInteractions::write_data() const –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint¶

Bases: pybind11_object

property ang_U1D2¶

property ang_U2D1¶

property dis_U1D1¶

property tor_U1D3¶

property tor_U2D2¶

property tor_U3D1¶

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget¶

Bases: InvrotTarget

all_target_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTarget::all_target_res() const –> class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget¶: C++: protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget::operator=(const class protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget &) –> class protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget &

generate_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶

generate constraints against a certain pose

C++: protocols::toolbox::match_enzdes_util::InvrotTarget::generate_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

get_self_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_ptr() –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::get_self_weak_ptr() –> class std::weak_ptr<class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

initialize_tree_nodes_from_enzcst_io(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → bool¶

can initialize tree nodes according to: an enzcst io note that this function presumes that representative_target_res_for_geom_cst_ and all_target_res_ have been set through calling the generate_representative_target_res_for_geom_cst() function as implemented by the child class

C++: protocols::toolbox::match_enzdes_util::InvrotTarget::initialize_tree_nodes_from_enzcst_io(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) –> bool

location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::location_in_parent_node() const –> unsigned long

parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) → pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::parent_node() const –> class std::weak_ptr<const class protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase>

set_location_in_parent_node(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location: int) → None¶: C++: protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase::set_location_in_parent_node(unsigned long) –> void

target_res_for_geom_cst(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, geom_cst: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: protocols::toolbox::match_enzdes_util::InvrotTarget::target_res_for_geom_cst(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree¶

Bases: InvrotTree

This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. It gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues…

assign(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree, : pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree) → pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree¶: C++: protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::operator=(const class protocols::toolbox::match_enzdes_util::TheozymeInvrotTree &) –> class protocols::toolbox::match_enzdes_util::TheozymeInvrotTree &

check_pose_tree_compatibility(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::check_pose_tree_compatibility(class core::pose::Pose &) const –> bool

collect_all_inverse_rotamers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotCollector_t¶

convenience access function: to the inverse rotamers in the tree note: the returned invrots can contain duplications, as every unique definition of the tree is returned

C++: protocols::toolbox::match_enzdes_util::InvrotTree::collect_all_inverse_rotamers() const –> class utility::vector1<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotCollector>, class std::allocator<class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::InvrotCollector> > >

dump_invrots_tree_as_multimodel_pdbs(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, filename_base: str) → None¶

visualization: this can lead to several files being written, depending on the ambiguities in the tree

C++: protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(std::string) const –> void

generate_inverse_rotamer_constraints(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose: pyrosetta.rosetta.core.pose.Pose, geomcst_seqpos: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) → None¶

the main function, generate the constraints

C++: protocols::toolbox::match_enzdes_util::InvrotTree::generate_inverse_rotamer_constraints(const class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst>) –> void

generate_targets_and_inverse_rotamers(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree) → None¶

this function generates the ‘target’ for the inverse rotamers,: i.e. in the case of enzdes, simply the coordinates for the ligand if in the future somebody wants to use this to build inverse rotamers against a protein, this function can be reimplemented. called from the constructor, is this really the best idea?

C++: protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers() –> void

get_constraint_for_target_state(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, target_state: int) → pyrosetta.rosetta.core.scoring.constraints.Constraint¶: C++: protocols::toolbox::match_enzdes_util::InvrotTree::get_constraint_for_target_state(unsigned long) const –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

num_target_states(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) → int¶: C++: protocols::toolbox::match_enzdes_util::InvrotTree::num_target_states() const –> unsigned long

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.assemble_remark_line(*args, **kwargs)¶

Overloaded function.

assemble_remark_line(chainA: str, resA: str, seqposA: int, chainB: str, resB: str, seqposB: int, cst_block: int) -> str
assemble_remark_line(chainA: str, resA: str, seqposA: int, chainB: str, resB: str, seqposB: int, cst_block: int, ex_geom_id: int) -> str

C++: protocols::toolbox::match_enzdes_util::assemble_remark_line(const std::string &, const std::string &, int, const std::string &, const std::string &, int, unsigned long, unsigned long) –> std::string

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.constrain_pose_res_to_invrots(*args, **kwargs)¶

Overloaded function.

constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint
constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose, constraint_func: pyrosetta.rosetta.core.scoring.func.Func) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint

fowarding function for function below

C++: protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(const class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, class std::shared_ptr<class core::scoring::func::Func>) –> class std::shared_ptr<const class core::scoring::constraints::AmbiguousConstraint>

constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose, fixed_pt: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint
constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t, seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose, fixed_pt: pyrosetta.rosetta.core.id.AtomID, constraint_func: pyrosetta.rosetta.core.scoring.func.Func) -> pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint

constraints each invrot to the: backbone of each seqpos and throws all those constraints into one ambiguous constraint.

C++: protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(const class std::list<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, const class core::id::AtomID &, class std::shared_ptr<class core::scoring::func::Func>) –> class std::shared_ptr<const class core::scoring::constraints::AmbiguousConstraint>

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.cst_residue_in_pose(pose: pyrosetta.rosetta.core.pose.Pose, geomcst: int, geomcst_template_res: int) → pyrosetta.rosetta.core.conformation.Residue¶

convenience function that returns a residue: of the desired cst interaction in case there are no constraints in the pose, returns null pointer

C++: protocols::toolbox::match_enzdes_util::cst_residue_in_pose(const class core::pose::Pose &, unsigned long, unsigned long) –> class std::shared_ptr<const class core::conformation::Residue>

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.get_enzdes_observer(*args, **kwargs)¶

Overloaded function.

get_enzdes_observer(pose: pyrosetta.rosetta.core.pose.Pose) -> protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver

convenience function to get a cacheable observer from a pose

C++: protocols::toolbox::match_enzdes_util::get_enzdes_observer(class core::pose::Pose &) –> class std::shared_ptr<class protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver>

get_enzdes_observer(pose: pyrosetta.rosetta.core.pose.Pose) -> protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver

C++: protocols::toolbox::match_enzdes_util::get_enzdes_observer(const class core::pose::Pose &) –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver>

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.get_first_protein_residue(pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::toolbox::match_enzdes_util::get_first_protein_residue(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.get_last_protein_residue(pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::toolbox::match_enzdes_util::get_last_protein_residue(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.replace_residue_keeping_all_atom_positions(pose: pyrosetta.rosetta.core.pose.Pose, new_res: pyrosetta.rosetta.core.conformation.Residue, res_pos: int) → None¶: C++: protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(class core::pose::Pose &, class core::conformation::Residue, unsigned long) –> void

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.sort_residue_type_pointers_by_name(restype_temp_set: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶: C++: protocols::toolbox::match_enzdes_util::sort_residue_type_pointers_by_name(const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &) –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.split_up_remark_line(line: str, chainA: str, resA: str, seqposA: int, chainB: str, resB: str, seqposB: int, cst_block: int, ex_geom_id: int) → bool¶: C++: protocols::toolbox::match_enzdes_util::split_up_remark_line(std::string, std::string &, std::string &, int &, std::string &, std::string &, int &, unsigned long &, unsigned long &) –> bool