match_enzdes_util

Bindings for protocols::toolbox::match_enzdes_util namespace

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

small mover that takes an invrot tree

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, invrot_tree: protocols::toolbox::match_enzdes_util::InvrotTree, seqpos: protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

name() → str

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(class std::basic_ostream<char> &) 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.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

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

2. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst

Bases: pybind11_builtins.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst, seqpos_for_geomcst: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

1. initialize_from_command_line(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> None
2. 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_builtins.pybind11_object

helper class to allow for removal of covalent constraints

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, resA_base_in: str, resB_base_in: str, resA_var_in: str, resB_var_in: str, Apos_in: int, Bpos_in: int, restype_set_in: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.EnzConstraintParameters

Bases: pybind11_builtins.pybind11_object

class that holds all the parameters for one specific constraint

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_less_std_string_std_allocator_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 &

convert_GeomSampleInfo_to_FuncOP(gsi: pyrosetta.rosetta.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) → pyrosetta.rosetta.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) → pyrosetta.rosetta.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.

1. 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

2. 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) → pyrosetta.rosetta.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) → pyrosetta.rosetta.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) → pyrosetta.rosetta.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) → pyrosetta.rosetta.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: pyrosetta.rosetta.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_builtins.pybind11_object

helper class for class EnzConstraintParameters, gathers information

from cst input and pdb input

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, src_enzio_param: pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) -> None
3. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, other: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, new_ref_param: pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) -> None
4. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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> > &

atom_inds_for_restype_begin(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → std::_Rb_tree_const_iterator<std::pair<std::shared_ptr<core::chemical::ResidueType const> const, utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > > > >

Iterator to the map from ResidueType pointers (addresses) to the set of atoms

that are used to build from; this returns ResidueTypes in an indeterminant order as they are going to be sorted based on where in memory the ResidueTypes happened to be allocated.

C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_begin() const –> struct std::_Rb_tree_const_iterator<struct std::pair<const class std::shared_ptr<const class core::chemical::ResidueType>, class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > >

atom_inds_for_restype_end(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) → std::_Rb_tree_const_iterator<std::pair<std::shared_ptr<core::chemical::ResidueType const> const, utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > > > >

End iterator to the map from ResidueType pointers to the set of atoms

that are used to build from.

C++: protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::atom_inds_for_restype_end() const –> struct std::_Rb_tree_const_iterator<struct std::pair<const class std::shared_ptr<const class core::chemical::ResidueType>, class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<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 class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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_builtins.pybind11_object

helper class for EnzCstTemplateRes, holds atom ids corresponding

to the residue types in a certain pose

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.EnzdesCstCache

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, enz_cstio: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, num_cst_blocks: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.EnzdesLoopsFile

Bases: pybind11_builtins.pybind11_object

class to process an enzdes loops file

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_string<char>) –> bool

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

Bases: pybind11_builtins.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

1. 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

2. 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.

1. 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

2. 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.

1. 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

2. 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.

1. 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

2. 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.

1. 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

2. 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.

1. 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

2. 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.GeomSampleInfo

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, tag: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, arg0: float, arg1: float, arg2: float, arg3: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, ideal_val: float, tolerance: float, force_k: float, periodicity: float, num_steps: int) -> None
4. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

C++: protocols::toolbox::match_enzdes_util::GeomSampleInfo::tag(const class std::basic_string<char> &) –> void

2. 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_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector, num_residue_lists: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector, arg0: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_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

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_std_allocator_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: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

all_target_res(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_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_builtins.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_string<char>) 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.InvrotTreeNodeBase

Bases: pybind11_builtins.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.MatchConstraintFileInfoList

Bases: pybind11_builtins.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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList, restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_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.TheozymeInvrotTree

Bases: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.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…

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree, enzcst_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_string<char>) 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.

1. assemble_remark_line(chainA: str, resA: str, seqposA: int, chainB: str, resB: str, seqposB: int, cst_block: int) -> str
2. 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(class std::basic_string<char>, class std::basic_string<char>, int, class std::basic_string<char>, class std::basic_string<char>, int, unsigned long, unsigned long) –> std::string

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

Overloaded function.

1. constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_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
2. constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_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>

3. constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_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
4. constrain_pose_res_to_invrots(invrots: pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_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.

1. 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>

2. 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(class std::basic_string<char>, class std::basic_string<char> &, class std::basic_string<char> &, int &, class std::basic_string<char> &, class std::basic_string<char> &, int &, unsigned long &, unsigned long &) –> bool