scoring

• methods

Bindings for protocols::scoring namespace

class pyrosetta.rosetta.protocols.scoring.InterchainPotential

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t

Singleton class to hold the interface-derived statistics for residue-pair scores at protein/protein interfaces.

This previously derived from the EnvPairPotential, which is in no way necessary because the two classes have nothing in common; rather, the InterchainPairEnergy and InterchainEnvEnergy classes can hold a pointer to both the InterchainPotential and the EnvPairPotential.

__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).

compute_interface(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::scoring::InterchainPotential::compute_interface(class core::pose::Pose &) const –> void

evaluate_contact_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, contact_score: float) → None

C++: protocols::scoring::InterchainPotential::evaluate_contact_score(const class core::pose::Pose &, double &) const –> void

evaluate_env_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, rsd: pyrosetta.rosetta.core.conformation.Residue, env_score: float) → None

C++: protocols::scoring::InterchainPotential::evaluate_env_score(const class core::pose::Pose &, const class core::conformation::Residue &, double &) const –> void

evaluate_pair_and_vdw_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pair_score: float, vdw_score: float) → None

C++: protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, double &, double &) const –> void

finalize(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::scoring::InterchainPotential::finalize(class core::pose::Pose &) const –> void

get_instance() → protocols::scoring::InterchainPotential

C++: utility::SingletonBase<protocols::scoring::InterchainPotential>::get_instance() –> class protocols::scoring::InterchainPotential *

interface_from_pose(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, : pyrosetta.rosetta.core.pose.Pose) → protocols::scoring::InterfaceInfo

C++: protocols::scoring::InterchainPotential::interface_from_pose(const class core::pose::Pose &) const –> const class protocols::scoring::InterfaceInfo &

nonconst_interface_from_pose(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, : pyrosetta.rosetta.core.pose.Pose) → protocols::scoring::InterfaceInfo

C++: protocols::scoring::InterchainPotential::nonconst_interface_from_pose(class core::pose::Pose &) const –> class protocols::scoring::InterfaceInfo &

class pyrosetta.rosetta.protocols.scoring.InterfaceInfo

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of the interface information

__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.scoring.InterfaceInfo) -> None
2. __init__(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rb_jump_in: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rb_jump_in: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
4. __init__(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, arg0: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) -> 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_jump(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, jump_in: int) → None

Adds another jump to the interface calculation, for example for multi-body docking

C++: protocols::scoring::InterfaceInfo::add_jump(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, : pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → pyrosetta.rosetta.protocols.scoring.InterfaceInfo

C++: protocols::scoring::InterfaceInfo::operator=(const class protocols::scoring::InterfaceInfo &) –> class protocols::scoring::InterfaceInfo &

calculate(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, pose: pyrosetta.rosetta.core.pose.Pose) → None

Calculates the interface for all jumps specified in rb_jump_

C++: protocols::scoring::InterfaceInfo::calculate(const class core::pose::Pose &) –> void

calculated(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → bool

Returns if interface calculation is up to date

C++: protocols::scoring::InterfaceInfo::calculated() –> bool &

clear_jumps(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → None

Removes all jumps from the interface calculation

C++: protocols::scoring::InterfaceInfo::clear_jumps() –> void

clone(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::InterfaceInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

closest_interface_residue(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, pose: pyrosetta.rosetta.core.pose.Pose, src_rsd: int, distance: float) → int

C++: protocols::scoring::InterfaceInfo::closest_interface_residue(const class core::pose::Pose &, unsigned long, double &) const –> unsigned long

distance(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, distance_in: float) → None

Sets the distance cutoff for interface calculations

C++: protocols::scoring::InterfaceInfo::distance(double) –> void

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

initialize(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → None

Sets up InterfaceInfo members such as interface_list_ based on variables from construction

C++: protocols::scoring::InterfaceInfo::initialize() –> void

interface(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, interface_num: int) → pyrosetta.rosetta.protocols.scoring.Interface

C++: protocols::scoring::InterfaceInfo::interface(unsigned long) const –> class std::shared_ptr<const class protocols::scoring::Interface>

interface_nres(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, jump_num: int) → int

Returns the number of resides at the interface defined by jump_num

C++: protocols::scoring::InterfaceInfo::interface_nres(unsigned long) const –> unsigned long

is_interface(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) → bool

Returns whether a residue is at any of the interfaces

C++: protocols::scoring::InterfaceInfo::is_interface(class core::conformation::Residue) const –> bool

is_pair(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → bool

Returns whether the two residues are considered a residue pair at any of the interfaces

C++: protocols::scoring::InterfaceInfo::is_pair(class core::conformation::Residue, class core::conformation::Residue) const –> bool

num_jump(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) → int

Returns the number of jumps that are being used

in interface calculations

C++: protocols::scoring::InterfaceInfo::num_jump() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

ResidualDipolarCouplingRigidSegmentss are mainly handled by this class

related classed: RDC — a single line in an RDC file - representing a single dipolar coupling

ResidualDipolarCouplingRigidSegmentsEnergy – an energy method which triggers computations handled by this class.

__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.scoring.ResidualDipolarCouplingRigidSegments) -> None
2. __init__(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, arg0: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) -> 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__(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) → str

__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.scoring.ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) → pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::operator=(const class protocols::scoring::ResidualDipolarCouplingRigidSegments &) –> class protocols::scoring::ResidualDipolarCouplingRigidSegments &

clone(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

compute_pairwise_score(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) → float

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_pairwise_score() const –> double

compute_total_score(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, pose: pyrosetta.rosetta.core.pose.Pose) → float

compute dipolar score for given segment definition

alignment tensor optimization will be performed for each segment individually

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_total_score(const class core::pose::Pose &) const –> double

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

show(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.std.ostream) → None

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::show(class std::basic_ostream<char> &) const –> void

pyrosetta.rosetta.protocols.scoring.const_vdw_cached_rep_screen_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(const class core::pose::Pose &) –> const class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.fill_vdw_cached_rep_screen_info_from_command_line(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.fill_vdw_cached_rep_screen_info_from_options(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) → None

C++: protocols::scoring::fill_vdw_cached_rep_screen_info_from_options(class core::pose::Pose &, const class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.protocols.scoring.make_sure_vdw_cached_rep_screen_info_is_setup(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::make_sure_vdw_cached_rep_screen_info_is_setup(class core::pose::Pose &) –> const class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.nonconst_vdw_cached_rep_screen_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::nonconst_vdw_cached_rep_screen_info_from_pose(class core::pose::Pose &) –> class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.option_vdw_rep_screen_info_user(options: pyrosetta.rosetta.utility.options.OptionCollection) → bool

C++: protocols::scoring::option_vdw_rep_screen_info_user(const class utility::options::OptionCollection &) –> bool

pyrosetta.rosetta.protocols.scoring.retrieve_RDC_segments_from_pose(*args, **kwargs)

Overloaded function.

1. retrieve_RDC_segments_from_pose(: pyrosetta.rosetta.core.pose.Pose) -> protocols::scoring::ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::retrieve_RDC_segments_from_pose(class core::pose::Pose &) –> class std::shared_ptr<class protocols::scoring::ResidualDipolarCouplingRigidSegments>

2. retrieve_RDC_segments_from_pose(: pyrosetta.rosetta.core.pose.Pose) -> protocols::scoring::ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::retrieve_RDC_segments_from_pose(const class core::pose::Pose &) –> class std::shared_ptr<const class protocols::scoring::ResidualDipolarCouplingRigidSegments>

pyrosetta.rosetta.protocols.scoring.set_vdw_cached_rep_screen_info(pose: pyrosetta.rosetta.core.pose.Pose, vdw_cached_rep_screen_info: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) → None

C++: protocols::scoring::set_vdw_cached_rep_screen_info(class core::pose::Pose &, class std::shared_ptr<class protocols::scoring::VDW_CachedRepScreenInfo> &) –> void

pyrosetta.rosetta.protocols.scoring.set_vdw_cached_rep_screen_info_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::scoring::set_vdw_cached_rep_screen_info_from_pose(class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.store_RDC_segments_in_pose(: protocols::scoring::ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::scoring::store_RDC_segments_in_pose(class std::shared_ptr<class protocols::scoring::ResidualDipolarCouplingRigidSegments>, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.vdw_cached_rep_screen_info_is_setup(pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::scoring::vdw_cached_rep_screen_info_is_setup(const class core::pose::Pose &) –> bool