hybridization

Bindings for protocols::hybridization namespace

class pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged

Bases: pyrosetta.rosetta.protocols.moves.PoseCondition

(helper) functor class which keeps track of initial phi/psi values.

calls of operator ( pose ) compare the initial phi/psi values

/to the current values of the given pose. Returns false once all phi/psi values

have been modified.

__call__(self: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::hybridization::AllResiduesChanged::operator()(const class core::pose::Pose &) –> bool

__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.hybridization.AllResiduesChanged, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.utility.vector1_double) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose, residue_weights: pyrosetta.rosetta.utility.vector1_double, anchor_residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
3. __init__(self: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose) -> None
4. __init__(self: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged, arg0: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged) -> 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.hybridization.AllResiduesChanged, : pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged) → pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged

C++: protocols::hybridization::AllResiduesChanged::operator=(const class protocols::hybridization::AllResiduesChanged &) –> class protocols::hybridization::AllResiduesChanged &

show_unmoved(self: pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::hybridization::AllResiduesChanged::show_unmoved(const class core::pose::Pose &, class std::basic_ostream<char> &) –> void

class pyrosetta.rosetta.protocols.hybridization.TemplateHistory

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

__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.hybridization.TemplateHistory, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. __init__(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory, arg0: pyrosetta.rosetta.protocols.hybridization.TemplateHistory) -> 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.hybridization.TemplateHistory, : pyrosetta.rosetta.protocols.hybridization.TemplateHistory) → pyrosetta.rosetta.protocols.hybridization.TemplateHistory

C++: protocols::hybridization::TemplateHistory::operator=(const class protocols::hybridization::TemplateHistory &) –> class protocols::hybridization::TemplateHistory &

clone(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory) → pyrosetta.rosetta.basic.datacache.CacheableData

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

get(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory, resid: int) → int

C++: protocols::hybridization::TemplateHistory::get(unsigned long) –> int

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>

set(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory, res_start: int, res_stop: int, template_id: int) → None

C++: protocols::hybridization::TemplateHistory::set(unsigned long, unsigned long, int) –> void

setall(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory, template_id: int) → None

C++: protocols::hybridization::TemplateHistory::setall(int) –> void

size(self: pyrosetta.rosetta.protocols.hybridization.TemplateHistory) → int

C++: protocols::hybridization::TemplateHistory::size() –> unsigned long

pyrosetta.rosetta.protocols.hybridization.add_non_protein_cst(pose: pyrosetta.rosetta.core.pose.Pose, tmpl: pyrosetta.rosetta.core.pose.Pose, self_cst_weight: float, het_prot_cst_weight: float) → None

C++: protocols::hybridization::add_non_protein_cst(class core::pose::Pose &, class core::pose::Pose &, const double, const double) –> void

pyrosetta.rosetta.protocols.hybridization.add_strand_pairs_cst(pose: pyrosetta.rosetta.core.pose.Pose, strand_pairs: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

C++: protocols::hybridization::add_strand_pairs_cst(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >) –> void

pyrosetta.rosetta.protocols.hybridization.apply_transformation(mod_pose: pyrosetta.rosetta.core.pose.Pose, residue_list: pyrosetta.rosetta.std.list_unsigned_long_t, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, preT: pyrosetta.rosetta.numeric.xyzVector_double_t, postT: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::hybridization::apply_transformation(class core::pose::Pose &, const class std::list<unsigned long, class std::allocator<unsigned long> > &, const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.hybridization.atom_map_valid_size(pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) → int

C++: protocols::hybridization::atom_map_valid_size(const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &) –> unsigned long

pyrosetta.rosetta.protocols.hybridization.create_fragment_set(pose: pyrosetta.rosetta.core.pose.Pose, len: int, nfrag: int) → pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::hybridization::create_fragment_set(const class core::pose::Pose &, unsigned long, unsigned long) –> class std::shared_ptr<class core::fragment::FragSet>

pyrosetta.rosetta.protocols.hybridization.create_fragment_set_no_ssbias(*args, **kwargs)

Overloaded function.

1. create_fragment_set_no_ssbias(pose: pyrosetta.rosetta.core.pose.Pose, len: int, nfrag: int) -> pyrosetta.rosetta.core.fragment.FragSet
2. create_fragment_set_no_ssbias(pose: pyrosetta.rosetta.core.pose.Pose, len: int, nfrag: int, force_ss: str) -> pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::hybridization::create_fragment_set_no_ssbias(const class core::pose::Pose &, unsigned long, unsigned long, char) –> class std::shared_ptr<class core::fragment::FragSet>

3. create_fragment_set_no_ssbias(pose: pyrosetta.rosetta.core.pose.Pose, user_pos: pyrosetta.rosetta.std.set_unsigned_long_t, len: int, nfrag: int) -> pyrosetta.rosetta.core.fragment.FragSet
4. create_fragment_set_no_ssbias(pose: pyrosetta.rosetta.core.pose.Pose, user_pos: pyrosetta.rosetta.std.set_unsigned_long_t, len: int, nfrag: int, force_ss: str) -> pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::hybridization::create_fragment_set_no_ssbias(const class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, unsigned long, unsigned long, char) –> class std::shared_ptr<class core::fragment::FragSet>

5. create_fragment_set_no_ssbias(seq: str, len: int, nfrag: int) -> pyrosetta.rosetta.core.fragment.FragSet
6. create_fragment_set_no_ssbias(seq: str, len: int, nfrag: int, force_ss: str) -> pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::hybridization::create_fragment_set_no_ssbias(class std::basic_string<char>, unsigned long, unsigned long, char) –> class std::shared_ptr<class core::fragment::FragSet>

pyrosetta.rosetta.protocols.hybridization.discontinued_lower(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → bool

C++: protocols::hybridization::discontinued_lower(const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.protocols.hybridization.discontinued_upper(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → bool

C++: protocols::hybridization::discontinued_upper(const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.protocols.hybridization.downstream_residues_from_jump(pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int) → pyrosetta.rosetta.std.list_unsigned_long_t

C++: protocols::hybridization::downstream_residues_from_jump(const class core::pose::Pose &, const unsigned long) –> class std::list<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.hybridization.generate_centroid_constraints(*args, **kwargs)

Overloaded function.

1. generate_centroid_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double) -> None
2. generate_centroid_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double, ignore_res: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: protocols::hybridization::generate_centroid_constraints(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > >, class utility::vector1<double, class std::allocator<double> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.hybridization.generate_fullatom_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::hybridization::generate_fullatom_constraints(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > >, class utility::vector1<double, class std::allocator<double> >) –> void

pyrosetta.rosetta.protocols.hybridization.get_gdtmm(native: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment) → float

C++: protocols::hybridization::get_gdtmm(class core::pose::Pose &, class core::pose::Pose &, class std::shared_ptr<class core::sequence::SequenceAlignment> &) –> double

pyrosetta.rosetta.protocols.hybridization.get_num_residues_nonvirt(pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::hybridization::get_num_residues_nonvirt(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.hybridization.get_num_residues_prot(pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::hybridization::get_num_residues_prot(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.hybridization.get_superposition_transformation(mod_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, preT: pyrosetta.rosetta.numeric.xyzVector_double_t, postT: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::hybridization::get_superposition_transformation(const class core::pose::Pose &, const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.hybridization.natom_aligned(*args, **kwargs)

Overloaded function.

1. natom_aligned(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> int
2. natom_aligned(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, distance_squared_threshold: float) -> int

C++: protocols::hybridization::natom_aligned(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &, double) –> unsigned long

pyrosetta.rosetta.protocols.hybridization.partial_align(*args, **kwargs)

Overloaded function.

1. partial_align(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, iterate_convergence: bool, distance_thresholds: pyrosetta.rosetta.utility.vector1_double, min_coverage: float) -> None

C++: protocols::hybridization::partial_align(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &, bool, class utility::vector1<double, class std::allocator<double> >, double) –> void

2. partial_align(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, residue_list: pyrosetta.rosetta.std.list_unsigned_long_t) -> None
3. partial_align(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, residue_list: pyrosetta.rosetta.std.list_unsigned_long_t, iterate_convergence: bool) -> None
4. partial_align(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, residue_list: pyrosetta.rosetta.std.list_unsigned_long_t, iterate_convergence: bool, distance_thresholds: pyrosetta.rosetta.utility.vector1_double) -> None
5. partial_align(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, residue_list: pyrosetta.rosetta.std.list_unsigned_long_t, iterate_convergence: bool, distance_thresholds: pyrosetta.rosetta.utility.vector1_double, min_coverage: float) -> None

C++: protocols::hybridization::partial_align(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &, const class std::list<unsigned long, class std::allocator<unsigned long> > &, bool, class utility::vector1<double, class std::allocator<double> >, double) –> void

pyrosetta.rosetta.protocols.hybridization.renumber_with_pdb_info(template_chunk: pyrosetta.rosetta.protocols.loops.Loops, template_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::hybridization::renumber_with_pdb_info(class protocols::loops::Loops &, class std::shared_ptr<const class core::pose::Pose>) –> class protocols::loops::Loops

pyrosetta.rosetta.protocols.hybridization.setup_centroid_constraints(*args, **kwargs)

Overloaded function.

1. setup_centroid_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double, cen_cst_file: str) -> None
2. setup_centroid_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double, cen_cst_file: str, ignore_res_for_AUTO: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: protocols::hybridization::setup_centroid_constraints(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > >, class utility::vector1<double, class std::allocator<double> >, class std::basic_string<char>, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.hybridization.setup_constraints(pose: pyrosetta.rosetta.core.pose.Pose, cst_in: str) → None

C++: protocols::hybridization::setup_constraints(class core::pose::Pose &, class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.hybridization.setup_fullatom_constraints(pose: pyrosetta.rosetta.core.pose.Pose, templates: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_weights: pyrosetta.rosetta.utility.vector1_double, cen_cst_file: str, fa_cst_file: str) → None

C++: protocols::hybridization::setup_fullatom_constraints(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > >, class utility::vector1<double, class std::allocator<double> >, class std::basic_string<char>, class std::basic_string<char>) –> void

pyrosetta.rosetta.protocols.hybridization.setup_user_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose, reses_to_cst: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::hybridization::setup_user_coordinate_constraints(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.hybridization.update_atom_map(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, distance_squared_threshold: float) → pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

C++: protocols::hybridization::update_atom_map(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::AtomID_Map<class core::id::AtomID> &, double) –> class core::id::AtomID_Map<class core::id::AtomID>