frags

Bindings for protocols::frags namespace

class pyrosetta.rosetta.protocols.frags.FragLib

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.frags.FragLib, : pyrosetta.rosetta.protocols.frags.FragLib) → pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::FragLib::operator=(const class protocols::frags::FragLib &) –> class protocols::frags::FragLib &

clear(self: pyrosetta.rosetta.protocols.frags.FragLib) → None

C++: protocols::frags::FragLib::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.FragLib, src: pyrosetta.rosetta.protocols.frags.FragLib) → None

C++: protocols::frags::FragLib::copy_fragments(const class protocols::frags::FragLib &) –> void

delete_residue(self: pyrosetta.rosetta.protocols.frags.FragLib, seqpos: int) → None

C++: protocols::frags::FragLib::delete_residue(const unsigned long) –> void

frag_sizes(self: pyrosetta.rosetta.protocols.frags.FragLib) → pyrosetta.rosetta.utility.vector1_unsigned_long

slow

C++: protocols::frags::FragLib::frag_sizes() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

library(self: pyrosetta.rosetta.protocols.frags.FragLib, size: int) → pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

C++: protocols::frags::FragLib::library(const unsigned long) –> class protocols::frags::TorsionFragmentLibrary &

shift(self: pyrosetta.rosetta.protocols.frags.FragLib, current2desired_offset: int) → None

C++: protocols::frags::FragLib::shift(const int) –> void

class pyrosetta.rosetta.protocols.frags.RMSVallData

Bases: pybind11_object

X(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::frags::RMSVallData::X() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

add_line(self: pyrosetta.rosetta.protocols.frags.RMSVallData, sq: str, ss: str, x: float, y: float, z: float, ph: float, ps: float, om: float) → None

read in one more line from Vall input file

C++: protocols::frags::RMSVallData::add_line(const char, const char, const double, const double, const double, const double, const double, const double) –> void

get_frags(*args, **kwargs)

Overloaded function.

  1. get_frags(self: pyrosetta.rosetta.protocols.frags.RMSVallData, nfrags: int, templ: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pref_seq: str, force_ss: str, frame: pyrosetta.rosetta.core.fragment.Frame) -> None

  2. get_frags(self: pyrosetta.rosetta.protocols.frags.RMSVallData, nfrags: int, templ: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pref_seq: str, force_ss: str, frame: pyrosetta.rosetta.core.fragment.Frame, randomness: float) -> None

  3. get_frags(self: pyrosetta.rosetta.protocols.frags.RMSVallData, nfrags: int, templ: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, pref_seq: str, force_ss: str, frame: pyrosetta.rosetta.core.fragment.Frame, randomness: float, oversample: float) -> None

C++: protocols::frags::RMSVallData::get_frags(const unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const std::string &, const char, class std::shared_ptr<class core::fragment::Frame> &, double, double) const –> void

omega(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::RMSVallData::omega() const –> const class utility::vector1<double, class std::allocator<double> > &

phi(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::RMSVallData::phi() const –> const class utility::vector1<double, class std::allocator<double> > &

psi(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::RMSVallData::psi() const –> const class utility::vector1<double, class std::allocator<double> > &

read_file(self: pyrosetta.rosetta.protocols.frags.RMSVallData, filename: str) → None

C++: protocols::frags::RMSVallData::read_file(const std::string &) –> void

secstruct(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::RMSVallData::secstruct() const –> const class utility::vector1<char, class std::allocator<char> > &

sequence(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::RMSVallData::sequence() const –> const class utility::vector1<char, class std::allocator<char> > &

shrink(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → None

removes excess storage capacity to minimize memory usage

C++: protocols::frags::RMSVallData::shrink() –> void

size(self: pyrosetta.rosetta.protocols.frags.RMSVallData) → int

number of lines in Vall database

C++: protocols::frags::RMSVallData::size() const –> int

class pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary

Bases: pybind11_object

a class for collection of fragments for a single residue position

essentially a vector of TorsionFragment (owning pointers)

append_fragment(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, fragment: pyrosetta.rosetta.protocols.frags.TorsionFragment) → None

append one piece of fragment at the end

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::append_fragment(class std::shared_ptr<class protocols::frags::TorsionFragment>) –> void

assign(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, : pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::operator=(const class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> class protocols::frags::SingleResidueTorsionFragmentLibrary &

clear(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, src: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::copy_fragments(const class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> void

erase(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, index: int) → None

erase a single fragment

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::erase(const unsigned long) –> void

insert_fragment(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, fragment: pyrosetta.rosetta.protocols.frags.TorsionFragment) → None

insert one piece of fragment in the front

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::insert_fragment(class std::shared_ptr<class protocols::frags::TorsionFragment>) –> void

size(self: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → int

number of available fragment pieces for this position

C++: protocols::frags::SingleResidueTorsionFragmentLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.TorsionFragment

Bases: pybind11_object

a class for single piece of torsion fragment

It stores torsion angles and secondary structure. Torsions are stored as vector of vector, such as TorsionFragment[frag_size][n_bb_torsion]; SS are stored as vector, such as TorsionFragment[frag_length]

assign(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, : pyrosetta.rosetta.protocols.frags.TorsionFragment) → pyrosetta.rosetta.protocols.frags.TorsionFragment

C++: protocols::frags::TorsionFragment::operator=(const class protocols::frags::TorsionFragment &) –> class protocols::frags::TorsionFragment &

clone(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → pyrosetta.rosetta.protocols.frags.TorsionFragment

C++: protocols::frags::TorsionFragment::clone() const –> class std::shared_ptr<class protocols::frags::TorsionFragment>

get_secstruct(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int) → str

C++: protocols::frags::TorsionFragment::get_secstruct(const unsigned long) const –> char

get_sequence(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int) → str

C++: protocols::frags::TorsionFragment::get_sequence(const unsigned long) const –> char

get_torsion(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, tor: int) → float

get value for specific torsion in this piece of fragment

C++: protocols::frags::TorsionFragment::get_torsion(const unsigned long, const unsigned long) const –> double

insert(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pose: pyrosetta.rosetta.core.pose.Pose, begin: int) → None

C++: protocols::frags::TorsionFragment::insert(class core::pose::Pose &, const unsigned long) const –> void

nbb(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → int

number of backbone torsions.

C++: protocols::frags::TorsionFragment::nbb() const –> unsigned long

set_secstruct(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, setting: str) → None

set secstruct for this position

C++: protocols::frags::TorsionFragment::set_secstruct(const unsigned long, const char) –> void

set_sequence(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, setting: str) → None

set seq for this position

C++: protocols::frags::TorsionFragment::set_sequence(const unsigned long, const char) –> void

set_size_and_nbb(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, size: int, nbb: int) → None

C++: protocols::frags::TorsionFragment::set_size_and_nbb(const unsigned long, const unsigned long) –> void

set_torsion(self: pyrosetta.rosetta.protocols.frags.TorsionFragment, pos: int, tor: int, setting: float) → None

set value for specific torsion in this piece of fragment.

C++: protocols::frags::TorsionFragment::set_torsion(const unsigned long, const unsigned long, const double) –> void

size(self: pyrosetta.rosetta.protocols.frags.TorsionFragment) → int

fragment size, 3mer or 9mer?

C++: protocols::frags::TorsionFragment::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

Bases: pybind11_object

a class for classic Rosetta fragment library

essentially a collection of SingleResidueTorsionFragmentLibrary (indexed by residue position)

assign(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, : pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary

C++: protocols::frags::TorsionFragmentLibrary::operator=(const class protocols::frags::TorsionFragmentLibrary &) –> class protocols::frags::TorsionFragmentLibrary &

clear(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → None

C++: protocols::frags::TorsionFragmentLibrary::clear() –> void

copy_fragments(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, src: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → None

C++: protocols::frags::TorsionFragmentLibrary::copy_fragments(const class protocols::frags::TorsionFragmentLibrary &) –> void

delete_residue(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, seqpos: int) → None

C++: protocols::frags::TorsionFragmentLibrary::delete_residue(const unsigned long) –> void

derive_from_src_lib(*args, **kwargs)

Overloaded function.

  1. derive_from_src_lib(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, my_size: int, src_size: int, src_lib_op: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> bool

C++: protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(const unsigned long, const unsigned long, class std::shared_ptr<const class protocols::frags::TorsionFragmentLibrary>) –> bool

  1. derive_from_src_lib(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, my_size: int, src_size: int, src_lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> bool

C++: protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(const unsigned long, const unsigned long, const class protocols::frags::TorsionFragmentLibrary &) –> bool

print(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, os: pyrosetta.rosetta.std.ostream) → None

Show some info – right now just for debugging, ie not a full dump of the library

C++: protocols::frags::TorsionFragmentLibrary::print(std::ostream &) const –> void

read_file(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, name: str, frag_size: int, nbb: int) → bool

C++: protocols::frags::TorsionFragmentLibrary::read_file(const std::string &, const unsigned long, const unsigned long) –> bool

resize(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, new_size: int) → None

change the size of fragment library

C++: protocols::frags::TorsionFragmentLibrary::resize(const unsigned long) –> void

shift(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, current2desired_offset: int) → None

C++: protocols::frags::TorsionFragmentLibrary::shift(const int) –> void

size(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) → int

number of residues

C++: protocols::frags::TorsionFragmentLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.frags.TorsionFragmentMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::frags::TorsionFragmentMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, : pyrosetta.rosetta.protocols.frags.TorsionFragmentMover) → pyrosetta.rosetta.protocols.frags.TorsionFragmentMover

C++: protocols::frags::TorsionFragmentMover::operator=(const class protocols::frags::TorsionFragmentMover &) –> class protocols::frags::TorsionFragmentMover &

check_ss_lengths(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, setting: bool) → None

C++: protocols::frags::TorsionFragmentMover::check_ss_lengths(const bool) –> void

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.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>

frag_size(*args, **kwargs)

Overloaded function.

  1. frag_size(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover) -> int

C++: protocols::frags::TorsionFragmentMover::frag_size() const –> unsigned long

  1. frag_size(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, setting: int) -> None

C++: protocols::frags::TorsionFragmentMover::frag_size(const unsigned long) –> void

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

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

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

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

fpd

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

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover) → str

C++: protocols::frags::TorsionFragmentMover::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

last_inserted_frag_begin(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover) → int

C++: protocols::frags::TorsionFragmentMover::last_inserted_frag_begin() const –> unsigned long

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

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

min_len_helix(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, setting: int) → None

C++: protocols::frags::TorsionFragmentMover::min_len_helix(const unsigned long) –> void

min_len_strand(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, setting: int) → None

C++: protocols::frags::TorsionFragmentMover::min_len_strand(const unsigned long) –> void

static name() → str

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

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

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

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

pose_passes_ss_length_check(self: pyrosetta.rosetta.protocols.frags.TorsionFragmentMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::frags::TorsionFragmentMover::pose_passes_ss_length_check(const class core::pose::Pose &) const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None
Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.frags.VallData

Bases: pybind11_object

/

add_line(self: pyrosetta.rosetta.protocols.frags.VallData, sq: str, ss: str, ph: float, ps: float, om: float) → None

read in one more line from Vall input file

C++: protocols::frags::VallData::add_line(const char, const char, const double, const double, const double) –> void

bigbin(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::bigbin() const –> const class utility::vector1<char, class std::allocator<char> > &

chain(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::frags::VallData::chain() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_cheating_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, target_phi: pyrosetta.rosetta.utility.vector1_double, target_psi: pyrosetta.rosetta.utility.vector1_double, target_omega: pyrosetta.rosetta.utility.vector1_double, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::VallData::get_cheating_frags(const unsigned long, const std::string &, const std::string &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &) const –> void

get_frags(*args, **kwargs)

Overloaded function.

  1. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None

  2. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None

  3. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

C++: protocols::frags::VallData::get_frags(const unsigned long, const std::string &, const std::string &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const std::string &) const –> void

  1. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None

  2. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None

  3. get_frags(self: pyrosetta.rosetta.protocols.frags.VallData, nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

C++: protocols::frags::VallData::get_frags(const unsigned long, const std::string &, const class utility::vector1<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >, class std::allocator<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > > > > &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const std::string &) const –> void

num_chains(self: pyrosetta.rosetta.protocols.frags.VallData) → int

number of chains

C++: protocols::frags::VallData::num_chains() const –> unsigned long

omega(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::omega() const –> const class utility::vector1<double, class std::allocator<double> > &

phi(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::phi() const –> const class utility::vector1<double, class std::allocator<double> > &

psi(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::frags::VallData::psi() const –> const class utility::vector1<double, class std::allocator<double> > &

read_file(self: pyrosetta.rosetta.protocols.frags.VallData, filename: str) → None

C++: protocols::frags::VallData::read_file(const std::string &) –> void

secstruct(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::secstruct() const –> const class utility::vector1<char, class std::allocator<char> > &

sequence(self: pyrosetta.rosetta.protocols.frags.VallData) → pyrosetta.rosetta.utility.vector1_char

C++: protocols::frags::VallData::sequence() const –> const class utility::vector1<char, class std::allocator<char> > &

shrink(self: pyrosetta.rosetta.protocols.frags.VallData) → None

removes excess storage capacity to minimize memory usage

C++: protocols::frags::VallData::shrink() –> void

size(self: pyrosetta.rosetta.protocols.frags.VallData) → int

number of lines in Vall database

C++: protocols::frags::VallData::size() const –> int

pyrosetta.rosetta.protocols.frags.add_vall_cheating_fragments(*args, **kwargs)

Overloaded function.

  1. add_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None

  2. add_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::frags::add_vall_cheating_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const std::string &, const double, const double, const double, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.frags.add_vall_fragments(*args, **kwargs)

Overloaded function.

  1. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None

  2. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  3. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float) -> None

  4. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str) -> None

  5. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str, inputseq: str) -> None

C++: protocols::frags::add_vall_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const std::string &, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const std::string &, const std::string &) –> void

  1. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None

  2. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  3. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float) -> None

  4. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str) -> None

  5. add_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, bb_weight: float, bigbins: str, inputseq: str) -> None

C++: protocols::frags::add_vall_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const class utility::vector1<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >, class std::allocator<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > > > > &, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.frags.dump_vall_fasta(fasta_filename: str) → None

C++: protocols::frags::dump_vall_fasta(const std::string &) –> void

pyrosetta.rosetta.protocols.frags.fill_in_gaps(*args, **kwargs)

Overloaded function.

  1. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib) -> None

  2. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  3. fill_in_gaps(nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, seq_weight: float, ss_weight: float, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, allow_uninitialized_secstruct: bool) -> None

C++: protocols::frags::fill_in_gaps(const unsigned long, const class core::pose::Pose &, const std::string &, const double, const double, class protocols::frags::FragLib &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.frags.get_cheating_frags(nfrags: int, target_seq: str, target_ss: str, target_phi: pyrosetta.rosetta.utility.vector1_double, target_psi: pyrosetta.rosetta.utility.vector1_double, target_omega: pyrosetta.rosetta.utility.vector1_double, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) → None

C++: protocols::frags::get_cheating_frags(const unsigned long, const std::string &, const std::string &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &) –> void

pyrosetta.rosetta.protocols.frags.get_frags(*args, **kwargs)

Overloaded function.

  1. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None

  2. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None

  3. get_frags(nfrags: int, target_seq: str, target_ss: str, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

handles loading the vall if necessary

C++: protocols::frags::get_frags(const unsigned long, const std::string &, const std::string &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const std::string &) –> void

  1. get_frags(nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary) -> None

  2. get_frags(nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float) -> None

  3. get_frags(nfrags: int, target_seq: str, target_ss: pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t, seq_weight: float, ss_weight: float, exclude_gly: bool, exclude_pro: bool, exclude_cis_peptides: bool, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long, library: pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary, bb_weight: float, target_bb: str) -> None

handles loading the vall if necessary

C++: protocols::frags::get_frags(const unsigned long, const std::string &, const class utility::vector1<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >, class std::allocator<class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > > > > &, const double, const double, const bool, const bool, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class protocols::frags::SingleResidueTorsionFragmentLibrary &, const double, const std::string &) –> void

pyrosetta.rosetta.protocols.frags.heap_down(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, index_in: int) → None

C++: protocols::frags::heap_down(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int) –> void

pyrosetta.rosetta.protocols.frags.heap_extract(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, val: int, coval: float, err: bool) → None

C++: protocols::frags::heap_extract(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int &, float &, bool &) –> void

pyrosetta.rosetta.protocols.frags.heap_init(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, max_items: int) → None

C++: protocols::frags::heap_init(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int) –> void

pyrosetta.rosetta.protocols.frags.heap_insert(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, val: int, coval: float, err: bool) → None

C++: protocols::frags::heap_insert(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int, float, bool &) –> void

pyrosetta.rosetta.protocols.frags.heap_replace(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, val: int, coval: float) → None

C++: protocols::frags::heap_replace(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int, float) –> void

pyrosetta.rosetta.protocols.frags.heap_up(heap: pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t, coheap: pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t, index_in: int) → None

C++: protocols::frags::heap_up(class ObjexxFCL::FArray1A<int>, class ObjexxFCL::FArray1A<float>, int &) –> void

pyrosetta.rosetta.protocols.frags.insert_fragment(*args, **kwargs)

Overloaded function.

  1. insert_fragment(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose, lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary) -> None

  2. insert_fragment(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose, lib: pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary, desired_insert_pos: int) -> None

C++: protocols::frags::insert_fragment(const unsigned long, const unsigned long, class core::pose::Pose &, const class protocols::frags::TorsionFragmentLibrary &, const unsigned long) –> void

pyrosetta.rosetta.protocols.frags.insert_random_fragments_in_flexible_protein_regions(flex_protein: pyrosetta.rosetta.utility.vector1_unsigned_long, frag_lib: pyrosetta.rosetta.protocols.frags.FragLib, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::frags::insert_random_fragments_in_flexible_protein_regions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class protocols::frags::FragLib &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.frags.setup_vall_cheating_fragments(*args, **kwargs)

Overloaded function.

  1. setup_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float) -> pyrosetta.rosetta.protocols.frags.FragLib

  2. setup_vall_cheating_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, torsion_weight: float, min_torsion_dev: float, max_torsion_dev: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::setup_vall_cheating_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const std::string &, const double, const double, const double, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<class protocols::frags::FragLib>

pyrosetta.rosetta.protocols.frags.setup_vall_fragments(*args, **kwargs)

Overloaded function.

  1. setup_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float) -> pyrosetta.rosetta.protocols.frags.FragLib

  2. setup_vall_fragments(frag_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long, nfrags: int, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, secstruct: str, seq_weight: float, ss_weight: float, homs_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.protocols.frags.FragLib

C++: protocols::frags::setup_vall_fragments(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const class core::pose::Pose &, const class core::kinematics::MoveMap &, const std::string &, const double, const double, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::shared_ptr<class protocols::frags::FragLib>

pyrosetta.rosetta.protocols.frags.ss_length_check(min_len_helix: int, min_len_strand: int, pose: pyrosetta.rosetta.core.pose.Pose) → bool

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

pyrosetta.rosetta.protocols.frags.torsion2big_bin(phi: float, psi: float, omega: float) → str

C++: protocols::frags::torsion2big_bin(const double, const double, const double) –> char