vall

Bindings for core::fragment::picking_old::vall namespace

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian

Bases: Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t

Librarian that picks fragments from the Vall

add_extent_eval(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t, val: core::fragment::picking_old::vall::eval::VallFragmentEval) → None

C++: core::fragment::picking_old::concepts::Librarian<core::fragment::picking_old::vall::scores::VallFragmentScore, core::fragment::picking_old::vall::eval::VallFragmentEval, core::fragment::picking_old::vall::gen::VallFragmentGen, core::fragment::picking_old::vall::VallLibrary>::add_extent_eval(class std::shared_ptr<const class core::fragment::picking_old::vall::eval::VallFragmentEval>) –> void

add_extent_gen(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t, gen: core::fragment::picking_old::vall::gen::VallFragmentGen) → None

C++: core::fragment::picking_old::concepts::Librarian<core::fragment::picking_old::vall::scores::VallFragmentScore, core::fragment::picking_old::vall::eval::VallFragmentEval, core::fragment::picking_old::vall::gen::VallFragmentGen, core::fragment::picking_old::vall::VallLibrary>::add_extent_gen(const class std::shared_ptr<const class core::fragment::picking_old::vall::gen::VallFragmentGen> &) –> void

add_fragment_eval(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, eval: pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval) → None

add a fragment evaluator (aka extent evaluator)

C++: core::fragment::picking_old::vall::VallLibrarian::add_fragment_eval(class std::shared_ptr<const class core::fragment::picking_old::vall::eval::VallFragmentEval>) –> void

add_fragment_gen(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, gen: pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen) → None

add a fragment generator (aka extent generator)

C++: core::fragment::picking_old::vall::VallLibrarian::add_fragment_gen(const class std::shared_ptr<const class core::fragment::picking_old::vall::gen::VallFragmentGen> &) –> void

catalog(*args, **kwargs)

Overloaded function.

  1. catalog(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, library: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary, lt: std::less<core::fragment::picking_old::vall::scores::VallFragmentScore>) -> bool

C++: core::fragment::picking_old::vall::VallLibrarian::catalog(const class core::fragment::picking_old::vall::VallLibrary &, const struct std::less<struct core::fragment::picking_old::vall::scores::VallFragmentScore> &) –> bool

  1. catalog(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, library: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) -> bool

create sorted list corresponding to fragments in Library

uses Score’s ‘<’ for evaluation

true if creation successful, false otherwise (e.g. no VallFragmentEval or VallFragmentGen found)

C++: core::fragment::picking_old::vall::VallLibrarian::catalog(const class core::fragment::picking_old::vall::VallLibrary &) –> bool

clear_extent_eval(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t) → None

C++: core::fragment::picking_old::concepts::Librarian<core::fragment::picking_old::vall::scores::VallFragmentScore, core::fragment::picking_old::vall::eval::VallFragmentEval, core::fragment::picking_old::vall::gen::VallFragmentGen, core::fragment::picking_old::vall::VallLibrary>::clear_extent_eval() –> void

clear_extent_gen(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t) → None

C++: core::fragment::picking_old::concepts::Librarian<core::fragment::picking_old::vall::scores::VallFragmentScore, core::fragment::picking_old::vall::eval::VallFragmentEval, core::fragment::picking_old::vall::gen::VallFragmentGen, core::fragment::picking_old::vall::VallLibrary>::clear_extent_gen() –> void

clear_fragment_eval(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → None

clear list of evaluators

C++: core::fragment::picking_old::vall::VallLibrarian::clear_fragment_eval() –> void

clear_fragment_gen(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → None

clear list of generators

C++: core::fragment::picking_old::vall::VallLibrarian::clear_fragment_gen() –> void

fragments(*args, **kwargs)

Overloaded function.

  1. fragments(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, from: int, to: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  2. fragments(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, from: int, to: int, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

get fragments from prior catalog() [from, to]

index of the first fragment in the list, indexing starts from ‘1’

index of the last fragment in the list (inclusive)

The BBTorsionSRFD type to use.

filled FragDataOPs if sort() was called successfully, otherwise empty FragDataOPs

C++: core::fragment::picking_old::vall::VallLibrarian::fragments(unsigned long, unsigned long, const class core::fragment::BBTorsionSRFD &) const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > >

n_fragment_eval(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → int

the number of currently defined fragment evaluators

C++: core::fragment::picking_old::vall::VallLibrarian::n_fragment_eval() const –> unsigned long

n_fragment_gen(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → int

the number of currently defined fragment generators

C++: core::fragment::picking_old::vall::VallLibrarian::n_fragment_gen() const –> unsigned long

n_scores(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → int

number of scores currently filed

C++: core::fragment::picking_old::vall::VallLibrarian::n_scores() const –> unsigned long

preallocate(*args, **kwargs)

Overloaded function.

  1. preallocate(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) -> bool

preallocate scores container prior to catalog() to attempt

speedup?, default true

C++: core::fragment::picking_old::vall::VallLibrarian::preallocate() const –> bool

  1. preallocate(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, flag: bool) -> None

set flag to preallocate scores container prior to catalog() to

attempt speedup

C++: core::fragment::picking_old::vall::VallLibrarian::preallocate(const bool) –> void

scores(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian) → pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore

return scores container

C++: core::fragment::picking_old::vall::VallLibrarian::scores() –> class utility::vector1<struct core::fragment::picking_old::vall::scores::VallFragmentScore, class std::allocator<struct core::fragment::picking_old::vall::scores::VallFragmentScore> > &

top_fragments(*args, **kwargs)

Overloaded function.

  1. top_fragments(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, n: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  2. top_fragments(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian, n: int, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

get top ‘N’ fragments from prior catalog()

The number of fragments to get.

The BBTorsionSRFD type to use.

C++: core::fragment::picking_old::vall::VallLibrarian::top_fragments(const unsigned long, const class core::fragment::BBTorsionSRFD &) const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > >

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary

Bases: Library_core_fragment_picking_old_vall_VallSections_t

Vall fragment library

add_section(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary, section: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection) → None

brief add a section to the end of this library

C++: core::fragment::picking_old::vall::VallLibrary::add_section(const class core::fragment::picking_old::vall::VallSection &) –> void

assign(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t, : pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t) → pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t

C++: core::fragment::picking_old::concepts::Library<core::fragment::picking_old::vall::VallSections>::operator=(const class core::fragment::picking_old::concepts::Library<class core::fragment::picking_old::vall::VallSections> &) –> class core::fragment::picking_old::concepts::Library<class core::fragment::picking_old::vall::VallSections> &

clear(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t) → None

C++: core::fragment::picking_old::concepts::Library<core::fragment::picking_old::vall::VallSections>::clear() –> void

last_section(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) → pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection

access the last section in thie library

C++: core::fragment::picking_old::vall::VallLibrary::last_section() –> class core::fragment::picking_old::vall::VallSection &

n_residues(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) → int

total number of residues in the library

C++: core::fragment::picking_old::vall::VallLibrary::n_residues() const –> unsigned long

reindex_sections(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) → None

re-index VallSections within this library so they number 1 .. n

C++: core::fragment::picking_old::vall::VallLibrary::reindex_sections() –> void

reserve(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary, n: int) → None
ensure storage currently allocated for VallSections is at least the

given size

C++: core::fragment::picking_old::vall::VallLibrary::reserve(unsigned long) –> void

size(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t) → int

C++: core::fragment::picking_old::concepts::Library<core::fragment::picking_old::vall::VallSections>::size() const –> unsigned long

tighten_memory(*args, **kwargs)

Overloaded function.

  1. tighten_memory(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) -> None

  2. tighten_memory(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary, sections_only: bool) -> None

tighten memory usage

if true, only tightens memory per-section and skips

the operation for the whole library

Shrinks the capacity of the library by calling

VallSection::tighten_memory() for each section. If ‘sections_only’ is false, will additionally perform a swap of the library, effectively requiring a similar amount of memory as the current library object.

The Vall libraries can be very large, so set ‘sections_only’

false only if you won’t be running on a constrained memory platform.

C++: core::fragment::picking_old::vall::VallLibrary::tighten_memory(const bool) –> void

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue

Bases: pybind11_object

class for managing a line of the Vall fragment library

aa(*args, **kwargs)

Overloaded function.

  1. aa(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> str

one letter amino acid code

C++: core::fragment::picking_old::vall::VallResidue::aa() const –> char

  1. aa(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, c: str) -> None

one letter amino acid code

C++: core::fragment::picking_old::vall::VallResidue::aa(const char) –> void

assign(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, rval: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) → pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue

copy assignment

C++: core::fragment::picking_old::vall::VallResidue::operator=(const class core::fragment::picking_old::vall::VallResidue &) –> class core::fragment::picking_old::vall::VallResidue &

bbtorsion_srfd(*args, **kwargs)

Overloaded function.

  1. bbtorsion_srfd(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> pyrosetta.rosetta.core.fragment.BBTorsionSRFD

  2. bbtorsion_srfd(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.core.fragment.BBTorsionSRFD

build a BBTorsionSRFD of the given type from this page

BBTorsionSRFD::create() will be called from this object.

A BBTorsionSRFD of the given type initialized with the backbone

torsion information from this page.

C++: core::fragment::picking_old::vall::VallResidue::bbtorsion_srfd(const class core::fragment::BBTorsionSRFD &) const –> class std::shared_ptr<class core::fragment::BBTorsionSRFD>

fill_from_string(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, line: str) → None

fill internal data from string

C++: core::fragment::picking_old::vall::VallResidue::fill_from_string(const std::string &) –> void

has_profile(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) → bool

has profile info?

C++: core::fragment::picking_old::vall::VallResidue::has_profile() const –> bool

id(*args, **kwargs)

Overloaded function.

  1. id(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> str

id of fragment source (e.g. pdb name)

C++: core::fragment::picking_old::vall::VallResidue::id() const –> const std::string &

  1. id(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, s: str) -> None

id of fragment source (e.g. pdb name)

C++: core::fragment::picking_old::vall::VallResidue::id(const std::string &) –> void

omega(*args, **kwargs)

Overloaded function.

  1. omega(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

omega backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::omega() const –> double

  1. omega(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

omega backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::omega(const double) –> void

phi(*args, **kwargs)

Overloaded function.

  1. phi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

phi backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::phi() const –> double

  1. phi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

phi backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::phi(const double) –> void

position_index(*args, **kwargs)

Overloaded function.

  1. position_index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> int

stores the 1-based indexing for accessing this residue

via VallSection::operator []

C++: core::fragment::picking_old::vall::VallResidue::position_index() const –> unsigned long

  1. position_index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, idx: int) -> None

stores the 1-based indexing for accessing this residue

via VallSection::operator []

C++: core::fragment::picking_old::vall::VallResidue::position_index(const unsigned long) –> void

profile(*args, **kwargs)

Overloaded function.

  1. profile(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> pyrosetta.rosetta.utility.vector1_double

per amino acid profile data

C++: core::fragment::picking_old::vall::VallResidue::profile() const –> const class utility::vector1<double, class std::allocator<double> > &

  1. profile(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, v: pyrosetta.rosetta.utility.vector1_double) -> None

per amino acid profile data

C++: core::fragment::picking_old::vall::VallResidue::profile(const class utility::vector1<double, class std::allocator<double> > &) –> void

psi(*args, **kwargs)

Overloaded function.

  1. psi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

psi backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::psi() const –> double

  1. psi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

psi backbone torsion in degrees

C++: core::fragment::picking_old::vall::VallResidue::psi(const double) –> void

resi(*args, **kwargs)

Overloaded function.

  1. resi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> int

residue sequence number in source

C++: core::fragment::picking_old::vall::VallResidue::resi() const –> unsigned long

  1. resi(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, i: int) -> None

residue sequence number in source

C++: core::fragment::picking_old::vall::VallResidue::resi(const unsigned long) –> void

section_index(*args, **kwargs)

Overloaded function.

  1. section_index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> int

stores the 1-based indexing for accessing the VallSection

this residue is located in via VallLibrary::operator []

C++: core::fragment::picking_old::vall::VallResidue::section_index() const –> unsigned long

  1. section_index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, idx: int) -> None

stores the 1-based indexing for accessing the VallSection

this residue is located in via VallLibrary::operator []

C++: core::fragment::picking_old::vall::VallResidue::section_index(const unsigned long) –> void

ss(*args, **kwargs)

Overloaded function.

  1. ss(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> str

one letter secondary structure code

C++: core::fragment::picking_old::vall::VallResidue::ss() const –> char

  1. ss(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, c: str) -> None

one letter secondary structure code

C++: core::fragment::picking_old::vall::VallResidue::ss(const char) –> void

x(*args, **kwargs)

Overloaded function.

  1. x(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

x-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::x() const –> double

  1. x(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

x-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::x(const double) –> void

y(*args, **kwargs)

Overloaded function.

  1. y(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

y-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::y() const –> double

  1. y(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

y-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::y(const double) –> void

z(*args, **kwargs)

Overloaded function.

  1. z(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) -> float

z-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::z() const –> double

  1. z(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue, val: float) -> None

z-coordinate of C-alpha

C++: core::fragment::picking_old::vall::VallResidue::z(const double) –> void

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues

Bases: vector1_core_fragment_picking_old_vall_VallResidue

wrapper for a collection of VallResidue

append(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue, arg0: core::fragment::picking_old::vall::VallResidue) → None

adds an element to the end

assign(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues, : pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues) → pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues

C++: core::fragment::picking_old::vall::VallResidues::operator=(const class core::fragment::picking_old::vall::VallResidues &) –> class core::fragment::picking_old::vall::VallResidues &

back(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → core::fragment::picking_old::vall::VallResidue

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → None

clears the contents

erase(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue, arg0: int) → None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → core::fragment::picking_old::vall::VallResidue

access the first element

l(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) -> core::fragment::picking_old::vall::VallResidue

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue, arg0: int) -> core::fragment::picking_old::vall::VallResidue

remove and return item at index

reserve(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue, arg0: int) → None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue, arg0: int) → None

changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue) → int

upper index

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection

Bases: Book_core_fragment_picking_old_vall_VallResidues_t

class implementing the Book concept for a continuous section of lines in the Vall library

append_residue(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection, r: pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue) → None

append a residue to the end of this section

C++: core::fragment::picking_old::vall::VallSection::append_residue(const class core::fragment::picking_old::vall::VallResidue &) –> void

assign(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t, : pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t) → pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t

C++: core::fragment::picking_old::concepts::Book<core::fragment::picking_old::vall::VallResidues>::operator=(const class core::fragment::picking_old::concepts::Book<class core::fragment::picking_old::vall::VallResidues> &) –> class core::fragment::picking_old::concepts::Book<class core::fragment::picking_old::vall::VallResidues> &

clear(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t) → None

C++: core::fragment::picking_old::concepts::Book<core::fragment::picking_old::vall::VallResidues>::clear() –> void

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection) -> int

stores the 1-based indexing for accessing this section

via VallLibrary::operator []

C++: core::fragment::picking_old::vall::VallSection::index() const –> unsigned long

  1. index(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection, idx: int) -> None

stores the 1-based indexing for accessing this section

via VallLibrary::operator []

C++: core::fragment::picking_old::vall::VallSection::index(const unsigned long) –> void

reindex_residues(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection) → None

re-index VallResidues within this library so they number 1 .. n

C++: core::fragment::picking_old::vall::VallSection::reindex_residues() –> void

reserve(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection, n: int) → None
ensure storage currently allocated for residues is at least the

given size

C++: core::fragment::picking_old::vall::VallSection::reserve(const unsigned long) –> void

size(self: pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t) → int

C++: core::fragment::picking_old::concepts::Book<core::fragment::picking_old::vall::VallResidues>::size() const –> unsigned long

tighten_memory(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection) → None

tighten memory usage

Shrinks the capacity of the VallResidues by performing

a swap, so this operation will effectively require a similar amount of memory as the current residue object.

C++: core::fragment::picking_old::vall::VallSection::tighten_memory() –> void

class pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections

Bases: vector1_core_fragment_picking_old_vall_VallSection

wrapper for a collection of VallSection

append(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection, arg0: core::fragment::picking_old::vall::VallSection) → None

adds an element to the end

assign(self: pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections, : pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections) → pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections

C++: core::fragment::picking_old::vall::VallSections::operator=(const class core::fragment::picking_old::vall::VallSections &) –> class core::fragment::picking_old::vall::VallSections &

back(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → core::fragment::picking_old::vall::VallSection

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → None

clears the contents

erase(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection, arg0: int) → None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → core::fragment::picking_old::vall::VallSection

access the first element

l(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) -> core::fragment::picking_old::vall::VallSection

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection, arg0: int) -> core::fragment::picking_old::vall::VallSection

remove and return item at index

reserve(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection, arg0: int) → None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection, arg0: int) → None

changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection) → int

upper index

pyrosetta.rosetta.core.fragment.picking_old.vall.pick_fragments(*args, **kwargs)

Overloaded function.

  1. pick_fragments(ss: str, aa: str, abego: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  2. pick_fragments(ss: str, aa: str, abego: pyrosetta.rosetta.utility.vector1_std_string, top_n: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  3. pick_fragments(ss: str, aa: str, abego: pyrosetta.rosetta.utility.vector1_std_string, top_n: int, randomize: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  4. pick_fragments(ss: str, aa: str, abego: pyrosetta.rosetta.utility.vector1_std_string, top_n: int, randomize: bool, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

pick fragments by default sec.struct IdentityScore

secondary structure string of desired frag length

amino acid string of same length as ss string

vector of string of desired frag length

return the top ‘n’ fragments, default 200

add random noise within [0, 0.001) to

The BBTorsionSRFD type to use.

score to break up equivalent scores

C++: core::fragment::picking_old::vall::pick_fragments(const std::string &, const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const unsigned long, const bool, const class core::fragment::BBTorsionSRFD &) –> class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > >

pyrosetta.rosetta.core.fragment.picking_old.vall.pick_fragments_by_ss(*args, **kwargs)

Overloaded function.

  1. pick_fragments_by_ss(ss: str, top_n: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  2. pick_fragments_by_ss(ss: str, top_n: int, randomize: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  3. pick_fragments_by_ss(ss: str, top_n: int, randomize: bool, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

pick fragments by default sec.struct IdentityScore

secondary structure string of desired frag length

return the top ‘n’ fragments, default 200

add random noise within [0, 0.001) to

The BBTorsionSRFD type to use.

score to break up equivalent scores

C++: core::fragment::picking_old::vall::pick_fragments_by_ss(const std::string &, const unsigned long, const bool, const class core::fragment::BBTorsionSRFD &) –> class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > >

pyrosetta.rosetta.core.fragment.picking_old.vall.pick_fragments_by_ss_plus_aa(*args, **kwargs)

Overloaded function.

  1. pick_fragments_by_ss_plus_aa(ss: str, aa: str, top_n: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  2. pick_fragments_by_ss_plus_aa(ss: str, aa: str, top_n: int, randomize: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

  3. pick_fragments_by_ss_plus_aa(ss: str, aa: str, top_n: int, randomize: bool, srfd_type: pyrosetta.rosetta.core.fragment.BBTorsionSRFD) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t

pick fragments by default sec.struct IdentityScore

secondary structure string of desired frag length

amino acid string of same length as ss string

return the top ‘n’ fragments, default 200

add random noise within [0, 0.001) to

The BBTorsionSRFD type to use.

score to break up equivalent scores

C++: core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(const std::string &, const std::string &, const unsigned long, const bool, const class core::fragment::BBTorsionSRFD &) –> class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > >

pyrosetta.rosetta.core.fragment.picking_old.vall.vall_library_from_file(*args, **kwargs)

Overloaded function.

  1. vall_library_from_file(filename: str, library: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary) -> None

  2. vall_library_from_file(filename: str, library: pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary, preallocate: int) -> None

load standard Vall library from file

C++: core::fragment::picking_old::vall::vall_library_from_file(const std::string &, class core::fragment::picking_old::vall::VallLibrary &, const unsigned long) –> void