quota

Bindings for protocols::frag_picker::quota namespace

class pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config

Bases: QuotaConfig

read a config file for quota selector

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config, : pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config) → pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config

C++: protocols::frag_picker::quota::ABEGO_SS_Config::operator=(const class protocols::frag_picker::quota::ABEGO_SS_Config &) –> class protocols::frag_picker::quota::ABEGO_SS_Config &

count_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig) → int

how many pools have been defined in a config file

C++: protocols::frag_picker::quota::QuotaConfig::count_pools() –> unsigned long

get_fraction(*args, **kwargs)

Overloaded function.

1. get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int) -> float

returns a fraction for a given pool

C++: protocols::frag_picker::quota::QuotaConfig::get_fraction(unsigned long) –> double

2. get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_name: str) -> float

returns a fraction for a given pool

if the given string is not a valid name of a quota pool, the method returns 0

C++: protocols::frag_picker::quota::QuotaConfig::get_fraction(std::string) –> double

get_pool_bins(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config, pool_id: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::frag_picker::quota::ABEGO_SS_Config::get_pool_bins(unsigned long) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int) → str

return a string id (name) assigned to a given pool

C++: protocols::frag_picker::quota::QuotaConfig::get_pool_name(unsigned long) –> std::string &

highest_probability(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config, : int) → float

C++: protocols::frag_picker::quota::ABEGO_SS_Config::highest_probability(unsigned long) –> double

is_valid_quota_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_name: str) → bool

returns true if a config file defined a given pool name

C++: protocols::frag_picker::quota::QuotaConfig::is_valid_quota_pool_name(std::string &) –> bool

most_probable_bin(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config, : int) → int

C++: protocols::frag_picker::quota::ABEGO_SS_Config::most_probable_bin(unsigned long) –> unsigned long

n_columns(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config) → int

C++: protocols::frag_picker::quota::ABEGO_SS_Config::n_columns() –> unsigned long

n_rows(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config) → int

C++: protocols::frag_picker::quota::ABEGO_SS_Config::n_rows() –> unsigned long

probability(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config, seq_pos: int, bin: int) → float

C++: protocols::frag_picker::quota::ABEGO_SS_Config::probability(unsigned long, unsigned long) –> double

set_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int, fraction: float) → None

returns a fraction for a given pool

C++: protocols::frag_picker::quota::QuotaConfig::set_fraction(unsigned long, double) –> void

size(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config) → int

C++: protocols::frag_picker::quota::ABEGO_SS_Config::size() –> unsigned long

source_file_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config) → str

C++: protocols::frag_picker::quota::ABEGO_SS_Config::source_file_name() –> std::string &

class pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map

Bases: pybind11_object

represents a single pool used by quota selector

abego_char(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, abego_bin: int) → str

C++: protocols::frag_picker::quota::ABEGO_SS_Map::abego_char(unsigned long) –> char

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, : pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map) → pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map

C++: protocols::frag_picker::quota::ABEGO_SS_Map::operator=(const class protocols::frag_picker::quota::ABEGO_SS_Map &) –> class protocols::frag_picker::quota::ABEGO_SS_Map &

check_status(*args, **kwargs)

Overloaded function.

1. check_status(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, ss_type: str, abego_type: str) -> bool

C++: protocols::frag_picker::quota::ABEGO_SS_Map::check_status(char, char) const –> bool

2. check_status(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, ss_type: str, abego_type: int) -> bool

C++: protocols::frag_picker::quota::ABEGO_SS_Map::check_status(char, unsigned long) const –> bool

3. check_status(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, ss_type: int, abego_type: str) -> bool

C++: protocols::frag_picker::quota::ABEGO_SS_Map::check_status(unsigned long, char) const –> bool

4. check_status(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, bin_index: Tuple[int, int]) -> bool

C++: protocols::frag_picker::quota::ABEGO_SS_Map::check_status(struct std::pair<unsigned long, unsigned long>) const –> bool

set_status(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map, bin_index: Tuple[int, int], new_status: bool) → None

C++: protocols::frag_picker::quota::ABEGO_SS_Map::set_status(struct std::pair<unsigned long, unsigned long>, bool) –> void

show_valid(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map) → str

C++: protocols::frag_picker::quota::ABEGO_SS_Map::show_valid() –> std::string

class pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool

Bases: QuotaPool

represents a single pool used by quota selector

accepts(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, ss_type: str, abego_type: str) → bool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::accepts(char, char) –> bool

add(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

Insert a fragment candidate to the container

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::add(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> bool

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::operator=(const class protocols::frag_picker::quota::ABEGO_SS_Pool &) –> class protocols::frag_picker::quota::ABEGO_SS_Pool &

clear(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → None

removes all candidates from the container

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::clear() –> void

could_be_accepted(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::could_be_accepted(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> bool

count_candidates(*args, **kwargs)

Overloaded function.

1. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : int) -> int

Check how many candidates have been already collected for a given position

This is a very special case - collector will be used only for a given position. Thus it returns the total number of inserted candidates, as count_candidates() does

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::count_candidates(unsigned long) const –> unsigned long

2. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) -> int

Check how many candidates have been already collected for all positions

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::count_candidates() const –> unsigned long

current_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → int

Says how many fragments are currently in this pool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::current_size() const –> unsigned long

get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : int) → pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t

Returns all the candidate in this pool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::get_candidates(unsigned long) –> class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &

get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → float

returns the fraction of this quota pool in the entire population of fragments

C++: protocols::frag_picker::quota::QuotaPool::get_fraction() const –> double

get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → str

returns the name assigned to this quota pool

C++: protocols::frag_picker::quota::QuotaPool::get_pool_name() const –> const std::string &

insert(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) → None

Inserts candidates from another Collector for a give position in the query

Candidates may or may not get inserted depending on the candidate

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void

print_report(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

Describes what has been collected

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void

push(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → None

Push a fragment candidate into the container

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::push(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> void

query_length(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → int

Check the size of query sequence that this object knows.

This is a very special case - collector will be used only for a given position and it does NOT know the tolal size. Thus it returns always 0

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::query_length() const –> unsigned long

quota_score(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → float

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::quota_score(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> double

resize(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, new_size: int) → None

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::resize(unsigned long) –> void

set_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool, new_fraction: float) → None

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::set_fraction(double) –> void

show_availability(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, where: pyrosetta.rosetta.std.ostream) → None

prints information on which fragments can be accepted by this pool and how many of them

base class’ impementation says the capacity that has left

C++: protocols::frag_picker::quota::QuotaPool::show_availability(std::ostream &) const –> void

size_left(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → int

Says how many fragments can still be inserted into this pool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::size_left() const –> unsigned long

total_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool) → int

Says how many fragments (in total) may fit into this pool

C++: protocols::frag_picker::quota::ABEGO_SS_Pool::total_size() const –> unsigned long

class pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector

Bases: CandidatesCollector

A base class for collecting fragments.

The purpose of a collector is to keep fragment candidates to the end of vall processing. Then a selector will go through all the candidates stored in a collector and select the final fragments

GrabAll collector for a possible implementation

add(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

Insert a fragment candidate to the container

C++: protocols::frag_picker::quota::QuotaCollector::add(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> bool

add_pool(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, position: int, the_pool: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → None

C++: protocols::frag_picker::quota::QuotaCollector::add_pool(unsigned long, class std::shared_ptr<class protocols::frag_picker::quota::QuotaPool>) –> void

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, : pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector) → pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector

C++: protocols::frag_picker::quota::QuotaCollector::operator=(const class protocols::frag_picker::quota::QuotaCollector &) –> class protocols::frag_picker::quota::QuotaCollector &

attach_secondary_structure_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, : float, : pyrosetta.rosetta.core.fragment.SecondaryStructure, : str, : int, : pyrosetta.rosetta.utility.vector1_unsigned_long, : pyrosetta.rosetta.utility.vector1_double, : int) → None

C++: protocols::frag_picker::quota::QuotaCollector::attach_secondary_structure_pools(double, class std::shared_ptr<class core::fragment::SecondaryStructure>, std::string, unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<double, class std::allocator<double> >, unsigned long) –> void

clear(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector) → None

removes all candidates from the container

C++: protocols::frag_picker::quota::QuotaCollector::clear() –> void

count_candidates(*args, **kwargs)

Overloaded function.

1. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, : int) -> int

Check how many candidates have been already collected for a given position

C++: protocols::frag_picker::quota::QuotaCollector::count_candidates(unsigned long) const –> unsigned long

2. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector) -> int

Check how many candidates have been already collected for all positions

C++: protocols::frag_picker::quota::QuotaCollector::count_candidates() const –> unsigned long

count_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, position: int) → int

prints the number of quota pools for a given positio in query

C++: protocols::frag_picker::quota::QuotaCollector::count_pools(unsigned long) const –> unsigned long

get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, position_in_query: int) → pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t

C++: protocols::frag_picker::quota::QuotaCollector::get_candidates(unsigned long) –> class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &

get_pool(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, position: int, pool_id: int) → pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool

C++: protocols::frag_picker::quota::QuotaCollector::get_pool(unsigned long, unsigned long) –> class std::shared_ptr<class protocols::frag_picker::quota::QuotaPool>

insert(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, pos: int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) → None

Inserts candidates from another QuotaCollector for a give position in the query

Candidates may or may not get inserted depending on the candidate

C++: protocols::frag_picker::quota::QuotaCollector::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void

list_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, where: pyrosetta.rosetta.std.ostream) → None

list all registered pools with their capacity

C++: protocols::frag_picker::quota::QuotaCollector::list_pools(std::ostream &) const –> void

print_report(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector, output: pyrosetta.rosetta.std.ostream, scoring: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

Describes what has been collected

C++: protocols::frag_picker::quota::QuotaCollector::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void

query_length(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector) → int

Check the size of query sequence that this object knows.

This is mainly to be ale to check if it is the same as in the other parts of fragment picking machinery.

C++: protocols::frag_picker::quota::QuotaCollector::query_length() const –> unsigned long

renormalize_quota_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector) → None

C++: protocols::frag_picker::quota::QuotaCollector::renormalize_quota_pools() –> void

class pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig

Bases: pybind11_object

read a config file for quota selector

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, : pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig) → pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig

C++: protocols::frag_picker::quota::QuotaConfig::operator=(const class protocols::frag_picker::quota::QuotaConfig &) –> class protocols::frag_picker::quota::QuotaConfig &

count_pools(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig) → int

how many pools have been defined in a config file

C++: protocols::frag_picker::quota::QuotaConfig::count_pools() –> unsigned long

get_fraction(*args, **kwargs)

Overloaded function.

1. get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int) -> float

returns a fraction for a given pool

C++: protocols::frag_picker::quota::QuotaConfig::get_fraction(unsigned long) –> double

2. get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_name: str) -> float

returns a fraction for a given pool

if the given string is not a valid name of a quota pool, the method returns 0

C++: protocols::frag_picker::quota::QuotaConfig::get_fraction(std::string) –> double

get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int) → str

return a string id (name) assigned to a given pool

C++: protocols::frag_picker::quota::QuotaConfig::get_pool_name(unsigned long) –> std::string &

is_valid_quota_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_name: str) → bool

returns true if a config file defined a given pool name

C++: protocols::frag_picker::quota::QuotaConfig::is_valid_quota_pool_name(std::string &) –> bool

set_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig, pool_id: int, fraction: float) → None

returns a fraction for a given pool

C++: protocols::frag_picker::quota::QuotaConfig::set_fraction(unsigned long, double) –> void

class pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool

Bases: CandidatesCollector

represents a single pool used by quota selector

add(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

Insert a fragment candidate to the container

C++: protocols::frag_picker::CandidatesCollector::add(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> bool

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, : pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool

C++: protocols::frag_picker::quota::QuotaPool::operator=(const class protocols::frag_picker::quota::QuotaPool &) –> class protocols::frag_picker::quota::QuotaPool &

clear(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → None

Makes the pool empty by removing all candidates

C++: protocols::frag_picker::quota::QuotaPool::clear() –> void

could_be_accepted(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

C++: protocols::frag_picker::quota::QuotaPool::could_be_accepted(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> bool

count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → int

Check how many candidates have been already collected for a given position

This is a very special case - collector will be used only for a given position. Thus it returns the total number of inserted candidates, as count_candidates() does

C++: protocols::frag_picker::quota::QuotaPool::count_candidates() const –> unsigned long

current_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → int

Says how many fragments are currently in this pool

C++: protocols::frag_picker::quota::QuotaPool::current_size() const –> unsigned long

get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, position_in_query: int) → pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t

C++: protocols::frag_picker::CandidatesCollector::get_candidates(unsigned long) –> class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &

get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → float

returns the fraction of this quota pool in the entire population of fragments

C++: protocols::frag_picker::quota::QuotaPool::get_fraction() const –> double

get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → str

returns the name assigned to this quota pool

C++: protocols::frag_picker::quota::QuotaPool::get_pool_name() const –> const std::string &

insert(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, : int, : pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) → None

inserts candidates from another collector

Candidates may or may not get inserted depending on the candidate and type of storage

C++: protocols::frag_picker::CandidatesCollector::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void

print_report(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, output: pyrosetta.rosetta.std.ostream, scoring: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

Describes what has been collected

C++: protocols::frag_picker::CandidatesCollector::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void

push(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → None

Push a fragment candidate into the pool container

C++: protocols::frag_picker::quota::QuotaPool::push(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> void

query_length(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) → int

Check the size of query sequence that this object knows.

This is mainly to be ale to check if it is the same as in the other parts of fragment picking machinery.

C++: protocols::frag_picker::CandidatesCollector::query_length() const –> unsigned long

quota_score(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → float

provides the score for a candidate that was used to sort a quota pool

This base class returns the most recent total score for a fragment

C++: protocols::frag_picker::quota::QuotaPool::quota_score(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> double

set_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, new_fraction: float) → None

Sets the fraction of this quota pool in the entire population of fragments

C++: protocols::frag_picker::quota::QuotaPool::set_fraction(double) –> void

show_availability(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, where: pyrosetta.rosetta.std.ostream) → None

prints information on which fragments can be accepted by this pool and how many of them

base class’ impementation says the capacity that has left

C++: protocols::frag_picker::quota::QuotaPool::show_availability(std::ostream &) const –> void

size_left(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → int

Says how many fragments can still be inserted into this pool

C++: protocols::frag_picker::quota::QuotaPool::size_left() const –> unsigned long

total_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → int

Says how many fragments (in total) may fit into this pool

C++: protocols::frag_picker::quota::QuotaPool::total_size() const –> unsigned long

class pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector

Bases: FragmentSelectingRule

selects a given number of fragments using a quota scheme

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector, : pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector) → pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector

C++: protocols::frag_picker::quota::QuotaSelector::operator=(const class protocols::frag_picker::quota::QuotaSelector &) –> class protocols::frag_picker::quota::QuotaSelector &

frags_per_pos(self: pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule) → int

Says how many fragments will be selected for each position in a query sequence

C++: protocols::frag_picker::FragmentSelectingRule::frags_per_pos() –> unsigned long

select_fragments(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector, in: pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, out: pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) → None

Selects desired number of fragments from a given candidates

C++: protocols::frag_picker::quota::QuotaSelector::select_fragments(const class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &, class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &) –> void

class pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool

Bases: QuotaPool

represents a single pool used by quota selector

add(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

Insert a fragment candidate to the container

C++: protocols::frag_picker::quota::SecondaryStructurePool::add(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> bool

assign(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool

C++: protocols::frag_picker::quota::SecondaryStructurePool::operator=(const class protocols::frag_picker::quota::SecondaryStructurePool &) –> class protocols::frag_picker::quota::SecondaryStructurePool &

clear(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → None

removes all candidates from the container

C++: protocols::frag_picker::quota::SecondaryStructurePool::clear() –> void

could_be_accepted(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → bool

C++: protocols::frag_picker::quota::SecondaryStructurePool::could_be_accepted(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> bool

count_candidates(*args, **kwargs)

Overloaded function.

1. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : int) -> int

Check how many candidates have been already collected for a given position

This is a very special case - collector will be used only for a given position. Thus it returns the total number of inserted candidates, as count_candidates() does

C++: protocols::frag_picker::quota::SecondaryStructurePool::count_candidates(unsigned long) const –> unsigned long

2. count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) -> int

Check how many candidates have been already collected for all positions

C++: protocols::frag_picker::quota::SecondaryStructurePool::count_candidates() const –> unsigned long

current_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → int

Says how many fragments are currently in this pool

C++: protocols::frag_picker::quota::SecondaryStructurePool::current_size() const –> unsigned long

get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : int) → pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t

Returns all the candidate in this pool

C++: protocols::frag_picker::quota::SecondaryStructurePool::get_candidates(unsigned long) –> class utility::vector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class std::allocator<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > > > &

get_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → float

returns the fraction of this quota pool in the entire population of fragments

C++: protocols::frag_picker::quota::QuotaPool::get_fraction() const –> double

get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool) → str

returns the name assigned to this quota pool

C++: protocols::frag_picker::quota::QuotaPool::get_pool_name() const –> const std::string &

get_ss_type(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → str

C++: protocols::frag_picker::quota::SecondaryStructurePool::get_ss_type() const –> char

insert(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) → None

Inserts candidates from another Collector for a give position in the query

Candidates may or may not get inserted depending on the candidate

C++: protocols::frag_picker::quota::SecondaryStructurePool::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void

print_report(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) → None

Describes what has been collected

C++: protocols::frag_picker::quota::SecondaryStructurePool::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void

push(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → None

Push a fragment candidate into the container

C++: protocols::frag_picker::quota::SecondaryStructurePool::push(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> void

query_length(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → int

Check the size of query sequence that this object knows.

This is a very special case - collector will be used only for a given position and it does NOT know the tolal size. Thus it returns always 0

C++: protocols::frag_picker::quota::SecondaryStructurePool::query_length() const –> unsigned long

quota_score(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, candidate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) → float

C++: protocols::frag_picker::quota::SecondaryStructurePool::quota_score(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) const –> double

resize(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, new_size: int) → None

C++: protocols::frag_picker::quota::SecondaryStructurePool::resize(unsigned long) –> void

set_fraction(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool, new_fraction: float) → None

C++: protocols::frag_picker::quota::SecondaryStructurePool::set_fraction(double) –> void

show_availability(self: pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool, where: pyrosetta.rosetta.std.ostream) → None

prints information on which fragments can be accepted by this pool and how many of them

base class’ impementation says the capacity that has left

C++: protocols::frag_picker::quota::QuotaPool::show_availability(std::ostream &) const –> void

size_left(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → int

Says how many fragments can still be inserted into this pool

C++: protocols::frag_picker::quota::SecondaryStructurePool::size_left() const –> unsigned long

total_size(self: pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool) → int

Says how many fragments (in total) may fit into this pool

C++: protocols::frag_picker::quota::SecondaryStructurePool::total_size() const –> unsigned long

pyrosetta.rosetta.protocols.frag_picker.quota.abego_index(: str) → int

C++: protocols::frag_picker::quota::abego_index(char) –> unsigned long

pyrosetta.rosetta.protocols.frag_picker.quota.ss_index(: str) → int

C++: protocols::frag_picker::quota::ss_index(char) –> unsigned long

pyrosetta.rosetta.protocols.frag_picker.quota.torsion2big_bin_id(phi: float, psi: float, omega: float) → int

C++: protocols::frag_picker::quota::torsion2big_bin_id(const double, const double, const double) –> unsigned long