frag_picker¶
Bindings for protocols::frag_picker namespace
- class pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter¶
Bases:
PdbIdChunkFilter
Accepts a chunk based on the pdb id of the source protein
If a given chunk comes from a registered pdb file then it will PASS the test. Otherwise it will be rejected
- add_pdb_id(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids: str) None ¶
Adds a pdb id to the filter.
What that PDB id means it depends on the filter implementation
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_id(std::string) –> void
- add_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Adds a bunch of pdb ids to the filter
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_ids(class utility::vector1<std::string, class std::allocator<std::string > >) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter, : pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter) pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter ¶
C++: protocols::frag_picker::AllowPdbIdFilter::operator=(const class protocols::frag_picker::AllowPdbIdFilter &) –> class protocols::frag_picker::AllowPdbIdFilter &
- load_pdb_id_from_file(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, : str) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::load_pdb_id_from_file(std::string) –> void
- show_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::show_pdb_ids(std::ostream &) –> void
- test_chunk(self: pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter, a_chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) bool ¶
say if a given chunk looks promising.
Simply if its pdb id is on a list then it will pass the test
C++: protocols::frag_picker::AllowPdbIdFilter::test_chunk(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
- class pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector¶
Bases:
FragmentSelectingRule
selects a given number of fragments using a quota scheme
- assign(self: pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector, : pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector) pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector ¶
C++: protocols::frag_picker::BestTotalScoreSelector::operator=(const class protocols::frag_picker::BestTotalScoreSelector &) –> class protocols::frag_picker::BestTotalScoreSelector &
- 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.BestTotalScoreSelector, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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::BestTotalScoreSelector::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.BoundedCollector_CompareTotalScore¶
Bases:
BoundedCollector_protocols_frag_picker_CompareTotalScore_t
- add(*args, **kwargs)¶
Overloaded function.
add(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, new_canditate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) -> bool
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::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(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : 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.BoundedCollector_CompareTotalScore, : pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore) pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore ¶
C++: protocols::frag_picker::BoundedCollector_CompareTotalScore::operator=(const class protocols::frag_picker::BoundedCollector_CompareTotalScore &) –> class protocols::frag_picker::BoundedCollector_CompareTotalScore &
- clear(*args, **kwargs)¶
Overloaded function.
clear(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::clear() –> void
clear(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> None
removes all candidates from the container
C++: protocols::frag_picker::CandidatesCollector::clear() –> void
- count_candidates(*args, **kwargs)¶
Overloaded function.
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, seq_pos: int) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::count_candidates() const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : int) -> int
Check how many candidates have been already collected for a given position
C++: protocols::frag_picker::CandidatesCollector::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
Check how many candidates have been already collected for all positions
C++: protocols::frag_picker::CandidatesCollector::count_candidates() const –> unsigned long
- get_candidates(*args, **kwargs)¶
Overloaded function.
get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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::BoundedCollector<protocols::frag_picker::CompareTotalScore>::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_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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> > > > &
- insert(*args, **kwargs)¶
Overloaded function.
insert(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, pos: int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void
insert(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : 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(*args, **kwargs)¶
Overloaded function.
print_report(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, out: pyrosetta.rosetta.std.ostream, scoring: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void
print_report(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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
- query_length(*args, **kwargs)¶
Overloaded function.
query_length(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::query_length() const –> unsigned long
query_length(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> 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
- class pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t¶
Bases:
CandidatesCollector
- add(*args, **kwargs)¶
Overloaded function.
add(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, new_canditate: Tuple[pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap]) -> bool
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::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(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : 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(*args, **kwargs)¶
Overloaded function.
assign(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::operator=(const class protocols::frag_picker::BoundedCollector<class protocols::frag_picker::CompareTotalScore> &) –> class protocols::frag_picker::BoundedCollector<class protocols::frag_picker::CompareTotalScore> &
assign(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) -> pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector
C++: protocols::frag_picker::CandidatesCollector::operator=(const class protocols::frag_picker::CandidatesCollector &) –> class protocols::frag_picker::CandidatesCollector &
- clear(*args, **kwargs)¶
Overloaded function.
clear(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::clear() –> void
clear(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> None
removes all candidates from the container
C++: protocols::frag_picker::CandidatesCollector::clear() –> void
- count_candidates(*args, **kwargs)¶
Overloaded function.
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, seq_pos: int) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::count_candidates() const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : int) -> int
Check how many candidates have been already collected for a given position
C++: protocols::frag_picker::CandidatesCollector::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
Check how many candidates have been already collected for all positions
C++: protocols::frag_picker::CandidatesCollector::count_candidates() const –> unsigned long
- get_candidates(*args, **kwargs)¶
Overloaded function.
get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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::BoundedCollector<protocols::frag_picker::CompareTotalScore>::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_candidates(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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> > > > &
- insert(*args, **kwargs)¶
Overloaded function.
insert(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, pos: int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void
insert(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, : 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(*args, **kwargs)¶
Overloaded function.
print_report(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, out: pyrosetta.rosetta.std.ostream, scoring: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) -> None
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void
print_report(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t, 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
- query_length(*args, **kwargs)¶
Overloaded function.
query_length(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> int
C++: protocols::frag_picker::BoundedCollector<protocols::frag_picker::CompareTotalScore>::query_length() const –> unsigned long
query_length(self: pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t) -> 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
- class pyrosetta.rosetta.protocols.frag_picker.CS2ndShift¶
Bases:
pybind11_object
- shifts(self: pyrosetta.rosetta.protocols.frag_picker.CS2ndShift) pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t ¶
C++: protocols::frag_picker::CS2ndShift::shifts() –> class utility::vector1<class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > > >
- class pyrosetta.rosetta.protocols.frag_picker.CSTalosIO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, : pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) pyrosetta.rosetta.protocols.frag_picker.CSTalosIO ¶
C++: protocols::frag_picker::CSTalosIO::operator=(const class protocols::frag_picker::CSTalosIO &) –> class protocols::frag_picker::CSTalosIO &
- get_first_residue_id(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) int ¶
C++: protocols::frag_picker::CSTalosIO::get_first_residue_id() const –> unsigned long
- get_last_residue_id(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) int ¶
C++: protocols::frag_picker::CSTalosIO::get_last_residue_id() const –> unsigned long
- get_sequence(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) str ¶
C++: protocols::frag_picker::CSTalosIO::get_sequence() const –> std::string
- get_shift(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, : int, : str) float ¶
C++: protocols::frag_picker::CSTalosIO::get_shift(unsigned long, const std::string &) const –> double
- has_atom(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, : int, : str) bool ¶
C++: protocols::frag_picker::CSTalosIO::has_atom(unsigned long, const std::string &) const –> bool
- has_entry(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, residue_id: int) bool ¶
C++: protocols::frag_picker::CSTalosIO::has_entry(unsigned long) –> bool
- read(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO, : str) None ¶
C++: protocols::frag_picker::CSTalosIO::read(const std::string &) –> void
- repack_to_matrix(self: pyrosetta.rosetta.protocols.frag_picker.CSTalosIO) pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t ¶
C++: protocols::frag_picker::CSTalosIO::repack_to_matrix() –> class utility::vector1<class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > > >
- class pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector¶
Bases:
pybind11_object
TODO write collector for mixed fragment lengths
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.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.CandidatesCollector, : pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector ¶
C++: protocols::frag_picker::CandidatesCollector::operator=(const class protocols::frag_picker::CandidatesCollector &) –> class protocols::frag_picker::CandidatesCollector &
- clear(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) None ¶
removes all candidates from the container
C++: protocols::frag_picker::CandidatesCollector::clear() –> void
- count_candidates(*args, **kwargs)¶
Overloaded function.
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, : int) -> int
Check how many candidates have been already collected for a given position
C++: protocols::frag_picker::CandidatesCollector::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) -> int
Check how many candidates have been already collected for all positions
C++: protocols::frag_picker::CandidatesCollector::count_candidates() 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> > > > &
- 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
- 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
- class pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination¶
Bases:
FragmentComparatorBase
comparator based on the linear combination of some score components
returns true if first pair has lower weighted score than the second one
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination, : pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination) pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination ¶
C++: protocols::frag_picker::CompareByScoreCombination::operator=(const class protocols::frag_picker::CompareByScoreCombination &) –> class protocols::frag_picker::CompareByScoreCombination &
- class pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition¶
Bases:
FragmentComparatorBase
comparator based on a sequence position in a query
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition, : pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition) pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition ¶
C++: protocols::frag_picker::CompareQueryPosition::operator=(const class protocols::frag_picker::CompareQueryPosition &) –> class protocols::frag_picker::CompareQueryPosition &
- class pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent¶
Bases:
FragmentComparatorBase
comparator based on one of the score components calculated for fragments
returns true if first pair has lower score component than the second one
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent, : pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent) pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent ¶
C++: protocols::frag_picker::CompareScoreComponent::operator=(const class protocols::frag_picker::CompareScoreComponent &) –> class protocols::frag_picker::CompareScoreComponent &
- class pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore¶
Bases:
FragmentComparatorBase
comparator based on the total score of fragments
returns true if first pair has lower total score than the second one
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore, : pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore) pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore ¶
C++: protocols::frag_picker::CompareTotalScore::operator=(const class protocols::frag_picker::CompareTotalScore &) –> class protocols::frag_picker::CompareTotalScore &
- class pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector¶
Bases:
FragmentSelectingRule
selects fragments by running several selectors
- add_selector(self: pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector, new_selector: pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule) None ¶
C++: protocols::frag_picker::CompositeFragmentSelector::add_selector(class std::shared_ptr<class protocols::frag_picker::FragmentSelectingRule>) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector, : pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector) pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector ¶
C++: protocols::frag_picker::CompositeFragmentSelector::operator=(const class protocols::frag_picker::CompositeFragmentSelector &) –> class protocols::frag_picker::CompositeFragmentSelector &
- 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.CompositeFragmentSelector, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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 set of candidates
C++: protocols::frag_picker::CompositeFragmentSelector::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.Contact¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.Contact, : pyrosetta.rosetta.protocols.frag_picker.Contact) pyrosetta.rosetta.protocols.frag_picker.Contact ¶
C++: protocols::frag_picker::Contact::operator=(const class protocols::frag_picker::Contact &) –> class protocols::frag_picker::Contact &
- dist(self: pyrosetta.rosetta.protocols.frag_picker.Contact) float ¶
C++: protocols::frag_picker::Contact::dist() –> double
- dist_squared(self: pyrosetta.rosetta.protocols.frag_picker.Contact) float ¶
C++: protocols::frag_picker::Contact::dist_squared() –> double &
- i(self: pyrosetta.rosetta.protocols.frag_picker.Contact) int ¶
C++: protocols::frag_picker::Contact::i() –> unsigned long &
- j(self: pyrosetta.rosetta.protocols.frag_picker.Contact) int ¶
C++: protocols::frag_picker::Contact::j() –> unsigned long &
- type(self: pyrosetta.rosetta.protocols.frag_picker.Contact) pyrosetta.rosetta.protocols.frag_picker.ContactType ¶
C++: protocols::frag_picker::Contact::type() –> enum protocols::frag_picker::ContactType &
- type_name(self: pyrosetta.rosetta.protocols.frag_picker.Contact) str ¶
C++: protocols::frag_picker::Contact::type_name() –> std::string
- class pyrosetta.rosetta.protocols.frag_picker.ContactCounts¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.ContactCounts, : pyrosetta.rosetta.protocols.frag_picker.ContactCounts) pyrosetta.rosetta.protocols.frag_picker.ContactCounts ¶
C++: protocols::frag_picker::ContactCounts::operator=(const class protocols::frag_picker::ContactCounts &) –> class protocols::frag_picker::ContactCounts &
- counts(self: pyrosetta.rosetta.protocols.frag_picker.ContactCounts) pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_unsigned_long_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_unsigned_long_t ¶
C++: protocols::frag_picker::ContactCounts::counts() –> class std::map<struct std::pair<unsigned long, unsigned long>, unsigned long, struct std::less<struct std::pair<unsigned long, unsigned long> >, class std::allocator<struct std::pair<const struct std::pair<unsigned long, unsigned long>, unsigned long> > > &
- class pyrosetta.rosetta.protocols.frag_picker.ContactType¶
Bases:
pybind11_object
Members:
CA
CB
CEN
UNK
num_contact_types
- CA = <ContactType.CA: 1>¶
- CB = <ContactType.CB: 2>¶
- CEN = <ContactType.CEN: 3>¶
- UNK = <ContactType.UNK: 4>¶
- property name¶
- num_contact_types = <ContactType.UNK: 4>¶
- property value¶
- class pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector¶
Bases:
FragmentSelectingRule
selects a given number of fragments using a quota scheme
- assign(self: pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector, : pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector) pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector ¶
C++: protocols::frag_picker::CustomScoreSelector::operator=(const class protocols::frag_picker::CustomScoreSelector &) –> class protocols::frag_picker::CustomScoreSelector &
- 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.CustomScoreSelector, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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::CustomScoreSelector::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.DenyPdbIdFilter¶
Bases:
PdbIdChunkFilter
Denies a chunk based on the pdb id of the source protein
If a given chunk comes from a registered pdb file then it will FAIL the test. Otherwise it will be accepted
- add_pdb_id(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids: str) None ¶
Adds a pdb id to the filter.
What that PDB id means it depends on the filter implementation
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_id(std::string) –> void
- add_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Adds a bunch of pdb ids to the filter
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_ids(class utility::vector1<std::string, class std::allocator<std::string > >) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter, : pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter) pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter ¶
C++: protocols::frag_picker::DenyPdbIdFilter::operator=(const class protocols::frag_picker::DenyPdbIdFilter &) –> class protocols::frag_picker::DenyPdbIdFilter &
- load_pdb_id_from_file(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, : str) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::load_pdb_id_from_file(std::string) –> void
- show_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::show_pdb_ids(std::ostream &) –> void
- test_chunk(self: pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter, a_chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) bool ¶
say if a given chunk looks promising.
Simply if its pdb id is on a list then it will be rejected
C++: protocols::frag_picker::DenyPdbIdFilter::test_chunk(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
- class pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering¶
Bases:
FragmentSelectingRule
selects fragments by running several selectors
- assign(self: pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering, : pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering) pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering ¶
C++: protocols::frag_picker::DiversifyCrmsdByClustering::operator=(const class protocols::frag_picker::DiversifyCrmsdByClustering &) –> class protocols::frag_picker::DiversifyCrmsdByClustering &
- 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.DiversifyCrmsdByClustering, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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 set of candidates
C++: protocols::frag_picker::DiversifyCrmsdByClustering::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.DiversifyCrmsdSelector¶
Bases:
FragmentSelectingRule
selects fragments by running several selectors
- assign(self: pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector, : pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector) pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector ¶
C++: protocols::frag_picker::DiversifyCrmsdSelector::operator=(const class protocols::frag_picker::DiversifyCrmsdSelector &) –> class protocols::frag_picker::DiversifyCrmsdSelector &
- 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.DiversifyCrmsdSelector, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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 set of candidates
C++: protocols::frag_picker::DiversifyCrmsdSelector::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.DiversifyDihedralsSelector¶
Bases:
FragmentSelectingRule
selects fragments by running several selectors
- assign(self: pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector, : pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector) pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector ¶
C++: protocols::frag_picker::DiversifyDihedralsSelector::operator=(const class protocols::frag_picker::DiversifyDihedralsSelector &) –> class protocols::frag_picker::DiversifyDihedralsSelector &
- dihedral_rmsd(self: pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) float ¶
C++: protocols::frag_picker::DiversifyDihedralsSelector::dihedral_rmsd(class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>) –> double
- 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.DiversifyDihedralsSelector, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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 set of candidates
C++: protocols::frag_picker::DiversifyDihedralsSelector::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.FragmentCandidate¶
Bases:
pybind11_object
Vector candidate says which X-mer from vall fits to a query sequence
Scores for a given fragment are stored separately in a FragmentScoreMap object Therefore fragment containers hold std::pair<FragmentCandidateOP,FragmentScoreMapOP>
- assign(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, : pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate ¶
C++: protocols::frag_picker::FragmentCandidate::operator=(const class protocols::frag_picker::FragmentCandidate &) –> class protocols::frag_picker::FragmentCandidate &
- get_chain_id(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) str ¶
returns a chain id of a protein from which the fragment has been extracted
C++: protocols::frag_picker::FragmentCandidate::get_chain_id() const –> char
- get_chunk(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) pyrosetta.rosetta.protocols.frag_picker.VallChunk ¶
returns a pointer to the original chunk from vall the fragment comes from
C++: protocols::frag_picker::FragmentCandidate::get_chunk() const –> class std::shared_ptr<class protocols::frag_picker::VallChunk>
- get_first_index_in_query(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns the index of a very first residue in a query sequence that is covered by this fragment
C++: protocols::frag_picker::FragmentCandidate::get_first_index_in_query() const –> unsigned long
- get_first_index_in_vall(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns the index of a very first residue in a Vall chunk that is covered by this fragment
C++: protocols::frag_picker::FragmentCandidate::get_first_index_in_vall() const –> unsigned long
- get_frag_data(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) pyrosetta.rosetta.core.fragment.FragData ¶
C++: protocols::frag_picker::FragmentCandidate::get_frag_data() –> class std::shared_ptr<class core::fragment::FragData>
- get_length(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns the length of this fragment
C++: protocols::frag_picker::FragmentCandidate::get_length() const –> unsigned long
- get_middle_residue(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) pyrosetta.rosetta.protocols.frag_picker.VallResidue ¶
returns the middle residue of this fragment candidate
C++: protocols::frag_picker::FragmentCandidate::get_middle_residue() const –> class std::shared_ptr<class protocols::frag_picker::VallResidue>
- get_middle_ss(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) str ¶
returns secondary structure assigned to the middle residue of this fragment candidate
secondary structure of the middle residue of this fragment, as extracted from Vall data
C++: protocols::frag_picker::FragmentCandidate::get_middle_ss() const –> char
- get_pdb_id(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) str ¶
returns a PDB id of a protein from which the fragment has been extracted
C++: protocols::frag_picker::FragmentCandidate::get_pdb_id() const –> std::string
- get_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) str ¶
C++: protocols::frag_picker::FragmentCandidate::get_pool_name() –> std::string
- get_query_middle_res_id(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns a query index of a middle residue in this fragment
a position of the middle residue of this fragment in the query sequence
C++: protocols::frag_picker::FragmentCandidate::get_query_middle_res_id() –> unsigned long
- get_residue(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, whichOne: int) pyrosetta.rosetta.protocols.frag_picker.VallResidue ¶
returns a given residue from this fragment
the irgument is in the range [1,fragmentLength]
C++: protocols::frag_picker::FragmentCandidate::get_residue(unsigned long) const –> class std::shared_ptr<class protocols::frag_picker::VallResidue>
- get_vall_middle_res_id(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns a vall index of a middle residue in this fragment
a position of the middle residue of this fragment in the vall sequence
C++: protocols::frag_picker::FragmentCandidate::get_vall_middle_res_id() –> unsigned long
- key(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) int ¶
returns an integer key identifying a fragment
C++: protocols::frag_picker::FragmentCandidate::key() const –> unsigned long
- output_silent(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, sequence: str, silent_file_name: str, tag: str, sc: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, ms: protocols::frag_picker::scores::FragmentScoreManager) None ¶
Prints fragment to silent struct
C++: protocols::frag_picker::FragmentCandidate::output_silent(class core::io::silent::SilentFileData &, const std::string &, const std::string &, const std::string &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) –> void
- print_fragment(*args, **kwargs)¶
Overloaded function.
print_fragment(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, out: pyrosetta.rosetta.std.ostream) -> None
print_fragment(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, out: pyrosetta.rosetta.std.ostream, sc: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) -> None
print_fragment(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, out: pyrosetta.rosetta.std.ostream, sc: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, ms: protocols::frag_picker::scores::FragmentScoreManager) -> None
Prints fragment data, the output can be directly loaded to minirosetta
C++: protocols::frag_picker::FragmentCandidate::print_fragment(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) –> void
- print_fragment_index(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, out: pyrosetta.rosetta.std.ostream, vall_index_database_exists: bool) None ¶
C++: protocols::frag_picker::FragmentCandidate::print_fragment_index(std::ostream &, bool) –> void
- print_fragment_seq(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, out: pyrosetta.rosetta.std.ostream) None ¶
Prints fragment sequence, used for generating structure based sequence profiles
C++: protocols::frag_picker::FragmentCandidate::print_fragment_seq(std::ostream &) –> void
- same_chain(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, fr: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) bool ¶
C++: protocols::frag_picker::FragmentCandidate::same_chain(class std::shared_ptr<const class protocols::frag_picker::FragmentCandidate>) –> bool
- sequence(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate) str ¶
creates a new string object that contains a sequence of this fragment
C++: protocols::frag_picker::FragmentCandidate::sequence() –> std::string
- set_pool_name(self: pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate, pool_name: str) None ¶
C++: protocols::frag_picker::FragmentCandidate::set_pool_name(const std::string &) –> void
- class pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase, : pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase) pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase ¶
C++: protocols::frag_picker::FragmentComparatorBase::operator=(const class protocols::frag_picker::FragmentComparatorBase &) –> class protocols::frag_picker::FragmentComparatorBase &
- class pyrosetta.rosetta.protocols.frag_picker.FragmentPicker¶
Bases:
pybind11_object
The core of the fragment picking machinery
- FragmentPicker class does:
know about query data: sequence, sequence profile, secondary structure. All other query data must be loaded directly to the relevant scoring methods
provide slots for ‘plugable’ parts of the machinery, like chunk filters, scoring methods and so on.
pick fragments
- add_chunk_filter(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, filter: protocols::frag_picker::VallChunkFilter) None ¶
adds a chunk filter that will be used to screen chunks before they are cut into fragments
C++: protocols::frag_picker::FragmentPicker::add_chunk_filter(class std::shared_ptr<class protocols::frag_picker::VallChunkFilter>) –> void
- add_query_ss(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str, : str) None ¶
Sets the query secondary structure
C++: protocols::frag_picker::FragmentPicker::add_query_ss(std::string, std::string) –> void
- add_scoring_method(*args, **kwargs)¶
Overloaded function.
add_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, scoring_term: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, weight: float) -> None
add_scoring_method(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, scoring_term: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod, weight: float, index: int) -> None
adds a new scoring method to the scoring scheme
C++: protocols::frag_picker::FragmentPicker::add_scoring_method(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoringMethod>, double, unsigned long) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.protocols.frag_picker.FragmentPicker ¶
C++: protocols::frag_picker::FragmentPicker::operator=(const class protocols::frag_picker::FragmentPicker &) –> class protocols::frag_picker::FragmentPicker &
- bounded_protocol(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
Picks fragments and saves them into proper files - uses bounded queue.
This protocol scores all vall data against all query positions and keeps a limited number of candidates per position using a bounded queue. When all candidates for all positions are scored, it selects final fragments.
C++: protocols::frag_picker::FragmentPicker::bounded_protocol() –> void
- count_query_ss(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) int ¶
Sets the query secondary structure
C++: protocols::frag_picker::FragmentPicker::count_query_ss() –> unsigned long
- create_scores(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, file_name: str) None ¶
- Creates scoring methods from score file, same as using
frags::scoring::config command-line option
C++: protocols::frag_picker::FragmentPicker::create_scores(std::string) –> void
- property frag_sizes_¶
- fragment_contacts(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, fragment_size: int, fragment_set: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) None ¶
C++: protocols::frag_picker::FragmentPicker::fragment_contacts(const unsigned long, const class utility::vector1<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 std::allocator<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
- get_candidates_collector(*args, **kwargs)¶
Overloaded function.
get_candidates_collector(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, frag_size: int) -> pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector
get_candidates_collector(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, frag_size: int, index: int) -> pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector
returns a pointer to the candidates collector currently used
one may need this instance to access the candidates that have been found by the picker
C++: protocols::frag_picker::FragmentPicker::get_candidates_collector(unsigned long, unsigned long) –> class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>
- get_final_fragments(*args, **kwargs)¶
Overloaded function.
get_final_fragments(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, qPos: int, frag_size: int, out: pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> None
C++: protocols::frag_picker::FragmentPicker::get_final_fragments(unsigned long, 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> > > > &) –> void
get_final_fragments(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, qPos: int, out: pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) -> None
C++: protocols::frag_picker::FragmentPicker::get_final_fragments(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> > > > &) –> void
- get_frag_sizes(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
getter for frag_sizes_
C++: protocols::frag_picker::FragmentPicker::get_frag_sizes() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- get_n_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) int ¶
Gets n_candidates_
C++: protocols::frag_picker::FragmentPicker::get_n_candidates() const –> unsigned long
- get_n_frags(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) int ¶
Gets n_frags_
C++: protocols::frag_picker::FragmentPicker::get_n_frags() const –> unsigned long
- get_picked_positions(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
returns vector of picked positions
C++: protocols::frag_picker::FragmentPicker::get_picked_positions() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- get_query_phi_prediction(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns the phi prediction
C++: protocols::frag_picker::FragmentPicker::get_query_phi_prediction() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_phi_prediction_conf(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns the phi prediction confidence
C++: protocols::frag_picker::FragmentPicker::get_query_phi_prediction_conf() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_psi_prediction(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns the psi prediction
C++: protocols::frag_picker::FragmentPicker::get_query_psi_prediction() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_psi_prediction_conf(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns the psi prediction confidence
C++: protocols::frag_picker::FragmentPicker::get_query_psi_prediction_conf() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_residue_depth(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns residue depth values
C++: protocols::frag_picker::FragmentPicker::get_query_residue_depth() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_sa_prediction(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.utility.vector1_double ¶
Returns the solvent accessibility prediction
C++: protocols::frag_picker::FragmentPicker::get_query_sa_prediction() –> class utility::vector1<double, class std::allocator<double> > &
- get_query_seq(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.core.sequence.SequenceProfile ¶
C++: protocols::frag_picker::FragmentPicker::get_query_seq() –> class std::shared_ptr<class core::sequence::SequenceProfile>
- get_query_seq_string(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) str ¶
Returns the sequence we are picking fragments for (as a string)
C++: protocols::frag_picker::FragmentPicker::get_query_seq_string() –> std::string &
- get_query_ss(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_name: str) pyrosetta.rosetta.core.fragment.SecondaryStructure ¶
Returns the query secondary structure as a SecondaryStructure object
C++: protocols::frag_picker::FragmentPicker::get_query_ss(std::string) –> class std::shared_ptr<class core::fragment::SecondaryStructure>
- get_query_ss_string(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, prediction_name: str) str ¶
Returns the query secondary structure as a string
C++: protocols::frag_picker::FragmentPicker::get_query_ss_string(std::string) –> std::string &
- get_score_manager(*args, **kwargs)¶
Overloaded function.
get_score_manager(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) -> pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager
get_score_manager(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, index: int) -> pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager
returns a pointer to a scoring manager
C++: protocols::frag_picker::FragmentPicker::get_score_manager(unsigned long) –> class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>
- get_self_ptr(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.protocols.frag_picker.FragmentPicker ¶
C++: protocols::frag_picker::FragmentPicker::get_self_ptr() –> class std::shared_ptr<class protocols::frag_picker::FragmentPicker>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_FragmentPicker_t ¶
C++: protocols::frag_picker::FragmentPicker::get_self_weak_ptr() –> class std::weak_ptr<class protocols::frag_picker::FragmentPicker>
- get_vall(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) protocols::frag_picker::VallProvider ¶
a pointer to Vall provider
C++: protocols::frag_picker::FragmentPicker::get_vall() –> class std::shared_ptr<class protocols::frag_picker::VallProvider>
- is_valid_chunk(*args, **kwargs)¶
Overloaded function.
is_valid_chunk(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) -> bool
C++: protocols::frag_picker::FragmentPicker::is_valid_chunk(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
is_valid_chunk(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, frag_len: int, chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) -> bool
C++: protocols::frag_picker::FragmentPicker::is_valid_chunk(const unsigned long, class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
- keep_all_protocol(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
Picks fragments and saves them into proper files - independently for each query position.
This protocol scores all vall data against a given position and keeps all the candidates unless they fail an energy filter When all candidates for a positions are scored, it selects fragments for the position and proceeds to the next position. Bounded queue is not used
C++: protocols::frag_picker::FragmentPicker::keep_all_protocol() –> void
- max_frag_len(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) int ¶
How long is the longest fragment?
C++: protocols::frag_picker::FragmentPicker::max_frag_len() –> unsigned long
- property n_candidates_¶
- property n_frags_¶
- nonlocal_pairs(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, fragment_size: int, fragment_set: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) None ¶
C++: protocols::frag_picker::FragmentPicker::nonlocal_pairs(const unsigned long, const class utility::vector1<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 std::allocator<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
- output_fragments(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, fragment_size: int, final_fragments: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t) None ¶
C++: protocols::frag_picker::FragmentPicker::output_fragments(const unsigned long, const class utility::vector1<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 std::allocator<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
- parse_command_line(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::parse_command_line() –> void
- parse_quota_command_line(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::parse_quota_command_line() –> void
- pick_candidates(*args, **kwargs)¶
Overloaded function.
pick_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) -> None
C++: protocols::frag_picker::FragmentPicker::pick_candidates() –> void
pick_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, i_pos: int, frag_len: int) -> None
C++: protocols::frag_picker::FragmentPicker::pick_candidates(unsigned long, unsigned long) –> void
- pick_chunk_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk, assignments: pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo) None ¶
multi-threaded task
C++: protocols::frag_picker::FragmentPicker::pick_chunk_candidates(class std::shared_ptr<class protocols::frag_picker::VallChunk>, const class basic::thread_manager::RosettaThreadAssignmentInfo &) –> void
- property prefix_¶
- quota_protocol(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::quota_protocol() –> void
- read_depth(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, file_name: str) None ¶
Reads DEPTH residue depth values
C++: protocols::frag_picker::FragmentPicker::read_depth(const std::string &) –> void
- read_psipred_ss2(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str, : str) None ¶
Reads query secondary structure prediction from a PsiPred file
C++: protocols::frag_picker::FragmentPicker::read_psipred_ss2(const std::string &, std::string) –> void
- read_spine_x(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, file_name: str) None ¶
Reads spine-x phi, psi, and solvent accessibility predictions
C++: protocols::frag_picker::FragmentPicker::read_spine_x(const std::string &) –> void
- read_ss_file(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str, : str) None ¶
Identifies if the ss file is psipred or talos, calls appropriate reader
C++: protocols::frag_picker::FragmentPicker::read_ss_file(const std::string &, const std::string &) –> void
- read_ss_files(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, sec_str_input: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Reads a bunch of ss predicitons from files and plugs them into the picker
C++: protocols::frag_picker::FragmentPicker::read_ss_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void
- read_talos_ss(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : str, : str) None ¶
Reads query secondary structure prediction from a Talos+ file
C++: protocols::frag_picker::FragmentPicker::read_talos_ss(const std::string &, std::string) –> void
- read_vall(*args, **kwargs)¶
Overloaded function.
read_vall(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, fn: str) -> None
reads a vall file
C++: protocols::frag_picker::FragmentPicker::read_vall(const std::string &) –> void
read_vall(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, fns: pyrosetta.rosetta.utility.vector1_std_string) -> None
C++: protocols::frag_picker::FragmentPicker::read_vall(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void
- save_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::save_candidates() –> void
- save_fragments(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::save_fragments() –> void
- property selector_¶
- set_candidates_collector(*args, **kwargs)¶
Overloaded function.
set_candidates_collector(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, frag_size: int, sink: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) -> None
set_candidates_collector(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, frag_size: int, sink: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector, index: int) -> None
sets a collector where fragment candidates will be kept until final selection
C++: protocols::frag_picker::FragmentPicker::set_candidates_collector(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>, unsigned long) –> void
- set_frag_sizes(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, size: pyrosetta.rosetta.utility.vector1_unsigned_long, clear: bool) None ¶
Lets you set frag sizes outside the command line
C++: protocols::frag_picker::FragmentPicker::set_frag_sizes(class utility::vector1<unsigned long, class std::allocator<unsigned long> >, bool) –> void
- set_max_threads(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, setting: int) None ¶
Set the number of threads to use.
A value of zero means use all available threads.
Vikram K. Mulligan (vmulligan.org)
C++: protocols::frag_picker::FragmentPicker::set_max_threads(const unsigned long) –> void
- set_n_candidates(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, n_candidates: int) None ¶
Sets n_candidates_
C++: protocols::frag_picker::FragmentPicker::set_n_candidates(unsigned long) –> void
- set_n_frags(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, n_frags: int) None ¶
Sets n_frags_
C++: protocols::frag_picker::FragmentPicker::set_n_frags(unsigned long) –> void
- set_picked_positions(*args, **kwargs)¶
Overloaded function.
set_picked_positions(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : int, : int) -> None
Asks the picker to pick fragments from a given range in a query sequence
C++: protocols::frag_picker::FragmentPicker::set_picked_positions(unsigned long, unsigned long) –> void
set_picked_positions(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Asks the picker to pick fragments for given positions in a query sequence
C++: protocols::frag_picker::FragmentPicker::set_picked_positions(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- set_query_phi(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_phi: pyrosetta.rosetta.utility.vector1_double) None ¶
Sets the query phi angles
Directly sets the query phi angles instead of reading it from a file
C++: protocols::frag_picker::FragmentPicker::set_query_phi(class utility::vector1<double, class std::allocator<double> > &) –> void
- set_query_phi_conf(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_phi_conf: pyrosetta.rosetta.utility.vector1_double) None ¶
Sets the query phi angle confidence
Directly sets the query phi angle confidence instead of reading it from a file
C++: protocols::frag_picker::FragmentPicker::set_query_phi_conf(class utility::vector1<double, class std::allocator<double> > &) –> void
- set_query_profile(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, profile: pyrosetta.rosetta.core.sequence.SequenceProfile) None ¶
Sets the sequence object we are picking fragments for
C++: protocols::frag_picker::FragmentPicker::set_query_profile(class std::shared_ptr<class core::sequence::SequenceProfile>) –> void
- set_query_psi(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_psi: pyrosetta.rosetta.utility.vector1_double) None ¶
Sets the query psi angles
Directly sets the query psi angles isntead of reading it from a file
C++: protocols::frag_picker::FragmentPicker::set_query_psi(class utility::vector1<double, class std::allocator<double> > &) –> void
- set_query_psi_conf(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_psi_conf: pyrosetta.rosetta.utility.vector1_double) None ¶
Sets the query psi angle confidence
Directly sets the query psi angle confidence instead of reading it form a file
C++: protocols::frag_picker::FragmentPicker::set_query_psi_conf(class utility::vector1<double, class std::allocator<double> > &) –> void
- set_query_sa(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_sa: pyrosetta.rosetta.utility.vector1_double) None ¶
Sets the query surface area
Directly sets the query surface area instead of reading it from a file
C++: protocols::frag_picker::FragmentPicker::set_query_sa(class utility::vector1<double, class std::allocator<double> > &) –> void
- set_query_seq(*args, **kwargs)¶
Overloaded function.
set_query_seq(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_sequence: pyrosetta.rosetta.core.sequence.SequenceProfile) -> None
sets the query sequence
Well, it is a sequence profile, but the sequence can be extracted from it
C++: protocols::frag_picker::FragmentPicker::set_query_seq(class std::shared_ptr<class core::sequence::SequenceProfile>) –> void
set_query_seq(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, query_sequence: str) -> None
sets the query sequence
C++: protocols::frag_picker::FragmentPicker::set_query_seq(std::string &) –> void
- set_selector(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, selector: pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule) None ¶
Sets selector_
C++: protocols::frag_picker::FragmentPicker::set_selector(class std::shared_ptr<class protocols::frag_picker::FragmentSelectingRule>) –> void
- set_up_quota_nnmake_style(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style() –> void
- set_up_ss_abego_quota(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota() –> void
- set_vall(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, vall_chunks: protocols::frag_picker::VallProvider) None ¶
sets vall data
C++: protocols::frag_picker::FragmentPicker::set_vall(class std::shared_ptr<class protocols::frag_picker::VallProvider>) –> void
- show_scoring_methods(*args, **kwargs)¶
Overloaded function.
show_scoring_methods(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, out: pyrosetta.rosetta.std.ostream) -> None
show_scoring_methods(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, out: pyrosetta.rosetta.std.ostream, index: int) -> None
C++: protocols::frag_picker::FragmentPicker::show_scoring_methods(std::ostream &, unsigned long) –> void
- size_of_query(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) int ¶
C++: protocols::frag_picker::FragmentPicker::size_of_query() –> unsigned long
- total_score(*args, **kwargs)¶
Overloaded function.
total_score(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, f: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap) -> float
total_score(self: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker, f: pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap, index: int) -> float
- Calculates total score for a given vector of small scores
(FragmentScoreMap object pointer)
FragmentScoreManager that is stored inside the picker is used for this calculation. It particular it provides weights
C++: protocols::frag_picker::FragmentPicker::total_score(class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap>, unsigned long) –> double
- class pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter¶
Bases:
Filter
–brief–
- apply(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
returns true if the structure passes the filter, false otherwise
C++: protocols::frag_picker::FragmentScoreFilter::apply(const class core::pose::Pose &) const –> bool
- static class_name() str ¶
C++: protocols::frag_picker::FragmentScoreFilter::class_name() –> std::string
- clear(self: pyrosetta.rosetta.protocols.filters.Filter) None ¶
used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual
C++: protocols::filters::Filter::clear() –> void
- clone(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
required in the context of the parser/scripting scheme
C++: protocols::frag_picker::FragmentScoreFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- compute(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::frag_picker::FragmentScoreFilter::compute(const class core::pose::Pose) const –> double
- fresh_instance(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
required in the context of the parser/scripting scheme
C++: protocols::frag_picker::FragmentScoreFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>
- get_result(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, : pyrosetta.rosetta.utility.vector1_double) float ¶
C++: protocols::frag_picker::FragmentScoreFilter::get_result(class utility::vector1<double, class std::allocator<double> >) const –> double
- get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_type() const –> std::string
- get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str ¶
C++: protocols::filters::Filter::get_user_defined_name() const –> std::string
- name(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter) str ¶
C++: protocols::frag_picker::FragmentScoreFilter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Filter in Rosetta Scripts)
C++: protocols::frag_picker::FragmentScoreFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.
C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::frag_picker::FragmentScoreFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
allows printing data to a stream
C++: protocols::frag_picker::FragmentScoreFilter::report(std::ostream &, const class core::pose::Pose &) const –> void
- report_sm(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
required for reporting score values
C++: protocols::frag_picker::FragmentScoreFilter::report_sm(const class core::pose::Pose &) const –> double
- rescore_fragment_crmsd(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose, candidates: pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, fc: protocols::frag_picker::scores::FragmentCrmsd) None ¶
C++: protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd(const class std::shared_ptr<class core::pose::Pose>, 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 protocols::frag_picker::scores::FragmentCrmsd *) const –> void
- score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double
- set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None ¶
C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void
- setup_fragment_picker(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose, picker: pyrosetta.rosetta.protocols.frag_picker.FragmentPicker) None ¶
C++: protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker(const class std::shared_ptr<class core::pose::Pose>, class std::shared_ptr<class protocols::frag_picker::FragmentPicker>) const –> void
- class pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator¶
Bases:
FilterCreator
- assign(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator, : pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator) pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator ¶
C++: protocols::frag_picker::FragmentScoreFilterCreator::operator=(const class protocols::frag_picker::FragmentScoreFilterCreator &) –> class protocols::frag_picker::FragmentScoreFilterCreator &
- create_filter(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::frag_picker::FragmentScoreFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- keyname(self: pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator) str ¶
C++: protocols::frag_picker::FragmentScoreFilterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule¶
Bases:
pybind11_object
selects a given number of fragments just by selecting the best ones
- assign(self: pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule, : pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule) pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule ¶
C++: protocols::frag_picker::FragmentSelectingRule::operator=(const class protocols::frag_picker::FragmentSelectingRule &) –> class protocols::frag_picker::FragmentSelectingRule &
- 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.FragmentSelectingRule, : pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t, : 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::FragmentSelectingRule::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.GrabAllCollector¶
Bases:
CandidatesCollector
Keeps all fragments candidates for the final selection
The purpose of a collector is to keep fragment candidates to the end of vall processing. This simple implementation keeps all candidates which might use huge memory
- add(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector, new_canditate: 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::GrabAllCollector::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.GrabAllCollector, : pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector) pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector ¶
C++: protocols::frag_picker::GrabAllCollector::operator=(const class protocols::frag_picker::GrabAllCollector &) –> class protocols::frag_picker::GrabAllCollector &
- clear(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector) None ¶
C++: protocols::frag_picker::GrabAllCollector::clear() –> void
- count_candidates(*args, **kwargs)¶
Overloaded function.
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector, seq_pos: int) -> int
Check how many candidates have been already collected for a given position
C++: protocols::frag_picker::GrabAllCollector::count_candidates(unsigned long) const –> unsigned long
count_candidates(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector) -> int
Check how many candidates have been already collected for all positions
C++: protocols::frag_picker::GrabAllCollector::count_candidates() const –> unsigned long
- get_candidates(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector, 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 ¶
returns all stored fragment candidates that begins at a given position in a query
C++: protocols::frag_picker::GrabAllCollector::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> > > > &
- insert(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector, pos: int, collector: pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector) None ¶
Inserts candidates from another Collector for a give position in the query
C++: protocols::frag_picker::GrabAllCollector::insert(unsigned long, class std::shared_ptr<class protocols::frag_picker::CandidatesCollector>) –> void
- print_report(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector, output: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager) None ¶
prints how many fragments have been collected for each position
C++: protocols::frag_picker::GrabAllCollector::print_report(std::ostream &, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreManager>) const –> void
- query_length(self: pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector) int ¶
- Check the size of query sequence that this object knows.
This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery.
C++: protocols::frag_picker::GrabAllCollector::query_length() const –> unsigned long
- class pyrosetta.rosetta.protocols.frag_picker.JCouplingIO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.JCouplingIO, : pyrosetta.rosetta.protocols.frag_picker.JCouplingIO) pyrosetta.rosetta.protocols.frag_picker.JCouplingIO ¶
C++: protocols::frag_picker::JCouplingIO::operator=(const class protocols::frag_picker::JCouplingIO &) –> class protocols::frag_picker::JCouplingIO &
- get_data(self: pyrosetta.rosetta.protocols.frag_picker.JCouplingIO, res_num: int, has_data: bool) Tuple[float, float] ¶
C++: protocols::frag_picker::JCouplingIO::get_data(const unsigned long, bool &) –> struct std::pair<double, double>
- get_length(self: pyrosetta.rosetta.protocols.frag_picker.JCouplingIO) int ¶
C++: protocols::frag_picker::JCouplingIO::get_length() –> unsigned long
- get_parameters(self: pyrosetta.rosetta.protocols.frag_picker.JCouplingIO) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::frag_picker::JCouplingIO::get_parameters() –> class utility::vector1<double, class std::allocator<double> >
- class pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO, : pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO) pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO ¶
C++: protocols::frag_picker::LAMBEGO_IO::operator=(const class protocols::frag_picker::LAMBEGO_IO &) –> class protocols::frag_picker::LAMBEGO_IO &
- matrix(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t ¶
C++: protocols::frag_picker::LAMBEGO_IO::matrix() const –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &
- nrows(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO) int ¶
C++: protocols::frag_picker::LAMBEGO_IO::nrows() const –> unsigned long
- prof_row(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO, idx: int) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::frag_picker::LAMBEGO_IO::prof_row(const unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &
- read(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO, input: pyrosetta.rosetta.std.istream) None ¶
C++: protocols::frag_picker::LAMBEGO_IO::read(std::istream &) –> void
- write(self: pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO, output: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::frag_picker::LAMBEGO_IO::write(std::ostream &) –> void
Bases:
pybind11_object
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::operator=(const class protocols::frag_picker::LazySortedVector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class protocols::frag_picker::CompareByScoreCombination> &) –> class protocols::frag_picker::LazySortedVector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class protocols::frag_picker::CompareByScoreCombination> &
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::clear() –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::count_inserted() const –> unsigned long
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::expose_data() –> 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> > > > &
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::peek_back() const –> struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::peek_front() const –> struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::push(const struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > &) –> bool
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::resize(unsigned long, unsigned long) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::set_boundary(unsigned long) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::set_worst(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::size() const –> unsigned long
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareByScoreCombination>::top() –> const struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > &
Bases:
pybind11_object
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::operator=(const class protocols::frag_picker::LazySortedVector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class protocols::frag_picker::CompareTotalScore> &) –> class protocols::frag_picker::LazySortedVector1<struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >, class protocols::frag_picker::CompareTotalScore> &
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::clear() –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::count_inserted() const –> unsigned long
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::expose_data() –> 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> > > > &
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::peek_back() const –> struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::peek_front() const –> struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::push(const struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > &) –> bool
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::resize(unsigned long, unsigned long) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::set_boundary(unsigned long) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::set_worst(struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> >) –> void
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::size() const –> unsigned long
C++: protocols::frag_picker::LazySortedVector1<std::pair<std::shared_ptr<protocols::frag_picker::FragmentCandidate>, std::shared_ptr<protocols::frag_picker::scores::FragmentScoreMap> >, protocols::frag_picker::CompareTotalScore>::top() –> const struct std::pair<class std::shared_ptr<class protocols::frag_picker::FragmentCandidate>, class std::shared_ptr<class protocols::frag_picker::scores::FragmentScoreMap> > &
- class pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter¶
Bases:
VallChunkFilter
- add_pdb_id(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, pdb_ids: str) None ¶
Adds a pdb id to the filter.
What that PDB id means it depends on the filter implementation
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_id(std::string) –> void
- add_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, list_of_pdb_ids: pyrosetta.rosetta.utility.vector1_std_string) None ¶
Adds a bunch of pdb ids to the filter
C++: protocols::frag_picker::PdbIdChunkFilter::add_pdb_ids(class utility::vector1<std::string, class std::allocator<std::string > >) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, : pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter) pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter ¶
C++: protocols::frag_picker::PdbIdChunkFilter::operator=(const class protocols::frag_picker::PdbIdChunkFilter &) –> class protocols::frag_picker::PdbIdChunkFilter &
- load_pdb_id_from_file(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, : str) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::load_pdb_id_from_file(std::string) –> void
- show_pdb_ids(self: pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::frag_picker::PdbIdChunkFilter::show_pdb_ids(std::ostream &) –> void
- test_chunk(self: pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) bool ¶
if a chunk seems to be interesting, return true. Otherwise say false
C++: protocols::frag_picker::VallChunkFilter::test_chunk(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
- class pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, : pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO ¶
C++: protocols::frag_picker::PhiPsiTalosIO::operator=(const class protocols::frag_picker::PhiPsiTalosIO &) –> class protocols::frag_picker::PhiPsiTalosIO &
- d_phi(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::d_phi(unsigned long) –> double
- d_psi(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::d_psi(unsigned long) –> double
- dist(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::dist(unsigned long) –> double
- get_first_residue_id(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) int ¶
C++: protocols::frag_picker::PhiPsiTalosIO::get_first_residue_id() const –> unsigned long
- get_last_residue_id(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) int ¶
C++: protocols::frag_picker::PhiPsiTalosIO::get_last_residue_id() const –> unsigned long
- get_sequence(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO) str ¶
C++: protocols::frag_picker::PhiPsiTalosIO::get_sequence() const –> const std::string &
- has_entry(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, residue_id: int) bool ¶
C++: protocols::frag_picker::PhiPsiTalosIO::has_entry(unsigned long) const –> bool
- phi(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::phi(unsigned long) –> double
- psi(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::psi(unsigned long) –> double
- quality(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) str ¶
C++: protocols::frag_picker::PhiPsiTalosIO::quality(unsigned long) –> std::string
- read(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, : str) None ¶
C++: protocols::frag_picker::PhiPsiTalosIO::read(const std::string &) –> void
- s2(self: pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO, res_id: int) float ¶
C++: protocols::frag_picker::PhiPsiTalosIO::s2(unsigned long) –> double
- class pyrosetta.rosetta.protocols.frag_picker.QuotaDebug¶
Bases:
ostringstream
- _M_write(self: pyrosetta.rosetta.std.ostringstream, __s: str, __n: int) None ¶
C++: std::basic_ostream<char, std::char_traits<char> >::_M_write(const char *, long) –> void
- bytes(self: pyrosetta.rosetta.std.ostringstream) bytes ¶
- flush(self: pyrosetta.rosetta.std.ostringstream) pyrosetta.rosetta.std.ostream ¶
C++: std::basic_ostream<char, std::char_traits<char> >::flush() –> std::ostream &
- log(self: pyrosetta.rosetta.protocols.frag_picker.QuotaDebug, : int, : int, : pyrosetta.rosetta.utility.vector1_double) None ¶
C++: protocols::frag_picker::QuotaDebug::log(unsigned long, unsigned long, class utility::vector1<double, class std::allocator<double> >) –> void
- max_pools(self: pyrosetta.rosetta.protocols.frag_picker.QuotaDebug) int ¶
C++: protocols::frag_picker::QuotaDebug::max_pools() –> unsigned long
- property nFrags_¶
- put(self: pyrosetta.rosetta.std.ostringstream, __c: str) pyrosetta.rosetta.std.ostream ¶
C++: std::basic_ostream<char, std::char_traits<char> >::put(char) –> std::ostream &
- rdbuf(self: pyrosetta.rosetta.std.ostringstream) pyrosetta.rosetta.std.stringbuf ¶
C++: std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::rdbuf() const –> class std::basic_stringbuf<char> *
- seekp(*args, **kwargs)¶
Overloaded function.
seekp(self: pyrosetta.rosetta.std.ostringstream, : pyrosetta.rosetta.std.fpos___mbstate_t_t) -> pyrosetta.rosetta.std.ostream
C++: std::basic_ostream<char, std::char_traits<char> >::seekp(class std::fpos<__mbstate_t>) –> std::ostream &
seekp(self: pyrosetta.rosetta.std.ostringstream, : int, : std::_Ios_Seekdir) -> pyrosetta.rosetta.std.ostream
C++: std::basic_ostream<char, std::char_traits<char> >::seekp(long, enum std::_Ios_Seekdir) –> std::ostream &
- class sentry¶
Bases:
pybind11_object
- setup_summary(self: pyrosetta.rosetta.protocols.frag_picker.QuotaDebug, collector_: protocols::frag_picker::quota::QuotaCollector) None ¶
C++: protocols::frag_picker::QuotaDebug::setup_summary(const class protocols::frag_picker::quota::QuotaCollector &) –> void
- str(*args, **kwargs)¶
Overloaded function.
str(self: pyrosetta.rosetta.std.ostringstream) -> str
C++: std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::str() const –> std::string
str(self: pyrosetta.rosetta.std.ostringstream, __s: str) -> None
C++: std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::str(const std::string &) –> void
- property tag_map_¶
- property tags_¶
- tellp(self: pyrosetta.rosetta.std.ostringstream) pyrosetta.rosetta.std.fpos___mbstate_t_t ¶
C++: std::basic_ostream<char, std::char_traits<char> >::tellp() –> class std::fpos<__mbstate_t>
- write(self: pyrosetta.rosetta.std.ostringstream, __s: str, __n: int) pyrosetta.rosetta.std.ostream ¶
C++: std::basic_ostream<char, std::char_traits<char> >::write(const char *, long) –> std::ostream &
- write_summary(self: pyrosetta.rosetta.protocols.frag_picker.QuotaDebug) None ¶
C++: protocols::frag_picker::QuotaDebug::write_summary() –> void
- class pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff¶
Bases:
pybind11_object
defines sidechain contact distance cutoffs.
provides amino acid pair specific distance cutoffs.
- assign(self: pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff, : pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff) pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff ¶
C++: protocols::frag_picker::SidechainContactDistCutoff::operator=(const class protocols::frag_picker::SidechainContactDistCutoff &) –> class protocols::frag_picker::SidechainContactDistCutoff &
- get_cutoff(self: pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff, aa_i: str, aa_j: str) float ¶
C++: protocols::frag_picker::SidechainContactDistCutoff::get_cutoff(char, char) –> double
- get_cutoff_squared(self: pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff, aa_i: str, aa_j: str) float ¶
C++: protocols::frag_picker::SidechainContactDistCutoff::get_cutoff_squared(char, char) –> double
- scale_factor(self: pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff) float ¶
C++: protocols::frag_picker::SidechainContactDistCutoff::scale_factor() –> double
- class pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO, : pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO) pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO ¶
C++: protocols::frag_picker::TorsionBinIO::operator=(const class protocols::frag_picker::TorsionBinIO &) –> class protocols::frag_picker::TorsionBinIO &
- matrix(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t ¶
C++: protocols::frag_picker::TorsionBinIO::matrix() const –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &
- nrows(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO) int ¶
C++: protocols::frag_picker::TorsionBinIO::nrows() const –> unsigned long
- prof_row(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO, idx: int) pyrosetta.rosetta.utility.vector1_double ¶
C++: protocols::frag_picker::TorsionBinIO::prof_row(const unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &
- read(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO, input: pyrosetta.rosetta.std.istream) None ¶
C++: protocols::frag_picker::TorsionBinIO::read(std::istream &) –> void
- write(self: pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO, output: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::frag_picker::TorsionBinIO::write(std::ostream &) –> void
- class pyrosetta.rosetta.protocols.frag_picker.VallChunk¶
Bases:
pybind11_object
represents a chunk of residues extracted from a vall.
VallChunk contains a vector of VallResidue objects and provides a basic ways to access them
- assign(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.protocols.frag_picker.VallChunk ¶
C++: protocols::frag_picker::VallChunk::operator=(const class protocols::frag_picker::VallChunk &) –> class protocols::frag_picker::VallChunk &
- at(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk, index: int) pyrosetta.rosetta.protocols.frag_picker.VallResidue ¶
returns i-th residue form this chunk. The first residue has index 1
C++: protocols::frag_picker::VallChunk::at(unsigned long) const –> class std::shared_ptr<class protocols::frag_picker::VallResidue>
- chunk_key(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) str ¶
returns a string that is unique for each chunk in vall
C++: protocols::frag_picker::VallChunk::chunk_key() –> std::string &
- get_chain_id(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) str ¶
returns protein chain ID
C++: protocols::frag_picker::VallChunk::get_chain_id() const –> char
- get_pdb_id(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) str ¶
returns a PDB id (a string of four letters, e.g. “4mba”)
C++: protocols::frag_picker::VallChunk::get_pdb_id() const –> std::string
- get_pose(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.core.pose.Pose ¶
returns a pose created for this chunk
the pose object is created when this function is called for the first time and then cached within a VallProvider object Every time this method is called for a new chunk, VallProvider caches new data
C++: protocols::frag_picker::VallChunk::get_pose() –> class std::shared_ptr<class core::pose::Pose>
- get_profile(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.core.sequence.SequenceProfile ¶
returns amino acid profile of this chunk
the profile object is created when this function is called for the first time and then cached within a VallProvider object. Every time this method is called for a new chunk, VallProvider caches new data
C++: protocols::frag_picker::VallChunk::get_profile() –> class std::shared_ptr<class core::sequence::SequenceProfile>
- get_self_ptr(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.protocols.frag_picker.VallChunk ¶
C++: protocols::frag_picker::VallChunk::get_self_ptr() –> class std::shared_ptr<class protocols::frag_picker::VallChunk>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_VallChunk_t ¶
C++: protocols::frag_picker::VallChunk::get_self_weak_ptr() –> class std::weak_ptr<class protocols::frag_picker::VallChunk>
- get_sequence(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) str ¶
returns amino acid sequence of this chunk
C++: protocols::frag_picker::VallChunk::get_sequence() –> std::string &
- get_vall_filename(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) str ¶
returns the Vall file used for this chunk
C++: protocols::frag_picker::VallChunk::get_vall_filename() –> std::string
- get_vall_provider(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) protocols::frag_picker::VallProvider ¶
returns the Vall Provider
C++: protocols::frag_picker::VallChunk::get_vall_provider() –> class std::shared_ptr<class protocols::frag_picker::VallProvider>
- key(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) int ¶
returns integer key of this chunk, which is the key of this chunk’s first residue
C++: protocols::frag_picker::VallChunk::key() const –> unsigned long
- push_back(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk, what: pyrosetta.rosetta.protocols.frag_picker.VallResidue) None ¶
appends a residue to this chunk
C++: protocols::frag_picker::VallChunk::push_back(class std::shared_ptr<class protocols::frag_picker::VallResidue>) –> void
- size(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) int ¶
returns the size of this chunk i.e. the number of residues stored in there
C++: protocols::frag_picker::VallChunk::size() const –> unsigned long
- vall_key(*args, **kwargs)¶
Overloaded function.
vall_key(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk) -> int
C++: protocols::frag_picker::VallChunk::vall_key() const –> unsigned long
vall_key(self: pyrosetta.rosetta.protocols.frag_picker.VallChunk, key: int) -> None
C++: protocols::frag_picker::VallChunk::vall_key(unsigned long) –> void
- class pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter¶
Bases:
pybind11_object
a base class for a chunk filtering mechanism
Chunk filtering is used to screen chunks before any fragment is evaluated Therefore it is the fastest way to excluded unwanted proteins
AllowPdbIdFilter and DenyPdbIdFilter for implementations
- assign(self: pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter, : pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter) pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter ¶
C++: protocols::frag_picker::VallChunkFilter::operator=(const class protocols::frag_picker::VallChunkFilter &) –> class protocols::frag_picker::VallChunkFilter &
- test_chunk(self: pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter, : pyrosetta.rosetta.protocols.frag_picker.VallChunk) bool ¶
if a chunk seems to be interesting, return true. Otherwise say false
C++: protocols::frag_picker::VallChunkFilter::test_chunk(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> bool
- class pyrosetta.rosetta.protocols.frag_picker.VallProvider¶
Bases:
pybind11_object
a vector of vall chunks
- assign(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, : pyrosetta.rosetta.protocols.frag_picker.VallProvider) pyrosetta.rosetta.protocols.frag_picker.VallProvider ¶
C++: protocols::frag_picker::VallProvider::operator=(const class protocols::frag_picker::VallProvider &) –> class protocols::frag_picker::VallProvider &
- at(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, index: int) pyrosetta.rosetta.protocols.frag_picker.VallChunk ¶
returns a certain chunk (starts from 1)
C++: protocols::frag_picker::VallProvider::at(unsigned long) –> class std::shared_ptr<class protocols::frag_picker::VallChunk>
- cache_pose(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, source_chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.core.pose.Pose ¶
cache a pose for a given chunk
C++: protocols::frag_picker::VallProvider::cache_pose(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> class std::shared_ptr<class core::pose::Pose>
- cache_profile(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, source_chunk: pyrosetta.rosetta.protocols.frag_picker.VallChunk) pyrosetta.rosetta.core.sequence.SequenceProfile ¶
cache a sequence profile for a given chunk
C++: protocols::frag_picker::VallProvider::cache_profile(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> class std::shared_ptr<class core::sequence::SequenceProfile>
- find_chunk(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, : str, : str, : int) pyrosetta.rosetta.protocols.frag_picker.VallChunk ¶
- tries to find a chunk defined by PDB id, chain id and a residue
sequence id
If this VallProvider does not contain a desired chunk, 0 is returned.
C++: protocols::frag_picker::VallProvider::find_chunk(std::string, char, unsigned long) –> class std::shared_ptr<class protocols::frag_picker::VallChunk>
- get_largest_chunk_size(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider) int ¶
- says what is the length of the largest chunk known to this
provider
C++: protocols::frag_picker::VallProvider::get_largest_chunk_size() –> unsigned long
- get_self_ptr(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider) pyrosetta.rosetta.protocols.frag_picker.VallProvider ¶
C++: protocols::frag_picker::VallProvider::get_self_ptr() –> class std::shared_ptr<class protocols::frag_picker::VallProvider>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider) pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_VallProvider_t ¶
C++: protocols::frag_picker::VallProvider::get_self_weak_ptr() –> class std::weak_ptr<class protocols::frag_picker::VallProvider>
- get_vall_by_key(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, index: int) str ¶
C++: protocols::frag_picker::VallProvider::get_vall_by_key(unsigned long) –> std::string
- get_vall_count(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider) int ¶
C++: protocols::frag_picker::VallProvider::get_vall_count() –> unsigned long
- get_vall_end_line_by_key(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, index: int) int ¶
C++: protocols::frag_picker::VallProvider::get_vall_end_line_by_key(unsigned long) –> unsigned long
- get_vall_last_residue_key_by_key(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, index: int) int ¶
C++: protocols::frag_picker::VallProvider::get_vall_last_residue_key_by_key(unsigned long) –> unsigned long
- get_vall_start_line_by_key(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, index: int) int ¶
C++: protocols::frag_picker::VallProvider::get_vall_start_line_by_key(unsigned long) –> unsigned long
- push_back(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, what: pyrosetta.rosetta.protocols.frag_picker.VallChunk) None ¶
adds a new chunk to this provider
C++: protocols::frag_picker::VallProvider::push_back(class std::shared_ptr<class protocols::frag_picker::VallChunk>) –> void
- size(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider) int ¶
says how many chunks do we have
C++: protocols::frag_picker::VallProvider::size() –> unsigned long
- vallChunksFromLibraries(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, fns: pyrosetta.rosetta.utility.vector1_std_string) int ¶
C++: protocols::frag_picker::VallProvider::vallChunksFromLibraries(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> unsigned long
- vallChunksFromLibrary(*args, **kwargs)¶
Overloaded function.
vallChunksFromLibrary(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, filename: str) -> int
vallChunksFromLibrary(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, filename: str, startline: int) -> int
vallChunksFromLibrary(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, filename: str, startline: int, endline: int) -> int
- Vall reader
THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end.
C++: protocols::frag_picker::VallProvider::vallChunksFromLibrary(const std::string &, unsigned long, unsigned long) –> unsigned long
- vallNumLines(self: pyrosetta.rosetta.protocols.frag_picker.VallProvider, filename: str) int ¶
Runs through the Vall and stores number of lines
C++: protocols::frag_picker::VallProvider::vallNumLines(const std::string &) –> unsigned long
- class pyrosetta.rosetta.protocols.frag_picker.VallResidue¶
Bases:
pybind11_object
class for managing a line of the Vall fragment library
- aa(*args, **kwargs)¶
Overloaded function.
aa(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> str
one letter amino acid code
C++: protocols::frag_picker::VallResidue::aa() const –> char
aa(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, c: str) -> None
one letter amino acid code
C++: protocols::frag_picker::VallResidue::aa(const char) –> void
- assign(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, rval: pyrosetta.rosetta.protocols.frag_picker.VallResidue) pyrosetta.rosetta.protocols.frag_picker.VallResidue ¶
copy assignment
C++: protocols::frag_picker::VallResidue::operator=(const class protocols::frag_picker::VallResidue &) –> class protocols::frag_picker::VallResidue &
- bF(*args, **kwargs)¶
Overloaded function.
bF(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
b factor average for backbone
C++: protocols::frag_picker::VallResidue::bF() const –> double
bF(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
b factor average for backbone
C++: protocols::frag_picker::VallResidue::bF(const double) –> void
- bbtorsion_srfd(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) pyrosetta.rosetta.core.fragment.BBTorsionSRFD ¶
build a BBTorsionSRFD from this page
C++: protocols::frag_picker::VallResidue::bbtorsion_srfd() const –> class std::shared_ptr<class core::fragment::BBTorsionSRFD>
- cbx(*args, **kwargs)¶
Overloaded function.
cbx(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
x-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cbx() const –> double
cbx(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
x-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cbx(const double) –> void
- cby(*args, **kwargs)¶
Overloaded function.
cby(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
y-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cby() const –> double
cby(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
y-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cby(const double) –> void
- cbz(*args, **kwargs)¶
Overloaded function.
cbz(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
z-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cbz() const –> double
cbz(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
z-coordinate of C-beta
C++: protocols::frag_picker::VallResidue::cbz(const double) –> void
- cenx(*args, **kwargs)¶
Overloaded function.
cenx(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
x-coordinate of centroid
C++: protocols::frag_picker::VallResidue::cenx() const –> double
cenx(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
x-coordinate of centroid
C++: protocols::frag_picker::VallResidue::cenx(const double) –> void
- ceny(*args, **kwargs)¶
Overloaded function.
ceny(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
y-coordinate of centroid
C++: protocols::frag_picker::VallResidue::ceny() const –> double
ceny(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
y-coordinate of centroid
C++: protocols::frag_picker::VallResidue::ceny(const double) –> void
- cenz(*args, **kwargs)¶
Overloaded function.
cenz(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
z-coordinate of centroid
C++: protocols::frag_picker::VallResidue::cenz() const –> double
cenz(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
z-coordinate of centroid
C++: protocols::frag_picker::VallResidue::cenz(const double) –> void
- depth(*args, **kwargs)¶
Overloaded function.
depth(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
all-atom residue depth
C++: protocols::frag_picker::VallResidue::depth() const –> double
depth(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, depth: float) -> None
all-atom residue depth
C++: protocols::frag_picker::VallResidue::depth(const double) –> void
- distance_squared(*args, **kwargs)¶
Overloaded function.
distance_squared(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, r: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
C++: protocols::frag_picker::VallResidue::distance_squared(class std::shared_ptr<const class protocols::frag_picker::VallResidue>) –> double
distance_squared(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, r: pyrosetta.rosetta.protocols.frag_picker.VallResidue, type: pyrosetta.rosetta.protocols.frag_picker.ContactType) -> float
C++: protocols::frag_picker::VallResidue::distance_squared(class std::shared_ptr<const class protocols::frag_picker::VallResidue>, const enum protocols::frag_picker::ContactType &) –> double
- distance_squared_cb(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, r: pyrosetta.rosetta.protocols.frag_picker.VallResidue) float ¶
C++: protocols::frag_picker::VallResidue::distance_squared_cb(class std::shared_ptr<const class protocols::frag_picker::VallResidue>) –> double
- distance_squared_cen(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, r: pyrosetta.rosetta.protocols.frag_picker.VallResidue) float ¶
C++: protocols::frag_picker::VallResidue::distance_squared_cen(class std::shared_ptr<const class protocols::frag_picker::VallResidue>) –> double
- dssp_phi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) float ¶
phi backbone torsion in degrees from DSSP
C++: protocols::frag_picker::VallResidue::dssp_phi() const –> double
- dssp_psi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) float ¶
psi backbone torsion in degrees from DSSP
C++: protocols::frag_picker::VallResidue::dssp_psi() const –> double
- fill_from_string(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, line: str) None ¶
fill internal data from string
C++: protocols::frag_picker::VallResidue::fill_from_string(const std::string &) –> void
- fill_from_string_cs(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, line: str) None ¶
fill internal data from string
C++: protocols::frag_picker::VallResidue::fill_from_string_cs(const std::string &) –> void
- fill_from_string_residue_depth_version1(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, line: str) None ¶
C++: protocols::frag_picker::VallResidue::fill_from_string_residue_depth_version1(const std::string &) –> void
- fill_from_string_version1(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, line: str) None ¶
fill internal data from string
C++: protocols::frag_picker::VallResidue::fill_from_string_version1(const std::string &) –> void
- has_chemical_shifts(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) bool ¶
C++: protocols::frag_picker::VallResidue::has_chemical_shifts() const –> bool
- has_profile(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) bool ¶
has profile info?
C++: protocols::frag_picker::VallResidue::has_profile() const –> bool
- has_profile_struct(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) bool ¶
has structure profile info?
C++: protocols::frag_picker::VallResidue::has_profile_struct() const –> bool
- id(*args, **kwargs)¶
Overloaded function.
id(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> str
id of fragment source (e.g. pdb name)
C++: protocols::frag_picker::VallResidue::id() const –> const std::string &
id(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, s: str) -> None
id of fragment source (e.g. pdb name)
C++: protocols::frag_picker::VallResidue::id(const std::string &) –> void
- key(*args, **kwargs)¶
Overloaded function.
key(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, key: int) -> None
sets the key id
C++: protocols::frag_picker::VallResidue::key(unsigned long) –> void
key(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> int
sets the key id
C++: protocols::frag_picker::VallResidue::key() –> unsigned long
- nali(*args, **kwargs)¶
Overloaded function.
nali(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> int
number of alignments
C++: protocols::frag_picker::VallResidue::nali() const –> unsigned long
nali(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: int) -> None
number of alignments
C++: protocols::frag_picker::VallResidue::nali(const unsigned long) –> void
- omega(*args, **kwargs)¶
Overloaded function.
omega(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
omega backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::omega() const –> double
omega(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
omega backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::omega(const double) –> void
- phi(*args, **kwargs)¶
Overloaded function.
phi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
phi backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::phi() const –> double
phi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
phi backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::phi(const double) –> void
- profile(*args, **kwargs)¶
Overloaded function.
profile(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> pyrosetta.rosetta.utility.vector1_double
per amino acid profile data
C++: protocols::frag_picker::VallResidue::profile() const –> const class utility::vector1<double, class std::allocator<double> > &
profile(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, v: pyrosetta.rosetta.utility.vector1_double) -> None
per amino acid profile data
C++: protocols::frag_picker::VallResidue::profile(const class utility::vector1<double, class std::allocator<double> > &) –> void
- profile_struct(*args, **kwargs)¶
Overloaded function.
profile_struct(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> pyrosetta.rosetta.utility.vector1_double
per amino acid structure profile data
C++: protocols::frag_picker::VallResidue::profile_struct() const –> const class utility::vector1<double, class std::allocator<double> > &
profile_struct(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, v: pyrosetta.rosetta.utility.vector1_double) -> None
per amino acid structure profile data
C++: protocols::frag_picker::VallResidue::profile_struct(const class utility::vector1<double, class std::allocator<double> > &) –> void
- psi(*args, **kwargs)¶
Overloaded function.
psi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
psi backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::psi() const –> double
psi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
psi backbone torsion in degrees
C++: protocols::frag_picker::VallResidue::psi(const double) –> void
- resi(*args, **kwargs)¶
Overloaded function.
resi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> int
residue sequence number in source
C++: protocols::frag_picker::VallResidue::resi() const –> unsigned long
resi(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, i: int) -> None
residue sequence number in source
C++: protocols::frag_picker::VallResidue::resi(const unsigned long) –> void
- sa(*args, **kwargs)¶
Overloaded function.
sa(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
solvent accessible area
C++: protocols::frag_picker::VallResidue::sa() const –> double
sa(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
solvent accessible area
C++: protocols::frag_picker::VallResidue::sa(const double) –> void
- sa_norm(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) float ¶
solvent accessible area normalized
C++: protocols::frag_picker::VallResidue::sa_norm() const –> double
- secondary_shifts(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) pyrosetta.rosetta.utility.vector1_double ¶
secondary chemical shifts
C++: protocols::frag_picker::VallResidue::secondary_shifts() –> const class utility::vector1<double, class std::allocator<double> > &
- set_ss_from_str(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) None ¶
C++: protocols::frag_picker::VallResidue::set_ss_from_str() –> void
- ss(*args, **kwargs)¶
Overloaded function.
ss(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> str
one letter secondary structure code
C++: protocols::frag_picker::VallResidue::ss() const –> char
ss(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, c: str) -> None
one letter secondary structure code
C++: protocols::frag_picker::VallResidue::ss(const char) –> void
- ss_str(*args, **kwargs)¶
Overloaded function.
ss_str(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> str
one letter secondary structure STR code
C++: protocols::frag_picker::VallResidue::ss_str() const –> char
ss_str(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, c: str) -> None
one letter secondary structure STR code
C++: protocols::frag_picker::VallResidue::ss_str(const char) –> void
- x(*args, **kwargs)¶
Overloaded function.
x(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
x-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::x() const –> double
x(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
x-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::x(const double) –> void
- y(*args, **kwargs)¶
Overloaded function.
y(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
y-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::y() const –> double
y(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
y-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::y(const double) –> void
- z(*args, **kwargs)¶
Overloaded function.
z(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue) -> float
z-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::z() const –> double
z(self: pyrosetta.rosetta.protocols.frag_picker.VallResidue, val: float) -> None
z-coordinate of C-alpha
C++: protocols::frag_picker::VallResidue::z(const double) –> void
- pyrosetta.rosetta.protocols.frag_picker.contact_name(type: pyrosetta.rosetta.protocols.frag_picker.ContactType) str ¶
give an enum type and return the string name
C++: protocols::frag_picker::contact_name(enum protocols::frag_picker::ContactType) –> std::string
- pyrosetta.rosetta.protocols.frag_picker.contact_type(name: str) pyrosetta.rosetta.protocols.frag_picker.ContactType ¶
give a string name and return its enum type
C++: protocols::frag_picker::contact_type(const std::string &) –> enum protocols::frag_picker::ContactType
- pyrosetta.rosetta.protocols.frag_picker.convert_binary_checkpoint(check_filename: str) None ¶
C++: protocols::frag_picker::convert_binary_checkpoint(const std::string &) –> void
- pyrosetta.rosetta.protocols.frag_picker.run_command(command: str) None ¶
C++: protocols::frag_picker::run_command(const std::string &) –> void
- pyrosetta.rosetta.protocols.frag_picker.sa_faraggi_max(aa: str) float ¶
C++: protocols::frag_picker::sa_faraggi_max(char) –> double