peptide_deriver¶

Bindings for protocols::peptide_deriver namespace

class pyrosetta.rosetta.protocols.peptide_deriver.CyclizationMethod¶

Bases: pybind11_object

Members:

CYCLIZATION_METHOD_DISULFIDE

CYCLIZATION_METHOD_END_TO_END

NUM_CYCLIZATION_METHODS

CYCLIZATION_METHOD_DISULFIDE = <CyclizationMethod.CYCLIZATION_METHOD_DISULFIDE: 0>¶

CYCLIZATION_METHOD_END_TO_END = <CyclizationMethod.CYCLIZATION_METHOD_END_TO_END: 1>¶

NUM_CYCLIZATION_METHODS = <CyclizationMethod.NUM_CYCLIZATION_METHODS: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo, : pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo) → pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo¶: C++: protocols::peptide_deriver::CyclizedPeptideInfo::operator=(const class protocols::peptide_deriver::CyclizedPeptideInfo &) –> class protocols::peptide_deriver::CyclizedPeptideInfo &

property cyc_comment¶

property cyc_isc¶

property cyc_pose¶

property is_cyclizable¶

property pre_cyc_pose¶

property was_cyclic_model_created¶

class pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry¶

Bases: pybind11_object

property lin_isc¶

property lin_pose¶

property pep_start¶

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter¶

Bases: PeptideDeriverOutputter

outputs a Peptiderive report to a stream in a basic, easily parsable format

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::operator=(const class protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter &) –> class protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter &

avoid_negative_zero(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, value: float, threshold: float) → float¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(const double, const double) –> double

begin_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, receptor_chain_letter: str, partner_chain_letter: str, total_isc: float, options_string: str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::begin_receptor_partner_pair(const char, const char, const double, const std::string &) –> void

begin_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, : pyrosetta.rosetta.core.pose.Pose, : str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::begin_structure(const class core::pose::Pose &, const std::string &) –> void

chain_pair_pose_prepared(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::chain_pair_pose_prepared(const class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::clone() const –> class std::shared_ptr<class protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter>

end_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::end_receptor_partner_pair() –> void

end_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::end_structure() –> void

peptide_entry(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, entry_type: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, total_isc: float, entry: pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_entry(enum protocols::peptide_deriver::PeptideDeriverEntryType, const double, class std::shared_ptr<const class protocols::peptide_deriver::DerivedPeptideEntry>) –> void

peptide_length(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, pep_length: int) → None¶: C++: protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_length(const unsigned long) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType¶

Bases: pybind11_object

an enum specifying whether the peptide entry encountered during the: sliding window run in known to be the “best” peptide, when calling PeptideDeriverOuputter::peptide_entry()

Members:

ET_GENERAL

ET_BEST_LINEAR

ET_BEST_CYCLIC

ET_BEST_CYCLIC = <PeptideDeriverEntryType.ET_BEST_CYCLIC: 2>¶

ET_BEST_LINEAR = <PeptideDeriverEntryType.ET_BEST_LINEAR: 1>¶

ET_GENERAL = <PeptideDeriverEntryType.ET_GENERAL: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter¶

Bases: Filter

implementation of the Peptiderive protocol - given a pose, it: evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides.

Data is either output to a log (using report()) or passed to the given PeptideDeriverOutputter (using derive_peptide()).

When calling report(), the output format is determined by a list of flags: - is_dump_peptide_pose - is_dump_cyclic_poses - is_dump_prepared_pose - is_dump_report_file - is_report_gzip See each flag’s documentation for their effect. These flags are settable via command-line or RosettaScripts options, and may also be set programmatically. These only affect the output coming from report(), since report() uses these to determine which PeptideDeriverOutputter instances it passes to derive_peptide().

When calling derive_peptide(), however, it is up to the consumer to provide the PeptideDeriverOutputter instance of choice. Naturally, it may use any of the subclasses provided in this file: - PeptideDeriverOutputterContainer - PeptideDeriverBasicStreamOutputter - PeptideDeriverMarkdownStreamOutputter - PeptideDeriverPoseOutputter

Note: the PeptideDeriverFilter doesn’t actually filter anything, so it might have been better to suffix it with -Reporter, but wasn’t so not to confuse it with the FeatureReporter class hierarchy.

apply(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::apply(const class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, rhs: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter¶

assignment operator

C++: protocols::peptide_deriver::PeptideDeriverFilter::operator=(const class protocols::peptide_deriver::PeptideDeriverFilter &) –> class protocols::peptide_deriver::PeptideDeriverFilter &

build_receptor_peptide_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, receptor_pose: pyrosetta.rosetta.core.pose.Pose, partner_pose: pyrosetta.rosetta.core.pose.Pose, peptide_start: int, peptide_end: int, jump_id: int) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, unsigned long &) const –> class std::shared_ptr<class core::pose::Pose>

calculate_interface_score(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int) → float¶

Calculate the interface score, i.e. addition to energy: resulting from the complex coming together.

C++: protocols::peptide_deriver::PeptideDeriverFilter::calculate_interface_score(const class core::pose::Pose &, const unsigned long) const –> double

calculate_per_residue_interface_score(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, chain_pair_pose: pyrosetta.rosetta.core.pose.Pose, interface_residues: pyrosetta.rosetta.std.set_unsigned_long_t, report_out: pyrosetta.rosetta.std.ostream, jump_id: int) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, std::ostream &, const unsigned long) const –> void

static class_name() → str¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::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.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

derive_peptide(*args, **kwargs)¶

Overloaded function.

derive_peptide(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: protocols::peptide_deriver::PeptideDeriverOutputter, pose: pyrosetta.rosetta.core.pose.Pose, first_chain_index: int, second_chain_index: int, both_ways: bool) -> None

overload of PeptideDeriverFilter::derive_peptide() which accepts: a many-chain pose and chain indices, rather than single-chain poses.

C++: protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(class protocols::peptide_deriver::PeptideDeriverOutputter &, const class core::pose::Pose &, const unsigned long, const unsigned long, const bool) const –> void

derive_peptide(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: protocols::peptide_deriver::PeptideDeriverOutputter, receptor_pose: pyrosetta.rosetta.core.pose.Pose, partner_pose: pyrosetta.rosetta.core.pose.Pose, total_isc: float) -> None

The core of the filter: calculate and output a table of the: energetic contribution of each linear segment of the pep_chain_pose chain (going through it with a sliding window), together with other interesting data.

C++: protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(class protocols::peptide_deriver::PeptideDeriverOutputter &, const class core::pose::Pose &, const class core::pose::Pose &, const double) const –> void

fresh_instance(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

generate_N2C_cyclic_peptide_protein_complex(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, receptor_peptide_pose: pyrosetta.rosetta.core.pose.Pose, pep_nter_idx: int, pep_cter_idx: int, scorefxn_N2C_minimize: pyrosetta.rosetta.core.scoring.ScoreFunction) → pyrosetta.rosetta.core.pose.Pose¶

Take a given linear peptide-protein complex and return a head-to-tail (N-ter to C-ter) cyclic peptide - receptor complex

C++: protocols::peptide_deriver::PeptideDeriverFilter::generate_N2C_cyclic_peptide_protein_complex(const class std::shared_ptr<class core::pose::Pose>, const unsigned long, const unsigned long, const class std::shared_ptr<class core::scoring::ScoreFunction>) const –> class std::shared_ptr<class core::pose::Pose>

get_is_do_minimize(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_do_minimize() const –> bool

get_is_dump_cyclic_poses(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_cyclic_poses() const –> bool

get_is_dump_peptide_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_peptide_pose() const –> bool

get_is_dump_prepared_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_prepared_pose() const –> bool

get_is_dump_report_file(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_dump_report_file() const –> bool

get_is_report_gzip(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_report_gzip() const –> bool

get_is_skip_zero_isc(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → bool¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_is_skip_zero_isc() const –> bool

get_optimize_cyclic_threshold(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → float¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_optimize_cyclic_threshold() const –> double

get_pep_lengths(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_pep_lengths() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_report_format(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_report_format() const –> enum protocols::peptide_deriver::PeptideDeriverReportFormat

get_restrict_partners_to_chains(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.utility.vector1_char¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_restrict_partners_to_chains() const –> class utility::vector1<char, class std::allocator<char> >

get_restrict_receptors_to_chains(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.utility.vector1_char¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_restrict_receptors_to_chains() const –> class utility::vector1<char, class std::allocator<char> >

get_scorefxn_deriver(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::get_scorefxn_deriver() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.peptide_deriver.PeptideDeriverFilter) → str¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static parse_report_format_string(value: str) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::parse_report_format_string(const std::string &) –> enum protocols::peptide_deriver::PeptideDeriverReportFormat

prepare_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: protocols::peptide_deriver::PeptideDeriverOutputter, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Prepare pose before derivation, by minimizing it and finding disulfides

C++: protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(class protocols::peptide_deriver::PeptideDeriverOutputter &, class core::pose::Pose &) const –> 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::peptide_deriver::PeptideDeriverFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double

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_is_do_minimize(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_do_minimize(const bool) –> void

set_is_dump_cyclic_poses(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_dump_cyclic_poses(const bool) –> void

set_is_dump_peptide_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_dump_peptide_pose(const bool) –> void

set_is_dump_prepared_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_dump_prepared_pose(const bool) –> void

set_is_dump_report_file(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_dump_report_file(const bool) –> void

set_is_report_gzip(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_report_gzip(const bool) –> void

set_is_skip_zero_isc(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: bool) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_is_skip_zero_isc(const bool) –> void

set_optimize_cyclic_threshold(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: float) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_optimize_cyclic_threshold(const double) –> void

set_pep_lengths(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, values: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_pep_lengths(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_report_format(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_report_format(const enum protocols::peptide_deriver::PeptideDeriverReportFormat) –> void

set_restrict_partners_to_chains(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, values: pyrosetta.rosetta.utility.vector1_char) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_restrict_partners_to_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_restrict_receptors_to_chains(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, values: pyrosetta.rosetta.utility.vector1_char) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_restrict_receptors_to_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_scorefxn_deriver(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, value: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilter::set_scorefxn_deriver(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator¶: C++: protocols::peptide_deriver::PeptideDeriverFilterCreator::operator=(const class protocols::peptide_deriver::PeptideDeriverFilterCreator &) –> class protocols::peptide_deriver::PeptideDeriverFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::peptide_deriver::PeptideDeriverFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator) → str¶: C++: protocols::peptide_deriver::PeptideDeriverFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::peptide_deriver::PeptideDeriverFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter¶

Bases: PeptideDeriverOutputter

outputs a Markdown formatted Peptiderive report to a stream

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::operator=(const class protocols::peptide_deriver::PeptideDeriverOutputter &) –> class protocols::peptide_deriver::PeptideDeriverOutputter &

avoid_negative_zero(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, value: float, threshold: float) → float¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(const double, const double) –> double

begin_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, receptor_chain_letter: str, partner_chain_letter: str, total_isc: float, options_string: str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::begin_receptor_partner_pair(const char, const char, const double, const std::string &) –> void

begin_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, pose: pyrosetta.rosetta.core.pose.Pose, : str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::begin_structure(const class core::pose::Pose &, const std::string &) –> void

chain_pair_pose_prepared(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::chain_pair_pose_prepared(const class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::clone() const –> class std::shared_ptr<class protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter>

end_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::end_receptor_partner_pair() –> void

end_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::end_structure() –> void

peptide_entry(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, entry_type: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, total_isc: float, entry: pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::peptide_entry(enum protocols::peptide_deriver::PeptideDeriverEntryType, const double, class std::shared_ptr<const class protocols::peptide_deriver::DerivedPeptideEntry>) –> void

peptide_length(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, pep_length: int) → None¶: C++: protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::peptide_length(const unsigned long) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter¶

Bases: pybind11_object

an abstract base class for handling calculation outputs from: PeptideDeriverFilter

Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class.

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::operator=(const class protocols::peptide_deriver::PeptideDeriverOutputter &) –> class protocols::peptide_deriver::PeptideDeriverOutputter &

avoid_negative_zero(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, value: float, threshold: float) → float¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(const double, const double) –> double

begin_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, receptor_chain_letter: str, partner_chain_letter: str, total_isc: float, options_string: str) → None¶

called by PeptideDeriverFilter when calculation commences on a receptor-partner pair

C++: protocols::peptide_deriver::PeptideDeriverOutputter::begin_receptor_partner_pair(const char, const char, const double, const std::string &) –> void

begin_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, : pyrosetta.rosetta.core.pose.Pose, : str) → None¶

called by PeptideDeriverFilter when processing of a strucuture (possibly multi-chain) starts

C++: protocols::peptide_deriver::PeptideDeriverOutputter::begin_structure(const class core::pose::Pose &, const std::string &) –> void

chain_pair_pose_prepared(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

called by PeptideDeriverFilter when a chain-pair pose is prepared (minimized and disulfide-bridge resolved)

C++: protocols::peptide_deriver::PeptideDeriverOutputter::chain_pair_pose_prepared(const class core::pose::Pose &) –> void

end_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) → None¶

called by PeptideDeriverFilter when calculation concludes for a receptor-partner pair (for all the different peptide lengths)

C++: protocols::peptide_deriver::PeptideDeriverOutputter::end_receptor_partner_pair() –> void

end_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) → None¶

called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends

C++: protocols::peptide_deriver::PeptideDeriverOutputter::end_structure() –> void

peptide_entry(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, entry_type: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, total_isc: float, entry: pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::peptide_entry(enum protocols::peptide_deriver::PeptideDeriverEntryType, const double, class std::shared_ptr<const class protocols::peptide_deriver::DerivedPeptideEntry>) –> void

peptide_length(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, pep_length: int) → None¶

called by PeptideDeriverFilter when calculation commences for: the specified peptide length

this is called for every peptide length specified to PeptideDeriverFilter, per each call to PeptideDeriverOutputter::begin_receptor_partner_pair()

C++: protocols::peptide_deriver::PeptideDeriverOutputter::peptide_length(const unsigned long) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer¶

Bases: PeptideDeriverOutputter

a container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::operator=(const class protocols::peptide_deriver::PeptideDeriverOutputterContainer &) –> class protocols::peptide_deriver::PeptideDeriverOutputterContainer &

avoid_negative_zero(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, value: float, threshold: float) → float¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(const double, const double) –> double

begin_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, receptor_chain_letter: str, partner_chain_letter: str, total_isc: float, options_string: str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::begin_receptor_partner_pair(const char, const char, const double, const std::string &) –> void

begin_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, pose: pyrosetta.rosetta.core.pose.Pose, : str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::begin_structure(const class core::pose::Pose &, const std::string &) –> void

chain_pair_pose_prepared(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::chain_pair_pose_prepared(const class core::pose::Pose &) –> void

clear(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer) → None¶

clear all outputters in the list.

C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::clear() –> void

clone(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::clone() const –> class std::shared_ptr<class protocols::peptide_deriver::PeptideDeriverOutputterContainer>

end_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::end_receptor_partner_pair() –> void

end_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::end_structure() –> void

peptide_entry(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, entry_type: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, total_isc: float, entry: pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::peptide_entry(enum protocols::peptide_deriver::PeptideDeriverEntryType, const double, class std::shared_ptr<const class protocols::peptide_deriver::DerivedPeptideEntry>) –> void

peptide_length(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, pep_length: int) → None¶: C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::peptide_length(const unsigned long) –> void

push_back(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer, item: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) → None¶

add an outputter to the list.

C++: protocols::peptide_deriver::PeptideDeriverOutputterContainer::push_back(const class std::shared_ptr<class protocols::peptide_deriver::PeptideDeriverOutputter>) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter¶

Bases: PeptideDeriverOutputter

outputs poses at different points of the Peptiderive protocol, according to the given set of options

assign(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, : pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::operator=(const class protocols::peptide_deriver::PeptideDeriverPoseOutputter &) –> class protocols::peptide_deriver::PeptideDeriverPoseOutputter &

avoid_negative_zero(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, value: float, threshold: float) → float¶: C++: protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(const double, const double) –> double

begin_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, receptor_chain_letter: str, partner_chain_letter: str, : float, : str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::begin_receptor_partner_pair(const char, const char, const double, const std::string &) –> void

begin_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, : pyrosetta.rosetta.core.pose.Pose, : str) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::begin_structure(const class core::pose::Pose &, const std::string &) –> void

chain_pair_pose_prepared(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::chain_pair_pose_prepared(const class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::clone() const –> class std::shared_ptr<class protocols::peptide_deriver::PeptideDeriverPoseOutputter>

end_receptor_partner_pair(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::end_receptor_partner_pair() –> void

end_structure(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::end_structure() –> void

peptide_entry(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, entry_type: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, total_isc: float, entry: pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::peptide_entry(enum protocols::peptide_deriver::PeptideDeriverEntryType, const double, class std::shared_ptr<const class protocols::peptide_deriver::DerivedPeptideEntry>) –> void

peptide_length(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, pep_length: int) → None¶: C++: protocols::peptide_deriver::PeptideDeriverPoseOutputter::peptide_length(const unsigned long) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat¶

Bases: pybind11_object

the output format that PeptideDeriverFilter reports in

Members:

PRF_MARKDOWN

PRF_BASIC

PRF_BASIC = <PeptideDeriverReportFormat.PRF_BASIC: 1>¶

PRF_MARKDOWN = <PeptideDeriverReportFormat.PRF_MARKDOWN: 0>¶

property name¶

property value¶