peptide_deriver

Bindings for protocols::peptide_deriver namespace

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter

Bases: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, out: pyrosetta.rosetta.utility.io.orstream, prefix: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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_builtins.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()

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) → int

__init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: int) -> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType, arg0: tuple) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter

Bases: pyrosetta.rosetta.protocols.filters.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) -> None
2. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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> >, class std::basic_ostream<char> &, const unsigned long) const –> void

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.

1. derive_peptide(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: pyrosetta.rosetta.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

2. derive_peptide(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: pyrosetta.rosetta.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>

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_report_format_string(value: str) → pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat

C++: protocols::peptide_deriver::PeptideDeriverFilter::parse_report_format_string(const class std::basic_string<char> &) –> enum protocols::peptide_deriver::PeptideDeriverReportFormat

prepare_pose(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter, output: pyrosetta.rosetta.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_xml_schema(xsd: pyrosetta.rosetta.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(class std::basic_ostream<char> &, 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 class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter

Bases: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter

outputs a Markdown formatted Peptiderive report to a stream

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter, out: pyrosetta.rosetta.utility.io.orstream, prefix: str) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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_builtins.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) -> None
2. __init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter, is_dump_best_peptide_pose: bool, is_dump_prepared_pose: bool, is_dump_cyclic_poses: bool, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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_builtins.pybind11_object

the output format that PeptideDeriverFilter reports in

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) → int

__init__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: int) -> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat, arg0: tuple) → None

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).