pdbinfo_manipulations¶

Bindings for protocols::pdbinfo_manipulations namespace

class pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences¶

Bases: Mover

Realign poses to sequences after losing pdb_info

apply(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply(class core::pose::Pose &) –> void

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

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_mode(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode() const –> const enum protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesMode &

get_mode_as_string(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → str¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode_as_string() const –> std::string

get_name(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → str¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_sequence_alignment_cut_max(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → int¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_sequence_alignment_cut_max() const –> unsigned long

get_target_sequences(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_target_sequences() –> class utility::vector1<struct protocols::pdbinfo_manipulations::SequenceSpecification, class std::allocator<struct protocols::pdbinfo_manipulations::SequenceSpecification> > &

get_throw_on_fail(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) → bool¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_throw_on_fail() const –> bool

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

load_json_file(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, json_fn: str) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::load_json_file(const std::string &) –> void

static mover_name() → str¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_target_tag(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, tag: pyrosetta.rosetta.utility.tag.Tag) → pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification¶: Rosetta Scripts Support ///

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_target_tag(const class std::shared_ptr<const class utility::tag::Tag> &) const –> struct protocols::pdbinfo_manipulations::SequenceSpecification

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : 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 movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_mode(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, mode: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode(const enum protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesMode &) –> void

set_mode_from_string(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, mode: str) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode_from_string(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_sequence_alignment_cut_max(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, sequence_alignment_cut_max: int) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_sequence_alignment_cut_max(const unsigned long) –> void

set_target_sequences(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, target_sequences: pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_target_sequences(const class utility::vector1<struct protocols::pdbinfo_manipulations::SequenceSpecification, class std::allocator<struct protocols::pdbinfo_manipulations::SequenceSpecification> > &) –> void

set_throw_on_fail(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, throw_on_fail: bool) → None¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_throw_on_fail(const bool) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences) -> None
show(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

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

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

class pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode¶

Bases: pybind11_object

Members:

unset

single

multiple

multiple = <AlignPDBInfoToSequencesMode.multiple: 2>¶

property name¶

single = <AlignPDBInfoToSequencesMode.single: 1>¶

unset = <AlignPDBInfoToSequencesMode.unset: 0>¶

property value¶

pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences_namer(name: str) → str¶: C++: protocols::pdbinfo_manipulations::AlignPDBInfoToSequences_namer(const std::string &) –> std::string

class pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification¶

Bases: pybind11_object

Rosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes.

assign(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification, : pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification) → pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification¶: C++: protocols::pdbinfo_manipulations::SequenceSpecification::operator=(const struct protocols::pdbinfo_manipulations::SequenceSpecification &) –> struct protocols::pdbinfo_manipulations::SequenceSpecification &

property chains_¶

check_single_format(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification) → None¶

make sure none of the non-sequence elements are larger than: the sequence_.

C++: protocols::pdbinfo_manipulations::SequenceSpecification::check_single_format() const –> void

property current_idx_¶

property insCodes_¶

property residue_numbers_¶

property segmentIDs_¶

property sequence_¶

set_1_to_1_format(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification, starting_number: int) → None¶

duplicate the last element (or default last element if not set) to: pad chains_, segmentIDs_, insCodes_, residue_numbers_, to be the same length as the sequence_.

C++: protocols::pdbinfo_manipulations::SequenceSpecification::set_1_to_1_format(const int) –> void

update_multiple_format_residue_numbering(self: pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification) → None¶

make sure residue numbering is set to be the same size as the sequence_

C++: protocols::pdbinfo_manipulations::SequenceSpecification::update_multiple_format_residue_numbering() –> void

pyrosetta.rosetta.protocols.pdbinfo_manipulations.alignpdbinfotosequencesmode_to_string(mode: pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode) → str¶: C++: protocols::pdbinfo_manipulations::alignpdbinfotosequencesmode_to_string(const enum protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesMode &) –> std::string

pyrosetta.rosetta.protocols.pdbinfo_manipulations.get_alignpdbinfotosequencesmode_from_string(str: str) → pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode¶: C++: protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string(const std::string &) –> enum protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesMode

pyrosetta.rosetta.protocols.pdbinfo_manipulations.pad_sequences(full_seq_1: str, aln_seq_1: pyrosetta.rosetta.core.sequence.Sequence, full_seq_2: str, aln_seq_2: pyrosetta.rosetta.core.sequence.Sequence) → None¶

Take two sequences that have been aligned, and their parent sequences

and align/pad them with ‘-’ as shown below:

given to align from SWAlign: query: CLGIGSCNDFAGCGYAVVCFW target: XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

from: (aka a result from SWAlign) query 1 CLGIGSCNDFAGCG——YAVVCFW target 15 CLGIGSCNDFAGCGXXXXXXYAVVCFW

to: query 1 ————–CLGIGSCNDFAGCG——YAVVCFW—– target 1 XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

C++: protocols::pdbinfo_manipulations::pad_sequences(const std::string &, const class std::shared_ptr<class core::sequence::Sequence> &, const std::string &, const class std::shared_ptr<class core::sequence::Sequence> &) –> void