contact_map

Bindings for protocols::contact_map namespace

class pyrosetta.rosetta.protocols.contact_map.Contact

Bases: pybind11_object

Simple class representing a contact between two atoms

add_distance(*args, **kwargs)

Overloaded function.

1. add_distance(self: pyrosetta.rosetta.protocols.contact_map.Contact) -> None

Adds distance to the contact

C++: protocols::contact_map::Contact::add_distance() –> void

2. add_distance(self: pyrosetta.rosetta.protocols.contact_map.Contact, distance: float) -> None

Adds distance to the contact

C++: protocols::contact_map::Contact::add_distance(double) –> void

assign(self: pyrosetta.rosetta.protocols.contact_map.Contact, : pyrosetta.rosetta.protocols.contact_map.Contact) → pyrosetta.rosetta.protocols.contact_map.Contact

C++: protocols::contact_map::Contact::operator=(const class protocols::contact_map::Contact &) –> class protocols::contact_map::Contact &

long_string_rep(*args, **kwargs)

Overloaded function.

1. long_string_rep(self: pyrosetta.rosetta.protocols.contact_map.Contact) -> str

2. long_string_rep(self: pyrosetta.rosetta.protocols.contact_map.Contact, n_poses: int) -> str

Returns string representation of the Contact including partner names

C++: protocols::contact_map::Contact::long_string_rep(unsigned long) const –> std::string

partner1(self: pyrosetta.rosetta.protocols.contact_map.Contact) → pyrosetta.rosetta.protocols.contact_map.ContactPartner

Accessor functions for private class variables

C++: protocols::contact_map::Contact::partner1() –> class protocols::contact_map::ContactPartner *

partner2(self: pyrosetta.rosetta.protocols.contact_map.Contact) → pyrosetta.rosetta.protocols.contact_map.ContactPartner

C++: protocols::contact_map::Contact::partner2() –> class protocols::contact_map::ContactPartner *

reset_count(self: pyrosetta.rosetta.protocols.contact_map.Contact) → None

Resets count to 0

C++: protocols::contact_map::Contact::reset_count() –> void

string_rep(*args, **kwargs)

Overloaded function.

1. string_rep(self: pyrosetta.rosetta.protocols.contact_map.Contact) -> str

Returns string representation of the Contact

C++: protocols::contact_map::Contact::string_rep() const –> std::string

2. string_rep(self: pyrosetta.rosetta.protocols.contact_map.Contact, n_poses: int) -> str

Returns string representation of the Contact as percentage value

C++: protocols::contact_map::Contact::string_rep(unsigned long) const –> std::string

class pyrosetta.rosetta.protocols.contact_map.ContactMap

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::contact_map::ContactMap::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, : pyrosetta.rosetta.protocols.contact_map.ContactMap) → pyrosetta.rosetta.protocols.contact_map.ContactMap

C++: protocols::contact_map::ContactMap::operator=(const class protocols::contact_map::ContactMap &) –> class protocols::contact_map::ContactMap &

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.contact_map.ContactMap) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::contact_map::ContactMap::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>

fill_contacts(*args, **kwargs)

Overloaded function.

1. fill_contacts(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, region: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Initializes ContactMap within a single region

C++: protocols::contact_map::ContactMap::fill_contacts(const class core::select::residue_selector::ResidueSelector &, const class core::pose::Pose &) –> void

2. fill_contacts(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, region1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, region2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Initializes ContactMap between two separate regions

C++: protocols::contact_map::ContactMap::fill_contacts(const class core::select::residue_selector::ResidueSelector &, const class core::select::residue_selector::ResidueSelector &, const class core::pose::Pose &) –> void

fill_contacts_all_atom2(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, region1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, region2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initializes ContactMap between a single region and all atoms of a ligand

(region2 must resolve to a single residue).

C++: protocols::contact_map::ContactMap::fill_contacts_all_atom2(const class core::select::residue_selector::ResidueSelector &, const class core::select::residue_selector::ResidueSelector &, const class core::pose::Pose &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.contact_map.ContactMap) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::contact_map::ContactMap::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_contact(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, row: int, col: int) → protocols::contact_map::Contact

Get the contact for a particular row and column

The identity contact (the contact of a residue with itself) is shared between all identity contacts. (The last identity contact in region.)

C++: protocols::contact_map::ContactMap::get_contact(unsigned long, unsigned long) –> const class protocols::contact_map::Contact &

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_name(self: pyrosetta.rosetta.protocols.contact_map.ContactMap) → str

C++: protocols::contact_map::ContactMap::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_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

static mover_name() → str

C++: protocols::contact_map::ContactMap::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

parse_region_string(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, : str) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

:

Parses region string end sets the boundaries accordingly

:

Possible formats for the region definition are “<int seqpos>” (e.g ‘12’), “<int begin>-<int end>” (e.g. ‘1-10’) or “<char chainID>”(e.g. ‘A’)

C++: protocols::contact_map::ContactMap::parse_region_string(const std::string &) const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

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::contact_map::ContactMap::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(self: pyrosetta.rosetta.protocols.contact_map.ContactMap) → None

Resets the movers n_poses_ variable and the counts of all contacts to 0

C++: protocols::contact_map::ContactMap::reset() –> void

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_distance_cutoff(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, cutoff: float) → None

C++: protocols::contact_map::ContactMap::set_distance_cutoff(double) –> void

set_distance_matrix(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, setting: bool) → None

C++: protocols::contact_map::ContactMap::set_distance_matrix(bool) –> 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_models_per_file(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, setting: int) → None

C++: protocols::contact_map::ContactMap::set_models_per_file(unsigned long) –> 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_output_prefix(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, prefix: str) → None

Setter functions for private class variables

C++: protocols::contact_map::ContactMap::set_output_prefix(std::string) –> void

set_reference_pose(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, setting: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::contact_map::ContactMap::set_reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_region2_all_atom(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, setting: bool) → None

C++: protocols::contact_map::ContactMap::set_region2_all_atom(bool) –> void

set_regions(*args, **kwargs)

Overloaded function.

1. set_regions(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, region1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

2. set_regions(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, region1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, region2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::contact_map::ContactMap::set_regions(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_row_format(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, setting: bool) → None

C++: protocols::contact_map::ContactMap::set_row_format(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.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::contact_map::ContactMap::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

write_to_file(*args, **kwargs)

Overloaded function.

1. write_to_file(self: pyrosetta.rosetta.protocols.contact_map.ContactMap) -> None

2. write_to_file(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, filename: str) -> None

Output function that writes the ContactMap to the specified file

C++: protocols::contact_map::ContactMap::write_to_file(std::string) –> void

write_to_stream(self: pyrosetta.rosetta.protocols.contact_map.ContactMap, output_stream: pyrosetta.rosetta.std.ostream) → None

C++: protocols::contact_map::ContactMap::write_to_stream(std::ostream &) –> void

class pyrosetta.rosetta.protocols.contact_map.ContactMapCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.contact_map.ContactMapCreator, : pyrosetta.rosetta.protocols.contact_map.ContactMapCreator) → pyrosetta.rosetta.protocols.contact_map.ContactMapCreator

C++: protocols::contact_map::ContactMapCreator::operator=(const class protocols::contact_map::ContactMapCreator &) –> class protocols::contact_map::ContactMapCreator &

create_mover(self: pyrosetta.rosetta.protocols.contact_map.ContactMapCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::contact_map::ContactMapCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.contact_map.ContactMapCreator) → str

C++: protocols::contact_map::ContactMapCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.contact_map.ContactMapCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::contact_map::ContactMapCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.contact_map.ContactPartner

Bases: pybind11_object

Simple class that holds the information on an atom involved in a contact

assign(self: pyrosetta.rosetta.protocols.contact_map.ContactPartner, : pyrosetta.rosetta.protocols.contact_map.ContactPartner) → pyrosetta.rosetta.protocols.contact_map.ContactPartner

C++: protocols::contact_map::ContactPartner::operator=(const class protocols::contact_map::ContactPartner &) –> class protocols::contact_map::ContactPartner &

atomname(self: pyrosetta.rosetta.protocols.contact_map.ContactPartner) → str

C++: protocols::contact_map::ContactPartner::atomname() const –> std::string

resname(self: pyrosetta.rosetta.protocols.contact_map.ContactPartner) → str

C++: protocols::contact_map::ContactPartner::resname() const –> std::string

seqpos(self: pyrosetta.rosetta.protocols.contact_map.ContactPartner) → int

Accessor functions for private class variables

C++: protocols::contact_map::ContactPartner::seqpos() const –> unsigned long

string_rep(self: pyrosetta.rosetta.protocols.contact_map.ContactPartner) → str

Returns string representation of the ContactPartner

C++: protocols::contact_map::ContactPartner::string_rep() const –> std::string