connection

Bindings for protocols::denovo_design::connection namespace

class pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate, : pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate) → pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate

C++: protocols::denovo_design::connection::AreConnectablePredicate::operator=(const class protocols::denovo_design::connection::AreConnectablePredicate &) –> class protocols::denovo_design::connection::AreConnectablePredicate &

class pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect

Bases: StructureArchitect

Architect for covalently joining two segments of a pose

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) -> None

does the work of modifying the StructureData

C++: protocols::denovo_design::connection::ConnectionArchitect::apply(class protocols::denovo_design::components::StructureData &) const –> void

  1. apply(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, random: float) -> None

applies with a specific random number

C++: protocols::denovo_design::connection::ConnectionArchitect::apply(class protocols::denovo_design::components::StructureData &, double &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, : pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect

C++: protocols::denovo_design::connection::ConnectionArchitect::operator=(const class protocols::denovo_design::connection::ConnectionArchitect &) –> class protocols::denovo_design::connection::ConnectionArchitect &

static attributes_for_parse_my_tag(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::denovo_design::connection::ConnectionArchitect::attributes_for_parse_my_tag(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

static class_name() → str

C++: protocols::denovo_design::connection::ConnectionArchitect::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect

C++: protocols::denovo_design::connection::ConnectionArchitect::clone() const –> class std::shared_ptr<class protocols::denovo_design::connection::ConnectionArchitect>

id(self: pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect) → str

C++: protocols::denovo_design::architects::StructureArchitect::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

segment1_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → pyrosetta.rosetta.std.vector_std_string

returns list of allowed segment 1 ids

C++: protocols::denovo_design::connection::ConnectionArchitect::segment1_ids() const –> const class std::vector<std::string, class std::allocator<std::string > > &

segment2_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → pyrosetta.rosetta.std.vector_std_string

returns list of allowed segment2 ids

C++: protocols::denovo_design::connection::ConnectionArchitect::segment2_ids() const –> const class std::vector<std::string, class std::allocator<std::string > > &

set_bridge(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, bridge: bool) → None
sets whether to always try to bridge. If true, a random cutpoint will be selected in the connection

if the chains to be connected have different movable groups

C++: protocols::denovo_design::connection::ConnectionArchitect::set_bridge(const bool) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect, new_id: str) → None

C++: protocols::denovo_design::architects::StructureArchitect::set_id(const std::string &) –> void

set_ideal_abego(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, use_ideal_abego: bool, extend_ss: str) → None

sets whether to use “ideal abego” loops according to Koga papers

C++: protocols::denovo_design::connection::ConnectionArchitect::set_ideal_abego(const bool, const std::string &) –> void

set_motifs(*args, **kwargs)

Overloaded function.

  1. set_motifs(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, motif_str: str, cutpoints_str: str) -> None

sets motifs using a motif string and a string of cutpoints

C++: protocols::denovo_design::connection::ConnectionArchitect::set_motifs(const std::string &, const std::string &) –> void

  1. set_motifs(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, motifs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_t) -> None

sets motifs via a vector

C++: protocols::denovo_design::connection::ConnectionArchitect::set_motifs(const class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > &) –> void

set_segment1_ids(*args, **kwargs)

Overloaded function.

  1. set_segment1_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, segment1_str: str) -> None

sets list of segment1 ids from string

C++: protocols::denovo_design::connection::ConnectionArchitect::set_segment1_ids(const std::string &) –> void

  1. set_segment1_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, segments: pyrosetta.rosetta.std.vector_std_string) -> None

sets list of segment1 ids from list

C++: protocols::denovo_design::connection::ConnectionArchitect::set_segment1_ids(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

set_segment2_ids(*args, **kwargs)

Overloaded function.

  1. set_segment2_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, segment2_str: str) -> None

sets list of segment2 ids from string

C++: protocols::denovo_design::connection::ConnectionArchitect::set_segment2_ids(const std::string &) –> void

  1. set_segment2_ids(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, segments: pyrosetta.rosetta.std.vector_std_string) -> None

sets list of segment1 ids from list

C++: protocols::denovo_design::connection::ConnectionArchitect::set_segment2_ids(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

set_use_hh_abego_rules(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, use_rules: bool) → None

sets whether or not to use the newer HH rules (https://doi.org/10.1101/2021.03.10.434454)

C++: protocols::denovo_design::connection::ConnectionArchitect::set_use_hh_abego_rules(const bool) –> void

set_user_chain1(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, chain: int) → None

sets user-specified chain number for the lower chain to be connected. 0 if unspecified

C++: protocols::denovo_design::connection::ConnectionArchitect::set_user_chain1(const unsigned long) –> void

set_user_chain2(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, chain: int) → None

sets user-specified chain number for the upper chain to be connected. 0 if unspecified

C++: protocols::denovo_design::connection::ConnectionArchitect::set_user_chain2(const unsigned long) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → str

C++: protocols::denovo_design::connection::ConnectionArchitect::type() const –> std::string

user_chain1(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → int

gets user-specified chain number for the lower chain to be connected. 0 if not specified

C++: protocols::denovo_design::connection::ConnectionArchitect::user_chain1() const –> unsigned long

user_chain2(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) → int

gets user-specified chain number for the upper chain to be connected. 0 if not specified

C++: protocols::denovo_design::connection::ConnectionArchitect::user_chain2() const –> unsigned long

class pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed

Bases: Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed, : pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed) → pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed

C++: protocols::denovo_design::connection::EXCN_ConnectionSetupFailed::operator=(const class protocols::denovo_design::connection::EXCN_ConnectionSetupFailed &) –> class protocols::denovo_design::connection::EXCN_ConnectionSetupFailed &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str

C++: std::exception::what() const –> const char *

pyrosetta.rosetta.protocols.denovo_design.connection.parse_segment_names(segment_name_str: str) → pyrosetta.rosetta.std.vector_std_string

C++: protocols::denovo_design::connection::parse_segment_names(const std::string &) –> class std::vector<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.protocols.denovo_design.connection.retrieve_connection_architect(architect_name: str, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect

C++: protocols::denovo_design::connection::retrieve_connection_architect(const std::string &, class basic::datacache::DataMap &) –> class std::shared_ptr<const class protocols::denovo_design::connection::ConnectionArchitect>

pyrosetta.rosetta.protocols.denovo_design.connection.store_connection_architect(architect: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::connection::store_connection_architect(class std::shared_ptr<class protocols::denovo_design::connection::ConnectionArchitect>, class basic::datacache::DataMap &) –> void