connection

Bindings for protocols::denovo_design::connection namespace

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

Bases: pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect

Architect for covalently joining two segments of a pose

__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.denovo_design.connection.ConnectionArchitect, id_value: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect, arg0: pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect) -> 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(*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

2. 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 &

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

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

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

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

C++: protocols::denovo_design::connection::ConnectionArchitect::set_ideal_abego(const bool, const bool) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> void

2. 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 class std::basic_string<char> &) –> void

2. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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 class std::basic_string<char> &) –> void

2. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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

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