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Rosetta
2020.50
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TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure. More...
#include <DsspDesignOperation.hh>
Public Types | |
typedef core::pack::task::operation::TaskOperation | parent |
typedef core::pack::task::operation::TaskOperationOP | TaskOperationOP |
typedef protocols::parser::BluePrint | BluePrint |
typedef protocols::parser::BluePrintOP | BluePrintOP |
typedef std::map< std::string, std::string > | SecStructResidues |
typedef std::pair< std::string, std::string > | SecStruct |
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typedef utility::tag::TagCOP | TagCOP |
typedef basic::datacache::DataMap | DataMap |
typedef pose::Pose | Pose |
Public Member Functions | |
DsspDesignOperation () | |
default constructor More... | |
DsspDesignOperation (DsspDesignOperation const &rval) | |
copy constructor More... | |
~DsspDesignOperation () override | |
destructor More... | |
TaskOperationOP | clone () const override |
make clone More... | |
void | set_blueprint (BluePrintOP const bp) |
define secondary structure from a blueprint More... | |
void | set_restrictions_aa (std::string const &sse, std::string const &aas) |
define allowed residues for some SSE More... | |
void | set_restrictions_append (std::string const &sse, std::string const &aas) |
append allowed residues for some SSE More... | |
void | set_restrictions_exclude (std::string const &sse, std::string const &aas) |
exclude allowed residues for some SSE More... | |
void | parse_tag (TagCOP tag, DataMap &) override |
parse RosettaScripts XML More... | |
void | apply (Pose const &pose, core::pack::task::PackerTask &task) const override |
apply More... | |
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~TaskOperation () override | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
static std::string | keyname () |
Private Member Functions | |
void | set_default_sse_residues () |
initialize allowed residue sets with defaults More... | |
utility::vector1< bool > | get_restrictions (std::string const &ss_type) const |
get the set of allowed residues for some secondary structure element More... | |
Private Attributes | |
SecStructResidues | sse_residues_ |
map sets of allowed residues to secondary structure elements More... | |
BluePrintOP | blueprint_ |
std::string | pose_secstruct_ |
Friends | |
class | ::DsspDesignOperationTests |
TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure.
typedef core::pack::task::operation::TaskOperation protocols::task_operations::DsspDesignOperation::parent |
typedef std::pair< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStruct |
typedef std::map< std::string, std::string > protocols::task_operations::DsspDesignOperation::SecStructResidues |
typedef core::pack::task::operation::TaskOperationOP protocols::task_operations::DsspDesignOperation::TaskOperationOP |
protocols::task_operations::DsspDesignOperation::DsspDesignOperation | ( | ) |
default constructor
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default |
copy constructor
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overridedefault |
destructor
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overridevirtual |
apply
Implements core::pack::task::operation::TaskOperation.
References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::pack::task::PackerTask::nonconst_residue_task(), core::pose::Pose::residue(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pose::Pose::size(), and protocols::task_operations::TR().
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overridevirtual |
make clone
Implements core::pack::task::operation::TaskOperation.
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private |
get the set of allowed residues for some secondary structure element
References core::chemical::aa_from_oneletter_code(), and core::chemical::num_canonical_aas.
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inlinestatic |
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overridevirtual |
parse RosettaScripts XML
Reimplemented from core::pack::task::operation::TaskOperation.
References protocols::task_operations::TR().
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static |
void protocols::task_operations::DsspDesignOperation::set_blueprint | ( | BluePrintOP const | bp | ) |
define secondary structure from a blueprint
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private |
initialize allowed residue sets with defaults
References protocols::task_operations::TR().
void protocols::task_operations::DsspDesignOperation::set_restrictions_aa | ( | std::string const & | sse, |
std::string const & | aas | ||
) |
define allowed residues for some SSE
void protocols::task_operations::DsspDesignOperation::set_restrictions_append | ( | std::string const & | sse, |
std::string const & | aas | ||
) |
append allowed residues for some SSE
void protocols::task_operations::DsspDesignOperation::set_restrictions_exclude | ( | std::string const & | sse, |
std::string const & | aas | ||
) |
exclude allowed residues for some SSE
References protocols::cluster::calibur::aa.
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friend |
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private |
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private |
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private |
map sets of allowed residues to secondary structure elements