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Rosetta
2020.50
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#include <FragData.hh>
Public Member Functions | |
FragData () | |
FragData (SingleResidueFragDataOP, core::Size n) | |
~FragData () override=default | |
virtual FragDataOP | clone () const |
FragDataCOP | get_self_ptr () const |
self pointers More... | |
FragDataOP | get_self_ptr () |
virtual Size | apply (kinematics::MoveMap const &, pose::Pose &, Size start, Size end) const |
virtual Size | apply (kinematics::MoveMap const &, pose::Pose &, Frame const &) const |
virtual Size | apply (pose::Pose &, Frame const &) const |
virtual Size | apply (pose::Pose &, Size start, Size end) const |
virtual Size | apply_ss (kinematics::MoveMap const &, std::string &ss, Frame const &) const |
virtual Size | is_applicable (kinematics::MoveMap const &, Size start, Size end) const |
virtual Size | is_applicable (kinematics::MoveMap const &, Frame const &) const |
virtual bool | steal (pose::Pose const &, Size start, Size end) |
virtual bool | steal (pose::Pose const &, Frame const &) |
virtual void | copy (FragData const &frag_data) |
bool | is_compatible (FragData const &frag_data) const |
bool | is_valid () const |
Size | size () const |
char | secstruct (Size const pos) const |
char | sequence (Size const pos) const |
std::string | secstruct () const |
std::string | sequence () const |
void | set_sequence (Size const pos, char const setting) |
void | set_residue (Size pos, SingleResidueFragDataOP res) |
void | add_residue (SingleResidueFragDataOP res) |
SingleResidueFragDataCOP | get_residue (core::Size pos) const |
virtual FragDataOP | generate_sub_fragment (Size start, Size stop) const |
virtual void | show (std::ostream &out) const |
virtual void | show (std::ostream &out, Frame const &) const |
virtual void | show_classic (std::ostream &out) const |
void | set_valid (bool setting=true) |
virtual std::string | pdbid () const |
Returns the PDB identifier if it has been specified, "no_pdb" otherwise. More... | |
virtual char | chain () const |
Returns the chain if it has been specified, '_' otherwise. More... | |
virtual Size | pdbpos () const |
void | set_score (Real score) |
Set a score value for this fragment. More... | |
Real | score () const |
Returns the score for this fragment. More... | |
Protected Member Functions | |
FragData (Size nr_res) | |
Protected Attributes | |
SRFD_List | data_ |
Private Types | |
typedef utility::vector1 < SingleResidueFragDataOP > | SRFD_List |
Private Attributes | |
bool | valid_ |
Real | score_ |
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private |
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inline |
Referenced by clone().
core::fragment::FragData::FragData | ( | SingleResidueFragDataOP | SRFD, |
core::Size | n | ||
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References data_.
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overridedefault |
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inlineprotected |
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inline |
References data_.
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virtual |
References data_, is_valid(), core::pose::Pose::size(), and protocols::loops::start.
Referenced by protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody::H3CterInsert::apply(), apply(), core::fragment::Frame::apply(), protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::GunnCost::compute_gunn(), and core::fragment::Frame::fragment_as_pose().
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virtual |
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virtual |
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References data_, is_valid(), and protocols::loops::start.
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References data_, and is_valid().
Referenced by core::fragment::Frame::apply_ss().
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inlinevirtual |
Returns the chain if it has been specified, '_' otherwise.
Reimplemented in core::fragment::AnnotatedFragData.
Referenced by core::fragment::AnnotatedFragData::copy().
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Reimplemented in core::fragment::AnnotatedFragData.
References data_, FragData(), and size().
Referenced by core::fragment::AnnotatedFragData::clone().
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Reimplemented in core::fragment::AnnotatedFragData.
References data_, score_, and valid_.
Referenced by core::fragment::AnnotatedFragData::copy().
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Reimplemented in core::fragment::AnnotatedFragData.
References data_, size(), and protocols::loops::stop.
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inline |
References data_.
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inline |
self pointers
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inline |
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References data_, and core::sequence::end.
Referenced by is_applicable(), and core::fragment::Frame::is_applicable().
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Referenced by core::fragment::Frame::is_mergeable().
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inline |
References valid_.
Referenced by apply(), apply_ss(), core::fragment::FragID::is_valid(), core::fragment::Frame::is_valid(), and show().
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inlinevirtual |
Returns the PDB identifier if it has been specified, "no_pdb" otherwise.
Reimplemented in core::fragment::AnnotatedFragData.
Referenced by core::fragment::AnnotatedFragData::copy(), protocols::fold_from_loops::utils::Nub::fix_fragment(), and show().
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inlinevirtual |
Reimplemented in core::fragment::AnnotatedFragData.
Referenced by core::fragment::AnnotatedFragData::copy(), and show().
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inline |
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inline |
References data_.
Referenced by protocols::loop_grower::LoopGrower::single_grow().
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inline |
References size(), and protocols::kinmatch::str().
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inline |
References data_, and sequence().
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inline |
References size(), and protocols::kinmatch::str().
Referenced by sequence().
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inline |
References data_.
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inline |
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inline |
References data_.
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inline |
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References data_, is_valid(), pdbid(), and pdbpos().
Referenced by core::fragment::operator<<(), core::fragment::Frame::show_classic(), and core::fragment::Frame::show_fragments().
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References data_, is_valid(), pdbid(), pdbpos(), and core::fragment::Frame::seqpos().
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virtual |
References data_.
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inline |
References data_.
Referenced by apply(), clone(), generate_sub_fragment(), core::fragment::AnnotatedFragData::generate_sub_fragment(), is_applicable(), is_compatible(), secstruct(), sequence(), and steal().
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References data_, core::sequence::end, set_valid(), and core::pose::Pose::size().
Referenced by steal().
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Referenced by add_residue(), apply(), apply_ss(), clone(), copy(), FragData(), generate_sub_fragment(), core::fragment::AnnotatedFragData::generate_sub_fragment(), get_residue(), is_applicable(), is_compatible(), secstruct(), sequence(), set_residue(), set_sequence(), show(), show_classic(), size(), and steal().
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Referenced by copy(), score(), and set_score().
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private |
Referenced by copy(), is_valid(), and set_valid().