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protocols::denovo_design Namespace Reference

Namespaces

 architects
 
 calculators
 
 components
 
 connection
 
 constraints
 
 filters
 
 movers
 
 residue_selectors
 
 task_operations
 

Classes

class  DisulfidizeMover
 
class  DisulfidizeMoverCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< DisulfidizerMover > 
DisulfidizerMoverOP
 
typedef
utility::pointer::shared_ptr
< DisulfidizerMover const > 
DisulfidizerMoverCOP
 
typedef
utility::pointer::weak_ptr
< DisulfidizerMover > 
DisulfidizerMoverAP
 
typedef
utility::pointer::weak_ptr
< DisulfidizerMover const > 
DisulfidizerMoverCAP
 
typedef std::string SegmentName
 
typedef std::vector< SegmentNameSegmentNames
 
typedef std::list< SegmentNameSegmentNameList
 
typedef std::set< SegmentNameSegmentNameSet
 
typedef std::pair< core::Size,
core::Size
SizePair
 
typedef std::map< std::string,
core::Size
StrandNameToNumberMap
 

Functions

void add_to_list (DisulfidizeMover::DisulfideList &disulf_partners, core::Size const r1, core::Size const r2)
 
bool same_pose (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 Tells whether the two given poses are identical based on # resides and dihedrals. More...
 
core::kinematics::FoldTree remove_all_jump_atoms (core::kinematics::FoldTree const &orig)
 
core::kinematics::FoldTree remove_missing_jump_atoms (core::pose::Pose const &pose, core::kinematics::FoldTree const &orig)
 removes atoms missing from the current pose More...
 
void construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, core::select::residue_selector::ResidueSubset const &set1, core::select::residue_selector::ResidueSubset const &set2, bool const keep_chirality)
 creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...
 
void construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, std::set< core::Size > const &res_set, bool const keep_chirality)
 creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...
 
core::pose::PoseOP construct_dummy_pose (std::string const &restype_name)
 builds an extended-conformation poly-XXX pose More...
 
core::pose::PoseOP construct_dummy_pose (std::string const &restype_name, core::Size const length)
 
core::pose::PoseOP construct_dummy_pose (core::chemical::ResidueType const &restype)
 
core::pose::PoseOP construct_dummy_pose (core::chemical::ResidueType const &restype, core::Size length)
 
core::select::residue_selector::ResidueSelectorCOP get_residue_selector (basic::datacache::DataMap const &data, std::string const &name)
 
std::string abego_str (utility::vector1< std::string > const &abego)
 
utility::vector1< std::string > abego_vector (std::string const &ab)
 
std::string get_remark_line (core::io::Remarks::const_iterator &it_rem, core::io::Remarks::const_iterator const &end)
 
void add_remark (core::io::Remarks &remarks, core::Size const num, std::string const &str_val)
 adds a remark to a Remarks object, splitting it into multiple remarks if it is too long More...
 
core::Size loop_stop_without_overlap (core::pose::Pose const &pose, core::Size stopres, core::Size const overlap)
 
core::Size loop_start_without_overlap (core::pose::Pose const &pose, core::Size startres, core::Size const overlap)
 
void rebuild_missing_atoms (core::pose::Pose &pose, core::Size const resi)
 given a residue, rebuilds all missing atoms More...
 
int find_jump_rec (core::kinematics::FoldTree const &ft, core::Size const residue)
 helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs More...
 
void insert_peptide_edges (core::kinematics::FoldTree &ft, core::kinematics::Edge const &jedge)
 inserts the peptide edges to accomodate the new jump edge given More...
 
utility::vector1< core::Sizeparse_length_string (std::string const &len_str)
 
core::Size extract_int (core::Real &num, core::Size const m, core::Size const n)
 given a number 0 <= x < 1, calculate an integer M <= x <= N NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER More...
 
std::pair< std::string,
std::string > 
parse_strand_pair (std::string const &strand_pair_str)
 
core::Size count_bulges (components::StructureData const &perm, std::string const &segment)
 counts the beta-bulges in the given segment. This simply counts all abego A's in the segment More...
 
void add_chain_from_pose (core::pose::PoseCOP to_add, core::pose::PoseOP combined)
 dumps a pose into another pose as a new chain More...
 
void add_residues_to_pose (core::pose::Pose &pose, core::pose::Pose const &template_pose, bool const new_chain)
 adds residues from template_pose to pose. If new_chain == true, creates covalent bond More...
 
core::Size get_resid (components::StructureData const &perm, std::string const &resid_str)
 
core::Real linear_chainbreak (core::pose::Pose const &pose, core::Size const pos)
 evaluate linear chainbreak at a position More...
 
core::kinematics::FoldTree slide_jump (core::kinematics::FoldTree const &ft_orig, core::Size const jump_idx, core::Size const new_start, core::Size const new_stop)
 
void add_cutpoints (core::pose::Pose &pose, components::StructureData const &sd)
 
std::string symmetric_secstruct (core::pose::Pose const &pose, std::string const &asymm_secstruct)
 Given a symmetric pose and a secstruct for the asymmetric unit, constructs and returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit. More...
 
core::kinematics::FoldTree symmetric_fold_tree (core::pose::Pose const &pose, core::kinematics::FoldTree const &asymm_ft)
 Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and returns a symmetric fold tree while preserving the topology of the aysmmetric unit's fold tree. More...
 
core::select::residue_selector::ResidueSubset symmetric_residue_subset (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &asymm_subset)
 Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset. More...
 
void parse_motif_string (std::string const &motif_str, std::string &secstruct, std::string &abego)
 Computes secondary structure string from the given motifs. More...
 
template<typename Container , typename T >
Container set_difference (typename std::set< T >::const_iterator begin1, typename std::set< T >::const_iterator const &end1, typename std::set< T >::const_iterator begin2, typename std::set< T >::const_iterator const &end2)
 Returns vector of elements found in v1 but not in v2. More...
 
template<typename Container >
Container csv_to_container (std::string const &csv, char const delim=',')
 Given a comma-seperated string, convert to container. More...
 

Variables

static char const PARENT_DELIMETER = '.'
 

Typedef Documentation

typedef utility::pointer::weak_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverAP
typedef utility::pointer::weak_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCAP
typedef utility::pointer::shared_ptr< DisulfidizerMover const > protocols::denovo_design::DisulfidizerMoverCOP
typedef utility::pointer::shared_ptr< DisulfidizerMover > protocols::denovo_design::DisulfidizerMoverOP

Function Documentation

std::string protocols::denovo_design::abego_str ( utility::vector1< std::string > const &  abego)
utility::vector1< std::string > protocols::denovo_design::abego_vector ( std::string const &  ab)
void protocols::denovo_design::add_chain_from_pose ( core::pose::PoseCOP  to_add,
core::pose::PoseOP  combined 
)

dumps a pose into another pose as a new chain

References protocols::TR().

void protocols::denovo_design::add_cutpoints ( core::pose::Pose pose,
components::StructureData const &  sd 
)
void protocols::denovo_design::add_remark ( core::io::Remarks remarks,
core::Size const  num,
std::string const &  str_val 
)

adds a remark to a Remarks object, splitting it into multiple remarks if it is too long

References core::io::RemarkInfo::num, and core::io::RemarkInfo::value.

Referenced by protocols::denovo_design::components::StructureDataFactory::add_perm_remark().

void protocols::denovo_design::add_residues_to_pose ( core::pose::Pose pose,
core::pose::Pose const &  template_pose,
bool const  new_chain 
)
void protocols::denovo_design::add_to_list ( DisulfidizeMover::DisulfideList &  disulf_partners,
core::Size const  r1,
core::Size const  r2 
)
core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( std::string const &  restype_name)

builds an extended-conformation poly-XXX pose

Referenced by construct_dummy_pose().

core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( std::string const &  restype_name,
core::Size const  length 
)
core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( core::chemical::ResidueType const &  restype)
core::pose::PoseOP protocols::denovo_design::construct_dummy_pose ( core::chemical::ResidueType const &  restype,
core::Size  length 
)
void protocols::denovo_design::construct_poly_ala_pose ( core::pose::Pose pose,
bool const  keep_disulf,
core::select::residue_selector::ResidueSubset const &  set1,
core::select::residue_selector::ResidueSubset const &  set2,
bool const  keep_chirality 
)

creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine

If keep_chirality is true, the D-amino acids are mutated to D-alanine.

Referenced by protocols::forge::components::BDR::centroid_build(), and protocols::denovo_design::DisulfidizeMover::find_possible_disulfides().

void protocols::denovo_design::construct_poly_ala_pose ( core::pose::Pose pose,
bool const  keep_disulf,
std::set< core::Size > const &  res_set,
bool const  keep_chirality 
)
core::Size protocols::denovo_design::count_bulges ( components::StructureData const &  perm,
std::string const &  segment 
)
template<typename Container >
Container protocols::denovo_design::csv_to_container ( std::string const &  csv,
char const  delim = ',' 
)

Given a comma-seperated string, convert to container.

core::Size protocols::denovo_design::extract_int ( core::Real num,
core::Size const  m,
core::Size const  n 
)
int protocols::denovo_design::find_jump_rec ( core::kinematics::FoldTree const &  ft,
core::Size const  residue 
)
std::string protocols::denovo_design::get_remark_line ( core::io::Remarks::const_iterator &  it_rem,
core::io::Remarks::const_iterator const &  end 
)
core::Size protocols::denovo_design::get_resid ( components::StructureData const &  perm,
std::string const &  resid_str 
)
core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::get_residue_selector ( basic::datacache::DataMap const &  data,
std::string const &  name 
)
void protocols::denovo_design::insert_peptide_edges ( core::kinematics::FoldTree ft,
core::kinematics::Edge const &  jedge 
)
core::Real protocols::denovo_design::linear_chainbreak ( core::pose::Pose const &  pose,
core::Size const  pos 
)

evaluate linear chainbreak at a position

Remarks
If necessary, will evaluate using a copy of the Pose with a cut fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished. Eventually this should be merged into protocols/forge/methods/linear_chainbreak.cc However, the changes I needed to make to that file break certain parts of remodel

References protocols::forge::methods::add_cutpoint_variants(), core::pose::Pose::fold_tree(), core::scoring::linear_chainbreak, core::kinematics::FoldTree::num_cutpoint(), core::kinematics::Edge::PEPTIDE, and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::rna::get_modeler_scorefxn().

core::Size protocols::denovo_design::loop_start_without_overlap ( core::pose::Pose const &  pose,
core::Size  startres,
core::Size const  overlap 
)
core::Size protocols::denovo_design::loop_stop_without_overlap ( core::pose::Pose const &  pose,
core::Size  stopres,
core::Size const  overlap 
)
utility::vector1< core::Size > protocols::denovo_design::parse_length_string ( std::string const &  len_str)
void protocols::denovo_design::parse_motif_string ( std::string const &  motif_str,
std::string &  secstruct,
std::string &  abego 
)

Computes secondary structure string from the given motifs.

Parameters
[in]motif_strMotif string to be parsed (e.g. "5EB-2LG-5EB")
[out]secstructSecondary structure string to be cleared and filled
[out]abegoABEGO string to be cleared and filled

References core::pack::dunbrack::c, and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_motifs(), and protocols::denovo_design::components::Segment::parse_motif().

std::pair< std::string, std::string > protocols::denovo_design::parse_strand_pair ( std::string const &  strand_pair_str)
void protocols::denovo_design::rebuild_missing_atoms ( core::pose::Pose pose,
core::Size const  resi 
)
core::kinematics::FoldTree protocols::denovo_design::remove_all_jump_atoms ( core::kinematics::FoldTree const &  orig)
core::kinematics::FoldTree protocols::denovo_design::remove_missing_jump_atoms ( core::pose::Pose const &  pose,
core::kinematics::FoldTree const &  orig 
)
bool protocols::denovo_design::same_pose ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)
template<typename Container , typename T >
Container protocols::denovo_design::set_difference ( typename std::set< T >::const_iterator  begin1,
typename std::set< T >::const_iterator const &  end1,
typename std::set< T >::const_iterator  begin2,
typename std::set< T >::const_iterator const &  end2 
)

Returns vector of elements found in v1 but not in v2.

Referenced by core::io::mmtf::add_ters_via_bonds(), and protocols::rna::movers::clean_res_list().

core::kinematics::FoldTree protocols::denovo_design::slide_jump ( core::kinematics::FoldTree const &  ft_orig,
core::Size const  jump_idx,
core::Size const  new_start,
core::Size const  new_stop 
)
core::kinematics::FoldTree protocols::denovo_design::symmetric_fold_tree ( core::pose::Pose const &  pose,
core::kinematics::FoldTree const &  asymm_ft 
)
core::select::residue_selector::ResidueSubset protocols::denovo_design::symmetric_residue_subset ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  asymm_subset 
)

Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset.

References core::pose::Pose::conformation(), and core::pose::Pose::size().

Referenced by protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply().

std::string protocols::denovo_design::symmetric_secstruct ( core::pose::Pose const &  pose,
std::string const &  asymm_secstruct 
)

Given a symmetric pose and a secstruct for the asymmetric unit, constructs and returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit.

References core::pose::Pose::conformation(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

Referenced by protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::apply().

Variable Documentation

char const protocols::denovo_design::PARENT_DELIMETER = '.'
static