Rosetta 3.4
Classes | Typedefs | Functions
protocols::dna Namespace Reference

Classes

class  DesignProteinBackboneAroundDNA
class  DesignProteinBackboneAroundDNACreator
class  DnaPosition
class  DnaChains
class  DnaDesignDef
 command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience More...
class  DnaNeighbor
class  DnaInterfaceFinder
class  DnaInterfaceMinMover
class  DnaInterfaceMinMoverCreator
class  DnaInterfaceMultiStateDesign
 wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework More...
class  DnaInterfaceMultiStateDesignCreator
class  Reversion
class  ResTypeSequence_lt
class  DnaInterfacePacker
class  DnaInterfacePackerCreator
class  PDBOutput
class  RestrictDesignToProteinDNAInterface
class  RestrictDesignToProteinDNAInterfaceCreator
class  RotamerDNAHBondFilter
class  SeparateDnaFromNonDna
class  SeparateDnaFromNonDnaCreator
class  PositionType
 basic struct for remembering position/type information before/during/after design More...
class  WatsonCrickRotamerCouplings
class  WatsonCrickRotamerCouplingsCreator

Typedefs

typedef
utility::pointer::owning_ptr
< DnaChains
DnaChainsOP
typedef
utility::pointer::owning_ptr
< DnaChains const > 
DnaChainsCOP
typedef std::map< core::Size,
DnaPosition
DnaPositions
typedef
utility::pointer::owning_ptr
< DnaDesignDef
DnaDesignDefOP
typedef
utility::pointer::owning_ptr
< DnaDesignDef const > 
DnaDesignDefCOP
typedef utility::vector1
< DnaDesignDef
DnaDesignDefs
typedef utility::vector1
< DnaDesignDefOP
DnaDesignDefOPs
typedef
utility::pointer::owning_ptr
< DnaInterfaceFinder
DnaInterfaceFinderOP
typedef
utility::pointer::owning_ptr
< DnaInterfaceFinder const > 
DnaInterfaceFinderCOP
typedef std::map< core::Size,
DnaNeighbor
DnaNeighbors
typedef
utility::pointer::owning_ptr
< DnaInterfaceMinMover
DnaInterfaceMinMoverOP
typedef
utility::pointer::owning_ptr
< DnaInterfaceMinMover const > 
DnaInterfaceMinMoverCOP
typedef
utility::pointer::owning_ptr
< DnaInterfaceMultiStateDesign
DnaInterfaceMultiStateDesignOP
typedef
utility::pointer::owning_ptr
< DnaInterfaceMultiStateDesign
const > 
DnaInterfaceMultiStateDesignCOP
typedef vector1< ReversionReversions
typedef
utility::pointer::owning_ptr
< DnaInterfacePacker
DnaInterfacePackerOP
typedef
utility::pointer::owning_ptr
< DnaInterfacePacker const > 
DnaInterfacePackerCOP
typedef std::map
< ResTypeSequence, core::Real,
ResTypeSequence_lt
SequenceScores
typedef
utility::pointer::owning_ptr
< PDBOutput
PDBOutputOP
typedef
utility::pointer::owning_ptr
< PDBOutput const > 
PDBOutputCOP
typedef
utility::pointer::owning_ptr
< RestrictDesignToProteinDNAInterface
RestrictDesignToProteinDNAInterfaceOP
typedef
utility::pointer::owning_ptr
< RotamerDNAHBondFilter
RotamerDNAHBondFilterOP
typedef
utility::pointer::owning_ptr
< SeparateDnaFromNonDna
SeparateDnaFromNonDnaOP
typedef
utility::pointer::owning_ptr
< SeparateDnaFromNonDna const > 
SeparateDnaFromNonDnaCOP
typedef std::map< core::Size,
core::chemical::ResidueTypeCAP
ResTypeSequence
typedef utility::vector1
< ResTypeSequence
ResTypeSequences
typedef std::map< core::Size,
core::chemical::ResidueTypeCAPs
TypesMap
typedef utility::vector1
< core::Size
Positions
typedef utility::vector1
< std::string > 
Strings
typedef utility::vector1
< PositionType
PositionTypes
typedef
utility::pointer::owning_ptr
< WatsonCrickRotamerCouplings
WatsonCrickRotamerCouplingsOP
typedef
utility::pointer::owning_ptr
< ProteinInterfaceMultiStateDesignMover > 
ProteinInterfaceMultiStateDesignMoverOP
typedef
utility::pointer::owning_ptr
< ProteinInterfaceMultiStateDesignMover
const > 
ProteinInterfaceMultiStateDesignMoverCOP

Functions

static basic::Tracer TR ("protocols.dna.DesignProteinBackboneAroundDNA", t_info)
std::ostream & operator<< (std::ostream &os, DnaDesignDef const &def)
std::ostream & operator<< (std::ostream &os, DnaDesignDefs const &defs)
static basic::Tracer TR ("protocols.dna.DnaInterfaceMinMover", t_info)
static basic::Tracer TR ("protocols.dna.DnaInterfaceMultiStateDesign", t_info)
int const PRECISION (3)
static basic::Tracer TR ("protocols.dna.DnaInterfacePacker")
static basic::Tracer TR_spec ("protocols.dna.Specificity")
static basic::Tracer TR ("protocols.dna.PDBOutput", t_info)
std::string string_join (PDBOutput::Strings const &list, std::string sep=", ")
void make_subdirs (std::string const &name)
static basic::Tracer TR ("protocols.dna.RestrictDesignToProteinDNAInterface", t_info)
static basic::Tracer TR ("protocols.dna.SeparateDnaFromNonDna", basic::t_info)
static basic::Tracer TR ("protocols.dna.util", basic::t_info)
bool close_to_dna (Residue const &pres, Residue const &dres, Real threshold, bool base_only)
Real argrot_dna_dis2 (pose::Pose const &pose, Size presid, Residue const &pres, Residue const &dres, Real threshold, bool base_only)
Real contact_distance2 (Atoms::const_iterator a_begin, Atoms::const_iterator a_end, Atoms::const_iterator b_begin, Atoms::const_iterator b_end, Real threshold)
Real z_axis_dist (Residue const &pres, Residue const &dres)
std::string dna_comp_name_str (std::string const &dna)
 also consider using the dna_base_partner function below
std::string dna_full_name3 (std::string const &name3)
 intended to convert any DNA "threeletter code" into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns " N" format as of Dec 2008)
chemical::AA dna_base_partner (chemical::AA const &na)
 helper function
void find_basepairs (pose::Pose const &pose, DnaChains &dna_chains, bool include_unpaired)
void make_sequence_combinations (utility::vector1< Size >::const_iterator seqset_iter, utility::vector1< Size > const &seq_indices, task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
void make_single_mutants (ResTypeSequence const &sequence, task::PackerTaskCOP ptask, ResTypeSequences &sequences)
 make a list of all single mutants from a base sequence
void design_residues_list (std::list< PositionType > &design_residues, pose::Pose const &pose, task::PackerTask const &ptask)
std::ostream & operator<< (std::ostream &os, ResTypeSequence const &seq)
std::string seq_to_str (ResTypeSequence const &seq)
std::string seq_pdb_str (ResTypeSequence const &seq, pose::Pose const &pose)
void print_sequence_pdb_nums (ResTypeSequence const &seq, pose::Pose const &pose, std::ostream &os)
void print_sequences_pdb_nums (ResTypeSequences const &seqs, pose::Pose const &pose, std::ostream &os)
void restrict_dna_rotamers (RotamerSetsCOP rotamer_sets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
void restrict_to_single_sequence (rotamer_set::RotamerSetsCOP rotamer_sets, vector1< ResidueTypeCAP > const &single_sequence, utility::vector0< int > &rot_to_pack)
void substitute_residue (pose::Pose &pose, Size index, ResidueType const &new_type)
void write_checkpoint (pose::Pose &pose, Size iter)
void load_checkpoint (pose::Pose &pose, Size &iter)
void checkpoint_cleanup ()
void load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, Strings const &str_defs)
 loads command-line dna design definitions (shorthand alternative to using resfile) option value is string vector i.e. -dna_defs C.-6 C.-5 or -dna_defs C.-6.GUA C.-5.CYT
void load_dna_design_defs_from_file (DnaDesignDefOPs &defs, std::string const &filename, std::string const &pdb_prefix)
void load_dna_design_defs_from_options (DnaDesignDefOPs &defs, std::string pdb_prefix)
void add_constraints_from_file (pose::Pose &pose)
core::Real contact_distance2 (core::conformation::Atoms::const_iterator a_begin, core::conformation::Atoms::const_iterator a_end, core::conformation::Atoms::const_iterator b_begin, core::conformation::Atoms::const_iterator b_end, core::Real threshold=0.0)
void make_single_mutants (ResTypeSequence const &sequence, core::pack::task::PackerTaskCOP ptask, ResTypeSequences &sequences)
void design_residues_list (std::list< PositionType > &design_residues, core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask)
void make_sequence_combinations (utility::vector1< core::Size >::const_iterator seqset_iter, utility::vector1< core::Size > const &seq_indices, core::pack::task::PackerTaskCOP ptask, ResTypeSequence &sequence, ResTypeSequences &sequences)
void restrict_dna_rotamers (core::pack::rotamer_set::RotamerSetsCOP rotsets, ResTypeSequence const &seq, utility::vector0< int > &rot_to_pack)
void restrict_to_single_sequence (core::pack::rotamer_set::RotamerSetsCOP rotamer_sets, utility::vector1< core::chemical::ResidueTypeCAP > const &single_sequence, utility::vector0< int > &rot_to_pack)
void load_dna_design_defs_from_strings (DnaDesignDefOPs &defs, utility::vector1< std::string > const &str_defs)
static basic::Tracer TR ("protocols.dna.WatsonCrickRotamerCouplings", t_info)

Typedef Documentation

typedef utility::pointer::owning_ptr< ProteinInterfaceMultiStateDesignMover const > protocols::dna::ProteinInterfaceMultiStateDesignMoverCOP
typedef utility::vector1< std::string > protocols::dna::Strings

Function Documentation

void protocols::dna::add_constraints_from_file ( pose::Pose pose)
core::Real protocols::dna::argrot_dna_dis2 ( pose::Pose const &  pose,
Size  presid,
Residue const &  pres,
Residue const &  dres,
Real  threshold,
bool  base_only 
)
void protocols::dna::checkpoint_cleanup ( )
bool protocols::dna::close_to_dna ( Residue const &  pres,
Residue const &  dres,
Real  threshold,
bool  base_only 
)
Real protocols::dna::contact_distance2 ( Atoms::const_iterator  a_begin,
Atoms::const_iterator  a_end,
Atoms::const_iterator  b_begin,
Atoms::const_iterator  b_end,
Real  threshold 
)

contact_distance2

distance check for contact between two sets of atoms

Authors:
ashworth

Referenced by argrot_dna_dis2().

core::Real protocols::dna::contact_distance2 ( core::conformation::Atoms::const_iterator  a_begin,
core::conformation::Atoms::const_iterator  a_end,
core::conformation::Atoms::const_iterator  b_begin,
core::conformation::Atoms::const_iterator  b_end,
core::Real  threshold = 0.0 
)
void protocols::dna::design_residues_list ( std::list< PositionType > &  design_residues,
core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  ptask 
)
void protocols::dna::design_residues_list ( std::list< PositionType > &  design_residues,
pose::Pose const &  pose,
task::PackerTask const &  ptask 
)
core::chemical::AA protocols::dna::dna_base_partner ( chemical::AA const &  na)
std::string protocols::dna::dna_comp_name_str ( std::string const &  dna)

also consider using the dna_base_partner function below

dna_comp_name_str

Authors:
ashworth

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply().

std::string protocols::dna::dna_full_name3 ( std::string const &  name3)
void protocols::dna::find_basepairs ( pose::Pose const &  pose,
DnaChains &  dna_chains,
bool  include_unpaired 
)
void protocols::dna::load_checkpoint ( pose::Pose pose,
Size iter 
)
void protocols::dna::load_dna_design_defs_from_file ( DnaDesignDefOPs &  defs,
std::string const &  filename,
std::string const &  pdb_prefix 
)
void protocols::dna::load_dna_design_defs_from_options ( DnaDesignDefOPs &  defs,
std::string  pdb_prefix 
)
void protocols::dna::load_dna_design_defs_from_strings ( DnaDesignDefOPs &  defs,
Strings const &  str_defs 
)
void protocols::dna::load_dna_design_defs_from_strings ( DnaDesignDefOPs &  defs,
utility::vector1< std::string > const &  str_defs 
)
void protocols::dna::make_sequence_combinations ( utility::vector1< Size >::const_iterator  seqset_iter,
utility::vector1< Size > const &  seq_indices,
task::PackerTaskCOP  ptask,
ResTypeSequence &  sequence,
ResTypeSequences &  sequences 
)

make_sequence_combinations

populates a set of all possible sequence combinations over a given range of positions. recursive.

Authors:
ashworth

References core::chemical::ADDUCT.

void protocols::dna::make_sequence_combinations ( utility::vector1< core::Size >::const_iterator  seqset_iter,
utility::vector1< core::Size > const &  seq_indices,
core::pack::task::PackerTaskCOP  ptask,
ResTypeSequence &  sequence,
ResTypeSequences &  sequences 
)
void protocols::dna::make_single_mutants ( ResTypeSequence const &  sequence,
core::pack::task::PackerTaskCOP  ptask,
ResTypeSequences &  sequences 
)
void protocols::dna::make_single_mutants ( ResTypeSequence const &  sequence,
task::PackerTaskCOP  ptask,
ResTypeSequences &  sequences 
)

make a list of all single mutants from a base sequence

make_single_mutants

Authors:
ashworth

References core::chemical::ADDUCT.

Referenced by protocols::dna::DnaInterfacePacker::measure_specificity().

void protocols::dna::make_subdirs ( std::string const &  name)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
DnaDesignDef const &  def 
)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
ResTypeSequence const &  seq 
)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
DnaDesignDefs const &  defs 
)

References core::sequence::end.

int const protocols::dna::PRECISION ( )
void protocols::dna::print_sequence_pdb_nums ( ResTypeSequence const &  seq,
pose::Pose const &  pose,
std::ostream &  os 
)

References seq_pdb_str().

Referenced by print_sequences_pdb_nums().

void protocols::dna::print_sequences_pdb_nums ( ResTypeSequences const &  seqs,
pose::Pose const &  pose,
std::ostream &  os 
)
void protocols::dna::restrict_dna_rotamers ( RotamerSetsCOP  rotamer_sets,
ResTypeSequence const &  seq,
utility::vector0< int > &  rot_to_pack 
)

restrict_dna_rotamers

for packing a single DNA sequence out of a multi-DNA-sequence RotamerSet

Authors:
ashworth
void protocols::dna::restrict_dna_rotamers ( core::pack::rotamer_set::RotamerSetsCOP  rotsets,
ResTypeSequence const &  seq,
utility::vector0< int > &  rot_to_pack 
)
void protocols::dna::restrict_to_single_sequence ( rotamer_set::RotamerSetsCOP  rotamer_sets,
vector1< ResidueTypeCAP > const &  single_sequence,
utility::vector0< int > &  rot_to_pack 
)

restrict_to_single_sequence

for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability

Authors:
ashworth

Referenced by protocols::dna::DnaInterfacePacker::measure_specificities(), and protocols::dna::DnaInterfacePacker::reversion_scan().

void protocols::dna::restrict_to_single_sequence ( core::pack::rotamer_set::RotamerSetsCOP  rotamer_sets,
utility::vector1< core::chemical::ResidueTypeCAP > const &  single_sequence,
utility::vector0< int > &  rot_to_pack 
)
std::string protocols::dna::seq_pdb_str ( ResTypeSequence const &  seq,
pose::Pose const &  pose 
)
std::string protocols::dna::seq_to_str ( ResTypeSequence const &  seq)
std::string protocols::dna::string_join ( PDBOutput::Strings const &  list,
std::string  sep = ", " 
)

References core::sequence::end.

void protocols::dna::substitute_residue ( pose::Pose pose,
Size  index,
ResidueType const &  new_type 
)
static basic::Tracer protocols::dna::TR ( "protocols.dna.WatsonCrickRotamerCouplings"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.SeparateDnaFromNonDna"  ,
basic::t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.RestrictDesignToProteinDNAInterface"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfacePacker"  ) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfaceMinMover"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.PDBOutput"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfaceMultiStateDesign"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.util"  ,
basic::t_info   
) [static]
static basic::Tracer protocols::dna::TR ( "protocols.dna.DesignProteinBackboneAroundDNA"  ,
t_info   
) [static]
static basic::Tracer protocols::dna::TR_spec ( "protocols.dna.Specificity"  ) [static]
void protocols::dna::write_checkpoint ( pose::Pose pose,
Size  iter 
)
core::Real protocols::dna::z_axis_dist ( Residue const &  pres,
Residue const &  dres 
)

z_axis_dist

A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis ('laterally').

Authors:
ashworth

References core::conformation::Residue::first_sidechain_atom(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), core::conformation::Residue::nbr_atom_xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::dna::DnaInterfaceFinder::determine_dna_interface(), and protocols::dna::DnaInterfaceFinder::determine_protein_interface().

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