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protocols::dna Namespace Reference

Classes

class  DesignProteinBackboneAroundDNA
 
class  DesignProteinBackboneAroundDNACreator
 
class  DNABase
 
class  DNABasepair
 
class  DNABasestep
 
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  DnaInterfaceFinder
 
class  DnaInterfaceMinMover
 
class  DnaInterfaceMinMoverCreator
 
class  DnaInterfaceMultiStateDesign
 wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework More...
 
class  DnaInterfaceMultiStateDesignCreator
 
class  DnaInterfacePacker
 
class  DnaInterfacePackerCreator
 
class  DnaNeighbor
 
class  DNAParameters
 
class  DnaPosition
 
class  PDBOutput
 
class  PositionType
 basic struct for remembering position/type information before/during/after design More...
 
class  RestrictDesignToProteinDNAInterface
 
class  RestrictDesignToProteinDNAInterfaceCreator
 
class  ResTypeSequence_lt
 
class  Reversion
 
class  RotamerDNAHBondFilter
 
class  SeparateDnaFromNonDna
 
class  SeparateDnaFromNonDnaCreator
 
class  WatsonCrickRotamerCouplings
 
class  WatsonCrickRotamerCouplingsCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< DnaChains
DnaChainsOP
 
typedef
utility::pointer::shared_ptr
< DnaChains const > 
DnaChainsCOP
 
typedef std::map< core::Size,
DnaPosition
DnaPositions
 
typedef
utility::pointer::shared_ptr
< DnaDesignDef
DnaDesignDefOP
 
typedef
utility::pointer::shared_ptr
< DnaDesignDef const > 
DnaDesignDefCOP
 
typedef utility::vector1
< DnaDesignDef
DnaDesignDefs
 
typedef utility::vector1
< DnaDesignDefOP
DnaDesignDefOPs
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceFinder
DnaInterfaceFinderOP
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceFinder const > 
DnaInterfaceFinderCOP
 
typedef std::map< core::Size,
DnaNeighbor
DnaNeighbors
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceMinMover
DnaInterfaceMinMoverOP
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceMinMover const > 
DnaInterfaceMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceMultiStateDesign
DnaInterfaceMultiStateDesignOP
 
typedef
utility::pointer::shared_ptr
< DnaInterfaceMultiStateDesign
const > 
DnaInterfaceMultiStateDesignCOP
 
using Reversions = vector1< Reversion >
 
typedef
utility::pointer::shared_ptr
< DnaInterfacePacker
DnaInterfacePackerOP
 
typedef
utility::pointer::shared_ptr
< DnaInterfacePacker const > 
DnaInterfacePackerCOP
 
typedef std::map
< ResTypeSequence, core::Real,
ResTypeSequence_lt
SequenceScores
 
typedef
utility::pointer::shared_ptr
< DNAParameters
DNAParametersOP
 
typedef
utility::pointer::shared_ptr
< DNAParameters const > 
DNAParametersCOP
 
typedef
utility::pointer::shared_ptr
< PDBOutput
PDBOutputOP
 
typedef
utility::pointer::shared_ptr
< PDBOutput const > 
PDBOutputCOP
 
typedef
utility::pointer::shared_ptr
< RestrictDesignToProteinDNAInterface
RestrictDesignToProteinDNAInterfaceOP
 
typedef
utility::pointer::shared_ptr
< RotamerDNAHBondFilter
RotamerDNAHBondFilterOP
 
typedef
utility::pointer::shared_ptr
< SeparateDnaFromNonDna
SeparateDnaFromNonDnaOP
 
typedef
utility::pointer::shared_ptr
< SeparateDnaFromNonDna const > 
SeparateDnaFromNonDnaCOP
 
typedef std::map< core::Size,
core::chemical::ResidueTypeCOP
ResTypeSequence
 
typedef utility::vector1
< ResTypeSequence
ResTypeSequences
 
typedef std::map< core::Size,
core::chemical::ResidueTypeCOPs
TypesMap
 
typedef utility::vector1
< core::Size
Positions
 
using Strings = utility::vector1< std::string >
 
typedef utility::vector1
< PositionType
PositionTypes
 
typedef
utility::pointer::shared_ptr
< WatsonCrickRotamerCouplings
WatsonCrickRotamerCouplingsOP
 
typedef
utility::pointer::shared_ptr
< ProteinInterfaceMultiStateDesignMover > 
ProteinInterfaceMultiStateDesignMoverOP
 
typedef
utility::pointer::shared_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)
 
std::ostream & operator<< (std::ostream &os, DnaDesignDefOPs 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 const &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, core::Size presid, Residue const &, 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 More...
 
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) More...
 
chemical::AA dna_base_partner (chemical::AA const &na)
 helper function More...
 
void find_basepairs (pose::Pose const &pose, DnaChains &dna_chains, bool include_unpaired)
 
void make_sequence_combinations (utility::vector1< core::Size >::const_iterator seqset_iter, utility::vector1< core::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 More...
 
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::ostream & operator<< (std::ostream &os, ResTypeSequences const &seqs)
 
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< ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack)
 
void substitute_residue (pose::Pose &pose, core::Size index, ResidueType const &new_type)
 
void write_checkpoint (pose::Pose &pose, core::Size iter)
 
void load_checkpoint (pose::Pose &pose, core::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 More...
 
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 const &pdb_prefix)
 
void add_constraints_from_file (pose::Pose &pose)
 
kinematics::FoldTree make_base_pair_aware_fold_tree (pose::Pose const &pose)
 
bool not_already_connected (pose::Pose const &pose, core::Size const num_jumps, char const this_chain, char const other_chain, ObjexxFCL::FArray2D< core::Size > &jump_pairs)
 
void set_base_segment_chainbreak_constraints (pose::Pose &pose, core::Size const start_base, core::Size const end_base)
 
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)
 make a list of all single mutants from a base sequence More...
 
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::ResidueTypeCOP > const &single_sequence, utility::vector0< int > &rot_to_pack)
 
static basic::Tracer TR ("protocols.dna.WatsonCrickRotamerCouplings", t_info)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< DnaChains const > protocols::dna::DnaChainsCOP
typedef utility::pointer::shared_ptr< DnaChains > protocols::dna::DnaChainsOP
typedef utility::pointer::shared_ptr< DnaDesignDef const > protocols::dna::DnaDesignDefCOP
typedef utility::pointer::shared_ptr< DnaDesignDef > protocols::dna::DnaDesignDefOP
typedef utility::vector1< DnaDesignDefOP > protocols::dna::DnaDesignDefOPs
typedef utility::vector1< DnaDesignDef > protocols::dna::DnaDesignDefs
typedef utility::pointer::shared_ptr< DnaInterfaceFinder const > protocols::dna::DnaInterfaceFinderCOP
typedef utility::pointer::shared_ptr< DnaInterfaceFinder > protocols::dna::DnaInterfaceFinderOP
typedef utility::pointer::shared_ptr< DnaInterfaceMinMover const > protocols::dna::DnaInterfaceMinMoverCOP
typedef utility::pointer::shared_ptr< DnaInterfaceMinMover > protocols::dna::DnaInterfaceMinMoverOP
typedef utility::pointer::shared_ptr< DnaInterfacePacker const > protocols::dna::DnaInterfacePackerCOP
typedef utility::pointer::shared_ptr< DnaInterfacePacker > protocols::dna::DnaInterfacePackerOP
typedef utility::pointer::shared_ptr< DNAParameters const > protocols::dna::DNAParametersCOP
typedef utility::pointer::shared_ptr< DNAParameters > protocols::dna::DNAParametersOP
typedef utility::pointer::shared_ptr< PDBOutput const > protocols::dna::PDBOutputCOP
typedef utility::pointer::shared_ptr< PDBOutput > protocols::dna::PDBOutputOP
typedef utility::vector1< core::Size > protocols::dna::Positions
typedef utility::vector1< PositionType > protocols::dna::PositionTypes
typedef utility::pointer::shared_ptr< ProteinInterfaceMultiStateDesignMover const > protocols::dna::ProteinInterfaceMultiStateDesignMoverCOP
typedef utility::pointer::shared_ptr< ProteinInterfaceMultiStateDesignMover > protocols::dna::ProteinInterfaceMultiStateDesignMoverOP
using protocols::dna::Reversions = typedef vector1<Reversion>
typedef utility::pointer::shared_ptr< RotamerDNAHBondFilter > protocols::dna::RotamerDNAHBondFilterOP
typedef utility::pointer::shared_ptr< SeparateDnaFromNonDna const > protocols::dna::SeparateDnaFromNonDnaCOP
typedef utility::pointer::shared_ptr< SeparateDnaFromNonDna > protocols::dna::SeparateDnaFromNonDnaOP
using protocols::dna::Strings = typedef utility::vector1<std::string>

Function Documentation

void protocols::dna::add_constraints_from_file ( pose::Pose pose)
core::Real protocols::dna::argrot_dna_dis2 ( pose::Pose const &  pose,
core::Size  presid,
Residue const &  ,
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 
)
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 
)

distance check for contact between two sets of atoms

Author
ashworth
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 
)

distance check for contact between two sets of atoms

Author
ashworth

Referenced by argrot_dna_dis2().

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

Author
ashworth

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), and 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,
core::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 const &  pdb_prefix 
)
void protocols::dna::load_dna_design_defs_from_strings ( DnaDesignDefOPs &  defs,
Strings const &  str_defs 
)
core::kinematics::FoldTree protocols::dna::make_base_pair_aware_fold_tree ( pose::Pose const &  pose)
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_sequence_combinations ( utility::vector1< core::Size >::const_iterator  seqset_iter,
utility::vector1< core::Size > const &  seq_indices,
task::PackerTaskCOP  ptask,
ResTypeSequence &  sequence,
ResTypeSequences &  sequences 
)

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

Author
ashworth

References core::chemical::ADDUCT_VARIANT.

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

void protocols::dna::make_single_mutants ( ResTypeSequence const &  sequence,
core::pack::task::PackerTaskCOP  ptask,
ResTypeSequences &  sequences 
)

make a list of all single mutants from a base sequence

Author
ashworth
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

Author
ashworth

References core::chemical::ADDUCT_VARIANT.

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

void protocols::dna::make_subdirs ( std::string const &  name)
bool protocols::dna::not_already_connected ( pose::Pose const &  pose,
core::Size const  num_jumps,
char const  this_chain,
char const  other_chain,
ObjexxFCL::FArray2D< core::Size > &  jump_pairs 
)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
DnaDesignDef const &  def 
)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
DnaDesignDefs const &  defs 
)

References core::sequence::end.

std::ostream & protocols::dna::operator<< ( std::ostream &  os,
DnaDesignDefOPs const &  defs 
)

References core::sequence::end.

std::ostream & protocols::dna::operator<< ( std::ostream &  os,
ResTypeSequence const &  seq 
)
std::ostream & protocols::dna::operator<< ( std::ostream &  os,
ResTypeSequences const &  seqs 
)
int const protocols::dna::PRECISION ( )
void protocols::dna::print_sequence_pdb_nums ( ResTypeSequence const &  seq,
pose::Pose const &  pose,
std::ostream &  os 
)
void protocols::dna::print_sequences_pdb_nums ( ResTypeSequences const &  seqs,
pose::Pose const &  pose,
std::ostream &  os 
)
void protocols::dna::restrict_dna_rotamers ( core::pack::rotamer_set::RotamerSetsCOP  rotsets,
ResTypeSequence const &  seq,
utility::vector0< int > &  rot_to_pack 
)

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

Author
ashworth
void protocols::dna::restrict_dna_rotamers ( RotamerSetsCOP  rotamer_sets,
ResTypeSequence const &  seq,
utility::vector0< int > &  rot_to_pack 
)

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

Author
ashworth

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

void protocols::dna::restrict_to_single_sequence ( core::pack::rotamer_set::RotamerSetsCOP  rotamer_sets,
utility::vector1< core::chemical::ResidueTypeCOP > const &  single_sequence,
utility::vector0< int > &  rot_to_pack 
)

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

Author
ashworth
void protocols::dna::restrict_to_single_sequence ( rotamer_set::RotamerSetsCOP  rotamer_sets,
vector1< ResidueTypeCOP > const &  single_sequence,
utility::vector0< int > &  rot_to_pack 
)

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

Author
ashworth

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

std::string protocols::dna::seq_pdb_str ( ResTypeSequence const &  seq,
pose::Pose const &  pose 
)
std::string protocols::dna::seq_to_str ( ResTypeSequence const &  seq)
void protocols::dna::set_base_segment_chainbreak_constraints ( pose::Pose pose,
core::Size const  start_base,
core::Size const  end_base 
)
std::string protocols::dna::string_join ( PDBOutput::Strings const &  list,
std::string const &  sep = ", " 
)
void protocols::dna::substitute_residue ( pose::Pose pose,
core::Size  index,
ResidueType const &  new_type 
)
static basic::Tracer protocols::dna::TR ( "protocols.dna.SeparateDnaFromNonDna"  ,
basic::t_info   
)
static
static basic::Tracer protocols::dna::TR ( "protocols.dna.WatsonCrickRotamerCouplings"  ,
t_info   
)
static
static basic::Tracer protocols::dna::TR ( "protocols.dna.DnaInterfaceMinMover"  ,
t_info   
)
static
static basic::Tracer protocols::dna::TR ( "protocols.dna.RestrictDesignToProteinDNAInterface"  ,
t_info   
)
static
static basic::Tracer protocols::dna::TR ( "protocols.dna.PDBOutput"  ,
t_info   
)
static
static basic::Tracer protocols::dna::TR ( "protocols.dna.DesignProteinBackboneAroundDNA"  ,
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.DnaInterfacePacker"  )
static
static basic::Tracer protocols::dna::TR_spec ( "protocols.dna.Specificity"  )
static
void protocols::dna::write_checkpoint ( pose::Pose pose,
core::Size  iter 
)
core::Real protocols::dna::z_axis_dist ( Residue const &  pres,
Residue const &  dres 
)

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').

Author
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().