Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Types | Private Attributes | List of all members
core::io::silent::BinarySilentStruct Class Reference

why this inheritance pathway? this makes no sense! More...

#include <BinarySilentStruct.hh>

Inheritance diagram for core::io::silent::BinarySilentStruct:
Inheritance graph
[legend]

Public Member Functions

 BinarySilentStruct (SilentFileOptions const &opts, Size const nres_in)
 Constructors. More...
 
 BinarySilentStruct (SilentFileOptions const &opts)
 
 BinarySilentStruct (SilentFileOptions const &opts, core::pose::Pose const &pose, std::string tag="empty_tag")
 
 BinarySilentStruct (BinarySilentStruct const &src)
 
BinarySilentStructOP shared_from_this ()
 
SilentStructOP clone () const override
 
BinarySilentStructoperator= (BinarySilentStruct const &src)
 Assignment operator. More...
 
void resize (Size const nres_in)
 Re-dimension the storage capacity of this BinarySilentStruct to the given number of residues. More...
 
 ~BinarySilentStruct () override
 
bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container) override
 Initialize object from a set of lines. More...
 
bool init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container, bool const skip_read_from_container)
 Initialize object from a set of lines. More...
 
void fill_pose (core::pose::Pose &pose, bool const metapatches=true) const override
 Configure the conformation of the given Pose with the conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types. More...
 
void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) const override
 Configure the conformation of the given Pose with the conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types. More...
 
void fill_struct (core::pose::Pose const &pose, std::string tag) override
 opposite of fill_pose More...
 
void setup_other_poses (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const
 for stepwise modeling, setup other_poses inside full_model_info More...
 
void print_header (std::ostream &out) const override
 print header information More...
 
void print_conformation (std::ostream &output) const override
 Prints the conformation information within this BinarySilentStruct to the given std::ostream. More...
 
ObjexxFCL::FArray2D< Realget_CA_xyz () const override
 returns the positions of the CA atoms More...
 
virtual Real CA_rmsd (BinarySilentStruct other_pss)
 
core::Real get_debug_rmsd () override
 calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this ProteinSilentStruct and the C-alpha atoms from this ProteinSilentStruct. More...
 
void add_jump (kinematics::Jump jump)
 
kinematics::RT const & jump (Size jump_num) const
 
void fold_tree (kinematics::FoldTree f)
 
kinematics::FoldTree const & fold_tree () const
 
bool fullatom () const
 
void fullatom (bool fullatom)
 
char secstruct (unsigned int seqpos) const
 
void secstruct (unsigned int seqpos, char ss)
 
void symmetry_info (core::conformation::symmetry::SymmetryInfo &s)
 
core::conformation::symmetry::SymmetryInfoCOP symmetry_info () const
 
bool is_symmetric () const
 
void parse_chain_endings (std::istream &stream)
 
void chain_endings (utility::vector1< Size > const &endings)
 
std::string chain_endings_str () const
 
utility::vector1< Size > const & chain_endings () const
 
void add_chain_ending (Size const seqpos)
 
- Public Member Functions inherited from core::io::silent::SilentStruct
 SilentStruct (SilentFileOptions const &opts)
 
 ~SilentStruct () override
 
 SilentStruct (SilentStruct const &)
 
SilentStructoperator= (SilentStruct const &)
 
SilentStructCOP get_self_ptr () const
 self pointers More...
 
SilentStructOP get_self_ptr ()
 
void fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSetCOP residue_set, bool const metapatches=true) const
 non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one) and invokes the virtual method that takes the const &. More...
 
void set_tag_from_pose (const core::pose::Pose &pose)
 Sets the tag from the Pose DataCache. More...
 
void precision (core::Size precision)
 
core::Size precision () const
 
void scoreline_prefix (std::string const &prefix)
 
std::string scoreline_prefix () const
 
void finish_pose (core::pose::Pose &pose) const
 calls optH if command line requests optH. must be called by derived classes. More...
 
virtual void print_score_header (std::ostream &out) const
 only print SCORE: header line More...
 
virtual void print_scores (std::ostream &out) const
 print out a SCORE line to the given ozstream. More...
 
virtual void print_comments (std::ostream &out) const
 print the comments in this SilentStruct. More...
 
virtual void print_residue_numbers (std::ostream &out) const
 print the resnum in this SilentStruct, if filled. More...
 
virtual void print_submotif_info (std::ostream &out) const
 print the submotif_info in this SilentStruct, if filled. More...
 
virtual Size nres () const
 returns the number of residues contained by this SilentStruct. More...
 
void set_decoy_tag (std::string const &tag)
 set the tag associate with this SilentStruct More...
 
std::string decoy_tag () const
 returns the tag associated with this SilentStruct. More...
 
core::sequence::AnnotatedSequence
const & 
sequence () const
 returns the sequence associated with this SilentStruct. More...
 
void nres (Size nres)
 returns the number of residues in this SilentStruct. More...
 
void decoy_tag (std::string const &tag)
 sets the tag associated with this SilentStruct. More...
 
void sequence (core::sequence::AnnotatedSequence const &sequence)
 sets the sequence for this SilentStruct. More...
 
void silent_energies (utility::vector1< SilentEnergy > const &new_se)
 sets the silent_energies for this SilentStruct. More...
 
void sort_silent_scores ()
 sort all the silent energies by their name. More...
 
bool has_energy (std::string const &scorename) const
 returns true if this SilentStruct has an energy for the given scorename, returns false otherwise. More...
 
core::Real get_energy (std::string const &scorename) const
 Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...
 
std::string const & get_string_value (std::string const &scorename) const
 Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...
 
SilentEnergy const & get_silent_energy (std::string const &scorename) const
 Returns the SilentEnergy associated with this scorename. More...
 
utility::vector1< SilentEnergyget_silent_energies ()
 
void set_valid_energies (utility::vector1< std::string > valid)
 
virtual void clear_energies ()
 Clear all of the energies in the SilentStruct. Doesn't just zero the energies, it entirely removes all knowledge of all energies from this SilentStruct. More...
 
void add_energy (std::string const &scorename, Real value, Real weight=1.0)
 add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0. More...
 
void add_string_value (std::string const &scorename, std::string const &value, int const index=-1)
 add a non-floating point score of a given name and value to this SilentStruct. More...
 
void copy_scores (const SilentStruct &src_ss)
 Copy the score information in the given SilentStruct into this SilentStruct. More...
 
void add_comment (std::string name, std::string value)
 add a named comment to this SilentStruct object. Similar to methods for playing with energies, but mapping is string => string rather than string => Real. More...
 
bool has_comment (std::string const &name) const
 
std::string get_comment (std::string const &name) const
 
void comment_from_line (std::string const &line)
 
void comment_from_line (std::string const &line, bool const include_silentfile_comments)
 Creates and adds a comment from an input REMARK line. More...
 
void erase_comment (std::string const &name)
 
void clear_comments ()
 
std::map< std::string,
std::string > 
get_all_comments () const
 
void parse_energies (std::istream &input, utility::vector1< std::string > const &energy_names)
 
void energies_from_pose (core::pose::Pose const &pose)
 Initialize this SilentStruct's energies from the given Pose. This sets energies, energy weights, and the output widths for the energies. More...
 
void energies_into_pose (core::pose::Pose &pose) const
 Put the energy information from this SilentStruct into the pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct. More...
 
utility::vector1< SilentEnergyenergies () const
 Returns the vector of SilentEnergy objects associated with this SilentStruct object. More...
 
EnergyNames energy_names () const
 Returns the EnergyNames that this SilentStruct contains. More...
 
void rename_energies ()
 
bool read_sequence (std::string const &line)
 
void read_score_headers (std::string const &line, utility::vector1< std::string > &enames, SilentFileData &container)
 
std::string one_letter_sequence () const
 strip [...] comment from seqeunce_ and return pure one-letter sequence More...
 
virtual core::Size mem_footprint () const
 
void print_parent_remarks (std::ostream &out) const
 
std::string get_parent_remark (std::string const &name) const
 
bool has_parent_remark (std::string const &name) const
 
void add_parent_remark (std::string const &name, std::string const &value)
 
void get_parent_remark_from_line (std::string const &line)
 
void set_residue_numbers (utility::vector1< int > const &residue_numbers)
 
void set_chains (utility::vector1< char > const &chains)
 
void set_full_model_parameters (core::pose::full_model_info::FullModelParametersCOP setting)
 
core::pose::full_model_info::FullModelParametersCOP full_model_parameters () const
 
void set_segment_IDs (utility::vector1< std::string > const &segids)
 
void fill_struct_with_residue_numbers (pose::Pose const &pose)
 
void fill_other_struct_list (pose::Pose const &pose)
 
void residue_numbers_into_pose (pose::Pose &pose) const
 
void full_model_info_into_pose (pose::Pose &pose) const
 
void figure_out_residue_numbers_from_line (std::istream &line_stream)
 
void figure_out_segment_ids_from_line (std::istream &line_stream)
 
void add_submotif_info_from_line (std::istream &line_stream)
 
void fill_struct_with_submotif_info_list (pose::Pose const &pose)
 
utility::vector1
< SilentStructOP > const & 
other_struct_list () const
 
utility::vector1
< SilentStructOP > & 
nonconst_other_struct_list ()
 
void add_other_struct (SilentStructOP silent_struct)
 
virtual void set_force_bitflip (bool const setting)
 Sets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...
 
virtual bool force_bitflip () const
 Gets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...
 
SilentFileOptions const & options () const
 

Private Types

typedef SilentStruct Parent
 

Private Attributes

bool fullatom_
 
utility::vector1< char > secstruct_
 
utility::vector1< std::pair
< core::id::NamedAtomID,
core::id::NamedAtomID > > 
noncanonical_residue_connections_
 
utility::vector1< kinematics::RTjumps_
 
bool bJumps_use_IntraResStub_
 
kinematics::FoldTree fold_tree_
 
core::conformation::symmetry::SymmetryInfoOP symminfo_
 
utility::vector1< Sizechain_endings_
 
utility::vector1
< utility::vector1
< numeric::xyzVector< float > > > 
atm_coords_
 

Additional Inherited Members

- Protected Member Functions inherited from core::io::silent::SilentStruct
void detect_fullatom (core::Size pos, core::Size natoms, bool &fullatom, bool &well_defined)
 @ brief helper to detect fullatom input More...
 
void extract_writeable_cacheable_data (core::pose::Pose const &pose)
 add string serialization of all WriteableCacheableData in as comments. More...
 

Detailed Description

why this inheritance pathway? this makes no sense!

Member Typedef Documentation

Constructor & Destructor Documentation

core::io::silent::BinarySilentStruct::BinarySilentStruct ( SilentFileOptions const &  opts,
Size const  nres_in 
)
core::io::silent::BinarySilentStruct::BinarySilentStruct ( SilentFileOptions const &  opts)
core::io::silent::BinarySilentStruct::BinarySilentStruct ( SilentFileOptions const &  opts,
core::pose::Pose const &  pose,
std::string  tag = "empty_tag" 
)
core::io::silent::BinarySilentStruct::BinarySilentStruct ( BinarySilentStruct const &  src)
default
core::io::silent::BinarySilentStruct::~BinarySilentStruct ( )
overridedefault

Member Function Documentation

void core::io::silent::BinarySilentStruct::add_chain_ending ( Size const  seqpos)
void core::io::silent::BinarySilentStruct::add_jump ( kinematics::Jump  jump)
inline
Real core::io::silent::BinarySilentStruct::CA_rmsd ( BinarySilentStruct  other_pss)
virtual
void core::io::silent::BinarySilentStruct::chain_endings ( utility::vector1< Size > const &  endings)
utility::vector1< Size > const& core::io::silent::BinarySilentStruct::chain_endings ( ) const
inline
std::string core::io::silent::BinarySilentStruct::chain_endings_str ( ) const

References chain_endings().

Referenced by print_conformation().

SilentStructOP core::io::silent::BinarySilentStruct::clone ( ) const
inlineoverridevirtual

Implements core::io::silent::SilentStruct.

Referenced by fill_struct().

void core::io::silent::BinarySilentStruct::fill_pose ( core::pose::Pose pose,
bool const  metapatches = true 
) const
overridevirtual

Configure the conformation of the given Pose with the conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

Reimplemented from core::io::silent::SilentStruct.

References core::chemical::CENTROID_t, core::chemical::FULL_ATOM_t, fullatom(), core::pose::Pose::residue_type_set_for_pose(), and core::io::silent::tr().

Referenced by core::pack::interaction_graph::generate_pose_from_packer_description(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), and get_debug_rmsd().

void core::io::silent::BinarySilentStruct::fill_pose ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set,
bool const  metapatches = true 
) const
overridevirtual

Configure the conformation of the given Pose with the conformational data within this BinarySilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

Reimplemented from core::io::silent::SilentStruct.

References core::pose::Pose::annotated_sequence(), atm_coords_, core::pose::Pose::batch_set_xyz(), bJumps_use_IntraResStub_, core::chemical::C_METHYLAMIDATION, chain_endings(), core::conformation::Conformation::chain_endings(), core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::declare_chemical_bond(), core::io::silent::SilentStruct::decoy_tag(), core::pose::Pose::energies(), core::io::silent::SilentStruct::finish_pose(), fold_tree(), core::pose::Pose::fold_tree(), fullatom(), core::conformation::Residue::has_variant_type(), core::pose::initialize_disulfide_bonds(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_mirror_symmetric(), core::pose::symmetry::is_symmetric(), is_symmetric(), jump(), core::kinematics::FoldTree::jump_edge(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_sequence(), core::pose::symmetry::make_symmetric_pose(), protocols::mean_field::min(), core::chemical::N_ACETYLATION, core::conformation::Residue::name(), core::pose::named_stub_id_to_stub_id(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), noncanonical_residue_connections_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::io::silent::SilentStruct::one_letter_sequence(), core::pose::Pose::residue(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::set_jump(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), setup_other_poses(), core::kinematics::Edge::start(), protocols::loops::start, core::kinematics::Edge::stop(), protocols::loops::stop, symmetry_info(), and core::io::silent::tr().

void core::io::silent::BinarySilentStruct::fill_struct ( core::pose::Pose const &  pose,
std::string  tag 
)
overridevirtual

opposite of fill_pose

Reimplemented from core::io::silent::SilentStruct.

References add_jump(), atm_coords_, core::conformation::Residue::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), chain_endings(), core::conformation::Conformation::chain_endings(), clone(), core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::io::silent::SilentStruct::fill_other_struct_list(), core::io::silent::SilentStruct::fill_struct(), core::io::silent::SilentStruct::fill_struct_with_residue_numbers(), core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(), fold_tree(), core::pose::Pose::fold_tree(), fold_tree_, fullatom(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), is_symmetric(), core::pose::Pose::jump(), jumps_, core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::natoms(), noncanonical_residue_connections_, core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection(), core::pose::Pose::residue_type(), resize(), core::pose::Pose::secstruct(), secstruct_, core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), symmetry_info(), core::io::silent::tr(), core::chemical::ResidueType::upper_connect_id(), and core::conformation::Atom::xyz().

Referenced by BinarySilentStruct().

void core::io::silent::BinarySilentStruct::fold_tree ( kinematics::FoldTree  f)
inline

References fold_tree_.

kinematics::FoldTree const& core::io::silent::BinarySilentStruct::fold_tree ( ) const
inline
bool core::io::silent::BinarySilentStruct::fullatom ( ) const
inline

References fullatom_.

Referenced by fill_pose(), fill_struct(), and fullatom().

void core::io::silent::BinarySilentStruct::fullatom ( bool  fullatom)
inline

References fullatom(), and fullatom_.

ObjexxFCL::FArray2D< Real > core::io::silent::BinarySilentStruct::get_CA_xyz ( ) const
overridevirtual

returns the positions of the CA atoms

Implements core::io::silent::SilentStruct.

References atm_coords_, and core::io::silent::SilentStruct::nres().

Referenced by CA_rmsd().

Real core::io::silent::BinarySilentStruct::get_debug_rmsd ( )
overridevirtual

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this ProteinSilentStruct and the C-alpha atoms from this ProteinSilentStruct.

Implements core::io::silent::SilentStruct.

References atm_coords_, fill_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

bool core::io::silent::BinarySilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
SilentFileData container 
)
overridevirtual
bool core::io::silent::BinarySilentStruct::init_from_lines ( utility::vector1< std::string > const &  lines,
SilentFileData container,
bool const  skip_read_from_container 
)

Initialize object from a set of lines.

If skip_read_from_container is true, then the container object is not used.

References add_jump(), core::io::silent::SilentStruct::add_submotif_info_from_line(), atm_coords_, bJumps_use_IntraResStub_, chain_endings_, core::io::silent::SilentStruct::comment_from_line(), core::io::silent::SilentStruct::decoy_tag(), core::io::silent::SilentStruct::detect_fullatom(), core::sequence::end, core::io::silent::energynames, core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(), core::io::silent::SilentStruct::figure_out_segment_ids_from_line(), fold_tree(), fold_tree_, core::io::silent::SilentStruct::force_bitflip(), fullatom_, core::io::silent::SilentFileData::get_shared_silent_data(), core::io::silent::SilentFileOptions::in_fullatom(), jump(), jumps_, noncanonical_residue_connections_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::io::silent::SilentStruct::one_letter_sequence(), core::io::silent::SilentStruct::options(), parse_chain_endings(), core::io::silent::SilentStruct::parse_energies(), core::kinematics::FoldTree::put_jump_stubs_intra_residue(), resize(), core::io::silent::SilentStruct::scoreline_prefix(), secstruct_, core::io::silent::SilentStruct::sequence(), core::io::silent::SilentFileData::set_shared_silent_data(), core::kinematics::FoldTree::simple_tree(), core::io::silent::simplesequencedata, core::scoring::electron_density::swap4_aligned(), symmetry_info(), and core::io::silent::tr().

bool core::io::silent::BinarySilentStruct::is_symmetric ( ) const
inline
kinematics::RT const& core::io::silent::BinarySilentStruct::jump ( Size  jump_num) const
inline

References jumps_.

Referenced by fill_pose(), init_from_lines(), and print_conformation().

BinarySilentStruct & core::io::silent::BinarySilentStruct::operator= ( BinarySilentStruct const &  src)
default

Assignment operator.

void core::io::silent::BinarySilentStruct::parse_chain_endings ( std::istream &  stream)

References add_chain_ending().

Referenced by init_from_lines().

void core::io::silent::BinarySilentStruct::print_conformation ( std::ostream &  output) const
overridevirtual
void core::io::silent::BinarySilentStruct::print_header ( std::ostream &  out) const
overridevirtual
void core::io::silent::BinarySilentStruct::resize ( Size const  nres_in)

Re-dimension the storage capacity of this BinarySilentStruct to the given number of residues.

Resize this silent-struct to the appropriate number of residues.

References atm_coords_, fold_tree_, core::kinematics::FoldTree::is_simple_tree(), core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().

Referenced by BinarySilentStruct(), fill_struct(), and init_from_lines().

char core::io::silent::BinarySilentStruct::secstruct ( unsigned int  seqpos) const
inline

References secstruct_.

void core::io::silent::BinarySilentStruct::secstruct ( unsigned int  seqpos,
char  ss 
)
inline

References secstruct_.

void core::io::silent::BinarySilentStruct::setup_other_poses ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  residue_set 
) const

for stepwise modeling, setup other_poses inside full_model_info

for stepwise modeling, setup other_poses inside full_model_info. this could go into SilentStruct parent class, if needed.

References core::pose::full_model_info::FullModelInfo::add_other_pose(), core::pose::full_model_info::nonconst_full_model_info(), core::scoring::other_pose, and core::io::silent::SilentStruct::other_struct_list().

Referenced by fill_pose().

BinarySilentStructOP core::io::silent::BinarySilentStruct::shared_from_this ( )
inline
void core::io::silent::BinarySilentStruct::symmetry_info ( core::conformation::symmetry::SymmetryInfo s)
inline

References symminfo_.

core::conformation::symmetry::SymmetryInfoCOP core::io::silent::BinarySilentStruct::symmetry_info ( ) const
inline

Member Data Documentation

utility::vector1< utility::vector1< numeric::xyzVector<float> > > core::io::silent::BinarySilentStruct::atm_coords_
private
bool core::io::silent::BinarySilentStruct::bJumps_use_IntraResStub_
private
utility::vector1< Size > core::io::silent::BinarySilentStruct::chain_endings_
private
kinematics::FoldTree core::io::silent::BinarySilentStruct::fold_tree_
private
bool core::io::silent::BinarySilentStruct::fullatom_
private
utility::vector1< kinematics::RT > core::io::silent::BinarySilentStruct::jumps_
private
utility::vector1< std::pair <core::id::NamedAtomID, core::id::NamedAtomID> > core::io::silent::BinarySilentStruct::noncanonical_residue_connections_
private
utility::vector1< char > core::io::silent::BinarySilentStruct::secstruct_
private
core::conformation::symmetry::SymmetryInfoOP core::io::silent::BinarySilentStruct::symminfo_
private

The documentation for this class was generated from the following files: