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Rosetta
2016.11
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#include <ScoreFileSilentStruct.hh>
Public Member Functions | |
ScoreFileSilentStruct () | |
Constructors. More... | |
ScoreFileSilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag") | |
virtual SilentStructOP | clone () const |
~ScoreFileSilentStruct () | |
Re-dimension the storage capacity of this ScoreFileSilentStruct to the given number of residues. More... | |
ScoreFileSilentStruct & | operator= (ScoreFileSilentStruct const &src) |
Test if this ScoreFileSilentStruct is equal to the given ScoreFileSilentStruct in terms of conformation. Doesn't check energies. More... | |
virtual bool | init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container) |
Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines. Only initializes energies. More... | |
virtual void | fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const |
Configure the conformation of the given Pose with the conformational data within this ScoreFileSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types. More... | |
virtual void | fill_struct (core::pose::Pose const &pose, std::string tag) |
opposite of fill_pose More... | |
virtual void | print_conformation (std::ostream &output) const |
Prints the conformation information within this ScoreFileSilentStruct to the given std::ostream. More... | |
virtual void | print_header (std::ostream &out) const |
Prints the header information within this ScoreFileSilentStruct to the given std::ostream. More... | |
virtual ObjexxFCL::FArray2D< Real > | get_CA_xyz () const |
returns the positions of the CA atoms in this ScoreFileSilentStruct. Useful for RMS calculations. More... | |
virtual Real | get_debug_rmsd () |
calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this ScoreFileSilentStruct and the C-alpha atoms from this ScoreFileSilentStruct. More... | |
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SilentStruct () | |
virtual | ~SilentStruct () |
SilentStruct (SilentStruct const &) | |
SilentStruct & | operator= (SilentStruct const &) |
SilentStructCOP | get_self_ptr () const |
self pointers More... | |
SilentStructOP | get_self_ptr () |
virtual void | fill_pose (core::pose::Pose &pose) const |
void | fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSetCOP residue_set) 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< SilentEnergy > | get_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 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 scorename, std::string const &value) |
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 | 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< SilentEnergy > | energies () 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< Size > 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... | |
Additional Inherited Members | |
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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... | |
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inline |
core::io::silent::ScoreFileSilentStruct::ScoreFileSilentStruct | ( | core::pose::Pose const & | pose, |
std::string | tag = "empty_tag" |
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inline |
Re-dimension the storage capacity of this ScoreFileSilentStruct to the given number of residues.
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inlinevirtual |
Implements core::io::silent::SilentStruct.
References ScoreFileSilentStruct().
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virtual |
Configure the conformation of the given Pose with the conformational data within this ScoreFileSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.
Reimplemented from core::io::silent::SilentStruct.
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virtual |
opposite of fill_pose
Reimplemented from core::io::silent::SilentStruct.
References core::pose::Pose::sequence().
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virtual |
returns the positions of the CA atoms in this ScoreFileSilentStruct. Useful for RMS calculations.
Implements core::io::silent::SilentStruct.
References core::io::silent::tr().
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virtual |
calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this ScoreFileSilentStruct and the C-alpha atoms from this ScoreFileSilentStruct.
Implements core::io::silent::SilentStruct.
References core::io::silent::tr().
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virtual |
Tells this ScoreFileSilentStruct object to initialize itself from the given set of lines. Only initializes energies.
Implements core::io::silent::SilentStruct.
References core::io::silent::energynames, core::io::silent::SilentFileData::get_shared_silent_data(), and core::io::silent::SilentFileData::set_shared_silent_data().
ScoreFileSilentStruct & core::io::silent::ScoreFileSilentStruct::operator= | ( | ScoreFileSilentStruct const & | src | ) |
Test if this ScoreFileSilentStruct is equal to the given ScoreFileSilentStruct in terms of conformation. Doesn't check energies.
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virtual |
Prints the conformation information within this ScoreFileSilentStruct to the given std::ostream.
Implements core::io::silent::SilentStruct.
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virtual |
Prints the header information within this ScoreFileSilentStruct to the given std::ostream.
Reimplemented from core::io::silent::SilentStruct.