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protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions Class Reference

Options for the application. More...

#include <HelicalBundlePredictApplication.hh>

Inheritance diagram for protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions:
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Public Member Functions

 HelicalBundlePredictApplicationOptions ()
 Constructor. More...
 
 ~HelicalBundlePredictApplicationOptions () override
 Destructor. More...
 
HelicalBundlePredictApplicationOptionsOP clone () const
 Clone operator: copy this object and return a smart pointer to the copy. More...
 
void initialize_from_options ()
 Read from the options system to initialize this object. More...
 
void set_fasta_file (std::string const &file_in)
 Set the file containing the FASTA sequence. More...
 
void set_sequence_file (std::string const &file_in)
 Set the file containing the full-basename sequence. More...
 
void set_helix_assignment_file (std::string const &file_in)
 Set the file containing the helix assignments. More...
 
void set_fasta_file_contents (std::string const &contents_in)
 Set the contents of the FASTA file. More...
 
void set_sequence_file_contents (std::string const &contents_in)
 Set the contents of the seqeunce file. More...
 
void set_helix_assignment_file_contents (std::string const &contents_in)
 Set the contents of the helix assignment file. More...
 
void set_rmsd_residues_to_ignore_native (utility::vector1< signed long > const &input)
 Get the residues to ignore in the native pose when setting up the alignment for RMSD. More...
 
void set_rmsd_residues_to_ignore_prediction (utility::vector1< signed long > const &input)
 Get the residues to ignore in the generated poses when setting up the alignment for RMSD. More...
 
std::string const & fasta_file () const
 Get the file containing the sequence. More...
 
std::string const & helix_assignment_file () const
 Get the file containing the helix assignments. More...
 
std::string const & fasta_file_contents () const
 Get the contents of the FASTA file. More...
 
std::string const & sequence_file_contents () const
 Get the contents of the sequence file. More...
 
std::string const & helix_assignment_file_contents () const
 Get the contents of the helix assignment file. More...
 
void read_inputs ()
 Given input filenames, read the files. More...
 
core::Size num_simulated_annealing_rounds_centroid () const
 Get the number of simulated annealing rounds in centroid mode. More...
 
core::Size num_steps_per_simulated_annealing_round_centroid () const
 Get the number of steps per simulated annealing round in centroid mode. More...
 
core::Real const & centroid_max_temperature () const
 Get the max temperature during simulated annealing steps in centroid mode. More...
 
core::Real const & centroid_min_temperature () const
 Get the min temperature during simulated annealing steps in centroid mode. More...
 
core::Size nstruct () const
 Get the number of repeated applications of this protocol. More...
 
bool do_fullatom_refinement () const
 Will be doing fullatom refinement? More...
 
core::Size fullatom_fast_relax_rounds () const
 If we are doing fullatom refinement, how many rounds of FastRelax should we apply? More...
 
bool fullatom_find_disulfides () const
 If we are doing fullatom refinement, should we try disulfide permutations? More...
 
std::string const & native_file () const
 Get the native filename. More...
 
utility::vector1< core::Size >
const & 
rmsd_residues_to_ignore_native () const
 Get the residues to ignore in the native pose when setting up the alignment for RMSD. More...
 
utility::vector1< core::Size >
const & 
rmsd_residues_to_ignore_prediction () const
 Get the residues to ignore in the generated poses when setting up the alignment for RMSD. More...
 

Static Public Member Functions

static void register_options ()
 Indicate which commandline flags are relevant (i.e. which should be listed with the –help flag). More...
 

Private Member Functions

void read_fasta ()
 Read a FASTA file from disk. More...
 
void read_sequence_file ()
 Read a sequence file from disk. More...
 
core::Size findchar (std::string const &curstring, utility::vector1< char > const &chars) const
 Given a set of characters, find the first instance of any of them in a string and return the (zero-based) index of that character. More...
 
void clean_fasta_file_contents ()
 Given FASTA file contents, remove comment lines. More...
 
void read_helix_assignments ()
 Read a helix assignemnt file from disk. More...
 

Private Attributes

std::string native_file_
 The native structure. More...
 
std::string fasta_file_
 The file containing the sequence (in FASTA format). More...
 
std::string sequence_file_
 The file containing the sequence (in full name format). More...
 
std::string helix_assignment_file_
 The file containing the helix assignments. More...
 
std::string fasta_file_contents_
 The contents of the FASTA file. More...
 
std::string sequence_file_contents_
 The contents of the sequence file. More...
 
std::string helix_assignment_file_contents_
 The contents of the helix assignment file. More...
 
core::Size num_simulated_annealing_rounds_centroid_ =3
 Number of simulated annealing rounds in centroid mode. More...
 
core::Size num_steps_per_simulated_annealing_round_centroid_ =1000
 Number of steps in each simulated annealing round in centroid mode. More...
 
core::Real centroid_max_temperature_ =50
 The max temperature during simulated annealing steps in centroid mode. More...
 
core::Real centroid_min_temperature_ =0.62
 The min temperature during simulated annealing steps in centroid mode. More...
 
core::Size nstruct_ =1
 The number of attempts to make. More...
 
bool do_fullatom_refinement_ =true
 Will be doing fullatom refinement? More...
 
core::Size fullatom_fast_relax_rounds_ =3
 If we are doing fullatom refinement, how many rounds of FastRelax should we apply? More...
 
bool fullatom_find_disulfides_ =true
 If we are doing fullatom refinement, should we try disulfide permutations? More...
 
utility::vector1< core::Sizermsd_residues_to_ignore_native_
 Residues to ignore in the native pose when setting up the alignment for RMSD. More...
 
utility::vector1< core::Sizermsd_residues_to_ignore_prediction_
 Residues to ignore in the generated poses when setting up the alignment for RMSD. More...
 

Detailed Description

Options for the application.

Prevents repeated calls to the global options system.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Constructor & Destructor Documentation

protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::HelicalBundlePredictApplicationOptions ( )

Constructor.

Triggers read from options system!

References initialize_from_options().

protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::~HelicalBundlePredictApplicationOptions ( )
overridedefault

Destructor.

Destructor

Member Function Documentation

core::Real const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_max_temperature ( ) const
inline

Get the max temperature during simulated annealing steps in centroid mode.

References centroid_max_temperature_.

core::Real const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_min_temperature ( ) const
inline

Get the min temperature during simulated annealing steps in centroid mode.

References centroid_min_temperature_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::clean_fasta_file_contents ( )
private

Given FASTA file contents, remove comment lines.

References fasta_file_contents_, findchar(), and protocols::TR().

Referenced by set_fasta_file_contents().

HelicalBundlePredictApplicationOptionsOP protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::clone ( ) const

Clone operator: copy this object and return a smart pointer to the copy.

Create a copy and return smart pointer to copy.

bool protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::do_fullatom_refinement ( ) const
inline

Will be doing fullatom refinement?

References do_fullatom_refinement_.

std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file ( ) const
inline

Get the file containing the sequence.

References fasta_file_.

std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file_contents ( ) const
inline

Get the contents of the FASTA file.

References fasta_file_contents_.

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::findchar ( std::string const &  curstring,
utility::vector1< char > const &  chars 
) const
private

Given a set of characters, find the first instance of any of them in a string and return the (zero-based) index of that character.

Referenced by clean_fasta_file_contents().

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_fast_relax_rounds ( ) const
inline

If we are doing fullatom refinement, how many rounds of FastRelax should we apply?

References fullatom_fast_relax_rounds_.

bool protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_find_disulfides ( ) const
inline

If we are doing fullatom refinement, should we try disulfide permutations?

References fullatom_find_disulfides_.

std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file ( ) const
inline

Get the file containing the helix assignments.

References helix_assignment_file_.

std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file_contents ( ) const
inline

Get the contents of the helix assignment file.

References helix_assignment_file_contents_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::initialize_from_options ( )
std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::native_file ( ) const
inline

Get the native filename.

References native_file_.

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::nstruct ( ) const
inline

Get the number of repeated applications of this protocol.

References nstruct_.

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_simulated_annealing_rounds_centroid ( ) const
inline

Get the number of simulated annealing rounds in centroid mode.

References num_simulated_annealing_rounds_centroid_.

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_steps_per_simulated_annealing_round_centroid ( ) const
inline

Get the number of steps per simulated annealing round in centroid mode.

References num_steps_per_simulated_annealing_round_centroid_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::read_fasta ( )
private

Read a FASTA file from disk.

References fasta_file_, and set_fasta_file_contents().

Referenced by read_inputs().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::read_helix_assignments ( )
private

Read a helix assignemnt file from disk.

References helix_assignment_file_, and helix_assignment_file_contents_.

Referenced by read_inputs().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::read_inputs ( )

Given input filenames, read the files.

INVOLVES READS FROM DISK! WARNING!

References fasta_file_, read_fasta(), read_helix_assignments(), and read_sequence_file().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::read_sequence_file ( )
private

Read a sequence file from disk.

References sequence_file_, and set_sequence_file_contents().

Referenced by read_inputs().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::register_options ( )
static

Indicate which commandline flags are relevant (i.e. which should be listed with the –help flag).

This is a static function that must be called BEFORE devel_init().

utility::vector1< core::Size > const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_native ( ) const
inline

Get the residues to ignore in the native pose when setting up the alignment for RMSD.

References rmsd_residues_to_ignore_native_.

utility::vector1< core::Size > const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_prediction ( ) const
inline

Get the residues to ignore in the generated poses when setting up the alignment for RMSD.

References rmsd_residues_to_ignore_prediction_.

std::string const& protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::sequence_file_contents ( ) const
inline

Get the contents of the sequence file.

References sequence_file_contents_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_fasta_file ( std::string const &  file_in)

Set the file containing the FASTA sequence.

References fasta_file_, and sequence_file_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_fasta_file_contents ( std::string const &  contents_in)

Set the contents of the FASTA file.

References clean_fasta_file_contents(), fasta_file_contents_, and sequence_file_contents_.

Referenced by read_fasta().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_helix_assignment_file ( std::string const &  file_in)

Set the file containing the helix assignments.

References helix_assignment_file_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_helix_assignment_file_contents ( std::string const &  contents_in)

Set the contents of the helix assignment file.

References helix_assignment_file_contents_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_native ( utility::vector1< signed long > const &  input)

Get the residues to ignore in the native pose when setting up the alignment for RMSD.

Throws errors if any are zero or negative.

References rmsd_residues_to_ignore_native_, and core::id::to_string().

Referenced by initialize_from_options().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_prediction ( utility::vector1< signed long > const &  input)

Get the residues to ignore in the generated poses when setting up the alignment for RMSD.

Throws errors if any are zero or negative.

References rmsd_residues_to_ignore_prediction_, and core::id::to_string().

Referenced by initialize_from_options().

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_sequence_file ( std::string const &  file_in)

Set the file containing the full-basename sequence.

References fasta_file_, and sequence_file_.

void protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_sequence_file_contents ( std::string const &  contents_in)

Set the contents of the seqeunce file.

References fasta_file_contents_, and sequence_file_contents_.

Referenced by read_sequence_file().

Member Data Documentation

core::Real protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_max_temperature_ =50
private

The max temperature during simulated annealing steps in centroid mode.

Referenced by centroid_max_temperature(), and initialize_from_options().

core::Real protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_min_temperature_ =0.62
private

The min temperature during simulated annealing steps in centroid mode.

Referenced by centroid_min_temperature(), and initialize_from_options().

bool protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::do_fullatom_refinement_ =true
private

Will be doing fullatom refinement?

Referenced by do_fullatom_refinement(), and initialize_from_options().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file_
private

The file containing the sequence (in FASTA format).

Referenced by fasta_file(), read_fasta(), read_inputs(), set_fasta_file(), and set_sequence_file().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file_contents_
private
core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_fast_relax_rounds_ =3
private

If we are doing fullatom refinement, how many rounds of FastRelax should we apply?

Referenced by fullatom_fast_relax_rounds(), and initialize_from_options().

bool protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_find_disulfides_ =true
private

If we are doing fullatom refinement, should we try disulfide permutations?

Referenced by fullatom_find_disulfides(), and initialize_from_options().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file_
private

The file containing the helix assignments.

Referenced by helix_assignment_file(), read_helix_assignments(), and set_helix_assignment_file().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file_contents_
private

The contents of the helix assignment file.

Referenced by helix_assignment_file_contents(), read_helix_assignments(), and set_helix_assignment_file_contents().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::native_file_
private

The native structure.

Referenced by initialize_from_options(), and native_file().

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::nstruct_ =1
private

The number of attempts to make.

Referenced by initialize_from_options(), and nstruct().

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_simulated_annealing_rounds_centroid_ =3
private

Number of simulated annealing rounds in centroid mode.

Referenced by initialize_from_options(), and num_simulated_annealing_rounds_centroid().

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_steps_per_simulated_annealing_round_centroid_ =1000
private

Number of steps in each simulated annealing round in centroid mode.

Referenced by initialize_from_options(), and num_steps_per_simulated_annealing_round_centroid().

utility::vector1< core::Size > protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_native_
private

Residues to ignore in the native pose when setting up the alignment for RMSD.

Referenced by rmsd_residues_to_ignore_native(), and set_rmsd_residues_to_ignore_native().

utility::vector1< core::Size > protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_prediction_
private

Residues to ignore in the generated poses when setting up the alignment for RMSD.

Referenced by rmsd_residues_to_ignore_prediction(), and set_rmsd_residues_to_ignore_prediction().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::sequence_file_
private

The file containing the sequence (in full name format).

Referenced by read_sequence_file(), set_fasta_file(), and set_sequence_file().

std::string protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::sequence_file_contents_
private

The contents of the sequence file.

Referenced by sequence_file_contents(), set_fasta_file_contents(), and set_sequence_file_contents().


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