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core::io::sequence_comparation::DesignContrast Class Reference

DesignContrast contains information for comparing the native protein sequence to designed protein sequence. And output the compare resultes to a special formated file which can be used for statistics calculations. More...

#include <DesignContrast.hh>

Public Member Functions

 DesignContrast ()
 default constructor More...
 
 DesignContrast (DesignContrast const &dc)
 
virtual ~DesignContrast ()
 default de-constructor More...
 
void setNeighbors (pose::Pose &pose)
 Set number of neighbors for all residues in pose. More...
 
utility::vector1< int > & getNeighbors ()
 Get number of neighbors for all residues in pose. More...
 
utility::vector1< int > const & getNeighbors () const
 
void setSecStruct (pose::Pose &pose)
 Set secondary structure for all residues in pose. More...
 
utility::vector1< std::string > & getSecStruct ()
 Get secondary structure for all residues in pose. More...
 
utility::vector1< std::string >
const & 
getSecStruct () const
 
void setNames ()
 Get pdb file names from the pdb list files. More...
 
utility::vector1
< utility::file::FileName > & 
getPdbNames ()
 
utility::vector1
< utility::file::FileName >
const & 
getPdbNames () const
 
utility::vector1
< utility::file::FileName > & 
getListNames ()
 
utility::vector1
< utility::file::FileName >
const & 
getListNames () const
 
void setPdbCodes ()
 
utility::vector1< std::string > & getPdbCodes ()
 
utility::vector1< std::string >
const & 
getPdbCodes () const
 
void output_sqc_file (pose::Pose &native_pose, pose::Pose &decoy_pose, std::string const &single_code, std::ofstream &sqc)
 this function will output the sequence comparing result between native pose and designed pose More...
 
void clear ()
 clear function to clear all datas in this class. More...
 

Private Attributes

utility::vector1
< utility::file::FileName > 
list_file_names_
 
utility::vector1
< utility::file::FileName > 
pdb_file_names_
 
utility::vector1< int > nneighbs_
 
utility::vector1< std::string > secstructs_
 
utility::vector1< std::string > pdb_codes_
 

Detailed Description

DesignContrast contains information for comparing the native protein sequence to designed protein sequence. And output the compare resultes to a special formated file which can be used for statistics calculations.

Constructor & Destructor Documentation

core::io::sequence_comparation::DesignContrast::DesignContrast ( )
inline

default constructor

core::io::sequence_comparation::DesignContrast::DesignContrast ( DesignContrast const &  dc)
virtual core::io::sequence_comparation::DesignContrast::~DesignContrast ( )
inlinevirtual

default de-constructor

References clear().

Member Function Documentation

void core::io::sequence_comparation::DesignContrast::clear ( )

clear function to clear all datas in this class.

Referenced by ~DesignContrast().

vector1< utility::file::FileName > & core::io::sequence_comparation::DesignContrast::getListNames ( )

Referenced by DesignContrast().

vector1< utility::file::FileName > const & core::io::sequence_comparation::DesignContrast::getListNames ( ) const
vector1< int > & core::io::sequence_comparation::DesignContrast::getNeighbors ( )

Get number of neighbors for all residues in pose.

Referenced by DesignContrast().

vector1< int > const & core::io::sequence_comparation::DesignContrast::getNeighbors ( ) const
vector1< std::string > & core::io::sequence_comparation::DesignContrast::getPdbCodes ( )

Referenced by DesignContrast().

vector1< std::string > const & core::io::sequence_comparation::DesignContrast::getPdbCodes ( ) const
vector1< utility::file::FileName > & core::io::sequence_comparation::DesignContrast::getPdbNames ( )

Referenced by DesignContrast().

vector1< utility::file::FileName > const & core::io::sequence_comparation::DesignContrast::getPdbNames ( ) const
vector1< std::string > & core::io::sequence_comparation::DesignContrast::getSecStruct ( )

Get secondary structure for all residues in pose.

Referenced by DesignContrast().

vector1< std::string > const & core::io::sequence_comparation::DesignContrast::getSecStruct ( ) const
void core::io::sequence_comparation::DesignContrast::output_sqc_file ( pose::Pose native_pose,
pose::Pose decoy_pose,
std::string const &  single_code,
std::ofstream &  sqc 
)
void core::io::sequence_comparation::DesignContrast::setNames ( )

Get pdb file names from the pdb list files.

Copied the major parts of this function from Andrew. Read the lines of the list files and store the pdb names in pdb_file_names.

void core::io::sequence_comparation::DesignContrast::setNeighbors ( pose::Pose pose)

Set number of neighbors for all residues in pose.

go through residues in the pose, count the number of neighbors of each residue. currently using tenA neighbor graph to # neighbors within 10 Angstroms

References core::pose::Pose::energies(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::update_residue_neighbors().

void core::io::sequence_comparation::DesignContrast::setPdbCodes ( )
void core::io::sequence_comparation::DesignContrast::setSecStruct ( pose::Pose pose)

Set secondary structure for all residues in pose.

Set secondary structure for residues in the pose. Have to call set_ss_from_phipsi to set up the secondary structure infomation for pose.

References core::pose::Pose::secstruct(), core::pose::set_ss_from_phipsi(), and core::pose::Pose::size().

Member Data Documentation

utility::vector1<utility::file::FileName> core::io::sequence_comparation::DesignContrast::list_file_names_
private
utility::vector1<int> core::io::sequence_comparation::DesignContrast::nneighbs_
private
utility::vector1<std::string> core::io::sequence_comparation::DesignContrast::pdb_codes_
private
utility::vector1<utility::file::FileName> core::io::sequence_comparation::DesignContrast::pdb_file_names_
private
utility::vector1<std::string> core::io::sequence_comparation::DesignContrast::secstructs_
private

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