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...
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

DesignContrast()

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

inline

default constructor

~DesignContrast()

virtual core::io::sequence_comparation::DesignContrast::~DesignContrast ( )

inlinevirtual

default de-constructor

References clear().

Member Function Documentation

clear()

void core::io::sequence_comparation::DesignContrast::clear

(

)

clear function to clear all datas in this class.

Referenced by ~DesignContrast().

getListNames() [1/2]

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

(

)

getListNames() [2/2]

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

(

)

const

getNeighbors() [1/2]

vector1< int > & core::io::sequence_comparation::DesignContrast::getNeighbors

(

)

Get number of neighbors for all residues in pose.

getNeighbors() [2/2]

vector1< int > const & core::io::sequence_comparation::DesignContrast::getNeighbors

(

)

const

getPdbCodes() [1/2]

vector1< std::string > & core::io::sequence_comparation::DesignContrast::getPdbCodes

(

)

getPdbCodes() [2/2]

vector1< std::string > const & core::io::sequence_comparation::DesignContrast::getPdbCodes

(

)

const

getPdbNames() [1/2]

vector1< utility::file::FileName > & core::io::sequence_comparation::DesignContrast::getPdbNames

(

)

getPdbNames() [2/2]

vector1< utility::file::FileName > const & core::io::sequence_comparation::DesignContrast::getPdbNames

(

)

const

getSecStruct() [1/2]

vector1< std::string > & core::io::sequence_comparation::DesignContrast::getSecStruct

(

)

Get secondary structure for all residues in pose.

getSecStruct() [2/2]

vector1< std::string > const & core::io::sequence_comparation::DesignContrast::getSecStruct

(

)

const

output_sqc_file()

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
	)

this function will output the sequence comparing result between native pose and designed pose

References protocols::comparative_modeling::features::A, core::chemical::element::I, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::io::sequence_comparation::TR().

setNames()

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.

setNeighbors()

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().

setPdbCodes()

void core::io::sequence_comparation::DesignContrast::setPdbCodes

(

)

References core::io::sequence_comparation::TR().

setSecStruct()

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

list_file_names_

utility::vector1<utility::file::FileName> core::io::sequence_comparation::DesignContrast::list_file_names_

private

nneighbs_

utility::vector1<int> core::io::sequence_comparation::DesignContrast::nneighbs_

private

pdb_codes_

utility::vector1<std::string> core::io::sequence_comparation::DesignContrast::pdb_codes_

private

pdb_file_names_

utility::vector1<utility::file::FileName> core::io::sequence_comparation::DesignContrast::pdb_file_names_

private

secstructs_

utility::vector1<std::string> core::io::sequence_comparation::DesignContrast::secstructs_

private

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

• src/core/io/sequence_comparation/DesignContrast.hh
• src/core/io/sequence_comparation/DesignContrast.cc