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>

Collaboration diagram for core::io::sequence_comparation::DesignContrast:

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...
vector1< int > &	getNeighbors ()
	Get number of neighbors for all residues in pose. More...
vector1< int > const &	getNeighbors () const
void	setSecStruct (pose::Pose &pose)
	Set secondary structure for all residues in pose. More...
vector1< std::string > &	getSecStruct ()
	Get secondary structure for all residues in pose. More...
vector1< std::string > const &	getSecStruct () const
void	setNames ()
	Get pdb file names from the pdb list files. More...
vector1< FileName > &	getPdbNames ()
vector1< FileName > const &	getPdbNames () const
vector1< FileName > &	getListNames ()
vector1< FileName > const &	getListNames () const
void	setPdbCodes ()
vector1< std::string > &	getPdbCodes ()
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
vector1< FileName >	list_file_names_
vector1< FileName >	pdb_file_names_
vector1< int >	nneighbs_
vector1< std::string >	secstructs_
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.

Definition at line 50 of file DesignContrast.hh.

Constructor & Destructor Documentation

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

inline

default constructor

Definition at line 53 of file DesignContrast.hh.

core::io::sequence_comparation::DesignContrast::DesignContrast

(

DesignContrast const &

dc)

Definition at line 90 of file DesignContrast.cc.

References getListNames(), getNeighbors(), getPdbCodes(), getPdbNames(), and getSecStruct().

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

inlinevirtual

default de-constructor

Definition at line 59 of file DesignContrast.hh.

References clear().

Member Function Documentation

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

(

)

clear function to clear all datas in this class.

Definition at line 242 of file DesignContrast.cc.

Referenced by ~DesignContrast().

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

(

)

Definition at line 170 of file DesignContrast.cc.

Referenced by DesignContrast().

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

(

)

const

Definition at line 174 of file DesignContrast.cc.

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

(

)

Get number of neighbors for all residues in pose.

Definition at line 110 of file DesignContrast.cc.

Referenced by DesignContrast().

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

(

)

const

Definition at line 114 of file DesignContrast.cc.

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

(

)

Definition at line 187 of file DesignContrast.cc.

Referenced by DesignContrast().

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

(

)

const

Definition at line 191 of file DesignContrast.cc.

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

(

)

Definition at line 162 of file DesignContrast.cc.

Referenced by DesignContrast().

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

(

)

const

Definition at line 166 of file DesignContrast.cc.

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

(

)

Get secondary structure for all residues in pose.

Definition at line 131 of file DesignContrast.cc.

Referenced by DesignContrast().

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

(

)

const

Definition at line 134 of file DesignContrast.cc.

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

Definition at line 195 of file DesignContrast.cc.

References protocols::comparative_modeling::features::A, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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.

Definition at line 140 of file DesignContrast.cc.

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

Definition at line 100 of file DesignContrast.cc.

References core::pose::Pose::energies(), core::graph::Graph::get_node(), core::graph::Node::num_neighbors_counting_self(), core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

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

(

)

Definition at line 178 of file DesignContrast.cc.

References core::io::serialization::size().

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.

Definition at line 121 of file DesignContrast.cc.

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

Member Data Documentation

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

private

Definition at line 103 of file DesignContrast.hh.

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

private

Definition at line 106 of file DesignContrast.hh.

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

private

Definition at line 108 of file DesignContrast.hh.

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

private

Definition at line 105 of file DesignContrast.hh.

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

private

Definition at line 107 of file DesignContrast.hh.

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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