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Rosetta
2020.11
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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_ |
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.
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inline |
default constructor
core::io::sequence_comparation::DesignContrast::DesignContrast | ( | DesignContrast const & | dc | ) |
References getListNames(), getNeighbors(), getPdbCodes(), getPdbNames(), and getSecStruct().
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inlinevirtual |
default de-constructor
References clear().
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 | ||
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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(), and core::pose::Pose::size().
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().
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