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Public Member Functions | Private Attributes | List of all members
protocols::protein_interface_design::PatchdockReader Class Reference

#include <read_patchdock.hh>

Inheritance diagram for protocols::protein_interface_design::PatchdockReader:
Inheritance graph
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Public Member Functions

 PatchdockReader ()
 
 ~PatchdockReader () override
 
void read_poses (core::pose::Pose &input_pose, std::string &input_tag)
 if no native is read More...
 
void read_poses (core::pose::Pose &input_pose, core::pose::Pose &native_pose, std::string &input_tag, std::string &native_tag)
 reads input and native poses from file. If patchdock flags are used will read the patchdock transformation and transform the input pose accordingly More...
 
void read_patchdock (std::string &input_tag, std::string &native_tag)
 
Transformation read_patchdock_entry ()
 
void clear_internals ()
 
core::Size number_of_patchdock_entries ()
 
std::string patchdock_fname () const
 
void patchdock_fname (std::string const &s)
 
core::Size patchdock_entry_num () const
 
void patchdock_entry_num (core::Size const s)
 
void from_entry (core::Size const f)
 
core::Size from_entry () const
 
void to_entry (core::Size const t)
 
core::Size to_entry () const
 
bool random_entry () const
 
void random_entry (bool const b)
 
void transform_pose (core::pose::Pose &pose, core::Size const chain, Transformation const &t)
 

Private Attributes

std::string patchdock_fname_
 
core::Size patchdock_entry_num_
 
core::Size from_entry_
 
core::Size to_entry_
 
core::pose::PoseOP saved_input_pose_
 
core::pose::PoseOP saved_native_pose_
 
std::string saved_input_tag_
 
std::string saved_native_tag_
 
utility::vector1< Transformationsaved_transformations_
 
bool random_entry_
 

Constructor & Destructor Documentation

protocols::protein_interface_design::PatchdockReader::PatchdockReader ( )
protocols::protein_interface_design::PatchdockReader::~PatchdockReader ( )
overridedefault

Member Function Documentation

void protocols::protein_interface_design::PatchdockReader::clear_internals ( )
void protocols::protein_interface_design::PatchdockReader::from_entry ( core::Size const  f)
inline

References from_entry_.

core::Size protocols::protein_interface_design::PatchdockReader::from_entry ( ) const
inline

References from_entry_.

core::Size protocols::protein_interface_design::PatchdockReader::number_of_patchdock_entries ( )

how many entries are there in the patchdock file?

core::Size protocols::protein_interface_design::PatchdockReader::patchdock_entry_num ( ) const
inline

References patchdock_entry_num_.

void protocols::protein_interface_design::PatchdockReader::patchdock_entry_num ( core::Size const  s)
inline

References patchdock_entry_num_.

std::string protocols::protein_interface_design::PatchdockReader::patchdock_fname ( ) const
inline

References patchdock_fname_.

void protocols::protein_interface_design::PatchdockReader::patchdock_fname ( std::string const &  s)
inline

References patchdock_fname_.

bool protocols::protein_interface_design::PatchdockReader::random_entry ( ) const
inline

References random_entry_.

void protocols::protein_interface_design::PatchdockReader::random_entry ( bool const  b)
inline
void protocols::protein_interface_design::PatchdockReader::read_patchdock ( std::string &  input_tag,
std::string &  native_tag 
)
Transformation protocols::protein_interface_design::PatchdockReader::read_patchdock_entry ( )

read a rigid-body transformation from a patchdock file. caches transformations in saved_transformations_ to avoid multiple disk access

References protocols::hybridization::t, and core::scoring::TR().

void protocols::protein_interface_design::PatchdockReader::read_poses ( core::pose::Pose input_pose,
std::string &  input_tag 
)
void protocols::protein_interface_design::PatchdockReader::read_poses ( core::pose::Pose input_pose,
core::pose::Pose native_pose,
std::string &  input_tag,
std::string &  native_tag 
)

reads input and native poses from file. If patchdock flags are used will read the patchdock transformation and transform the input pose accordingly

If the native and input tags match those saved in the object, then the pose will not be read again from disk. Only the patchdock entry will be read.

References core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::fold_tree(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::hybridization::t, and core::scoring::TR().

void protocols::protein_interface_design::PatchdockReader::to_entry ( core::Size const  t)
inline
core::Size protocols::protein_interface_design::PatchdockReader::to_entry ( ) const
inline

References to_entry_.

void protocols::protein_interface_design::PatchdockReader::transform_pose ( core::pose::Pose pose,
core::Size const  chain,
Transformation const &  t 
)

Member Data Documentation

core::Size protocols::protein_interface_design::PatchdockReader::from_entry_
private

Referenced by from_entry().

core::Size protocols::protein_interface_design::PatchdockReader::patchdock_entry_num_
private

Referenced by patchdock_entry_num().

std::string protocols::protein_interface_design::PatchdockReader::patchdock_fname_
private

Referenced by patchdock_fname().

bool protocols::protein_interface_design::PatchdockReader::random_entry_
private

Referenced by random_entry().

core::pose::PoseOP protocols::protein_interface_design::PatchdockReader::saved_input_pose_
private
std::string protocols::protein_interface_design::PatchdockReader::saved_input_tag_
private
core::pose::PoseOP protocols::protein_interface_design::PatchdockReader::saved_native_pose_
private
std::string protocols::protein_interface_design::PatchdockReader::saved_native_tag_
private
utility::vector1< Transformation > protocols::protein_interface_design::PatchdockReader::saved_transformations_
private
core::Size protocols::protein_interface_design::PatchdockReader::to_entry_
private

Referenced by to_entry().


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