protocols::protein_interface_design::PatchdockReader Class Reference

#include <read_patchdock.hh>

Public Member Functions
	PatchdockReader ()
virtual	~PatchdockReader ()
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< Transformation >	saved_transformations_
bool	random_entry_

Constructor & Destructor Documentation

protocols::protein_interface_design::PatchdockReader::PatchdockReader

(

)

References option, parser::patchdock, parser::patchdock_random_entry, runtime_assert, and user.

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

virtual

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

(

)

Detailed: 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

References protocols::match::upstream::b, and random_entry_.

void protocols::protein_interface_design::PatchdockReader::read_patchdock	(	std::string &	input_tag,
		std::string &	native_tag
	)

References option, RG, runtime_assert, ss, core::scoring::TR, numeric::random::RandomGenerator::uniform(), out::user_tag, and utility_exit_with_message_status.

Transformation protocols::protein_interface_design::PatchdockReader::read_patchdock_entry

(

)

Detailed: read a rigid-body transformation from a patchdock file.

caches transformations in saved_transformations_ to avoid multiple disk access

References getline(), runtime_assert, t, core::scoring::TR, and utility_exit_with_message.

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

if no native is read

Referenced by protocols::protein_interface_design::ParserJobInputter::pose_from_job().

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 in::file::centroid_input, core::import_pose::centroid_pose_from_pdb(), in::file::fold_tree, core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), getline(), option, core::import_pose::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), runtime_assert, t, core::scoring::TR, and user.

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

inline

References to_entry_.

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
	)

References protocols::protein_interface_design::Transformation::alpha, protocols::protein_interface_design::Transformation::beta, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), in::detect_disulf, core::conformation::Conformation::detect_disulfides(), protocols::protein_interface_design::Transformation::gamma, core::pose::Pose::is_fullatom(), core::conformation::Residue::natoms(), option, core::pose::Pose::residue(), residue, rotation, core::scoring::sa, core::pose::Pose::set_xyz(), protocols::protein_interface_design::Transformation::translation, user, and core::pose::Pose::xyz().

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().

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

• src/protocols/protein_interface_design/read_patchdock.hh
• src/protocols/protein_interface_design/read_patchdock.cc