protocols::protein_interface_design::PatchdockReader Class Reference

#include <read_patchdock.hh>

Inheritance diagram for protocols::protein_interface_design::PatchdockReader:

Collaboration diagram for protocols::protein_interface_design::PatchdockReader:

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 ()

Private Attributes
std::string	patchdock_fname_
core::Size	patchdock_entry_num_
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_

Detailed Description

Definition at line 42 of file read_patchdock.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::PatchdockReader::PatchdockReader

(

)

Definition at line 62 of file read_patchdock.cc.

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

virtual

Definition at line 65 of file read_patchdock.cc.

Member Function Documentation

void protocols::protein_interface_design::PatchdockReader::clear_internals

(

)

Definition at line 68 of file read_patchdock.cc.

core::Size protocols::protein_interface_design::PatchdockReader::number_of_patchdock_entries

(

)

Detailed: how many entries are there in the patchdock file?

Definition at line 80 of file read_patchdock.cc.

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

Definition at line 204 of file read_patchdock.cc.

References core::conformation::symmetry::RG(), and core::TR().

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

Definition at line 92 of file read_patchdock.cc.

References core::scoring::hbonds::t(), and core::TR().

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

if no native is read

Definition at line 195 of file read_patchdock.cc.

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.

Definition at line 264 of file read_patchdock.cc.

References core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), core::import_pose::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), core::scoring::hbonds::t(), core::TR(), and protocols::protein_interface_design::transform_pose().

Member Data Documentation

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

private

Definition at line 61 of file read_patchdock.hh.

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

private

Definition at line 60 of file read_patchdock.hh.

core::pose::PoseOP protocols::protein_interface_design::PatchdockReader::saved_input_pose_

private

Definition at line 62 of file read_patchdock.hh.

std::string protocols::protein_interface_design::PatchdockReader::saved_input_tag_

private

Definition at line 63 of file read_patchdock.hh.

core::pose::PoseOP protocols::protein_interface_design::PatchdockReader::saved_native_pose_

private

Definition at line 62 of file read_patchdock.hh.

std::string protocols::protein_interface_design::PatchdockReader::saved_native_tag_

private

Definition at line 63 of file read_patchdock.hh.

utility::vector1< Transformation > protocols::protein_interface_design::PatchdockReader::saved_transformations_

private

Definition at line 64 of file read_patchdock.hh.

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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