core::membrane::MembraneProteinFactory Class Reference

Membrane Protein Factory. More...

#include <MembraneProteinFactory.hh>

Public Member Functions
	MembraneProteinFactory (std::string membrane_chains)
	Resource Manager Constructor (No Options Specified) More...
	MembraneProteinFactory (bool include_lips, std::string membrane_chains, bool fullatom)
	Resource Manager Constructor (Non-Default) More...
	MembraneProteinFactory (utility::vector1< PoseOP > chains, utility::vector1< SpanningTopologyOP > topologies, utility::vector1< EmbedConfigInfoOP > embeddings, utility::vector1< LipidAccInfoOP > lipid_acc)
	Interactive Constructor (With Default MP Options) More...
	MembraneProteinFactory (bool include_lips, bool fullatom, utility::vector1< PoseOP > chains, utility::vector1< SpanningTopologyOP > topologies, utility::vector1< EmbedConfigInfoOP > embeddings, utility::vector1< LipidAccInfoOP > lipid_acc)
	Interactive Constructor (with non default options) More...
	~MembraneProteinFactory ()
	Default Destructor. More...
core::pose::PoseOP	create_membrane_pose ()
	Create Membrane Protein. More...

Private Member Functions
	MembraneProteinFactory ()
	Default Constructor (Private. More...
void	initialize_chains ()
	Initialize Chains. More...
void	build_pose (core::pose::PoseOP pose)
	Build Pose. More...
void	initialize_topology (core::pose::PoseOP pose)
	Initialize Spanning Topology. More...
void	initialize_lips_exp (core::pose::PoseOP pose)
	Initialize Lipds Exposure Data. More...
void	show (std::ostream &out)
	Show Membrane Pose Info. More...
void	initialize_resources ()
	Initialize Resources from the Resource Manager. More...

Private Attributes
std::map< core::Size, std::string >	chains_map_
std::string	prefix_file_
bool	fullatom_
bool	include_lips_
utility::vector1 < core::pose::PoseOP >	chains_
utility::vector1 < SpanningTopologyOP >	topologies_
utility::vector1 < EmbedConfigInfoOP >	embeddings_
utility::vector1< LipidAccInfoOP >	lipid_acc_
core::membrane::geometry::MembraneResidueFactory	mrf_

Detailed Description

Membrane Protein Factory.

Initializes a pose as a membrane protein in Rosetta

Constructor & Destructor Documentation

core::membrane::MembraneProteinFactory::MembraneProteinFactory

(

std::string

membrane_chains

)

Resource Manager Constructor (No Options Specified)

Construct a Membrane Protein Factory loading all required resources from the resource manager using the default option settings

Exceptions

EXCN_Illegal_Arguments

if file is "" - cannot construct a membrane protein without chain refs for the resource manager

Returns

MembraneProteinFactory

References initialize_chains(), and initialize_resources().

core::membrane::MembraneProteinFactory::MembraneProteinFactory	(	bool	include_lips,
		std::string	membrane_chains,
		bool	fullatom
	)

Resource Manager Constructor (Non-Default)

Construct a Membrane Protein Factory loading all required resources from the resource manager

Parameters

include_lips	load and include lipid accessibility data in scoring
membrane_chains	text file storing references to membrane chains in the membrane protein
fullatom	specified fullatom residue typeset

Returns

MembraneProteinFactory

References initialize_chains(), and initialize_resources().

core::membrane::MembraneProteinFactory::MembraneProteinFactory	(	utility::vector1< PoseOP >	chains,
		utility::vector1< SpanningTopologyOP >	topologies,
		utility::vector1< EmbedConfigInfoOP >	embeddings,
		utility::vector1< LipidAccInfoOP >	lipid_acc
	)

Interactive Constructor (With Default MP Options)

Construct a Membrane Protein Factory loading all required resources from user specified inputs

Parameters

chians	list of pose chains to compose into a single pose
topologies	list of spannign topology objects for each chain
embeddings	list of embedding data objects for each chain
lipid_acc	list of lipid accessibility data objects for each chain

Returns

MembraneProteinFactory

References chains_, embeddings_, lipid_acc_, and topologies_.

core::membrane::MembraneProteinFactory::MembraneProteinFactory	(	bool	include_lips,
		bool	fullatom,
		utility::vector1< PoseOP >	chains,
		utility::vector1< SpanningTopologyOP >	topologies,
		utility::vector1< EmbedConfigInfoOP >	embeddings,
		utility::vector1< LipidAccInfoOP >	lipid_acc
	)

Interactive Constructor (with non default options)

Construct a Membrane Protein Factory loading all required resources from user specified inputs

Parameters

include_lips	load and include lipid accessibility data in scoring
fullatom	specified fullatom residue typeset
chians	list of pose chains to compose into a single pose
topologies	list of spannign topology objects for each chain
embeddings	list of embedding data objects for each chain
lipid_acc	list of lipid accessibility data objects for each chain

Returns

MembraneProteinFactory

References chains_, embeddings_, lipid_acc_, and topologies_.

core::membrane::MembraneProteinFactory::~MembraneProteinFactory

(

)

Default Destructor.

Note

core::membrane::MembraneProteinFactory::MembraneProteinFactory ( )

private

Default Constructor (Private.

Private Default constructor (DO NOT USE)

Member Function Documentation

void core::membrane::MembraneProteinFactory::build_pose ( core::pose::PoseOP  pose )

private

Build Pose.

Create pose containing membrane/embedding residues from multi- chain input.

Exceptions

EXCN_Resource_Manager,EXCN_Membrane_Bounds

References core::membrane::geometry::MembraneResidueFactory::add_membrane_residue(), core::pose::append_pose_to_pose(), center(), chains_, depth, embeddings_, fullatom_, initialize_lips_exp(), initialize_topology(), mrf_, core::conformation::symmetry::residue_center_of_mass(), topologies_, and TR.

Referenced by create_membrane_pose().

core::pose::PoseOP core::membrane::MembraneProteinFactory::create_membrane_pose

(

)

Create Membrane Protein.

Create a membrne proteins from a series of loaded membrane proteins

Returns

Pose (as starting structure)

References build_pose().

void core::membrane::MembraneProteinFactory::initialize_chains ( )

private

Initialize Chains.

Initialize membrane chains from initialized prefix file provided in the constructor

Exceptions

Argument

exception if chain list not specified (also this is well docuemnted, no excuse)

References chains_map_, utility::io::izstream::eof(), getline(), l, utility::io::izstream::open(), and prefix_file_.

Referenced by MembraneProteinFactory().

void core::membrane::MembraneProteinFactory::initialize_lips_exp ( core::pose::PoseOP  pose )

private

Initialize Lipds Exposure Data.

Initialize lipid exposure data in the final pose

References include_lips_, and lipid_acc_.

Referenced by build_pose().

void core::membrane::MembraneProteinFactory::initialize_resources ( )

private

Initialize Resources from the Resource Manager.

Load required resources for initializing a membrane protein

Note

Precondition: Initialized prefix list

Exceptions

EXCN_Resource_Manager

(missing reuqired resource)

References chains_, chains_map_, embeddings_, include_lips_, lipid_acc_, topologies_, TR, and utility_exit_with_message.

Referenced by MembraneProteinFactory().

void core::membrane::MembraneProteinFactory::initialize_topology ( core::pose::PoseOP  pose )

private

Initialize Spanning Topology.

Initialize spanning topology in the final pose

References topologies_.

Referenced by build_pose().

void core::membrane::MembraneProteinFactory::show ( std::ostream &  out )

private

Show Membrane Pose Info.

Show all ifnormation relevant to the new membrane pose

Member Data Documentation

utility::vector1< core::pose::PoseOP > core::membrane::MembraneProteinFactory::chains_

private

Referenced by build_pose(), initialize_resources(), and MembraneProteinFactory().

std::map< core::Size, std::string > core::membrane::MembraneProteinFactory::chains_map_

private

Referenced by initialize_chains(), and initialize_resources().

utility::vector1< EmbedConfigInfoOP > core::membrane::MembraneProteinFactory::embeddings_

private

Referenced by build_pose(), initialize_resources(), and MembraneProteinFactory().

bool core::membrane::MembraneProteinFactory::fullatom_

private

Referenced by build_pose().

bool core::membrane::MembraneProteinFactory::include_lips_

private

Referenced by initialize_lips_exp(), and initialize_resources().

utility::vector1< LipidAccInfoOP > core::membrane::MembraneProteinFactory::lipid_acc_

private

Referenced by initialize_lips_exp(), initialize_resources(), and MembraneProteinFactory().

core::membrane::geometry::MembraneResidueFactory core::membrane::MembraneProteinFactory::mrf_

private

Referenced by build_pose().

std::string core::membrane::MembraneProteinFactory::prefix_file_

private

Referenced by initialize_chains().

utility::vector1< SpanningTopologyOP > core::membrane::MembraneProteinFactory::topologies_

private

Referenced by build_pose(), initialize_resources(), initialize_topology(), and MembraneProteinFactory().

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

• symlinks/rosetta/src/core/membrane/MembraneProteinFactory.hh
• symlinks/rosetta/src/core/membrane/MembraneProteinFactory.cc