Create an embedding definition from opts. More...

#include <EmbeddingFactory.hh>

Public Member Functions
	EmbeddingFactory (core::pose::PoseOP pose, EmbedConfigInfoOP config, SpanningTopologyOP topology)
	Default Constructor. More...

	~EmbeddingFactory ()
	Default Destructor. More...

void	create_and_add_embedding (bool fullatom)
	Create Embedding Method. More...

void	create_and_add_embedding (bool fullatom, core::Size jump)
	Create Embedding Method. More...

void	embed_from_pdb (EmbedConfigInfoOP embedding)
	Embed from Defaults. More...

void	embed_from_topology (EmbedConfigInfoOP embedding)
	Embed from membrane spanning topology. More...

void	embed_from_search_and_score (EmbedConfigInfoOP embedding)
	Embedding Search and Score Method. More...

void	embed_for_FA (EmbedConfigInfoOP embedding)
	Compute Fullatom Projections for Fa Embedding. More...

Private Attributes
EmbedConfigInfoOP	embed_info_

SpanningTopologyOP	topology_

core::pose::PoseOP	pose_

Detailed Description

Create an embedding definition from opts.

Generate the correct protein emebdding using a user-specified method

Constructor & Destructor Documentation

core::membrane::geometry::EmbeddingFactory::EmbeddingFactory	(	core::pose::PoseOP	pose,
		EmbedConfigInfoOP	config,
		SpanningTopologyOP	topology
	)

Default Constructor.

Ways to fix the logic in the file format

POSE <PDB_ID> <type tag>=""> /// <== MEMBRANE or NON_MEMBRANE center x y z tag normal x y z tag depth x y z tag

References embed_info_, pose_, and topology_.

core::membrane::geometry::EmbeddingFactory::~EmbeddingFactory ( )

Default Destructor.

Member Function Documentation

void core::membrane::geometry::EmbeddingFactory::create_and_add_embedding ( bool fullatom )

Create Embedding Method.

Creates a membrane protein embedding definition from embedidng config object loaded at resource definiiton (cmd). The embedding definition is a final definition of the starting pose's definition in the membrane

Parameters

description	resource description
fullatom	residue typeset

References core::conformation::Conformation::chain_begin(), and pose_.

void core::membrane::geometry::EmbeddingFactory::create_and_add_embedding	(	bool	fullatom,
		core::Size	jump
	)

Create Embedding Method.

Creates a membrane protein embedding definition from embedidng config object loaded at resource definiiton (cmd). The embedding definition is a final definition of the starting pose's definition in the membrane

Parameters

description	resource description
fullatom	residue typeset

References core::conformation::membrane::EmbedConfigInfo::center, embed_from_pdb(), embed_from_search_and_score(), embed_from_topology(), embed_info_, pose_, and TR.

void core::membrane::geometry::EmbeddingFactory::embed_for_FA ( EmbedConfigInfoOP embedding )

Compute Fullatom Projections for Fa Embedding.

Computes Projections, depth, and stores coordinates. Computes fullatom center and corresponding normal from these computations

void core::membrane::geometry::EmbeddingFactory::embed_from_pdb ( EmbedConfigInfoOP embedding )

Embed from Defaults.

Define the membrane embedding from a pre-determined set of parameters Normal (0, 0, 1), Center (0, 0, 0)

Parameters

EmbedConfigInfoOP ref to an embed config info obj passed by the embedding factory

References TR.

Referenced by create_and_add_embedding().

void core::membrane::geometry::EmbeddingFactory::embed_from_search_and_score ( EmbedConfigInfoOP embedding )

Embedding Search and Score Method.

Starting from embedding defined from topology (see method above), score each conformation, perturb, score, and aver n trials and MC accept lowest. Takes the embed params resource loaded via resource loader (RM).

References TR.

Referenced by create_and_add_embedding().

void core::membrane::geometry::EmbeddingFactory::embed_from_topology ( EmbedConfigInfoOP embedding )

Embed from membrane spanning topology.

Determines embedding by finding the average point between Ca inner and Ca outer (distance between the intracellualr and extracellular region).

Parameters

EmbedConfigInfoOP embedding config info to modify

References core::sequence::end, pose_, start, topology_, and TR.

Referenced by create_and_add_embedding().