MembraneProteinFactory.cc File Reference

MembraneProteinFactory. More...

#include <core/membrane/MembraneProteinFactory.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <core/conformation/membrane/LipidAccInfo.hh>
#include <core/conformation/membrane/definitions.hh>
#include <core/conformation/membrane/Exceptions.hh>
#include <core/membrane/geometry/MembraneResidueFactory.hh>
#include <core/membrane/geometry/EmbeddingFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <basic/resource_manager/ResourceManager.hh>
#include <basic/resource_manager/util.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/tag/Tag.hh>
#include <utility/io/izstream.hh>
#include <cstdlib>
#include <string>
#include <cmath>
#include <algorithm>
#include <stdexcept>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::membrane

Macros
#define	INCLUDED_core_membrane_MembraneProteinFactory_cc
	Class: Membrane Protein Factory. More...

Variables
static basic::Tracer	TR ("core.membrane.MembraneProteinFactory")

Detailed Description

MembraneProteinFactory.

The membrane protein factory creates a single pose from various membrane proteins loaded on the front end and initialized as membrane proteins. This single framework will then be passed off to the MembraneHub (which coordinates I/O) and sent back to the protocol it was called from (usually in pose loading)

Author

Rebecca Alford (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om)

Macro Definition Documentation

#define INCLUDED_core_membrane_MembraneProteinFactory_cc

Class: Membrane Protein Factory.

Construct a membrane protein in Rosetta

Author

Rebecca Alford (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om)

The membrane protein factory constructs a membrane protein in Rosetta through the following steps: (1) Construct fold tree with pre-defined membrane fold tree topology (2) Add a MembraneConformation which maintains info about the membrane protein (3) Add a virtual residue to the root of the foldtree to define the membrane (4) Add a new virtual residue representing the embedding of each protein chain in the membrane

The membrane protein factory provides three constructors - single chain construction, multi chain construction via the resource manager and multi chain construction via the options system (existing system). The new membrane protein framework is not backwards compatible with the previous RosettaMembrane code (Yarov-Yaravoy et al. 2006) and uses a different set of options

Maintains the following invariants: (1) For an n chain pose, will return a pose with n+1 chains (n chains plus a membrane chain) (2) Initializes a correct membrane foldtree topology (initial) (3) Membrane chain is always the n+1 chain (4) Membrane fold tree is a valid fold tree

Notes:

• This class is not a mover. It will not move the backbone whatsoever (see MembraneRigidInitialMover)

Variable Documentation

basic::Tracer TR("core.membrane.MembraneProteinFactory")

static

Referenced by core::membrane::MembraneProteinFactory::build_pose(), and core::membrane::MembraneProteinFactory::initialize_resources().