Rosetta Core  2014.35
Classes | Typedefs | Functions
core::membrane::geometry Namespace Reference

Classes

class  Embedding
 
class  EmbeddingDef
 Embedding Setup Helper Class. More...
 

Typedefs

typedef
utility::pointer::owning_ptr
< Embedding
EmbeddingOP
 
typedef
utility::pointer::owning_ptr
< Embedding const > 
EmbeddingCOP
 
typedef
utility::pointer::owning_ptr
< EmbeddingDef
EmbeddingDefOP
 
typedef
utility::pointer::owning_ptr
< EmbeddingDef const > 
EmbeddingDefCOP
 

Functions

numeric::xyzVector< core::Realcenter_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
 Center of Mass. More...
 
core::SSize residue_center_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
 Residue Center of Mass. More...
 
core::SSize return_nearest_residue (pose::Pose const &pose, core::SSize const begin, core::SSize const end, Vector center)
 Return nearest residue. More...
 
std::pair< utility::vector1
< Real >, utility::vector1
< Real > > 
get_chain_and_z (pose::PoseOP pose)
 Get z-coord and chainID. More...
 
void membrane_normal_to_length_15 (pose::Pose &pose)
 Normalize normal vector to length 15 for visualization. More...
 

Typedef Documentation

Function Documentation

numeric::xyzVector< core::Real > core::membrane::geometry::center_of_mass ( pose::Pose const &  pose,
core::SSize const  start,
core::SSize const  stop 
)

Center of Mass.

Calculates the center of mass of a pose - Stop and start positions (or residues) used ot find the starting and finishing locations the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Author
Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::Residue::atom(), core::conformation::membrane::center, center_of_mass(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

std::pair< utility::vector1< Real >, utility::vector1< Real > > core::membrane::geometry::get_chain_and_z ( pose::PoseOP  pose)

Get z-coord and chainID.

Helper function that creates input for SpanningTopology which is not built at the time the Pose is built returns a pair of vectors: vector1 is z-coord of CA atoms of the pose vector2 is chainID of CA atoms of the pose

References core::conformation::TR.

void core::membrane::geometry::membrane_normal_to_length_15 ( pose::Pose pose)
core::SSize core::membrane::geometry::residue_center_of_mass ( pose::Pose const &  pose,
core::SSize const  start,
core::SSize const  stop 
)

Residue Center of Mass.

Calcualte the center of mass of a pose.

Author
Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::membrane::center, center_of_mass(), and core::pose::return_nearest_residue().

core::SSize core::membrane::geometry::return_nearest_residue ( pose::Pose const &  pose,
core::SSize const  begin,
core::SSize const  end,
Vector  center 
)

Return nearest residue.

Find the residue nearest some position passed in (normally a center of mass)

Author
Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::sequence::end, core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().