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IMP Reference Guide  2.9.0
The Integrative Modeling Platform
IMP::kinematics::ProteinKinematics Class Reference

#include <IMP/kinematics/ProteinKinematics.h>

+ Inheritance diagram for IMP::kinematics::ProteinKinematics:

Detailed Description

Kinematic structure over a protein, with backbone and side chain dihedrals

Note: Particles that are handled by this class should never be decorated with IMP::core::RigidBody externally, as this could lead to unexpected behavior (e.g., wrong coordinates) and it cannot be detected by IMP at the current time.

Definition at line 35 of file ProteinKinematics.h.

Public Member Functions

 ProteinKinematics (atom::Hierarchy mhd, bool flexible_backbone=true, bool flexible_side_chains=false)
 Constructor with all phi/psi rotatable. More...
 
 ProteinKinematics (atom::Hierarchy mhd, const atom::Residues &flexible_residues, const std::vector< atom::Atoms > &dihedral_angles, atom::Atoms open_loop_bond_atoms=atom::Atoms(), bool flexible_backbone=true, bool flexible_side_chains=false)
 
DihedralAngleRevoluteJoints get_joints ()
 
KinematicForestget_kinematic_forest ()
 
DihedralAngleRevoluteJoints get_loop_joints ()
 
DihedralAngleRevoluteJoints get_ordered_joints ()
 
double get_phi (const atom::Residue r) const
 
double get_psi (const atom::Residue r) const
 
core::RigidBodies get_rigid_bodies ()
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
void set_phi (const atom::Residue r, double angle)
 
void set_psi (const atom::Residue r, double angle)
 
- Public Member Functions inherited from IMP::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
void set_check_level (CheckLevel l)
 
void set_log_level (LogLevel l)
 Set the logging level used in this object. More...
 
void set_was_used (bool tf) const
 
void show (std::ostream &out=std::cout) const
 
const std::string & get_name () const
 
void set_name (std::string name)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Constructor & Destructor Documentation

IMP::kinematics::ProteinKinematics::ProteinKinematics ( atom::Hierarchy  mhd,
bool  flexible_backbone = true,
bool  flexible_side_chains = false 
)

Constructor with all phi/psi rotatable.

Member Function Documentation

core::RigidBodies IMP::kinematics::ProteinKinematics::get_rigid_bodies ( )

get all rigid bodies that were automatically generated in the tree

Definition at line 88 of file ProteinKinematics.h.

virtual ::IMP::VersionInfo IMP::kinematics::ProteinKinematics::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 106 of file ProteinKinematics.h.


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