OpenStructure
Public Member Functions | Protected Member Functions | Friends
XCSEditor Class Reference

#include <xcs_editor.hh>

Inherits EditorBase.

Public Member Functions

 XCSEditor ()
 
 ~XCSEditor ()
 
 XCSEditor (const XCSEditor &rhs)
 
XCSEditoroperator= (const XCSEditor &rhs)
 
void SetAtomOriginalPos (const AtomHandle &atom, const geom::Vec3 &position)
 
void SetAtomOriginalPos (const AtomHandleList &alist, float *positions)
 
void SetAtomOriginalPos (const AtomHandleList &alist, double *positions)
 
void SetAtomTransformedPos (const AtomHandle &atom, const geom::Vec3 &position)
 
void SetAtomTransformedPos (const AtomHandleList &alist, float *positions)
 
void SetAtomTransformedPos (const AtomHandleList &alist, double *positions)
 
void SetAtomPos (const AtomHandle &atom, const geom::Vec3 &position)
 
void SetAtomPos (const AtomHandleList &alist, float *positions)
 
void SetAtomPos (const AtomHandleList &alist, double *positions)
 
void ApplyTransform (const geom::Mat4 &transform)
 
void ApplyTransform (const geom::Transform &transform)
 
void SetTransform (const geom::Mat4 &transform)
 
void SetTransform (const geom::Transform &transform)
 
void FixTransform ()
 
void UpdateICS ()
 
void ForceUpdate ()
 
- Public Member Functions inherited from EditorBase
ChainHandle InsertChain (const String &chain_name)
 
ChainHandle InsertChain (const String &chain_name, ChainHandle chain, bool deep=false)
 
ResidueHandle AppendResidue (ChainHandle chain, const ResidueKey &k)
 
ResidueHandle AppendResidue (ChainHandle chain, const ResidueKey &k, const ResNum &num)
 
ResidueHandle AppendResidue (ChainHandle chain, ResidueHandle residue, bool deep=false)
 
ResidueHandle InsertResidueBefore (ChainHandle chain, int index, const ResNum &num, const ResidueKey &k)
 
ResidueHandle InsertResidueAfter (ChainHandle chain, int index, const ResNum &num, const ResidueKey &k)
 
AtomHandle InsertAtom (ResidueHandle residue, const String &name, const geom::Vec3 &pos, const String &ele="", Real occupancy=1.0, Real b_factor=0.0, bool is_hetatm=false)
 
AtomHandle InsertAtom (ResidueHandle residue, AtomHandle atom)
 
AtomHandle InsertAltAtom (ResidueHandle residue, const String &name, const String &alt_group, const geom::Vec3 &pos, const String &ele="", Real occ=1.0, Real b_factor=0.0)
 
AtomHandle InsertAltAtom (ResidueHandle residue, AtomHandle atom, const String &alt_group)
 
void AddAltAtomPos (const String &group, const AtomHandle &atom, const geom::Vec3 &position, Real occ=1.0, Real b_factor=0.0)
 
BondHandle Connect (const AtomHandle &first, const AtomHandle &second)
 
BondHandle Connect (const AtomHandle &first, const AtomHandle &second, unsigned char bond_order)
 
BondHandle Connect (const AtomHandle &first, const AtomHandle &second, Real len, Real theta, Real phi)
 
BondHandle Connect (const AtomHandle &first, const AtomHandle &second, Real len, Real theta, Real phi, unsigned char bond_order)
 
void RenameResidue (ResidueHandle res, const String &new_name)
 
void SetResidueNumber (ResidueHandle res, const ResNum &num)
 
void RenameChain (ChainHandle chain, const String &new_name)
 
void SetChainType (ChainHandle chain, const ChainType type)
 
void SetChainDescription (ChainHandle chain, const String desc)
 
void DeleteAllAtoms (ResidueHandle res)
 
void DeleteAtom (const AtomHandle &atom)
 
void DeleteAtoms (const AtomHandleList &atoms)
 
void DeleteBond (const BondHandle &bond)
 
void DeleteBonds (const BondHandleList &bonds)
 
TorsionHandle AddTorsion (const String &name, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4)
 
void DeleteChain (const ChainHandle &chain)
 
void DeleteResidue (const ResidueHandle &residue_handle)
 
void ReorderResidues (const ChainHandle &chain)
 
void ReorderAllResidues ()
 
void RenumberAllResidues (int start, bool keep_spacing)
 
void RenumberChain (ChainHandle chain, const ResNumList &new_numbers)
 
void RenumberChain (const ChainHandle &chain, int start, bool keep_spacing)
 
EditMode GetMode () const
 
EntityHandle GetEntity () const
 
void RenameAtom (AtomHandle atom, const String &new_name)
 
void Prune ()
 

Protected Member Functions

 XCSEditor (const EntityHandle &ent, EditMode mode)
 
void Update ()
 
- Protected Member Functions inherited from EditorBase
 EditorBase (const EntityHandle &ent, EditMode mode)
 
void UpdateTrace ()
 

Friends

class EntityHandle
 

Additional Inherited Members

- Protected Attributes inherited from EditorBase
EntityHandle ent_
 
EditMode mode_
 

Detailed Description

external coordinate system editor

For an introduction to editors go here.

Definition at line 36 of file xcs_editor.hh.

Constructor & Destructor Documentation

◆ XCSEditor() [1/3]

XCSEditor ( )

create invalid xcs editor

◆ ~XCSEditor()

~XCSEditor ( )

◆ XCSEditor() [2/3]

XCSEditor ( const XCSEditor rhs)

◆ XCSEditor() [3/3]

XCSEditor ( const EntityHandle ent,
EditMode  mode 
)
protected

Member Function Documentation

◆ ApplyTransform() [1/2]

void ApplyTransform ( const geom::Mat4 transform)

apply additional transformation to all atoms

This transformation is applied after the transformation already stored in the entity

◆ ApplyTransform() [2/2]

void ApplyTransform ( const geom::Transform transform)

◆ FixTransform()

void FixTransform ( )

set transformed pos to new original pos

◆ ForceUpdate()

void ForceUpdate ( )

force spatial organizer and ics update workaround for delayed dtor call from Python garbage collection

◆ operator=()

XCSEditor& operator= ( const XCSEditor rhs)

◆ SetAtomOriginalPos() [1/3]

void SetAtomOriginalPos ( const AtomHandle atom,
const geom::Vec3 position 
)

set original position of atom This function also updates the stores transformed coordinates

◆ SetAtomOriginalPos() [2/3]

void SetAtomOriginalPos ( const AtomHandleList alist,
double *  positions 
)

numpy double interface

the passed in double array must have a length of 3*alist.size()

◆ SetAtomOriginalPos() [3/3]

void SetAtomOriginalPos ( const AtomHandleList alist,
float *  positions 
)

numpy float interface

the passed in float array must have a length of 3*alist.size()

◆ SetAtomPos() [1/3]

void SetAtomPos ( const AtomHandle atom,
const geom::Vec3 position 
)

same as SetAtomTransformedPos(AtomHandle, geom::Vec3)

◆ SetAtomPos() [2/3]

void SetAtomPos ( const AtomHandleList alist,
double *  positions 
)

same as SetTransformedPos(AtomHandleList,double*)

◆ SetAtomPos() [3/3]

void SetAtomPos ( const AtomHandleList alist,
float *  positions 
)

same as SetTransformedPos(AtomHandleList,float*)

◆ SetAtomTransformedPos() [1/3]

void SetAtomTransformedPos ( const AtomHandle atom,
const geom::Vec3 position 
)

set transformed position of atom

This function also updates the original coordinates

◆ SetAtomTransformedPos() [2/3]

void SetAtomTransformedPos ( const AtomHandleList alist,
double *  positions 
)

numpy double interface

the passed in double array must have a length of 3*alist.size()

◆ SetAtomTransformedPos() [3/3]

void SetAtomTransformedPos ( const AtomHandleList alist,
float *  positions 
)

numpy float interface

the passed in float array must have a length of 3*alist.size()

◆ SetTransform() [1/2]

void SetTransform ( const geom::Mat4 transform)

apply a new transformation to all atoms

◆ SetTransform() [2/2]

void SetTransform ( const geom::Transform transform)

◆ Update()

void Update ( )
protected

◆ UpdateICS()

void UpdateICS ( )

immediately update internal coordinate system

Friends And Related Function Documentation

◆ EntityHandle

friend class EntityHandle
friend

Definition at line 38 of file xcs_editor.hh.


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