XCSEditor Class Reference

#include <xcs_editor.hh>

Inherits EditorBase.

Public Member Functions
	XCSEditor ()
	~XCSEditor ()
	XCSEditor (const XCSEditor &rhs)
XCSEditor &	operator= (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.

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

• build-2.9.0-doc/stage/include/ost/mol/xcs_editor.hh