#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)

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)

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)

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 ( )

create invalid xcs editor

~XCSEditor ( )

XCSEditor ( const XCSEditor & rhs )

XCSEditor	(	const EntityHandle &	ent,
		EditMode	mode
	)

protected

Member Function Documentation

void ApplyTransform ( const geom::Mat4 & transform )

apply additional transformation to all atoms

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

void ApplyTransform ( const geom::Transform & transform )

void FixTransform ( )

set transformed pos to new original pos

void ForceUpdate ( )

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

XCSEditor& operator= ( const XCSEditor & rhs )

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

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

void SetAtomOriginalPos	(	const AtomHandleList &	alist,
		float *	positions
	)

numpy float interface

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

void SetAtomOriginalPos	(	const AtomHandleList &	alist,
		double *	positions
	)

numpy double interface

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

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

same as SetAtomTransformedPos(AtomHandle, geom::Vec3)

void SetAtomPos	(	const AtomHandleList &	alist,
		float *	positions
	)

same as SetTransformedPos(AtomHandleList,float*)

void SetAtomPos	(	const AtomHandleList &	alist,
		double *	positions
	)

same as SetTransformedPos(AtomHandleList,double*)

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

set transformed position of atom

This function also updates the original coordinates

void SetAtomTransformedPos	(	const AtomHandleList &	alist,
		float *	positions
	)

numpy float interface

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

void SetAtomTransformedPos	(	const AtomHandleList &	alist,
		double *	positions
	)

numpy double interface

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

void SetTransform ( const geom::Mat4 & transform )

apply a new transformation to all atoms

void SetTransform ( const geom::Transform & transform )

void Update ( )

protected

void UpdateICS ( )

immediately update internal coordinate system

Friends And Related Function Documentation

friend class EntityHandle

friend

Definition at line 38 of file xcs_editor.hh.

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

stage/include/ost/mol/xcs_editor.hh

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation