ICSEditor Class Reference

#include <ics_editor.hh>

Inherits EditorBase.

Public Member Functions
	~ICSEditor ()
	ICSEditor (const ICSEditor &rhs)
ICSEditor &	operator= (const ICSEditor &rhs)
void	SetBondLength (const BondHandle &bond, Real length)
bool	SetAngle (const AtomHandle &atom_a, const AtomHandle &atom_b, const AtomHandle &atom_c, Real angle)
void	SetTorsionAngle (TorsionHandle torsion, Real angle, bool update_others=true)
void	RotateTorsionAngle (TorsionHandle torsion, Real delta, bool update_others=true)
void	RotateTorsionAngle (const AtomHandle &atom_a, const AtomHandle &atom_b, const AtomHandle &atom_c, const AtomHandle &atom_d, Real angle, bool update_others=true)
void	SetTorsionAngle (const AtomHandle &atom_a, const AtomHandle &atom_b, const AtomHandle &atom_c, const AtomHandle &atom_d, Real angle, bool update_others=true)
void	UpdateXCS ()
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
	ICSEditor (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

editor for internal molecule coordinates

See Also

Entity Editors, Roll Helix Example

Definition at line 34 of file ics_editor.hh.

Constructor & Destructor Documentation

~ICSEditor

(

)

ICSEditor ( const EntityHandle &  ent, EditMode  mode  )

protected

ICSEditor

(

const ICSEditor &

rhs

)

Member Function Documentation

ICSEditor& operator=

(

const ICSEditor &

rhs

)

void RotateTorsionAngle	(	TorsionHandle	torsion,
		Real	delta,
		bool	update_others = true
	)

rotate torsion angle

void RotateTorsionAngle	(	const AtomHandle &	atom_a,
		const AtomHandle &	atom_b,
		const AtomHandle &	atom_c,
		const AtomHandle &	atom_d,
		Real	angle,
		bool	update_others = true
	)

bool SetAngle	(	const AtomHandle &	atom_a,
		const AtomHandle &	atom_b,
		const AtomHandle &	atom_c,
		Real	angle
	)

Set angle of vectors formed by a12 and a13 to the given value.

The angle is adjusted in such a way that the plane given by the 3 atom positions is kept invariant (the vectors are rotated around the plane normal).

Setting the angle requires the 3 atoms to be connected with bond. If they are not, the method will fail. The method is solely based on the internal coordinate system.

void SetBondLength	(	const BondHandle &	bond,
		Real	length
	)

set the lengh of the bond, ie the distance of the second atom from the first

Calling BondHandle::SetLength will bring the external coordinate system out of sync. It will not be updated until EntityHandle::UpdateICS() is called.

See Also

EntityHandle::UpdateICS

void SetTorsionAngle	(	TorsionHandle	torsion,
		Real	angle,
		bool	update_others = true
	)

set absolute torsion angle

All connectors at the third atom (A3) will be adjusted accordingly. If you only want to adjust the bond between A3 and A4, and leave the other bonds untouched, use the SetDihedralAngle() function

See Also

RotateTorsionAngle

void SetTorsionAngle	(	const AtomHandle &	atom_a,
		const AtomHandle &	atom_b,
		const AtomHandle &	atom_c,
		const AtomHandle &	atom_d,
		Real	angle,
		bool	update_others = true
	)

void Update ( )

protected

void UpdateXCS

(

)

immediately update external coordinate system

Friends And Related Function Documentation

friend class EntityHandle

friend

Definition at line 36 of file ics_editor.hh.

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

• stage/include/ost/mol/ics_editor.hh