EditorBase Class Reference

#include <editor_base.hh>

Inherited by ICSEditor, and XCSEditor.

Public Member Functions
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)
void	Prune ()
Inserting, removing and modifying order of residues
Append residue to the end of the chain Append residue with residue key
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)
Adding/removing atoms
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
	EditorBase (const EntityHandle &ent, EditMode mode)
void	UpdateTrace ()

Protected Attributes
EntityHandle	ent_
EditMode	mode_

Detailed Description

base class for entity editors

Entities, chains, residues and atoms are assembled and modified via editors. Editors are usually used as one of the concrete subclasses of EditorBase: XCSEditor and ICSEditor. The former operates on the external carthesian coordinate system while the latter operates on the internal coordinate system. To create a new editor, use EntityHandle::EditXCS() and EntityHandle::EditICS(), respectively.

For an introduction to the concept of editors go here

Definition at line 46 of file editor_base.hh.

Constructor & Destructor Documentation

EditorBase ( const EntityHandle &  ent, EditMode  mode  )

protected

Member Function Documentation

void AddAltAtomPos	(	const String &	group,
		const AtomHandle &	atom,
		const geom::Vec3 &	position,
		Real	occ = 1.0,
		Real	b_factor = 0.0
	)

Add alternative atom position.

Parameters

group	is the name of the alternative atom position group. If no group of that name exists, it will be created.
atom	is the atom handle the additional location belongs to. It is required that the atom has been inserted via InsertAltAtom, If the atom is a conventional atom without alternative location, a Error will be thrown.
position	is the alternative position
occ
b_factor

See Also

EditorBase::InsertAltAtom(), ResidueHandle

TorsionHandle AddTorsion	(	const String &	name,
		const AtomHandle &	a1,
		const AtomHandle &	a2,
		const AtomHandle &	a3,
		const AtomHandle &	a4
	)

Add named torsion to entity.

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
	)

BondHandle Connect	(	const AtomHandle &	first,
		const AtomHandle &	second
	)

connect two atoms with bond

If there is already a bond between the two atoms, no new bond is created. Instead, the already existing bond is returned.

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 DeleteAllAtoms

(

ResidueHandle

res

)

Delete all atoms of residue.

All associated torsions and bonds will also be removed

void DeleteAtom

(

const AtomHandle &

atom

)

Delete specific atom from this residue.

All associated torsions and bonds will also be removed as well.

Parameters

atom	is the atom to remove. If no such atom exists, this method will have no effect

void DeleteAtoms

(

const AtomHandleList &

atoms

)

\ brief Delete a set of atoms

All associated torsions and bonds will be removed as well

void DeleteBond

(

const BondHandle &

bond

)

\ brief Delete bond

Parameters

bond	Is the bond to remove. If no such bond exists, this method will have no effect

void DeleteBonds

(

const BondHandleList &

bonds

)

\ brief Delete a set of bond

Parameters

bonds

bonds to remove. If no such bonds exist, this method will have no effect

void DeleteChain

(

const ChainHandle &

chain

)

delete chain

all associated atoms, residues, torsions and bonds will also be deleted.

void DeleteResidue

(

const ResidueHandle &

residue_handle

)

Delete residue.

Atoms, bonds and torsions involving this residue are removed as well

See Also

ChainHandle::DeleteResidue, DeleteAtom

EntityHandle GetEntity ( ) const

inline

\ brief return entity this editor works on

Definition at line 327 of file editor_base.hh.

EditMode GetMode ( ) const

inline

Get edit mode of editor.

Definition at line 324 of file editor_base.hh.

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
	)

Insert new atom with alternative position indicator.

See Also

EditorBase::AddAltAtomPos(), ResidueHandle

AtomHandle InsertAltAtom	(	ResidueHandle	residue,
		AtomHandle	atom,
		const String &	alt_group
	)

Insert new atom with alternative position indicator.

All informations will be copied over from atom, except bonds

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
	)

Insert new atom.

Insert new atom and add it to residue. For atoms with alternative atom locations use ResidueHandle::InsertAltAtom().

Parameters

residue	is the parent residue
name	is the atom name. While free to choose a name, it is adviced to properly name the residues according to IUPAC rules as several algorithms as well as most builders in the conop module rely on proper naming.
pos	is the position of the atom in global coordinates
ele
occupancy
b_factor
is_hetatm

AtomHandle InsertAtom	(	ResidueHandle	residue,
		AtomHandle	atom
	)

Insert new atom.

Inserts new atom with all properties from the provided atom handle.

Parameters

residue	is the parent residue
atom	from which all informations will be copied over to the newly created atom

Returns

the newly created AtomHandle

ChainHandle InsertChain

(

const String &

chain_name

)

create new chain

create new chain and attach it to entity.

Parameters

chain_name

The chain name. Can be an arbitrary String. However, if you intend to use the PDB export funtionality, the chain_name should be a single letter, preferably in the range A-Z.

Returns

The newly created chain handle

ChainHandle InsertChain	(	const String &	chain_name,
		ChainHandle	chain,
		bool	deep = false
	)

create new chain

create new chain with properties of a provided chain handle and attach it to entity.

Parameters

chain_name	The chain name. Can be an arbitrary String. However, if you intend to use the PDB export funtionality, the chain_name should be a single letter, preferably in the range A-Z.
chain	The newly created chain will take over all generic attached to this handle.
deep	If set to true, all residues and atoms of chain will be completely copied into the created chain. No bonds and angles are added.

Returns

The newly created chain handle

ResidueHandle InsertResidueAfter	(	ChainHandle	chain,
		int	index,
		const ResNum &	num,
		const ResidueKey &	k
	)

insert residue into chain

This method is identical to InsertResidueBefore() but inserts the residue after the specified position

See Also

InsertResidueBefore

ResidueHandle InsertResidueBefore	(	ChainHandle	chain,
		int	index,
		const ResNum &	num,
		const ResidueKey &	k
	)

void Prune

(

)

Removes all residues and chains in the attached entity that don't contain any atoms.

void RenameAtom	(	AtomHandle	atom,
		const String &	new_name
	)

change the name of the atom to the new name

void RenameChain	(	ChainHandle	chain,
		const String &	new_name
	)

void RenameResidue	(	ResidueHandle	res,
		const String &	new_name
	)

void RenumberAllResidues	(	int	start,
		bool	keep_spacing
	)

renumber residues of all chains

Parameters

start	Residues of every chain will be renumbered, whereas the first residue gets the residue number start.
keep_spacing	If set to false, residues will continously be renumbered ongoing from start. Otherwise the spacings between the residues are kept.

void RenumberChain	(	ChainHandle	chain,
		const ResNumList &	new_numbers
	)

void RenumberChain	(	const ChainHandle &	chain,
		int	start,
		bool	keep_spacing
	)

renumber residues of one chain

Parameters

chain	All residues of this chain will be renumbered according to the parameters start and keep_spacing
start	Residues of given chain will be renumbered, whereas the first residue gets the residue number start.
keep_spacing	If set to false, residues will continously be renumbered ongoing from start. Otherwise the spacings between the residues are kept.

void ReorderAllResidues

(

)

reorder residues of all chains based on their residue number

void ReorderResidues

(

const ChainHandle &

chain

)

reorder residues of given chain based on their residue number

void SetChainDescription	(	ChainHandle	chain,
		const String	desc
	)

Assign a description to a chain.

Parameters

chain	chain to assign to
desc	description

void SetChainType	(	ChainHandle	chain,
		const ChainType	type
	)

Assign type of chain according to ChainType.

Parameters

chain	chain to assign to
type	type of the chain

void SetResidueNumber	(	ResidueHandle	res,
		const ResNum &	num
	)

void UpdateTrace ( )

protected

Field Documentation

EntityHandle ent_

protected

Definition at line 339 of file editor_base.hh.

EditMode mode_

protected

Definition at line 340 of file editor_base.hh.

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

• stage/include/ost/mol/editor_base.hh