EditorBase Class Reference

base class for entity editors More...

#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)
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,
ResidueHandle  residue,
bool  deep = false 
)
ResidueHandle AppendResidue ( ChainHandle  chain,
const ResidueKey &  k,
const ResNum &  num 
)
ResidueHandle AppendResidue ( ChainHandle  chain,
const ResidueKey &  k 
)
BondHandle Connect ( const AtomHandle &  first,
const AtomHandle &  second,
Real  len,
Real  theta,
Real  phi,
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,
unsigned char  bond_order 
)
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.

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,
AtomHandle  atom,
const String &  alt_group 
)

Insert new atom with alternative position indicator.

All informations will be copied over from atom, except bonds

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 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
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 
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
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
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 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 ( 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 RenumberChain ( ChainHandle  chain,
const ResNumList &  new_numbers 
)
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 334 of file editor_base.hh.

EditMode mode_ [protected]

Definition at line 335 of file editor_base.hh.

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