Editors¶
The structure, topology and connectivity of entities is edited via editors. This includes operations such as changing atom positions, connecting atoms with bonds as well as adding and removing chains, residues and atoms. There are two flavors of editors, one for the internal coordinate system (ICSEditor) and one for the external coordinate system (XCSEditor).
Edit Modes¶
Editors support two modes: An unbuffered edit mode and a buffered edit mode. In the unbuffered edit mode, dependent information such as the spatial organizer and the internal coordinate system (in case of the XCSEditor) are updated after every change. In buffered edit mode, the updates are delayed until one of the following happens:
- The last editor goes out of scope.
- XCSEditor.UpdateICS() or ICSEditor.UpdateXCS() is called explicitly.
The editors follow the RIAA (resource allocation is initialization) principle: Whenever an editor is requested an internal reference counter is incremented. In the destructor, this reference count is decremented. When the count drops to zero, the dependent information is updated.
In Python, one can not rely on the destructors being called. It is advised to always put a call to XCSEditor.UpdateICS() or ICSEditor.UpdateXCS() when the editing is finished. Alternatively, starting from Python version 2.6, one can use the with statement to make sure the destructor are called and the dependent information is updated.
Basic Editing Operations¶
The basic functionality of editors is implemented in the EditorBase class.
- class EditorBase¶
Inherited by XCSEditor, ICSEditor.
- InsertChain(chain_name)¶
Add new chain to the entity
Parameters: chain_name (string) – The chain’s name. In the scope of an entity, chain names are unique. If a chain of the same already exists an IntegrityError is raised. Returns: ChainHandle
- AppendResidue(chain, residue_name[, res_num])¶
Append residue to the end of the chain. If res_num is not given, the residue number will be set to the residue number of the last added residue plus one. The insertion code is the same.
Parameters: - chain (ChainHandle) – Must be a valid chain
- residue_name (string) – 3-letter-code of the residue, e.g. GLY.
Returns:
- RenameResidue(residue, new_name)¶
Change the name of residue to new_name. Just overwrites the 3-letter-code without changing anything else. Be aware that the sequence/ 1-letter-code will not change automatically.
Parameters: - residue (ResidueHandle) – Must be a valid residue
- new_name (string) – is the new name. Free to choose and not verified to be a valid identifier.
- RenameChain(chain, new_name)¶
Change the name of a chain to new_name while avoiding duplicated identifiers. If new_name is already in use by any chain, an exception will be generated.
Parameters: - chain (ChainHandle) – Must be a valid chain
- new_name (string) – is the new name
- SetChainType(chain, type)¶
Parameters: - chain – Must be a valid chain
- type – Must be a value of enum ChainType (see ChainHandle.type)
- SetChainDescription(chain, description)¶
Parameters: - chain – Must be a valid chain
- description – Description to be added
- InsertAtom(residue, atom_name, pos,
- element="", occupancy=1.0, b_factor=0.0,
- is_hetatm=False)
Insert new atom and add it to residue. For atoms with alternative atom locations use InsertAltAtom(). If the element parameter is a valid element, the atom properties mass, charge, and radius are set to default values for that element. If element is an empty string (or an invalid element), the properties are set to rather meaningless default values. You may later set any of the properties manually.
Parameters: - residue (ResidueHandle) – is the parent residue and must be valid
- atom_name (string) – is the atom name. While free to choose a name, it is advised to properly name the atoms according to IUPAC rules as several algorithms as well as most builders in the conop module rely on proper naming.
- pos (Vec3) – is the position of the atom in global coordinates
- element (class:string) – is the atom’s element. If set to a a valid element, atom properties such as mass, charge, radius are set based on default values for that element. If the element string is empty, or unknown, the properties are filled with rather meaningless default values.
- occupancy (float) – The occupancy of the atom. between 0 and 1
- b_factor (float) – temperature factor.
- is_hetatm (bool) – whether the atom is an atom coming from a HETATM record.
Returns:
- AddTorsion(name, atom1, atom2, atom3, atom4)¶
Add a named torsion to the entity. The atoms must have bonds between atom1-atom2-atom3-atom4.
Parameters: - name (str) – The torsion name, e.g. PHI or PSI
- atom1 (AtomHandle) – First atom. must be valid
- atom2 (AtomHandle) – Second atom. must be valid
- atom3 (AtomHandle) – Third atom. must be valid
- atom4 (AtomHandle) – Fourth atom. must be valid
- DeleteAtom(atom)¶
Deletes the atom from the entity and removes all bonds and torsions this atom is involved.
Parameters: atom (EntityHandle) – A valid atom
- DeleteAllAtoms(residue)¶
Deletes all atoms of this residue from the entity and remove all bonds and torsions for where an atom of the residue is involved.
Parameters: residue (ResidueHandle) – A valid residue
- DeleteResidue(residue)¶
Deletes the residue, it’s atoms and removes all bonds and torsion where one atom of the residue is involved
Parameters: residue (ResidueHandle) – A valid residue
- DeleteChain(chain)¶
Delete the given chain, and all its residues
Parameters: chain (ChainHandle) – A valid chain
- ReorderResidues(chain)¶
- ReorderResidues()
Reorder residues of the chain (the entity) such that their residues numbers are continuously increasing. This function might be useful in cases of PDB files that do not list the residues from N to C terminus but rather use the residue number to describe their position in the chain.
Parameters: chain (ChainHandle) – A valid chain
- RenameAtom(atom, new_name)¶
Change the name of atom to new_name without changing anything else.
Parameters: - atom (AtomHandle) – Must be a valid atom
- new_name (string) – is the new name. Free to choose and not verified to be a valid atom identifier.
Editor for the External Coordinate System¶
The XCSEditor defines the interface for manipulating the external coordinate system. The external coordinate system directly operates on atom positions in Euclidian space.
- class XCSEditor¶
Inherits EditorBase
- ApplyTransform(transform)¶
Apply a transformation to the entity. The transformation is applied to all atoms positions.
Parameters: transform (geom.Mat4) – The transformation to be applied
- SetTransform(transform)¶
Set the entity transformation. See also ApplyTransform()
Parameters: transform (geom.Mat4) – The transformation to be applied
- SetAtomPos(atom, pos)¶
Set the (transformed) position of atom. This method will also update the original position of the atom by applying the inverse of the entity transform.
Parameters: - atom (ost.mol.AtomHandle) – must be a valid atom handle
- pos (Vec3) – The new position
- SetOriginalAtomPos(atom, pos)¶
Set the original (untransformed) position of the atom. This method will also update the transformed position by applying the entity transform to the original pos.
Parameters: - atom (ost.mol.AtomHandle) – must be a valid atom handle
- pos (Vec3) – The new untransformed position
Editor for the Internal Coordinate System¶
The ICSEditor is used to manipulate the internal coordinate system that is defined by bond lengths and angles. You can create an editor with the EditICS method of the EntityHandle.
The use XCSEditor and ICSEditor are mutually exclusive. This means that whenever a XCSEditor has pending changes, the results of using an ICSEditor is undefined and vice versa.
Note
For speed reasons, the internal coordinate system is not initialised until the first call to EntityHandle.EditICS(). This involves the build-up of a directed-graph for the bond network as well as calculating the internal coordinate matrices.
- class ICSEditor¶
Inherits EditorBase
- SetTorsionAngle(torsion, angle)¶
Set the angle of the given torsion. If the edit mode of the editor is set to buffered, the external coordinates remain unchanged. If set to unbuffered, the external coordinates are immediately recalculated.
See : Parameters: - torsion (TorsionHandle) – A valid torsion
- angle (float) – The angle in radians
Raises : RuntimeError when the torsion handle is invalid
- UpdateXCS()¶
Apply all remaining changes to the internal coordinate system and recalculate external coordinates. In unbuffered edit mode, calling this method has no effect.
- SetBondLength(bond, length)¶
Sets the length of a bond. If the edit mode of the editor is set to buffered, the external coordinates remain unchanged. If set to unbuffered, the external coordinates are immediately recalculated.
See : UpdateICS()
Parameters: - bond (BondHandle) – A valid bond handle
- length (float) – The bond length in Angstrom.
Raises : RuntimeError when the bond handle is invalid
- SetAngle(atom1, atom2, atom3, angle)¶
Sets the angle between 3 atoms. The first atom must be connected to the second, the second to the third with a bond. If the edit mode of the editor is set to buffered, the external coordinates remain unchanged. If set to unbuffered, the external coordinates are immediately recalculated.
See : UpdateICS()
Parameters: - atom1 (AtomHandle) – The first atom. Must be valid
- atom2 (AtomHandle) – The second atom. Must be valid
- atom3 (AtomHandle) – The third atom. Must be valid
- angle – The angle in radians
Raises : RuntimeError when one of the atoms is invalid or there is no bond between atom1 and atom2 or atom2 and atom3.