Editors
================================================================================
.. currentmodule:: ost.mol
The structure, topology and connectivity of :class:`entities <EntityHandle>` 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 (:class:`ICSEditor`) and one for the external coordinate system (:class:`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.
* :meth:`XCSEditor.UpdateICS` or :meth:`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 :meth:`XCSEditor.UpdateICS` or
:meth:`ICSEditor.UpdateXCS` when the editing is finished. Alternatively,
starting from Python version 2.6, one can use the \
`with <http://docs.python.org/reference/compound_stmts.html#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.
.. note::
To use the editing functions available in :class:`EditorBase`, it is
recommended to use the external coordinate system :class:`XCSEditor` for
performance reasons.
.. class:: EditorBase
Inherited by :class:`XCSEditor`, :class:`ICSEditor`.
.. method:: InsertChain(chain_name[, chain, deep=false])
Add new chain to the entity. Properties of :class:`ChainHandle` `chain` will be inherited, if provided.
:param chain_name: The chain's name. In the scope of an entity, chain names
are unique. If a chain of the same name already exists
an :class:`IntegrityError` is raised.
:type chain_name: :class:`string`
:param chain: The newly created chain will take over all generic
properties attached to this handle.
:type chain: :class:`ChainHandle`
:param 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.
:type deep:
:returns: :class:`ChainHandle`
.. method:: AppendResidue(chain, residue_name, [res_num])
AppendResidue(chain, residue, deep=False)
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.
It is possible to give a residue handle as second argument, instead of a
residue name. By default, atoms and bonds are not added. If deep is
`True`, atoms (but not bonds) are added to the new residue, including
alternative atoms.
:param chain: Must be a valid chain
:type chain: :class:`ChainHandle`
:param residue_name: 3-letter-code of the residue, e.g. ``GLY``.
:type residue_name: :class:`string`
:param residue: A residue handle to copy
:type residue: :class:`ResidueHandle`
:param deep: If set to true, insert atoms as well.
:type deep: :class:`bool`
:returns: :class:`ResidueHandle`
.. method:: 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.
:param residue: Must be a valid residue
:type residue: :class:`ResidueHandle`
:param new_name: is the new name. Free to choose and not verified to be a
valid identifier.
:type new_name: string
.. method:: 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.
:param chain: Must be a valid chain
:type chain: :class:`ChainHandle`
:param new_name: is the new name
:type new_name: string
.. method:: SetChainType(chain, type)
:param chain: Must be a valid chain
:type chain: :class:`ChainHandle`
:param type: Chain type to set
:type type: :class:`ChainType`
.. method:: SetChainDescription(chain, description)
:param chain: Must be a valid chain
:param description: Description to be added
.. method:: InsertAtom(residue, atom_name, pos, element="", occupancy=1.0, \
b_factor=0.0, is_hetatm=False)
Insert new atom and add it to residue. By convention, this should be the
chemical symbol in upper case. For atoms with alternative atom locations
use :meth:`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.
:param residue: is the parent residue and must be valid
:type residue: :class:`ResidueHandle`
:param atom_name: 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
:class:`builders <conop.Builder>` in the :mod:`conop`
module rely on proper naming.
:type atom_name: string
:param pos: is the position of the atom in global coordinates
:type pos: :class:`~ost.geom.Vec3`
:param element: 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.
:type element: class:`string`
:param occupancy: The occupancy of the atom. between 0 and 1
:type occupancy: float
:param b_factor: temperature factor.
:type b_factor: float
:param is_hetatm: whether the atom is an atom coming from a HETATM record.
:type is_hetatm: bool
:returns: :class:`AtomHandle`
.. method:: InsertAltAtom(residue, atom_name, alt_group, pos, element="", occupancy=1.0, b_factor=0.0)
Insert new atom with alternative position indicator
:param residue: is the parent residue and must be valid
:type residue: :class:`ResidueHandle`
:param atom_name: 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
:class:`builders <conop.Builder>` in the :mod:`conop`
module rely on proper naming.
:type atom_name: string
:param alt_group: group is the name of the alternative atom position group.
If no group of that name exists, it will be created.
:type alt_group: string
:param pos: is the position of the atom in global coordinates
:type pos: :class:`~ost.geom.Vec3`
:param element: 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.
:type element: class:`string`
:param occupancy: The occupancy of the atom. between 0 and 1
:type occupancy: float
:param b_factor: temperature factor.
:type b_factor: float
:returns: :class:`AtomHandle`
.. method:: InsertAltAtom(residue, atom, alt_group)
Insert new atom with alternative position indicator
:param residue: is the parent residue and must be valid
:type residue: :class:`ResidueHandle`
:param atom: Must be a valid Atom
:type atom: :class:`AtomHandle`
:param alt_group: group is the name of the alternative atom position group.
If no group of that name exists, it will be created.
:type alt_group: string
:returns: :class:`AtomHandle`
.. method:: AddAltAtomPos(alt_group, atom, pos, occupancy=1.0, b_factor=0.0)
Add an alternative atom position
:param alt_group: group is the name of the alternative atom position group.
If no group of that name exists, it will be created.
:type alt_group: string
:param atom: 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.
:type atom: :class:`AtomHandle`
:param pos: is the position of the atom in global coordinates
:type pos: :class:`~ost.geom.Vec3`
:param occupancy: The occupancy of the atom. between 0 and 1
:type occupancy: float
:param b_factor: temperature factor.
:type b_factor: float
.. method:: AddTorsion(name, atom1, atom2, atom3, atom4)
Add a named torsion to the entity. The atoms must have bonds between
atom1-atom2-atom3-atom4.
:param name: The torsion name, e.g. PHI or PSI
:type name: :class:`str`
:param atom1: First atom. must be valid
:type atom1: :class:`AtomHandle`
:param atom2: Second atom. must be valid
:type atom2: :class:`AtomHandle`
:param atom3: Third atom. must be valid
:type atom3: :class:`AtomHandle`
:param atom4: Fourth atom. must be valid
:type atom4: :class:`AtomHandle`
.. method:: DeleteAtom(atom)
Deletes the atom from the entity and removes all bonds and torsions this
atom is involved.
:param atom: A valid atom
:type atom: :class:`EntityHandle`
.. method:: 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.
:type residue: :class:`ResidueHandle`
:param residue: A valid residue
:type atom: The atom to be deleted
:type atom: :class:`EntityHandle`
.. method:: DeleteAtoms(atoms)
Deletes a set specified atoms. All associated torsions and bonds will be
removed as well
:type atoms: :class:`AtomHandleList`
:param atoms: A valid set of atoms
.. method:: DeleteResidue(residue)
Deletes the residue, it's atoms and removes all bonds and torsion where one
atom of the residue is involved
:type residue: :class:`ResidueHandle`
:param residue: A valid residue
.. method:: DeleteResidues(chain)
Deletes all the residues of given chain.
All associated atoms, residues, torsions and bonds will also be deleted
:type chain: :class:`ChainHandle`
:param chain: A valid chain
.. method:: DeleteChain(chain)
Delete the given chain, and all its residues
:param chain: `A valid chain`
:type chain: :class:`ChainHandle`
.. method:: 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.
:param chain: `A valid chain`
:type chain: :class:`ChainHandle`
.. method:: ReorderAllResidues()
Reorder residues of the all chains 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.
.. method:: RenumberAllResidues(start, keep_spacing)
Renumber residues of all chains
:param start: Residues of every chain will be renumbered,
whereas the first residue gets the residue number start.
:type start: int
:param keep_spacing: If set to false, residues will continously
Otherwise the spacings between the residues are kept
:type keep_spacing: bool
.. method:: RenumberChain(chain, new_numbers)
Renumber residues of the given chain
:param chain: A valid chain
:type chain: :class:`ChainHandle`
:param new_numbers: A valid ResNumList
:type new_numbers: :class:`ResNumList`
.. method:: RenumberChain(chain, start, keep_spacing)
Renumber residues of the given chain
:param chain: A valid chain
:type chain: :class:`ChainHandle`
:param start: Residues of given chain will be renumbered,
whereas the first residue gets the residue number start.
:type start: int
:param keep_spacing: If set to false, residues will continously
Otherwise the spacings between the residues are kept
:type keep_spacing: bool
.. method:: GetMode()
Get edit mode of editor
:returns: :class:`EditMode`
.. method:: RenameAtom(atom, new_name)
Change the name of atom to new_name without changing anything else.
:param atom: Must be a valid atom
:type atom: :class:`AtomHandle`
:param new_name: is the new name. Free to choose and not verified to be a
valid atom identifier.
:type new_name: string
.. method:: SetResidueNumber(residue, num)
Change the number of residue to num without changing anything else.
:param residue: Must be a valid residue
:type residue: :class:`ResidueHandle`
:param num: Residue number
:type num: :class: `ResNum`
.. method:: Connect(atom1, atom2)
Connect(atom1, atom2, bond_order)
Add a bond between two atoms.
:param atom1: Must be a valid atom
:type atom1: :class:`AtomHandle`
:param atom2: Must be a valid atom
:type atom2: :class:`AtomHandle`
:param bond_order: bond order (e.g. 1=single, 2=double, 3=triple)
:type bond_order: :class:`int`
.. method:: Prune()
Removes residues and chains that don't contain any atoms.
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 :class:`EditorBase`
.. method:: ApplyTransform(transform)
Apply a transformation to the entity. The transformation is applied to all
atoms positions.
:param transform: The transformation to be applied
:type transform: :class:`geom.Mat4`
.. method:: ApplyTransform(transform)
Apply a transformation to the entity. The transformation is applied to all
atoms positions.
:param transform: The transformation to be applied
:type transform: :class:`Transform`
.. method:: SetTransform(transform)
Set the entity transformation. See also :meth:`ApplyTransform`
:param transform: The transformation to be applied
:type transform: :class:`geom.Mat4`
.. method:: SetTransform(transform)
Set the entity transformation. See also :meth:`ApplyTransform`
:param transform: The transformation to be applied
:type transform: :class:`Transform`
.. method:: FixTransform()
Set transformed positions to new original positions
.. method:: UpdateICS()
Immediately update internal coordinate system
.. method:: ForceUpdate()
Force spatial organizer and ICS update workaround for delayed editor call from Python garbage collection
.. method:: SetAtomPos(atom, pos)
SetAtomPos(atom_list, pos_list)
SetAtomTransformedPos(atom, pos)
SetAtomTransformedPos(atom_list, pos_list)
Set the transformed position of atoms. This method will also update the
original position of atoms by applying the inverse of the entity transform.
Setting all positions at once is by far faster than call the function for
each atom, but it is only available if OpenStructure was compiled with an
enabled ``USE_NUMPY`` flag (see :ref:`here <cmake-flags>` for details). The
fastest option to work with all atom positions externally is to extract the
list of :attr:`~ost.mol.EntityHandle.atoms` with
:meth:`ost.mol.EntityHandle.GetPositions` (with *sort_by_index = False*).
Then extract a buffered editor and use the same list of atoms with a
modified numpy array as input to this function. Example:
.. code-block:: python
# get atom list and positions
atom_list = ent.atoms
positions = ent.GetPositions(False)
# modify positions but keep ent and atom_list unchanged
# ...
# apply changes to entity all at once
edi = ent.EditXCS(mol.BUFFERED_EDIT)
edi.SetAtomPos(atom_list, positions)
edi.UpdateICS()
:param atom: A valid atom handle
:type atom: :class:`ost.mol.AtomHandle`
:param atom_list: A valid atom handle list or a list of atom :attr:`indices
<ost.mol.AtomHandle.index>`.
:type atom_list: :class:`ost.mol.AtomHandleList` or :class:`list` of
:class:`int`
:param pos: The new position
:type pos: :class:`~ost.geom.Vec3`
:param pos_list: An array of positions (shape [*len(atom_list)*, 3],
preferably contiguous array in memory (C order)).
:type pos_list: :class:`numpy.array`
.. method:: SetAtomOriginalPos(atom, pos)
SetAtomOriginalPos(atom_list, pos_list)
Set the original (untransformed) position of atoms. This method will
also update the transformed position by applying the entity transform to
the original pos. See :meth:`SetAtomPos` for more details.
Editor for the Internal Coordinate System
--------------------------------------------------------------------------------
The :class:`ICSEditor` is used to manipulate the internal coordinate system that
is defined by bond lengths and angles. You can create an editor with the
:class:`~EntityHandle.EditICS` method of the :class:`EntityHandle`.
The use :class:`XCSEditor` and :class:`ICSEditor` are mutually exclusive. This
means that whenever a :class:`XCSEditor` has pending changes, the results of
using an :class:`ICSEditor` is undefined and vice versa.
.. note::
For speed reasons, the internal coordinate system is not initialised until
the first call to :meth:`EntityHandle.EditICS`. This involves the build-up of
a directed-graph for the bond network as well as calculating the internal
coordinate matrices.
.. warning::
The :class:`ICSEditor` has a very significant performance impact on the
structure, and can make subsequent access or modifications on the entity
extremely slow to keep the internal coordinate system up-to-date. The
:class:`ICSEditor` is never used in SWISS-MODEL, ProMod3 or CAMEO. Only
open one if you absolutely need to.
.. class:: ICSEditor
Inherits :class:`EditorBase`
.. method:: 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: :meth:`UpdateXCS`
:param torsion: A valid torsion
:type torsion: :class:`TorsionHandle`
:param angle: The angle in radians
:type angle: :class:`float`
:raises: :exc:`RuntimeError` when the torsion handle is invalid
.. method:: SetTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
Set the angles of the given atoms. 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 :meth:`SetDihedralAngle` function
:see: :meth:`UpdateXCS`
:param atom1: The first atom. Must be valid
:type atom1: :class:`AtomHandle`
:param atom2: The second atom. Must be valid
:type atom2: :class:`AtomHandle`
:param atom3: The third atom. Must be valid
:type atom3: :class:`AtomHandle`
:param atom4: The third atom. Must be valid
:type atom4: :class:`AtomHandle`
:param angle: The angle in radians
:type: angle: :class:`Real`
:param update_others: Update all the the other torsion angles consequently
:type update_others: bool
.. method:: RotateTorsionAngle(torsion, delta, update_others=True)
Rotate torsion angle
:see: :meth:`UpdateXCS`
:param torsion: A valid torsion
:type torsion: :class:`TorsionHandle`
:param delta: delta
:type delta: :class:`Real`
:param update_others: Update all the the other torsion angles consequently
:type update_others: bool
.. method:: RotateTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
Rotate torsion angle
:see: :meth:`UpdateXCS`
:param atom1: The first atom. Must be valid
:type atom1: :class:`AtomHandle`
:param atom2: The second atom. Must be valid
:type atom2: :class:`AtomHandle`
:param atom3: The third atom. Must be valid
:type atom3: :class:`AtomHandle`
:param atom4: The third atom. Must be valid
:type atom4: :class:`AtomHandle`
:param angle: The angle in radians
:type: angle: :class:`Real`
:param update_others: Update all the the other torsion angles consequently
:type update_others: bool
.. method:: UpdateXCS()
Apply all remaining changes to the internal coordinate system and
recalculate external coordinates. In unbuffered edit mode, calling this
method has no effect.
.. method:: 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: :meth:`UpdateICS`
:param bond: A valid bond handle
:type bond: :class:`BondHandle`
:param length: The bond length in Angstrom.
:type length: :class:`float`
:raises: :exc:`RuntimeError` when the bond handle is invalid
.. method:: 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: :meth:`UpdateICS`
:param atom1: The first atom. Must be valid
:type atom1: :class:`AtomHandle`
:param atom2: The second atom. Must be valid
:type atom2: :class:`AtomHandle`
:param atom3: The third atom. Must be valid
:type atom3: :class:`AtomHandle`
:param angle: The angle in radians
:raises: :exc:`RuntimeError` when one of the atoms is invalid or there is
no bond between atom1 and atom2 or atom2 and atom3.