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Commit 5076d713 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Cleaned up entity documentation.

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modules/mol/base/doc/editors.rst
+ 5
− 3
View file @ 5076d713
......@@ -93,15 +93,17 @@ The basic functionality of editors is implemented in the EditorBase class.
.. method:: SetChainType(chain, type)
:param chain: Must be a valid chain
:param type: Must be a value of enum ChainType
(see :attr:`ChainHandle.type`)
: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)
.. 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. 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
......
modules/mol/base/doc/entity.rst
+ 60
− 81
View file @ 5076d713
......@@ -194,10 +194,10 @@ The Handle Classes
# select atoms in a box of size 10, centred at the origin
in_box=ent.Select('x=-5:5 and y=-5:5 and z=-5:5')
:param query: The query to be executed. See :class:`Query` for details.
:type query: string or :class:`Query`
:param flags: An ORed combination of :class:`QueryFlags`.
:type flags: int
:param query: The query to be executed.
:type query: :class:`Query` / :class:`str`
:param flags: An ORed together combination of :class:`QueryFlag`
:type flags: :class:`int` / :class:`QueryFlag`
:returns: An :class:`entity view <EntityView>`.
:raises: :class:`QueryError` when the query could not be executed due
to syntactic errors.
......@@ -297,7 +297,9 @@ The Handle Classes
.. attribute:: type
Describes the type of the chain. See :ref:`chaintype`.
Describes the type of the chain.
:type: :class:`ChainType`.
.. attribute:: description
......@@ -916,7 +918,7 @@ The View Classes
See :meth:`EntityHandle.CreateEmptyView`
:rtype: EntityView
:rtype: :class:`EntityView`
.. method:: CreateFullView()
......@@ -948,8 +950,8 @@ The View Classes
:param chain_handle: The chain handle to be added.
:type chain_handle: :class:`ChainHandle`
:param view_add_flags: An ORed together combination of :ref:`viewaddflags`.
:type view_add_flags: :class:`int`
:param view_add_flags: An ORed together combination of :class:`ViewAddFlags`
:type view_add_flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`ChainView`
.. method:: AddResidue(residue_handle[, view_add_flags])
......@@ -957,12 +959,12 @@ The View Classes
Add residue to view. If the residue's chain is not already part of the
view, it will be added. By default, only the residue is added, but not its
atoms. This behaviour can be modified by passing in an appropriate
combination of :ref:`viewaddflags`.
combination of :class:`ViewAddFlags`.
:param residue_handle: The residue handle to be added
:type residue_handle: :class:`ResidueHandle`
:param view_add_flags: An ORed together combination of :ref:`viewaddflags`
:type view_add_flags: :class:`int`
:param view_add_flags: An ORed together combination of :class:`ViewAddFlags`
:type view_add_flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`ResidueView`
.. method:: AddAtom(atom_handle[, view_add_flags])
......@@ -972,8 +974,8 @@ The View Classes
:param atom_handle: The atom handle
:type atom_handle: :class:`AtomHandle`
:param view_add_flags: An ORed together combination of :ref:`viewaddflags`
:type view_add_flags: :class:`int`
:param view_add_flags: An ORed together combination of :class:`ViewAddFlags`
:type view_add_flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`AtomView`
.. method:: AddBond(bond_handle)
......@@ -1065,16 +1067,15 @@ The View Classes
:type atom_name: str
:rtype: :class:`AtomView`
.. method:: Select(query[, flags])
.. method:: Select(query, flags=0)
Perform selection on entity view. See :meth:`EntityHandle.Select`.
:param query: The query
:type query: (:class:`Query` or str)
:param flags: An ORed together combination of ViewAddFlags
:type flags: int
:rtype: EntityView
:type query: :class:`Query` / :class:`str`
:param flags: An ORed together combination of :class:`QueryFlag`
:type flags: :class:`int` / :class:`QueryFlag`
:rtype: :class:`EntityView`
.. method:: Copy()
......@@ -1084,7 +1085,7 @@ The View Classes
the_copy=view.Select(')
:rtype: EntityView
:rtype: :class:`EntityView`
.. method:: GetMass()
......@@ -1306,12 +1307,12 @@ The View Classes
Add atom to the view. If the residue of the atom is not already part of the
view, it will be added. If the atom does not belong to chain, the result is
undefined. Foo
undefined.
:param atom_handle: The atom to be added
:type atom_handle: :class:`AtomHandle`
:param view_add_flags: An ORed together combination of :ref:`viewaddflags`
:type view_add_flags: :class:`int`
:param view_add_flags: An ORed together combination of :class:`ViewAddFlags`
:type view_add_flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`AtomView`
.. method:: AddResidue(residue_handle[, view_add_flags])
......@@ -1319,12 +1320,12 @@ The View Classes
Add residue to the view. If the atom does not belong to chain, the result is
undefined. By default, only the residue, but no atoms are added to the
view. To change the behavior, pass in a suitable combination of
:ref:`viewaddflags`.
:class:`ViewAddFlags`.
:param residue_handle: The residue handle to be added.
:type residue_handle: :class:`ResidueHandle`
:param view_add_flags: An ORed together combination of :ref:`viewaddflags`
:type view_add_flags: :class:`int`
:param view_add_flags: An ORed together combination of :class:`ViewAddFlags`
:type view_add_flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`ResidueView`
.. method:: FindAtom(res_num, atom_name)
......@@ -1414,16 +1415,14 @@ The View Classes
Remove all residues from this chain view
.. method:: Select(query[, flags])
.. method:: Select(query, flags=0)
Perform query on chain. This will return an entity view containing atoms
and bonds of the residue view that match the residue. In case no atom
matches the predicate, an empty view is returned.
Perform query on chain view. See :meth:`EntityHandle.Select`.
:param query: The query
:type query: :class:`Query` or str
:param flags: An ORed together combination of query flags
:type flags: int
:type query: :class:`Query` / :class:`str`
:param flags: An ORed together combination of :class:`QueryFlag`
:type flags: :class:`int` / :class:`QueryFlag`
:rtype: :class:`EntityView`
.. class:: ResidueView
......@@ -1576,8 +1575,8 @@ The View Classes
:param atom_handle: Atom handle to be added
:type atom_handle: :class:`AtomHandle`
:param flags: An ORed together combination of :ref:`viewaddflags`
:type flags: :class:`int`
:param flags: An ORed together combination of :class:`ViewAddFlags`
:type flags: :class:`int` / :class:`ViewAddFlags`
:rtype: :class:`AtomView`
.. method:: GetCenterOfAtoms()
......@@ -1588,16 +1587,14 @@ The View Classes
See :attr:`atoms`
.. method:: Select(query[, flags])
.. method:: Select(query, flags=0)
Perform selection on residue view. This method will return an entity view
containing all atoms and bonds of the residue matching the predicate. In
case no atom matches the predicate, this will return an empty view.
Perform selection on residue view. See :meth:`EntityHandle.Select`.
:param query: The query
:type query: :class:`Query` or str
:param flags: An ORed together combination of query flags
:type flags: int
:type query: :class:`Query` / :class:`str`
:param flags: An ORed together combination of :class:`QueryFlag`
:type flags: :class:`int` / :class:`QueryFlag`
:rtype: :class:`EntityView`
......@@ -1741,40 +1738,26 @@ Residue Numbering
:returns: :attr:`ins_code`
.. _chaintype:
ChainType
--------------------------------------------------------------------------------
A ChainType fills the :attr:`ChainHandle.type` attribute. Different types are
described in the :ref:`ChainType enum <chaintype_enum>`. Functions for setting
a type belong to the :class:`EditorBase` class, getting is provided by the
:class:`ChainHandle` class, further convenience functions are described here.
described in the :class:`ChainType` enum. The type is set with an editor in
:meth:`EditorBase.SetChainType`. Further convenience functions are described
here.
.. _chaintype_enum:
The ChainType enum
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. class:: ChainType
The ChainType enum enumerates all types defined by the PDB for the MMCif file
format. Following values are supported:
The ChainType enum enumerates all types defined by the PDB for the MMCif file
format. Following values are supported:
``CHAINTYPE_POLY``, ``CHAINTYPE_NON_POLY``, ``CHAINTYPE_WATER``,
``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
``CHAINTYPE_POLY``, ``CHAINTYPE_NON_POLY``, ``CHAINTYPE_WATER``,
``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available.
Setter & Getter functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
:func:`EditorBase.SetChainType`, :func:`ChainHandle.GetType`
ChainType functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available.
.. function:: ChainTypeFromString(identifier)
......@@ -1796,23 +1779,19 @@ ChainType functions
:returns: :class:`str`
.. _viewaddflags:
ViewAddFlags
--------------------------------------------------------------------------------
Those are the flags controlling behaviour of routines adding handles to views.
* ``INCLUDE_ATOMS`` - Include all atoms when adding a residue handle to a view
* ``INCLUDE_RESIDUES`` - Include all residues when adding a chain to a view
.. class:: ViewAddFlags
* ``INCLUDE_CHAINS`` - Include all chains when creating a new entity view
Defines flags controlling behaviour of routines adding handles to views:
* ``INCLUDE_ALL`` = ``INCLUDE_ATOMS`` | ``INCLUDE_RESIDUES`` |
``INCLUDE_CHAINS`` - Convenience flags to include all substructures
* ``CHECK_DUPLICATES`` - If set, it will be checked that no duplicates are
created when adding a new handle
* ``INCLUDE_ATOMS`` - Include all atoms when adding a residue handle to a view
* ``INCLUDE_RESIDUES`` - Include all residues when adding a chain to a view
* ``INCLUDE_CHAINS`` - Include all chains when creating a new entity view
* ``INCLUDE_ALL`` = ``INCLUDE_ATOMS`` | ``INCLUDE_RESIDUES`` |
``INCLUDE_CHAINS`` - Convenience flags to include all substructures
* ``CHECK_DUPLICATES`` - If set, it will be checked that no duplicates are
created when adding a new handle
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