The Graphical Entity
================================================================================
.. currentmodule:: ost.gfx
.. note::
This document describes the API of the :class:`Entity` and related classes.
For an overview of the graphical entity, see :doc:`../intro-03`.
.. _render-mode:
Render Modes
--------------------------------------------------------------------------------
The entity supports different render modes. They are depicted in the following
images together with the options they support. To change the render mode of the
full entity or part of the entity, use the :meth:`Entity.SetRenderMode` method.
Render Modes at the Connectivity Level
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. data:: SIMPLE
.. image:: simple.png
Renders bonds as lines and single atoms as crosses.
.. data:: CPK
.. image:: cpk.png
Renders atoms as spheres with radii proportional to their van der Waals
radius.
.. data:: CUSTOM
.. image:: custom.png
Render Modes at the Trace Level
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. data:: TUBE
.. image:: tube.png
Renders a smooth backbone trace with circular profiles.
.. data:: SLINE
.. image:: sline.png
Renders a smooth backbone trace with lines.
.. data:: TRACE
.. image:: trace.png
Renders the Calpha atoms connected by tubes.
.. data:: LINE_TRACE
.. image:: line_trace.png
Renders the Calpha connected by lines.
.. data:: HSC
.. image:: hsc.png
Renders a helix/strand/coil cartoon.
.. _render-options:
Render Options
--------------------------------------------------------------------------------
**line_width**
The line width. Defaults to 1.0
:type: float
**aa_lines**
Controls whether antialiased lines are enabled. Only available when
compiled with shaders. Defaults to false.
:type: bool
**draw_bond_order**
Controls whether double/triple bonds are drawn as multiple lines. This
requires that the bond order information has been assigned. As of now,
only the :class:`~ost.conop.RuleBasedBuilder` assigns this information.
Defaults to off.
:type: bool
**bond_order_distance**
The distance between the lines depicting higher order bonds.
Loading and Displaying an Entity
--------------------------------------------------------------------------------
This code examples shows how to load a structure and display it on the screen. It also shows how to programmatically combine different render modes in one graphical entity.
.. literalinclude:: /../../examples/demos/load_and_display.py
Entity API Reference
--------------------------------------------------------------------------------
.. class:: Entity(name, entity)
Entity(name, render_mode, entity)
Graphical representation of entities.
:param name: Name of the entity.
:type name: str
:param render_mode: One of the :ref:`render-mode`.
Defaults to :obj:`SIMPLE`.
:param entity: The entity. Only atoms and bonds that part part of the entity
view (or handle) are rendered.
:type entity: :class:`~ost.mol.EntityView`, or :class:`~ost.mol.EntityHandle`
.. attribute:: name
The name of the entity. Read-only. Also available as :meth:`GetName`
:type: str
.. attribute:: selection
The selection of the entity is rendered with a green halo. As a shortcut,
the property an also be set as a string. The following two statements are
identical:
.. code-block:: python
go.selection = query
go.selection = go.view.Select(query)
:type: :class:`~ost.mol.EntityView`
.. attribute:: center
The geometric center of the graphical entity. Read-only.
:type: :class:`~ost.geom.Vec3`
.. method:: SetRenderMode(render_mode)
SetRenderMode(render_mode, view, keep=False)
Changes the render mode of the graphical entity. The first signature changes
the render mode of all atoms and bonds, whereas the second only changes the
display of atoms/bonds that are part of the view. If `keep` is set to false,
the atoms and bonds that are part of the view will only be displayed in the
new render mode. If keep is set to true, the atoms and bonds will be
rendered with the new render mode in addition to whatever render mode they
were rendered previously.
:param render_mode: One of the :ref:`render-mode`.
Defaults to :obj:`SIMPLE`.
:param view: A valid entity view.
:type view: :class:`~ost.mol.EntityView`
.. method:: SetColor(color, selection='')
Sets the atoms matching the selection predicates to `color`.
:param color: The new color
:type color: :class:`Color`
:param selection: A valid :doc:`query <../mol/base/query>`
:type selection: str
.. method:: ColorByElement()
Apply `CPK coloring <http://en.wikipedia.org/wiki/CPK_coloring>`_ coloring
to atoms. This will color the carbon atoms in white, nitrogen in blue,
oxygen in red, phosphorous in pink and sulfur in yellow.
.. method:: ColorBy(prop, color1, color2, min, max, hint='U')
ColorBy(prop, color1, color2, hint='U')
ColorBy(prop, gradient, min, max, hint='U')
ColorBy(prop, gradient, hint='U')
Colors the entity by mapping a numeric property to a color. This property
can be a built-in a property such as atomic b-factor, charge, residue number
or be a :doc:`custom property <../base/generic>` assigned by the user or an
algorithm and be defined at any level (chain, residue, atom). The naming of
the built-in properties is identical to the properties available in
:doc:`query language <../mol/base/query>`.
In case a generic property is undefined for a certain element, the property
value of min is used for that element.
:param prop: The name of the numeric property
:type prop: str
:param color1: Color corresponding to min value
:type color1: :class:`Color`
:param color2: Color corresponding to max value
:type color2: :class:`Color`
:param gradient: The gradient to be used
:type gradient: :class:`Gradient`
:type min: Value mapped to `color1`, or the color at 0.0 in the gradient
:type max: Value mapped to `color2` or the color at 1.0 in the gradient
:param hint: When `prop` refers to a generic property, hint must be set to
the hierarchy level at which the property is defined.
:type hint: str
.. method:: UpdatePositions()
Tells the graphical entity to update its vertex arrays. Use this function
when you modified coordinates of the underlying
:class:`~ost.mol.EntityHandle` and would like to see the changes on the
screen.
:see: :meth:`UpdateViews`
.. method:: UpdateView()
Tells the graphical object to recalculate all views and vertex arrays. Use
this function when you added new chains, residues, atoms or bonds to the
entity and would like to see the changes on the screen.
:see: :meth:`UpdatePositions`